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1.
Pedro Serrano Margaret A. Johnson Amarnath Chatterjee Benjamin W. Neuman Jeremiah S. Joseph Michael J. Buchmeier Peter Kuhn Kurt Wüthrich 《Journal of virology》2009,83(24):12998-13008
The nuclear magnetic resonance (NMR) structure of a globular domain of residues 1071 to 1178 within the previously annotated nucleic acid-binding region (NAB) of severe acute respiratory syndrome coronavirus nonstructural protein 3 (nsp3) has been determined, and N- and C-terminally adjoining polypeptide segments of 37 and 25 residues, respectively, have been shown to form flexibly extended linkers to the preceding globular domain and to the following, as yet uncharacterized domain. This extension of the structural coverage of nsp3 was obtained from NMR studies with an nsp3 construct comprising residues 1066 to 1181 [nsp3(1066-1181)] and the constructs nsp3(1066-1203) and nsp3(1035-1181). A search of the protein structure database indicates that the globular domain of the NAB represents a new fold, with a parallel four-strand β-sheet holding two α-helices of three and four turns that are oriented antiparallel to the β-strands. Two antiparallel two-strand β-sheets and two 310-helices are anchored against the surface of this barrel-like molecular core. Chemical shift changes upon the addition of single-stranded RNAs (ssRNAs) identified a group of residues that form a positively charged patch on the protein surface as the binding site responsible for the previously reported affinity for nucleic acids. This binding site is similar to the ssRNA-binding site of the sterile alpha motif domain of the Saccharomyces cerevisiae Vts1p protein, although the two proteins do not share a common globular fold.The coronavirus replication cycle begins with the translation of the 29-kb positive-strand genomic RNA to produce two large polyprotein species (pp1a and pp1ab), which are subsequently cleaved to produce 15 or possibly 16 nonstructural proteins (nsp''s) (11). Among these, nsp3 is the largest nsp and also the largest coronavirus protein. nsp3 is a glycosylated (16, 22), multidomain (36, 51), integral membrane protein (38). All known coronaviruses encode a homologue of severe acute respiratory syndrome coronavirus (SARS-CoV) nsp3, and sequence analysis suggests that at least some functions of nsp3 may be found in all members of the order Nidovirales (11). Hallmarks of the coronavirus nsp3 proteins include one or two papain-like proteinase domains (3, 12, 16, 31, 56, 62), one to three histone H2A-like macrodomains which may bind RNA or RNA-like substrates (5, 9, 48, 54, 55), and a carboxyl-terminal Y domain of unknown function (13). An extensive bioinformatics analysis of the coronavirus replicase proteins by Snijder et al. (51) provided detailed annotations of the then-recently sequenced SARS-CoV genome (35, 47), including the identification of a domain unique to SARS-CoV and the prediction of the ADP-ribose-1″-phosphatase (ADRP) activity of the X domain (since shown to be one of the macrodomains).Only limited information is so far available regarding the ways in which the functions of nsp3 are involved in the coronavirus replication cycle. Some functions of nsp3 appear to be directed toward protein; e.g., the nsp3 proteinase domain cleaves the amino-terminal two or three nsp''s from the polyprotein and has deubiquitinating activity (4, 6, 14, 30, 53, 60). Most homologues of the most conserved macrodomain of nsp3 appear to possess ADRP activity (9, 34, 41-43, 48, 59) and may act on protein-conjugated poly(ADP-ribose); however, this function appears to be dispensable for replication (10, 42) and may not be conserved in all coronaviruses (41). The potential involvement of nsp3 in RNA replication is suggested by the presence of several RNA-binding domains (5, 36, 49, 54, 55). nsp3 has been identified in convoluted membrane structures that are also associated with other replicase proteins and that have been shown to be involved in viral RNA synthesis (16, 24, 52), and nsp3 papain-like proteinase activity is essential for replication (14, 62). Other conserved structural features of nsp3 include two ubiquitin-like domains (UB1 and UB2) (45, 49). We have also recently reported that nsp3 is a structural protein, since it was identified as a minor component of purified SARS-CoV preparations, although it is not known whether nsp3 is directly involved in virogenesis or is incidentally incorporated due to protein-protein or protein-RNA interactions (36).A nucleic acid-binding region (NAB) is located within the polypeptide segment of residues 1035 to 1203 of nsp3. The NAB is expected to be located in the cytoplasm, along with the papain-like protease, ADRP, a region unique to SARS-CoV (the SARS-CoV unique domain [SUD]), and nsp3a, since both the N and C termini of nsp3 were shown previously to be cytoplasmic (38). Two hydrophobic segments are membrane spanning (38), and the NAB is located roughly 200 residues in the N-terminal direction from the first membrane-spanning segment. This paper presents the next step in the structural coverage of nsp3, with the determination of the NAB structure. The structural studies included nuclear magnetic resonance (NMR) characterization of two constructs, an nsp3 construct comprising residues 1035 to 1181 [nsp3(1035-1181)] and nsp3(1066-1203), and complete NMR structure determination for the construct nsp3(1066-1181) (see Fig. Fig.8).8). The structural data were then used as a platform from which to investigate the nature of the previously reported single-stranded RNA (ssRNA)-binding activity of the NAB (36). Since no three-dimensional (3D) structures for the corresponding domains in other group II coronaviruses are known and since the SARS-CoV NAB has only very-low-level sequence identity to other proteins, such data could not readily be derived from comparisons with structurally and functionally characterized homologues.Open in a separate windowFIG. 8.Sequence alignment of the polypeptide segment nsp3(1066-1181) that forms the globular domain of the SARS-CoV NAB with homologues from other group II coronaviruses. Protein multiple-sequence alignment was performed using ClustalW2 and included sequences from SARS-CoV Tor2 (accession no. ) and representatives of three protein clusters corresponding to three group II coronavirus lineages identified by a BLAST search: bat coronavirus HKU5-5 (BtCoV-HKU5-5; accession no. AAP41036), BtCoV-HKU9-1 (accession no. ABN10901), and human coronavirus HKU1-N16 (HCoV-HKU1-N16; accession no. P0C6T6). Above the sequences, the positions in full-length SARS-CoV nsp3, the locations of the regular secondary structures in the presently solved NMR structure of the SARS-CoV NAB globular domain, and the residue numbering in this domain are indicated. Amino acids are colored according to conservation and biochemical properties, following ClustalW conventions. Residues implicated in interactions with ssRNA are marked with inverted black triangles. In the present context, the key features are that there is only one position with conservation of K or R (red) and that there are extended sequences with conservation of hydrophobic residues (blue) (see the text). ABD75496相似文献
2.
3.
Matthew S. Miller Wendy E. Furlong Leesa Pennell Marc Geadah Laura Hertel 《Journal of virology》2010,84(13):6483-6496
The products of numerous open reading frames (ORFs) present in the genome of human cytomegalovirus (CMV) have not been characterized. Here, we describe the identification of a new CMV protein localizing to the nuclear envelope and in cytoplasmic vesicles at late times postinfection. Based on this distinctive localization pattern, we called this new protein nuclear rim-associated cytomegaloviral protein, or RASCAL. Two RASCAL isoforms exist, a short version of 97 amino acids encoded by the majority of CMV strains and a longer version of 176 amino acids encoded by the Towne, Toledo, HAN20, and HAN38 strains. Both isoforms colocalize with lamin B in deep intranuclear invaginations of the inner nuclear membrane (INM) and in novel cytoplasmic vesicular structures possibly derived from the nuclear envelope. INM infoldings have been previously described as sites of nucleocapsid egress, which is mediated by the localized disruption of the nuclear lamina, promoted by the activities of viral and cellular kinases recruited by the lamina-associated proteins UL50 and UL53. RASCAL accumulation at the nuclear membrane required the presence of UL50 but not of UL53. RASCAL and UL50 also appeared to specifically interact, suggesting that RASCAL is a new component of the nuclear egress complex (NEC) and possibly involved in mediating nucleocapsid egress from the nucleus. Finally, the presence of RASCAL within cytoplasmic vesicles raises the intriguing possibility that this protein might participate in additional steps of virion maturation occurring after capsid release from the nucleus.Cytomegalovirus (CMV) is a highly prevalent betaherpesvirus that can cause severe multiorgan disease in immunocompromised individuals (45). The ability of this virus to infect an exceptionally wide variety of different cell types substantially contributes to pathogenesis (5, 68). CMV tropism is largely determined by a finely tuned interplay between cellular and viral factors, many of which act at the earliest stages of infection (30, 68). We recently showed that the cellular protein vimentin is required for efficient onset of infection in primary human foreskin fibroblasts (HF). Interestingly, the degree of reliance on the presence and integrity of vimentin intermediate filaments is dependent on the virus strain, with the broadly tropic strain TB40/E being more negatively affected than the HF-adapted, attenuated strain AD169 (44).Serial passage of clinical isolates in HF or in endothelial cells (EC) has produced strains with different tropisms. The attenuated strains AD169 and Towne were developed as vaccine candidates by propagation in HF for more than 50 (AD169) and 125 (Towne) serial passages (19, 53, 61). During this process, both strains, compared to clinical isolates, accumulated multiple mutations and genomic deletions, resulting in the loss of more than 19 open reading frames (ORFs) (8). The number of serial passages in HF of another commonly used strain, Toledo, has been more moderate (19, 54, 58). This, however, did not prevent the emergence of numerous genomic mutations, including the inversion of an ∼15-kb fragment (8, 16, 56). As a consequence of these changes, productive infections by AD169, Towne, and Toledo are largely restricted to HF. In contrast, propagation of clinical isolates in EC has yielded a series of strains with more-intact genomes and broader tropisms, such as TB40/E, VHL/E, and FIX (VR1814) (25, 60, 71). These strains retain the ability to grow in a wider variety of cell types, including EC, epithelial cells, and dendritic cells (DC), in addition to HF (23, 28, 59, 60, 68).The UL128, UL130, and UL131A gene products were recently identified as essential mediators of CMV infection of EC and epithelial cells (26, 72, 73) and of virus transfer from infected EC to monocyte-derived DC (23). Each of these proteins is independently required for the broader tropisms of EC-propagated CMV isolates (63, 64), and the presence of mutations affecting their functionality has been directly linked to the inability of AD169, Towne, and Toledo to initiate productive infections in EC and epithelial cells (26, 72, 73).We have shown that mature Langerhans-type DC differentiated in vitro from CD34+ hematopoietic progenitor cells are highly permissive to direct infection with TB40/E or VHL/E, with 48 to 72% of cells in culture expressing the viral immediate-early genes IE1 and IE2 at 48 h postinfection (hpi) (28). In contrast, only 2 to 5% and 0% of mature Langerhans cells were IE1/IE2 positive after exposure to Towne and Toledo, respectively. However, productive infection was detected in 12 to 17% of cells infected with AD169, despite the fact that this strain lacks expression of the UL131A gene as a consequence of a frameshift mutation (26). These results suggested the existence of additional viral genes with products involved in mediating tropisms for specific cell types, such as DC. To identify possible candidates, we compared the amino acid sequence of each ORF found in the genome of TB40-BAC4, a sequenced clone of the TB40/E strain in a bacterial artificial chromosome (BAC) (GenBank accession number ) ( EF99992169), to the sequence of each ORF found in AD169 and AD169-BAC (accession numbers and X17403) ( AC14699910, 49), Towne and Towne-BAC (accession numbers , FJ616285, and AC146851) ( AY31519717, 18, 49), and Toledo-BAC (accession number ) ( AC14690549). The product of a putative ORF, originally identified by Murphy et al. and named conserved ORF 29 (c-ORF29) (49), was considered of particular interest because the amino acid sequence of the putative protein encoded by Toledo and Towne was extended by 79 residues compared to the putative protein encoded by TB40/E and AD169. This led to our speculation that that the extended version might result in a nonfunctional version of the c-ORF29-encoded protein. We thus focused our studies on the products of this ORF.Here, we show for the first time that CMV c-ORF29 encodes a protein expressed at early to late times postinfection (p.i.) and localizes to the nuclear rim in peculiar invaginations of the nuclear lamina and in cytoplasmic vesicular structures at late times p.i. Based on this localization pattern, we named this gene product nuclear rim-associated cytomegaloviral protein, or RASCAL. Surprisingly, no difference was observed in the distributions of RASCAL during infection of HF with TB40/E or Towne, suggesting that the intracellular trafficking of this protein is not affected by the presence of the additional residues at the C terminus of RASCAL from strain Towne (RASCALTowne). Ectopic expression of RASCAL in human embryo kidney 293T (HEK293T) cells further revealed that this protein requires the presence of the nuclear egress complex (NEC) member UL50 to reach the nuclear rim, while coimmunoprecipitation (co-IP) assays provided evidence for the existence of an interaction between RASCAL and UL50. These findings suggest that RASCAL may be a new component of the NEC with possible roles in remodeling the nuclear lamina during nucleocapsid egress from the nucleus. 相似文献
4.
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
Phylum Crenarchaeota
- Pyrobaculum strain 1860, sequence accession [ CP0030981]
Phylum Deinococcus-Thermus
- “Thermus sp.” Strain CCB_US3_UF1, sequence accession (chromosome), CP003126 (plasmid) [ CP0031272]
Phylum Proteobacteria
- “Achromobacter arsenitoxydans” SY8, sequence accession [ AGUF000000003]
- Acidovorax sp. Strain NO1, sequence accession [ AGTS000000004]
- Acinetobacter baumannii AB4857, sequence accession [ AHAG000000005]
- Acinetobacter baumannii AB5075, sequence accession [ AHAH000000005]
- Acinetobacter baumannii AB5256, sequence accession [ AHAI000000005]
- Acinetobacter baumannii AB5711, sequence accession [ AHAJ000000005]
- Aeromonas salmonicida, sequence accession [ AGVO000000006]
- Aggregatibacter actinomycetemcomitans RHAA1, sequence accession [ AHGR000000007]
- Agrobacterium tumefaciens 5A, sequence accession [ AGVZ000000008]
- Azoarcus sp. Strain KH32C, sequence accession , AP012304 [ AP0123059]
- Burkholderia sp. Strain YI23, sequence accession (Chromosome 1), CP003087 (Chromosome 2), CP003088 (Chromosome 3), CP003089 (plasmid BYI23_D), CP003090 (plasmid BYI23_E) CP003091 (plasmid BYI23_F) [ CP00309210]
- Brucella suis VBI22, sequence accession , CP003128 [ CP00312911]
- Comamonas testosteroni ATCC 11996, sequence accession [ AHIL0000000012]
- “Commensalibacter intestini” A911T, sequence accession [ AGFR0000000013]
- Edwardsiella ictaluri, sequence accession [ CP001600.114]
- Enterobacter cloacae subsp. dissolvens SDM, sequence accession [ AGSY0000000015]
- “Gluconobacter morbifer” G707T, sequence accession [ AGQV0000000016]
- Legionella dumoffii TEX-KL, sequence accession [ AGVT0000000017]
- Legionella dumoffii NY-23, sequence accession [ AGVU0000000017]
- Legionella pneumophila serogroup 12 Strain 570-CO-H, sequence accession [ CP00319218]
- Marinobacterium stanieri S30, sequence accession [ AFPL0000000019]
- “Marinobacter manganoxydans” MnI7-9, sequence accession [ CP001978 to CP00198020]
- Mesorhizobium alhagi CCNWXJ12-2T, sequence accession [ AHAM0000000021]
- Mesorhizobium amorphae, sequence accession [ AGSN0000000022]
- Methylomicrobium alcaliphilum 20Z, sequence accession and FO082060 [ FO08206123]
- Mitsuaria sp. Strain H24L5A, sequence accession [ CAFG01000001 to CAFG0100060724]
- Novosphingobium pentaromativorans US6-1, sequence accession [ AGFM0000000025]
- Pantoea ananatis B1-9, sequence accession [ CAEI01000001 to CAEI0100016926]
- Pantoea ananatis LMG 5342, sequence accession (chromosome), HE617160 (pPANA10) [ HE61716127]
- Pantoea ananatis Strain PA13, sequence accession and CP003085 [ CP00308628]
- Pseudomonas aeruginosa, sequence accession [ AFXI0000000029]
- Pseudomonas aeruginosa, sequence accession [ AFXJ0000000029]
- Pseudomonas aeruginosa, sequence accession [ AFXK0000000029]
- Pseudomonas chlororaphis GP72, sequence accession [ AHAY0100000030]
- Pseudomonas fluorescens F113, sequence accession [ CP00315031]
- Pseudomonas fluorescens Wayne 1R, sequence accession [ CADX01000001 to CADX0100009032]
- Pseudomonas fluorescens Wood1R, sequence accession to CAFF01000001 [ CAFF0100143732]
- Pseudomonas psychrotolerans L19, sequence accession [ AHBD0000000033]
- Pseudoalteromonas rubra ATCC 29570T, sequence accession [ AHCD0000000034]
- Pseudomonas stutzeri SDM-LAC, sequence accession [ AGSX0000000035]
- Pseudoxanthomonas spadix BD-a59, sequence accession [ CP00309336]
- Rickettsia slovaca, sequence accession [ CP00242837]
- Salmonella enterica serovar Pullorum RKS5078, sequence accession [ CP00304738]
- Sinorhizobium meliloti CCNWSX0020, sequence accession [ AGVV0000000039]
- Sphingobium sp. Strain SYK-6, sequence accession and AP012222 [ AP01222340]
- Sphingomonas sp. Strain PAMC 26605, sequence accession [ AHIS0000000041]
- Stenotrophomonas maltophilia RR-10, sequence accession [ AGRB0000000042]
- Strain HIMB30, sequence accession [ AGIG0000000043]
- Taylorella equigenitalis, sequence accession [ CP00305944]
- Vibrio campbellii DS40M4, sequence accession [ AGIE0000000045]
- Vibrio fischeri SR5, sequence accession [ AHIH0000000046]
- Yersinia enterocolitica, sequence accession [ AGQO0000000047]
Phylum Tenericutes
- Candidatus Mycoplasma haemominutum, sequence accession [ HE61325448]
- Mycoplasma haemocanis strain Illinois, sequence accession [ CP00319949]
- Mycoplasma iowae, sequence accession [ AGFP0000000050]
- Mycoplasma pneumoniae Type 2a Strain 309, sequence accession [ AP01230351]
Phylum Firmicutes
- Bacillus cereus F837/76, sequence accession (chromosome) CP003187 (pF837_55kb), CP003188 (pF837_10kb) [ CP00318952]
- Brevibacillus laterosporus Strain GI-9, sequence accession [ CAGD01000001 to CAGD0100006153]
- Clostridium sporogenes PA 3679, sequence accession [ AGAH0000000054]
- Enterococcus mundtii CRL1656, sequence accession [ AFWZ00000000.155]
- Geobacillus thermoleovorans CCB_US3_UF5, sequence accession [ CP00312556]
- Lactobacillus curvatus Strain CRL705, sequence accession [ AGBU0100000057]
- Lactobacillus rhamnosus ATCC 8530, sequence accession [ CP00309458]
- Lactobacillus rhamnosus R0011, sequence accession [ AGKC0000000059]
- Lactococcus garvieae TB25, sequence accession [ AGQX0100000060]
- Lactococcus garvieae LG9, sequence accession [ AGQY0100000060]
- Lactococcus lactis subsp. cremoris A76, sequence accession (chromosome), CP003132 (pQA505), CP003136 (PQA518), CP003135 (pQA549), CP003134 (pQA554) [ CP00313361]
- Leuconostoc citreum LBAE C10, sequence accession [ CAGE0000000062]
- Leuconostoc citreum LBAE C11, sequence accession [ CAGF0000000062]
- Leuconostoc citreum LBAE E16, sequence accession [ CAGG0000000062]
- Leuconostoc mesenteroides subsp. mesenteroides Strain J18, sequence accession [ CP00310163]
- Paenibacillus peoriae Strain KCTC 3763T, sequence accession [ AGFX0000000064]
- Pediococcus acidilactici MA18/5M, sequence accession [ AGKB0000000065]
- Pediococcus claussenii ATCC BAA-344T, sequence accession (chromosome), CP003137 (pPECL-1), CP003138 (pPECL-2), CP003139 (pPECL-3), CP003140 (pPECL-4), CP003141 (pPECL-5), CP003142 (pPECL-6), CP003143 (pPECL-7), CP003144 (pPECL-8) [ CP00314566]
- Staphylococcus aureus M013, sequence accession [ CP00316667]
- Staphylococcus aureus subsp. aureus TW20, sequence accession [ FN43359668]
- Weissella confusa LBAE C39-2, sequence accession [ CAGH0000000069]
Phylum Actinobacteria
- Corynebacterium casei, sequence accession [ CAFW01000001 to CAFW0100010670]
- Corynebacterium glutamicum, sequence accession [ AGQQ0000000071]
- Leucobacter chromiiresistens, sequence accession [ AGCW0000000072]
- Mycobacterium abscessus, sequence accession [ AGQU0000000073]
- Propionibacterium acnes ST9, sequence accession [ CP00319574]
- Propionibacterium acnes ST22, sequence accession [ CP00319674]
- Propionibacterium acnes ST27, sequence accession [ CP00319774]
- Saccharomonospora azurea SZMC 14600, sequence accession [ AHBX0000000075]
- Streptomyces sp. Strain TOR3209, sequence accession [ AGNH0000000076]
- Streptomyces sp. Strain W007, sequence accession [ AGSW0000000077]
Phylum Spirochaetes
- Borrelia valaisiana VS116, sequence accession (chromosome), ABCY02000001 (plasmid Ip17), CP001439 (Ip25), CP001437 (plasmid Ip 28-3), CP001440 (plasmid Ip28-8), CP001442 (Ip 36), CP001436 (plasmid Ip 54), CP001433 (plasmid cp9), CP001438 (plasmid cp26), CP001432 (plasmid cp32-5), CP001441 (plasmid cp32-7), CP001434 (plasmid cp32-10) [ CP00143578]
- “Borrelia bissettii” DN127, sequence accession (chromosome), CP002746 (plasmid Ip12), CP002756 (plasmid Ip25), CP002757 (plasmid 28-3), CP002758 (plasmid Ip 28-4), CP002759 (Ip28-7), CP002760 (plasmid Ip54), CP002761 (plasmid Ip56), CP002762 (plasmid cp9), CP002755 (plasmid cp26), CP002747 (plasmid cp32-3), CP002749 (plasmid cp32-4), CP002750 (plasmid 32-5), CP002751 (plasmid cp32-6), CP002752 (plasmid cp32-7), CP0027554 (plasmid cp32-9), CP002753 (plasmid cp32-11) [ CP00274878]
- Borrelia spielmanii A14S, sequence accession (chromosome), ABKB02000001 (plasmid Ip17), CP001468 (Ip28-3), CP001471 (plasmid Ip28-4), CP001470 (plasmid Ip28-2), CP001465 (plasmid Ip36), CP001466 (plasmid Ip38), CP001464 (plasmid Ip54), CP001469, ABKB02000016 (plasmid cp9), ABKB02000020 (plasmid cp26), CP001467 (plasmid cp32-3), ABKB02000026 (plasmid 32-5), ABKB02000031 (plasmid cp32-12), ABKB02000021 (unidentified) [ ABKB0200001478]
Non-Bacterial genomes
- Aspergillus flavus, sequence accession [ GSE3217779]
- Bacteriophage SPN3UB, sequence accession [ JQ28802180]
- Bamboo mitochondria, sequence accession [ JQ235166 to JQ23517981]
- Boea hygrometrica chloroplast, sequence accession [ JN10781182]
- Boea hygrometrica mitochondrial, sequence accession [ JN10781282]
- Canine Picornavirus, sequence accession [ JN83135683]
- Chandipura virus (CHPV) CIN0327, sequence accession [ GU212856.184]
- Chandipura virus (CHPV) CIN0451, sequence accession [ GU212857.184]
- Chandipura virus (CHPV) CIN0751, sequence accession [ GU212858.184]
- Chandipura virus (CHPV) CIN0755, sequence accession [ GU190711.184]
- Chinese Porcine Parvovirus Strain PPV2010, sequence accession [ JN87244885]
- Common midwife toad megavirus, sequence accession [ JQ23122286]
- Dengue Virus Serotype 4, sequence accession [ JN98381387]
- Duck Tembusu Virus, sequence accession [ JF27048088]
- Duck Tembusu Virus, sequence accession [ JQ31446488]
- Duck Tembusu Virus, sequence accession [ JQ31446588]
- Emiliania huxleyi Virus 202, sequence accession [ HQ63414589]
- Emiliania huxleyi Virus EhV-88, sequence accession [ JF97431089]
- Emiliania huxleyi EhV-201, sequence accession [ JF97431189]
- Emiliania huxleyi EhV-207, sequence accession [ JF97431789]
- Emiliania huxleyi EhV-208, sequence accession [ JF97431889]
- Glarea lozoyensis, sequence accession GUE00000000 [90]
- Nannochloropis gaditana, sequence accession [ AGNI0000000091]
- Oryza sativa cv., sequence accession DRA000499 [92]
- Partetravirus, sequence accession [ JN99026993]
- Porcine Bocavirus PBoV5, sequence accession [ JN83165194]
- Porcine epidemic diarrhea virus, sequence accession [ JQ28290995]
- Pseudomonas aeruginosa lytic bacteriophage PA1Ø, sequence accession [ HM62408096]
- Pseudomonas fluorescens phage OBP, sequence accesssion [ JN62716097]
- RNA Virus from Avocado, sequence accession [ JN88041498]
- Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S, sequence accession [ JN39118099]
- Schistosoma haematobium, sequence accession PRJNA78265 [100]
- Schistosoma mansoni, sequence accession [ ERP00038101]
- Stenopirates sp., sequence accession [ JN100019102]
- T7-Like Virus, sequence accession [ JN651747103]
- Vibrio harveyi siphophage VHS1, sequence accession [ JF713456104]
- Tyrolean ice man, sequence accession ERP001144 [105]
5.
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
- Phylum Crenarchaeota
- Thermoproteus tenax, strain Kra1, DSM 2078T sequence accession [ FN8698591]
- Phylum Euryarchaeota
- Haloarcula hispanica CGMCC 1.2049, sequence accession (chromosome I), CP002921 (chromosome II), and CP002922 (plasmid pHH400) [ CP0029232]
- Methanococcus maripaludis, strain X1 (unculturable) sequence accession [ CP0029133]
- Phylum Proteobacteria
- Acinetobacter baumannii strain 1656-2, sequence accession [ CP0019214]
- Arcobacter butzleri strain ED-1, sequence accession , AP012047, and AP012048 [ AP0120495]
- Brucella suis strain 1330, sequence accession and CP002997 [ CP0029986]
- Campylobacter fetus subsp. venerealis NCTC 10354, sequence accession [ AFGH010000007]
- “Chromobacterium sp.” strain C-61, sequence accession to CAEE01000001 [ CAEE010011188]
- Cronobacter sakazakii strain E899, sequence accession [ AFMO000000009]
- “Desulfovibrio sp.” strain A2, sequence accession [ AGFG0100000010]
- “Erythrobacter sp.” strain NAP1, sequence accession [ NZ_AAMW0000000011]
- Escherichia coli strain XH140A, sequence accession [ AFVX0100000012]
- Escherichia coli strain XH001, sequence accession [ AFYG0100000013]
- Haemophilus haemolyticus strain , sequence accession M19107 [ AFQN0000000014]
- Haemophilus haemolyticus strain , sequence accession M19501 [ AFQO0000000014]
- Haemophilus haemolyticus strain , sequence accession M21127 [ AFQP0000000014]
- Haemophilus haemolyticus strain , sequence accession M21621 [ AFQQ0000000014]
- Haemophilus haemolyticus strain , sequence accession M21639 [ AFQR0000000014]
- Idiomarina sp.” strain A28L, sequence accession [ AFPO01000001 to AFPO0100002815]
- Ketogulonicigenium vulgare” strain WSH-001, sequence accession (chromosome), CP002018 (plasmid pKVU_100), and CP002019 (plasmid pKVU_200) [ CP00202016]
- Methylobacter tundripaludum strain SV96, sequence accession [ AEGW0000000017]
- Pseudogulbenkiania sp.” strain NH8B, sequence accession [ AP01222418]
- Pseudomonas aeruginosa NCGM1179, sequence accession through DF126593 [ DF12661319]
- Pseudomonas putida strain B001, sequence accession to CAED01000001 [ CAEE0100026220]
- Pseudomonas putida strain B6-2, sequence accession [ AGCS0100000021]
- Pseudomonas stutzeri CGMCC 1.1803, sequence accession [ CP00288122]
- Ralstonia solanacearum phylotype IB, strain Y45, sequence accession [ AFWL0100000023]
- Rheinheimera sp.” strain A13L, sequence accession through AFHI01000001 [ AFHI0100007224]
- Sphingobium yanoikuyae strain XLDN2-5, sequence accession [ AFXE0100000025]
- Vibrio cholerae strain Amazonia, sequence accession [ AFSV0100000026]
- Phylum Firmicutes
- Bacillus coagulans strain XZL4, sequence accession [ AFWM0100000027]
- Bacillus megaterium strain WSH-002, sequence accession (chromosome), plasmids CP003017 (plasmid pBME_100), CP003018 (plasmid pBME_200), and CP003019 (plasmid pBME_300) [ CP00302028]
- Bacillus pumilus strain S-1, sequence accession [ AGBY0000000029]
- “Desulfosporosinus sp.” strain OT, sequence accession [ AGAF0100000030]
- Lentibacillus jeotgali strain Grbi, sequence accession [ AGAV0100000031]
- Leuconostoc carnosum KCTC 3525, sequence accession [ BACM0100000032]
- Listeria ivanovii subsp. ivanovii strain PAM 55, sequence accession [ FR68725333]
- Paenibacillus riograndensis strain SBR5, sequence accession [ AGBD0100000034]
- Sporolactobacillus inulinus strain CASD, sequence accession [ AFVQ0000000035]
- Streptococcus pseudopneumoniae strain IS7493, sequence accession and CP002925 [ CP00292636]
- Streptococcus salivarius strain 57.I, sequence accession and CP002888 [ CP00288937]
- Streptococcus salivarius strain M18, sequence accession [ AGBV0100000038]
- Streptococcus suis SS12, sequence accession [ CP00264039]
- Streptococcus suis D9, sequence accession [ CP00264139]
- Streptococcus suis D12, sequence accession [ CP00264439]
- Streptococcus suis ST1, sequence accession [ CP00265139]
- Weissella thailandensis strain fsh4-2, sequence accession through HE575133 [ HE57518240]
- Phylum Tenericutes
- Mycoplasma anatis strain 1340, sequence accession [ AFVJ0000000041]
- Mycoplasma capricolum subsp. capripneumoniae strain M1601, sequence accession [ AENG0100000042]
- Mycoplasma putrefaciens Type strain KS1, sequence accession [ CP00302143]
- Corynebacterium pseudotuberculosis strain PAT10, sequence accession [ CP00292444]
- Phylum Actinobacteria
- Bifidobacterium animalis subsp. lactis strain BLC1, sequence accession [ CP00303945]
- Bifidobacterium breve strain DPC 6330, sequence accession [ AFXX0100000046]
- Brachybacterium squillarum strain M-6-3, sequence accession [ AGBX0100000047]
- “Citricoccus sp.” strain CH26A, sequence accession [ AFXQ0100000048]
- Corynebacterium glutamicum strain S9114, sequence accession [ AFYA0100000049]
- Dietzia alimentaria strain 72, sequence accession [ AGFF0100000050]
- Mycobacterium colombiense CECT 3035, sequence accession [ AFVW0000000051]
- Mycobacterium tuberculosis NCGM2209, sequence accession and DF126614 [ DF12661552]
- Rhodococcus erythropolis strain XP, sequence accession [ AGCF0100000053]
- Serinicoccus profundi MCCC 1A05965T, sequence accession [ AFYF0000000054]
- Phylum Spirochaetes
- Leptospira interrogans, sequence accession (CI), CP001221 (CII) [ CP00122255]
- Phylum Bacteroidetes
- Bacteroides faecis Type strain MAJ27T, sequence accession [ AGDG0100000056]
- Bizionia argentinensis, Type strain JUB59T sequence accession [ AFXZ0100000057]
- Flavobacterium branchiophilum strain FL-15, sequence accession [ FQ85918358]
- “Flavobacteriaceae” strain S85, sequence accession [ AFPK0000000059]
- Phylum Thermotogae
- “Thermotoga sp.” strain RQ2, sequence accession [ CP00096960]
Non-Bacterial genomes
- Aspergillus kawachii IFO 4308, sequence accession through DF126447, BACL01000001 through BACL01001641, DF126592 [ AP01227261]
- Cajanus cajan pigeonpea, sequence accession PRJNA72815 [62]
- Coxsackievirus A22, sequence accession [ JN54251063]
- Gordonia phage GRU1, sequence accession [ JF92379764]
- Gordonia phage GTE5, sequence accession [ JF92379664]
- Heterocephalus glaber naked mole rat, sequence accession , AFSB00000000 [ AFSB0100000065]
- Human Adenovirus Prototype 17, sequence accession [ HQ91040766]
- Macaca mulatta lasiota rhesus macaque, sequence accession [ AEHL0000000067]
- Macaca mulatta mulatta rhesus macaque, sequence accession [ AEHK0000000067]
- Porcine epidemic diarrhea virus, sequence accession [ JN54722868]
6.
Catherine A. Blish D. Noah Sather George Sellhorn Leonidas Stamatatos Yide Sun Indresh Srivastava Susan W. Barnett Brad Cleveland Julie Overbaugh Shiu-lok Hu 《Journal of virology》2010,84(5):2573-2584
Development of broadly cross-reactive neutralizing antibodies (NAbs) remains a major goal of HIV-1 vaccine development, but most candidate envelope immunogens have had limited ability to cross-neutralize heterologous strains. To evaluate the immunogenicity of subtype A variants of HIV-1, rabbits were immunized with pairs of closely related subtype A envelopes from the same individual. In each immunogen pair, one variant was readily neutralized by a variety of monoclonal antibodies and plasma antibodies, while the other was neutralization resistant, suggesting differences in the exposures of key epitopes. The breadth of the antibody response was evaluated against subtype A, B, C, and D variants of HIV-1. The specificity of the immunogen-derived neutralizing antibody response was also compared to that of the infected individuals from whom these variants were cloned. None of the immunogens produced broad neutralizing antibodies in immunized animals, and most of the neutralizing antibodies were directed to the variable loops, particularly the V3 loop. No detectable antibodies to either of the potentially exposed conserved epitopes, the membrane proximal external region, or the CD4 binding site were found with immunized rabbits. In contrast, relatively little of the neutralizing activity within the plasma samples of the infected individuals was directed to linear epitopes within the variable loops. These data indicate that immunogens designed to expose conserved regions did not enhance generation of broadly neutralizing antibodies in comparison with the immunogens that failed to expose those regions using this immunization approach.The ability to elicit broadly cross-reactive neutralizing antibodies (NAbs) is likely to be an important component of an effective vaccine to human immunodeficiency virus type 1 (HIV-1). Unfortunately, the HIV-1 envelope (Env)-based vaccines developed to date do not elicit such antibodies. Initial vaccines based on soluble, monomeric gp120 generated antibodies capable of only weakly neutralizing the homologous virus, with a very narrow breadth of cross-reactivity (13, 30, 53). Subsequent modifications to the Env immunogens, including variable loop deletions (15, 20, 31, 34, 35, 61, 64-66), alterations in the glycosylation pattern (4, 10, 11, 14, 30, 43, 55, 56), epitope repositioning (39, 46), the use of consensus Envs (22, 36, 37, 47), and the use of soluble trimeric gp140 molecules as immunogens (1-3, 5, 14, 16, 20, 21, 24, 25) have led to only modest enhancements in NAb breadth or potency. These modified Env immunogens have failed to redirect NAbs from the variable loops to more conserved regions of Env (reviewed in reference 33).Differences in Env structure between HIV-1 subtypes may further hinder efforts to elicit broadly cross-reactive antibodies capable of protecting against transmitted strains worldwide. Most immunogens tested to date have been derived from subtype B Envs. However, there are clear antigenic differences between subtype B strains and the subtype A and C strains that account for most infections worldwide (6, 8, 27, 28, 40, 42). For instance, most transmitted subtype A Envs are resistant to the monoclonal antibodies 2G12, b12, 2F5, and 4E10, either because of alterations in the epitopes for these monoclonal antibodies (MAbs) or because the epitopes are shielded in these Envs (6, 8). It is therefore possible that even NAbs specific for a conserved region of subtype B Envs, such as the CD4 binding site, would not be able to access and neutralize a similar epitope on a subtype A Env.In order to evaluate the immunogenicity of subtype A Envs, which account for ∼25% of global HIV-1 infections (12), we previously investigated the types of antibody responses elicited following gp160 priming and gp140 boosting with immunogens derived from four subtype A Envs in comparison to the subtype B Env SF162 (38). These experiments were also designed to explore whether deriving immunogens from HIV-1 Envs isolated from early in infection would better target NAbs to transmitted strains. Although all of the subtype A-based immunogens and the SF162 immunogen elicited anti-V3 NAbs capable of neutralizing the easy-to-neutralize SF162 pseudovirus, only one of the four immunogens generated homologous NAbs (38). Even immunogens with shorter variable loops or fewer potential N-linked glycosylation sites (PNGS) did not lead to enhanced breadth of neutralization against heterologous subtype A or B Envs (38). However, the four subtype A Envs used in these immunizations were generally neutralization resistant to both plasma samples from HIV-1-infected individuals and to monoclonal antibodies (6), raising the possibility that the poor breadth observed could be related to the shielding of conserved epitopes within these Envs.In order to determine whether using subtype A Env immunogens that do not shield conserved epitopes could improve neutralization breadth, here we performed immunizations with pairs of Env immunogens derived from two individuals acutely infected with subtype A HIV-1. The Envs in each pair were very similar in their amino acid sequences yet differed dramatically in their neutralization phenotype (6, 9) (Fig. (Fig.1A).1A). The pair from subject Q461 had a neutralization-resistant Env, (termed Q461e2R to indicate neutralization resistance), and a neutralization-sensitive Env, Q461e2 (termed Q461d1S to indicate neutralization sensitivity), which was sensitive to neutralization by plasma, 2F5, 4E10, b12, and soluble CD4 (sCD4). We previously demonstrated that the neutralization sensitivity of the Q461d1S Env is mediated entirely by two amino acid substitutions in gp41, one in the first heptad repeat and one in the membrane proximal external region (MPER) ( Q461d19). These mutations led to enhanced exposure of both the CD4 binding site and the MPER (9). From subject Q168, the Env Q168b23S was sensitive to autologous and heterologous plasma and to the MPER antibodies 2F5 and 4E10 but resistant to b12 and sCD4, while R was weakly neutralized by the MPER antibodies, less sensitive to neutralization by autologous plasma, and resistant to heterologous plasma ( Q168a26). The R and Q168b23S Envs contain identical sequences in the MPER region yet have >500-fold differences in neutralization sensitivity to 2F5 and 4E10, indicating that the exposure of the MPER region, rather than the sequence, likely accounts for the enhanced neutralization of the Q168b23S Env. Q168a2Open in a separate windowFIG. 1.Analysis of S gp140 used for immunizations. (A) SDS-PAGE analysis of final preparation of Q461d1S gp140 from the GNA capture and DEAE and CHAP columns. Lane 1 contains molecular weight standards, lane 2 the concentrated DEAE flowthrough, and lane 3 the final concentrated protein. The purified Q461d1S gp140 protein is indicated by an arrow. The sizes of the molecular weight markers (in thousands) are indicated on the left. (B) Binding of purified gp140 subtype A to CD4 as determined by a high-pressure liquid chromatography (HPLC)-based assay. The bottom line represents the protein obtained after the GNA column, and the top line represents purified protein after all three steps. The trimer and monomer peaks are marked. (C) Summary of neutralization characteristics of all four HIV-1 subtype A Env variants used in the immunizations, adapted from reference Q461d16. The pseudovirus is shown in the far left column. IC50 values for plasma sample (left) and monoclonal antibodies (right) are displayed. The autologous plasma samples were taken 3.7 ypi for subject Q461 and 2.6 ypi for subject Q168. The Kenya pool was derived by pooling plasma from 30 HIV-1-infected individuals in Kenya and has been described previously (6).Thus, to directly test whether using Env immunogens that expose conserved epitopes could enhance neutralization breadth immunization, here we immunized with these pairs of related Envs, in which one variant exposes conserved regions, while the other does not. We also compared the specificity of the NAb responses following immunization with these Envs with the specificities of the NAbs that developed during natural infection in the individuals from whom these variants were cloned. 相似文献
7.
8.
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to this subsequent versions of this list are invited to provide the bibliometric data for such references to the SIGS editorial office.
- Phylum Crenarchaeota
- Phylum Euryarchaeota
- Pyrococcus yayanosii CH1, sequence accession [ CP0027791]
- Methanocella paludicola, sequence accession [ AP0115322]
- Halorhabdus tiamatea, sequence accession [ AFNT000000003]
- Thermococcus sp. Strain 4557, sequence accession [ CP0029204]
- Phylum Chloroflexi
- Phylum Proteobacteria
- Ralstonia solanacearum strain Po82, sequence accession (chromosome) and CP002819 (megaplasmid) [ CP0028205
- Desulfovibrio alaskensis G20, sequence accession [ CP0001126]
- Methylophaga aminisulfidivorans MPT, sequence accession [ AFIG000000007]
- Acinetobacter sp. P8-3-8, sequence accession [ AFIE000000008]
- Sphingomonas strain KC8, sequence accession [ AFMP010000009]
- Brucella pinnipedialis B2/94, sequence accession and CP002078 [ CP00207910]
- Salmonella enterica Serovar Typhimurium UK-1, sequence accession (chromosome), CP002614 (plasmid) [ CP00261511]
- Bordetella pertussis CS, sequence accession [ CP00269512]
- Alteromonas sp. Strain SN2, sequence accession [ CP00233913]
- Escherichia coli O104:H4, sequence accession ( AFOB00000000) and LB226692 (01-09591) [ AFPS0000000014]
- Acidithiobacillus caldus, sequence accession (Chromosome), CP002573 (pLAtcm), CP002574 (pLAtc1), CP002575 (pLAtc2), CP002576 (pLAtc3) [ CP00257715]
- Cupriavidus necator N-1, sequence accession (chromosome 1), CP002877 (chromosome 2), CP002878 (pBB1), and CP002879 (pBB2) [ CP00288016]
- Oligotropha carboxidovorans OM4, sequence accession (OM4 chromosome), CP002821 (pHCG3b), CP002822 (pOC167B) [ CP00282317]
- Oligotropha carboxidovorans OM5, sequence accession (OM5 chromosome), CP002826 (pHCG3), and CP002827 (pOC167) [17] CP002828
- Pantoea ananatis LMG20103, sequence accession [ CP00187518]
- Helicobacter bizzozeronii strain CIII-1, sequence accession (chromosome) and FR871757 (HBZ-1) [ FR87175819]
- Vibrio anguillarum 775, sequence accession [ CP002284 to CP00228520]
- Zymomonas mobilis subsp. pomaceae, sequence accession (chromosome), CP002865 (p29192_1), CP002866 (p29192_2) [ CP00286721]
- Agrobacterium sp. strain ATCC 31749, sequence accession [ AECL0100000022]
- Xanthomonas spp. strain Xrc, sequence accesssion [ CP00278923]
- Xanthomonas spp. strain Xoc, sequence accesssion [ AAQN0000000023]
- Glaciecola sp. Strain 4H-3-7+YE-5, sequence accession (chromosome) and CP002526 (plasmid) [ CP00252724]
- Escherichia coli Strain HM605, sequence accession through CADZ01000001 [ CADZ0100015425]
- Salinisphaera shabanensis, sequence accession [ AFNV0000000026]
- Methyloversatilis universalis FAM5T, sequence accession [ AFHG0000000027]
- Alicycliphilus denitrificans Strain BC, sequence accession (chromosome), CP002449 (megaplasmid), CP002450 (plasmid) [ CP00245128].
- Alicycliphilus denitrificans K601T, sequence accession (chromosome) and CP002657 (plasmid) [ CP00265828]
- Oligotropha carboxidovorans Strain OM4, sequence accession (chromosome), CP002821 (pHCG3b), CP002822 (pOC167B) [ CP00282329]
- Oligotropha carboxidovorans Strain OM5, sequence accession (chromosome), CP002826 (pHCG3), and CP002827 (pOC167) [ CP00282829]
- Bradyrhizobiaceae strain SG-6C, sequence accession [ AFOF0100000030]
- Hyphomicrobium sp. Strain MC1, sequence accession [ FQ85918131]
- Shewanella sp. Strain HN-41, sequence accession [ AFOZ0100000032]
- Myxococcus fulvus HW-1, sequence accession [ CP00283033]
- Nitrosomonas sp. Strain AL212, sequence accession (chromosome), NC_015222 pNAL21201), NC_015223 (pNAL21202) [ NC_01522134]
- Ruegeria sp. Strain KLH11, sequence accession [ ACCW0000000035]
- Acidovorax avenae subsp. avenae RS-1, sequence accession [ AFPT0100000036]
- Escherichia coli (ExPEC), sequence accession [ AFAT0000000037]
- Vibrio mimicus SX-4, sequence accession [ ADOO0100000038]
- Agrobacterium tumefaciens Strain F2, sequence accession [ AFSD0000000039]
- Pasteurella multocida subsp. gallicida [ AFRR01000001 to AFRR0100048940]
- Pseudomonas aeruginosa 138244, sequence accession [ AEVV0000000041]
- Pseudomonas aeruginosa 152504, sequence accession [ AEVW0000000041]
- Campylobacter jejuni strain 305, sequence accession [ ADHL0000000042]
- Campylobacter jejuni strain DFVF1099, sequence accession [ ADHK0000000042]
- Xanthomonas campestris pv. raphani strain 756C, sequence accession [ CP00278943]
- Xanthomonas campestris pv. raphani strain BLS256, sequence accession [ AAQN0100000143]
- Rickettsia heilongjiangensis, sequence accession [ CP00291244]
- Acidiphilium sp. Strain PM (DSM 24941), sequence accession [ AFPR0000000045]
- Pseudomonas putida Strain S16, sequence accession [ CP00287046]
- Acinetobacter lwoffii, sequence accession [ AFQY0100000047]
- Phylum Firmicutes
- Caldalkalibacillus thermarum strain TA2.A1, sequence accession [ AFCE0000000048]
- Listeria monocytogenes Scott A, sequence accession [ AFGI0000000049]
- Lactococcus garvieae 8831, sequence accession [ AFCD0000000050]
- Natranaerobius thermophilus JW/NM-WN-LF, sequence accession (chromosome), CP001034 (plasmid) [ CP00103551]
- Melissococcus plutonius ATCC 35311, sequence accession (chromosome) and AP012200 (plasmid) [ AP01220152]
- Lactobacillus buchneri NRRL B-30929, sequence accession (chromosome), CP002652 (plasmid pLBU01), CP002653 (plasmid pLBU02), and CP002654 (plasmid pLBU03) [ CP00265553]
- Lactobacillus kefiranofaciens ZW3 , sequence accession (chromosome), CP002764 (plasmid), and CP002765 (plasmid) [ CP00276654]
- Bacillus megaterium strain QM B1551, sequence accession (chromosome), CP001983 (plasmids pBM100 through pBM700) [ CP001984 to CP00199055]
- Bacillus megaterium strain DSM319, sequence accession (chromosome) [ CP00198255]
- Listeria monocytogenes serovar 4a strain M7, sequence accession [ CP00281656]
- Bacillus coagulans 2-6, sequence accession [ CP00247257]
- Streptococcus salivarius strain CCHSS3, sequence accession [ FR87348158]
- Paenibacillus elgii B69, sequence accession [ AFHW0100000059]
- Lactobacillus pentosus MP-10, sequence accession through FR871759 [ FR87184860]
- Leuconostoc pseudomesenteroides KCTC 3652, sequence accession AEOQ00000001 through AEOQ00001160 [61]
- Lactobacillus mali KCTC 3596, sequence accession through BACP01000001 [ BACP0100012262]
- Paenibacillus polymyxa Type Strain ATCC 842T, sequence accession [ AFOX0100000063]
- Streptococcus salivarius strain JIM8777, sequence accssion [ FR87348264]
- Lactobacillus cypricasei KCTC 13900, sequence accession [ BACS01000001 to BACS0100048765]
- Lactobacillus zeae KCTC 3804, sequence accession to BACQ101000113 [ BACQ0100000166]
- Listeria monocytogenes Serovar 4a Strain M7, sequence accession [ CP00281667]
- Lactobacillus salivarius GJ-24, sequence accession [ AFOI0000000068]
- Lactobacillus johnsonii PF01, sequence accession [ AFQJ0100000069]
- Clostridium acetobutylicum DSM 1731, sequence accession through CP002660 [ CP00266270]
- Lactobacillus suebicus KCTC 3549, sequence accession [ BACO0100000071]
- Brevibacillus laterosporus LMG 15441, sequence accession [ AFRV0000000072]
- Lactobacillus salivarius NIAS840, sequence accession [ AFMN0000000073]
- Bifidobacterium animalis subsp. lactis CNCM I-2494, sequence accession [ CP00291574]
- Megasphaera elsdenii, sequence accession [ HE57679475]
- Lactobacillus versmoldensis KCTC 3814, sequence accession [ BACR01000001 to BACR0100010276]
- Lactobacillus pentosus IG1, sequence accession [ FR874848 to FR87486077]
- Alicyclobacillus acidocaldarius Strain Tc-4-1, sequence accession [ CP00290278]
- Streptococcus thermophilus Strain JIM8232, sequence accession [ FR87517879]
- Streptococcus equi subsp. zooepidemicus Strain ATCC 35246, sequence accession [ CP00290480]
- Bacillus amyloliquefaciens XH7, sequence accession [ CP00292781]
- Leuconostoc kimchii Strain C2, sequence accession [ CP00289882]
- Lactobacillus malefermentans KCTC 3548, sequence accession [ BACN01000001 to BACN0100017283]
- Weissella koreensis KACC 15510, sequence accession [ CP00290084]
- Phylum Tenericutes
- Mycoplasma bovis Strain Hubei-1, sequence accession [ CP00251385]
- Mycoplasma fermentans Strain M64, sequence accession [ NC_01492186]
- Haloplasma contractile, sequence accession [ AFNU0000000087]
- Mycoplasma ovipneumoniae Strain SC01, sequence accession [ AFHO0100000088]
- Phylum Actinobacteria
- Kocuria rhizophila P7-4, sequence accession [ AFID0000000089]
- Streptomyces S4, sequence accession [ CADY0100000090]
- Corynebacterium nuruki S6-4T, sequence accession [ AFIZ0000000091]
- Propionibacterium humerusii, sequence accession [ AFAM00000000.192]
- Strain JDM601, sequence accession [ CP00232993]
- Streptomyces sp. strain Tü6071, sequence accession [ AFHJ0100000094]
- Bifidobacterium breve UCC2003, sequence accession [ CP00030395]
- Propionibacterium acnes, sequence accession [ CP00281596]
- Amycolicicoccus subflavus DQS3-9A1T, sequence accession (chromosome), CP002786 (plasmid pAS9A-1), and CP002787 (plasmid pAS9A-2). [ CP00278897]
- Gordonia neofelifaecis NRRL B-59395, sequence accession [ AEUD0100000098]
- Pseudonocardia dioxanivorans strain CB1190, sequence accession NC_015312-4 and CP002595-7 [99]
- Bifidobacterium longum subsp. longum KACC 91563, sequence accession [ CP002794 to CP002796100]
- Streptomyces cattleya NRRL 8057, sequence accession (chromosome) and FQ859185 (megaplasmid) [ FQ859184101]
- Rhodococcus sp. Strain R04, sequence accession [ AFAQ01000000102]
- Mycobacterium bovis BCG Moreau, sequence accession [103]
- Saccharopolyspora spinosa NRRL 18395, sequence accession [104]
- Mycobacterium tuberculosis CCDC5079, sequence accession [105]
- Mycobacterium tuberculosis CCDC5180, sequence accession [105]
- Amycolatopsis mediterranei S699, sequence accession [ CP002896106]
- Nesterenkonia sp. Strain F, sequence accession [ AFRW01000000107]
- Streptomyces xinghaiensis NRRL T, sequence accession B24674 [ AFRP01000000108]
- Phylum Chlamydiae
- Chlamydophila abortus variant strain LLG, sequence accession [ AFHM01000000109]
- Chlamydia psittaci 6BC, sequence accession (chromosome), CP002586 (plasmid) [ CP002587110]
- Chlamydia psittaci Cal10, sequence accession (draft chromosome and plasmid) [ AEZD00000000110]
- Chlamydia trachomatis, sequence accession [ CP002024111]
- Phylum Spirochaetes
- Spirochaeta thermophila DSM 6192, sequence accession [ CP001698112]
- Brachyspira intermedia, sequence accession (chromosome) and CP002874 (plasmid) [ CP002875113]
- Phylum Fibrobacteres
- Phylum Bacteroidetes
- Porphyromonas gingivalis TDC60, sequence accession [ AP012203114]
- Krokinobacter sp. strain 4H-3-7-5, sequence accession [ CP002528115]
- Lacinutrix sp. strain 5H-3-7-4, sequence accession [ CP002825115]
- Bacterium HQM9, sequence accession [ AFPB00000000116]
- Anaerophaga sp. Strain HS1, sequence accession [ AFSL00000000117]
- Capnocytophaga canimorsus Strain 5, sequence accession [ CP002113118]
- Mesoflavibacter zeaxanthinifaciens strain S86, sequence accession [ AFOE00000000119]
- Phylum Verrucomicrobia
- Phylum Lentisphaerae
- Phylum Thermotogae
- Kosmotoga olearia Strain TBF 19.5.1, sequence accession [ CP001634120]
- Domain Archaea
- "Candidatus Nitrosoarchaeum koreensis" MY1, sequence accession [ AFPU00000000121]
Non-Bacterial genomes
- North-European Cucumber Cucumis sativus L., sequence accession , FI132140-FI136208, GS765762-GS766880 [ GS815969-GS874855122]
- Castor bean Ricinus communis organelle genome, sequence accession (chloroplast), JF937588 (mitochondria) [ HQ874649123]
- Stretch Lagoon Orbivirus Umatilla, sequence accession through HQ842619 [ HQ842628124]
- Atlantic cod Gadus morhua, sequence accession through CAEA01000001 [ CAEA01554869125]
- Potato Solanum tuberosum L., sequence accession through GS025503 [ GS026177126]
- ΦCA82, sequence accession [ HQ264138127]
- Paramecium caudatumreveals mitochondria, sequence accession NC001324 [128]
- bacteriophage IME08, sequence accession [ NC_014260129]
- virus (ILTV), sequence accession HQ_630064 [130]
- Australian kangaroo Macropus eugenii, sequence accession [ ABQO000000000131]
- Aichi virus, sequence accession [ FJ890523132]
- "Candidatus Tremblaya princeps" Strain PCVAL, sequence accession [ CP002918133]
9.
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
Phylum Euryarchaeota
- Halococcus hamelinensis, sequence accession PRJNA80845 [1]
- “Methanocella conradii” HZ254, sequence accession [ CP0032432]
- Thermococcus litoralis NS-C, sequence accession [ AHVB000000003]
Phylum Crenarchaeota
- Candidatus Nitrosopumilus salaria” BD31, sequence accession [ AEXL000000004]
- Candidatus Nitrosoarchaeum limnia, sequence accession [ AHJG000000005]
Phylum Deinococcus-Thermus
- Deinococcus gobiensis, sequence accession [ CP0025366]
Phylum Proteobacteria
- Aggregatibacter actinomycetemcomitans strain ANH9381, sequence accession [ CP0030997]
- Alishewanella jeotgali, sequence accession [ AHTH000000008]
- Enterobacter aerogenes KCTC 2190, sequence accession [ CP0028249]
- Escherichia coli O104:H4, sequence accession [ AFOB0200009210]
- Helicobacter pylori strains 17874, sequence accession PRJNA76569 [11]
- Helicobacter pylori strains P79, sequence accession PRJNA76567 [11]
- Janthinobacterium sp. Strain PAMC 25724, sequence accession [ AHHB0000000012]
- Klebsiella oxytoca KCTC 1686, sequence accession [ CP00321813]
- Klebsiella pneumoniae subsp. pneumoniae HS11286, sequence accession (chromosome), CP003200 (plasmid pKPHS1), CP003223 (plasmid pKPHS2), CP003224 (plasmid pKPHS3), CP003225 (plasmid pKPHS4), CP003226 (plasmid pKPHS5), CP003227 (plasmid pKPHS6) [ CP00322814]
- Oceanimonas sp. GK1, sequence accession [ CP00317115]
- “Pseudogulbenkiania ferrooxidans” Strain 2002, sequence accession [ NZ_ACIS0100000016]
- Pseudomonas extremaustralis 14-3b, sequence accession [ AHIP0000000017]
- Pseudomonas sp. Strain PAMC 25886, sequence accession [ AHHC0000000018]
- Psychrobacter, sequence accession [ AHVZ0000000019]
- Rahnella sp. Strain Y9602, sequence accession [ CP00250520]
- Rhizobium sp. Strain PDO1-076, sequence accession [ AHZC0000000021]
- Rhodospirillum photometricum DSM122, sequence accession [ HE66349322]
- “Rickettsia sibirica sibirica”, sequence accession [ AHIZ0000000023]
- Rickettsia sibirica subsp. mongolitimonae strain HA-91, sequence accession [ AHZB0000000024]
- Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5, sequence accession [25]
- Salmonella enterica subsp. enterica Serotype Senftenberg Strain SS209, sequence accession [ CAGQ0000000026]
- Salmonella enterica subsp. enterica Serovar Typhi P-stx-12, sequence accession (chromosome) and CP003278 (plasmid) [ CP00327927]
- Sphingomonas echinoides ATCC 14820, sequence accession [ AHIR0000000028]
- Strain HIMB55, sequence accession [ AGIF0000000029]
- Vibrio harveyi CAIM 1792, sequence accession [ AHHQ0000000030]
- Wolbachia Strain wAlbB, sequence accession [ CAGB01000001 to CAGB0100016531]
- Xanthomonas axonopodis pv. punicae Strain LMG 859, sequence accession [ CAGJ01000001 to CAGJ0100021732]
Phylum Tenericutes
- Mycoplasma hyorhinis Strain GDL-1, sequence accession [ CP00323133]
Phylum Firmicutes
- Bacillus subtilis, sequence accession BGSCID 3A27 through BGSCID 28A4 [34]
- Clostridium difficile Strain CD37, sequence accession [ AHJJ0000000035]
- Clostridium perfringens, sequence accession [ AFES0000000036]
- Lactobacillus fructivorans KCTC 3543, sequence accession [ AEQY0000000037]
- Lactococcus lactis IO-1, sequence accession [ AP01228138]
- Lactobacillus plantarum strain NC8, sequence accession [ AGRI0000000039]
- Paenibacillus dendritiformis C454, sequence accession [ AHKH0000000040]
- Paenibacillus sp. Strain Aloe-11, sequence accession [ AGFI0000000041]
- “Peptoniphilus rhinitidis” 1-13T, sequence accession [ BAEW01000001 to BAEW0100005642]
- Streptococcus macedonicus ACA-DC 198, sequence accession and HE613569 [ HE61357043]
- Staphylococcus aureus VC40, sequence accession [ CP00303344]
- Streptococcus infantarius subsp. infantarius Strain CJ18, sequence accession (chromosome), CP003295 (plasmid) [ CP00329645]
- Streptococcus macedonicus ACA-DC 198, sequence accession (chromosome), HE613569 (plasmid pSMA198) [ HE61357046]
Phylum Actinobacteria
- Actinoplanes sp. SE50/110, sequence accession [ CP00317047]
- Amycolatopsis sp. Strain ATCC 39116, sequence accession [48]
- Nocardia cyriacigeorgica GUH-2, sequence accession [ FO08284349]
- Salinibacterium sp., sequence accession [ AHWA0000000050]
- Streptomyces acidiscabies 84-104, sequence accession [ AHBF0000000051]
Non-Bacterial genomes
- Bluetongue Virus Serotype 2, sequence accession (Seg-6) and AJ783905 (Seg-1), JQ681257 (Seg-1), JQ681257 (Seg-2), JQ681258 (Seg-3), JQ681259 (Seg-4), JQ681260 (Seg-5), JQ681261 (Seg-7), JQ6812563 (Seg-8), JQ6812564 (Seg-9), to JQ681262 (Seg-10) [ JQ68126552]
- Virus Serotype 1, sequence accession (Seg-2), AJ585111 (Seg-6), AJ586659 (Seg-1), JQ282770 (Seg-3), JQ282771 (Seg-4), JQ282772 (Seg-5), JQ282773 (Seg-7), JQ282774 (Seg-8), JQ282775 (Seg-9), and JQ282776 (Seg-10) [ JQ28277752]
- Chloroplast genome of Erycina pusilla, sequence accession JF_746994 [53]
- Danio rerio, sequence accession [ JQ43410154]
- Enterococcal Bacteriophage SAP6, sequence accession [ JF73112855]
- Eubenangee virus, sequence accession through JQ070376 [ JQ07038556]
- Fujian/411-like viruses, sequence accession [ CY087969 to CY08856857]
- Hantavirus Variant of Rio Mamoré Virus, Maripa Virus, sequence accession (segment S), JQ611712 (segment M), and JQ611713 (segment L) [ JQ61171458]
- Pata virus, sequence accession through JQ070386 [ JQ07039559]
- Porcine Circovirus 2, sequence accession [ JQ41380860]
- Porcine Reproductive and Respiratory Syndrome Virus, sequence accession [ JQ32627161]
- Streptococcus mutans Phage M102AD, sequence accession [ DQ38616262]
- Tilligery virus, sequence accession through JQ070366 [ JQ07037563]
10.
Xiaopeng Xu Shaoping Weng Ting Lin Junliang Tang Lichao Huang Jing Wang Xiaoqiang Yu Ling Lu Zhijian Huang Jianguo He 《Journal of virology》2010,84(22):11866-11875
Putative open reading frames (ORFs) encoding laminin-like proteins are found in all members of the genus Megalocytivirus, family Iridoviridae. This is the first study that identified the VP23R protein encoded by ORF23R of the infectious spleen and kidney necrosis virus (ISKNV), a member of these genes of megalocytiviruses. The VP23R mRNA covering the ISKNV genomic coordinates 19547 to 22273 was transcribed ahead of the major capsid protein. Immunofluorescence analysis demonstrated that VP23R was expressed on the plasma membrane of the ISKNV-infected cells and could not be a viral envelope protein. Residues 292 to 576 of VP23R are homologous to the laminin γ1III2-6 fragment, which covers the nidogen-binding site. An immunoprecipitation assay showed that VP23R could interact with nidogen-1, and immunohistochemistry showed that nidogen-1 was localized on the outer membrane of the infected cells. Electron microscopy showed that a virus-mock basement membrane (VMBM) was formed on the surface of the infected cells and a layer of endothelial cells (ECs) was attached to the VMBM. The VMBM contained VP23R and nidogen-1 but not collagen IV. The attached ECs were identified as lymphatic endothelial cells (LECs), which have unique feature of overlapping intercellular junctions and can be stained by immunohistochemistry using an antibody against a specific lymphatic marker, Prox-1. Such infection signs have never been described in viruses. Elucidating the functions of LECs attached to the surface of the infected cells may be useful for studies on the pathogenic mechanisms of megalocytiviruses and may also be important for studies on lymphangiogenesis and basement membrane functions.Basement membrane (BM), a dense and sheetlike structure that is always associated with cells, is a very important specialized form of extracellular matrix (31, 67). BMs mediate tissue compartmentalization and provide structural support to the epithelium, endothelium, peripheral nerve axons, fat cells, and muscle cells, as well as structural and functional foundations of the vasculature (25, 31, 52). BM is also an important regulator of cell behaviors, such as adhesion, migration, proliferation, and differentiation. BMs are highly cross-linked and insoluble materials. They are highly complex and are made up of more than 50 known components (31, 54). Although the molecular composition of BMs is unique in each tissue, their basic structures are similar. Even if many more isoforms exist in different species, the major BM proteins and their receptors are conserved from Caenorhabditis elegans to mammals. BM consists of a layer of laminin polymer, a layer of type IV collagen network, and the nidogen protein, which acts as a cross-linker of these two networks. Other BM components, such as perlecan and fibulin, interact with the laminin polymer and the type IV collagen network to organize a functional BM on the basolateral aspect of the cells (31, 45, 52).The components of BM are able to self-assemble and form a sheetlike structure, and laminin is the key molecule in this process (50). Laminin protein consists of three different chains (α, β, and γ), which comprise a cross-shaped molecular structure with three short amino-terminal arms and a long carboxyl-terminal triple-helical arm (58, 68). The three short arms of this cross-shaped structure can interact with each other in the presence of calcium. Through the binding of globular G domain at the carboxyl-terminal end of the α chain to the cell receptors (e.g., integrins and dystroglycans), laminin self-assembles into polygonal lattices on cell surfaces. This process initiates BM self-assembly (15, 21, 25, 38, 65, 66). To date, 17 laminin isoforms have been observed in different tissues (51). Among them, laminin-1, the crux of early embryonic BM assembly, has been well studied. Laminin-1 consists of α1, β1, and γ1 chains and can interact with nidogen-1 with high affinity through a laminin-type epidermal growth factor-like (LE) module, γ1III4, within the domain III of the γ1 chain (1, 42). The heptapeptide “NIDPNAV” within the γ1III4 motif of laminin-1 is essential for the interaction between laminin-1 and nidogen-1 (41, 46). Blocking the interactions between laminin-1 and nidogen-1 leads to the disruption of BMs. This indicates that the formation of laminin/nidogen complex is essential for BM assembly and stability (30, 61). Nidogen-1, also called entactin-1, is a dumbbell-shaped sulfated 150-kDa glycoprotein consisted of three domains (G1, G2, and G3) (12). By interacting with collagen IV through its G2 domain and binding with laminin γ1 chain through its G3 domain, nidogen-1 bridges the layers of the laminin network and the collagen IV network to construct the fundamental structure of BMs (48). Collagen IV is a triple-helical trimer composed of three α chains. Through the hexamer formation of the carboxyl-terminal globular non-collagenous-1 (NC1) domain of each α chain, two collagen IV proteins assemble into a dimer. Dimers of collagen IV connect with each other via their amino-terminal 7S domains and self-assemble into a network (24, 27, 31, 32). Six kinds of α chains of collagen IV have been identified in mammals. Among them, α1 and α2 chains are the most abundant forms of collagen IV found in all BMs (19, 23). They commonly form a collagen IV molecule with a α1 and α2 ratio of 2:1 (31, 35).Iridoviruses infect invertebrates and poikilothermic vertebrates, including insects, fish, amphibians, and reptiles. These viruses are a group of icosahedral cytoplasmic DNA viruses with circularly permuted and terminally redundant DNA genomes (6, 8, 9, 10, 57, 62). The family Iridoviridae has been subdivided into five genera: Iridovirus, Chloriridovirus, Ranavirus, Lymphocystisvirus, and Megalocystivirus (7). The genus Megalocystivirus, characterized by the ability to cause swelling of the infected cells, is one group of the most harmful viruses to cultured fish (7, 26, 29). Infectious spleen and kidney necrosis virus (ISKNV), the causative agent of a disease that causes high mortality rates in farmed mandarin fish, Siniperca chuatsi, and large-mouth bass, Micropterus salmoides, is regarded as the type species of Megalocystivirus (7). Similar to infection caused by other members of the Megalocystivirus, fish ISKNV infection is characterized by cell hypertrophy in the spleen, kidney, cranial connective tissue, and endocardium (16, 17). Aside from mandarin fish and large-mouth bass, ISKNV-like virus can also be detected in the tissues of more than 60 marine and freshwater fishes (14, 28, 59, 64). The entire genome of ISKNV has been sequenced, and the organization of open reading frames (ORFs) of ISKNV was analyzed by using DNASTAR Omiga 2.0 and Genescan (18). The ISKNV genome is about 110 kbp and contains 125 putative ORFs (GenBank accession no. ).Putative ORFs, encoding viral proteins containing a fragment homologous to laminin and a putative transmembrane fragment, were found in all of the sequenced genomes of the members of Megalocystivirus. These ORFs include ORF23R of ISKNV (GenBank accession no. AF371960), laminin-like protein gene of olive flounder iridovirus (GenBank accession no. AAL98747), ORF2 of sea perch iridovirus (GenBank accession no. AAT76907), predicted laminin-type epidermal growth factor-like protein of large yellow croaker iridovirus (GenBank accession no. AAV51313), an unknown gene of red sea bream iridovirus (GenBank accession no. ABI32391), ORF2 of rock bream iridovirus (GenBank accession no. AAQ07956), and laminin-type epidermal growth factor-like protein of orange-spotted grouper iridovirus (GenBank accession no. AAN86692). These putative proteins are highly homologous to each other in amino acid sequence (65 to 99% identity). However, the functions of these proteins have never been identified. This is the first study to identify that the VP23R protein encoded by ORF23R of ISKNV is a plasma membrane-localized viral protein. In addition, we discovered a new function of VP23R in a unique pathological phenomenon of virus infection: the attachment of lymphatic endothelial cells (LECs) to the infected cells. Nidogen-1 assisted VP23R in the construction of a BM-like structure, providing an attachment site for LECs. This unique pathological phenomenon has never been found in viruses and is an attractive direction for studies of pathogenic mechanisms of megalocystiviruses. Moreover, studies on the unique profiles of the virus-mock BM can help us learn more about the functions of BM components and the mechanisms of lymphangiogenesis. AAX82335相似文献
11.
12.
Vassili N. Kouvelis Elizabeth Saunders Thomas S. Brettin David Bruce Chris Detter Cliff Han Milton A. Typas Katherine M. Pappas 《Journal of bacteriology》2009,191(22):7140-7141
Zymomonas mobilis is an ethanol-producing alphaproteobacterium currently considered a major candidate organism for bioethanol production. Here we report the finished and annotated genome sequence of Z. mobilis subsp. mobilis strain NCIMB 11163, a British ale-infecting isolate. This is the first Z. mobilis strain whose genome, chromosomal and plasmid, is presented in its entirety.Zymomonas mobilis is a bacterium vigorously studied as a platform organism for bioethanol production in North America and other parts of the world. Z. mobilis converts sugars such as glucose or sucrose into ethanol and carbon dioxide to almost theoretical yields and to rates higher than those of yeasts (17). Genetically engineered strains that ferment pentoses in addition to naturally utilized hexoses also hold great promise for use in lignocellulosic biomass degradations (5, 22). Besides ethanol, Z. mobilis can produce other high-value chemicals such as sorbitol, levan, or phenylacetylcarbinol and has attracted interest for its unusual membrane steroid content (11). Lastly, Zymomonas is regarded as a safe organism and is even used for medicinal purposes (12, 20), which further facilitates its employment in large-scale biotechnological endeavors.The chromosomal sequence of the Z. mobilis subsp. mobilis industrial strain ATCC 31821 (ZM4) was recently published (19). Here we announce the first entire genome sequence of a Z. mobilis subsp. mobilis strain, that of the United Kingdom-originating strain NCIMB 11163 (B70) (20). Total DNA from NCIMB 11163 (16) was used for whole-genome shotgun sequencing at the U.S. DOE Joint Genome Institute. For this, an 8.7-kb DNA library and 454 and Solexa reads were used (http://www.jgi.doe.gov). Draft assemblies were based on 8,551 Sanger reads and 454 pyrosequencing to 20× coverage, whereas the Phred/Phrap/Consed software package was used for sequence assembly and quality assessment (6, 7, 9; http://www.phrap.com). After the shotgun stage, reads were assembled with parallel Phrap (High Performance Software, LLC), and misassemblies were corrected with Dupfinisher (10) or transposon bombing of bridging clones (Epicentre Biotechnologies, Madison, WI). A total of 144 primer walk reactions, five transposon bomb libraries, 53 PCR end reads, and two PCR shatter libraries were necessary to close gaps, resolve repetitive regions, and raise the quality of the finished sequence. The completed genome sequence of NCIMB 11163 was based on 11,048 reads, with an error rate of less than 6 bp out of 100,000 bp.Open reading frame prediction and annotation were performed using Prodigal (http://compbio.ornl.gov/prodigal/) and BLAST (1); tRNAscan-SE and RNAmmer (14, 15) were used for tRNA and rRNA recognition, respectively. Functional assignment of genes was performed by searching translated open reading frames against sequences in the SPTR (TrEMBL) (2), Pfam (8), TIGRFAMs (18), COG (21), and KEGG (13) databases.Z. mobilis NCIMB 11163 contains a single, circular chromosome of 2,124,771 bp and three plasmids, p11163_1, p11163_2, and p11163_3 of 53,380 bp, 40,818 bp, and 4,551 bp, respectively. The overall GC content of the chromosome is 46.83%, whereas those of the plasmids are 42.32%, 43.80%, and 36.37%, respectively. The entire genome of NCIMB 11163 contains 1,884 protein-encoding genes and 51 tRNA and nine rRNA genes, which are chromosomally located.The chromosome of NCIMB 11163 is 68,355 bp larger than that of ZM4 (GenBank accession number ) ( NC_00652619) and colinear at its largest part with that of ZM4 (genome structure comparisons were performed using ACT) (3). It bears several unique regions, among which are two genomic islands of ca. 25 and 79 kb, with no detectable nucleotide homology to same-species sequences and high regional similarity to chromosomal stretches of Paracoccus denitrificans PD1222 (GenBank accession number ), Xanthobacter autotrophicus Py2 (GenBank accession number CP000489.1), and Gluconacetobacter diazotrophicus PAl 5 (GenBank accession number CP000781.1). Genome plasticity in NCIMB 11163 is further indicated by the presence of a type IV secretion system on the 79-kb island, syntenous to the Agrobacterium tumefaciens Ti (IncRh1) conjugal trb system ( CP001189.14), and also by multiple transposase and phage-related genes.In plasmids, housekeeping genes implicated in replication, active partitioning, and plasmid addiction are recognized, as well as genes involved in metabolism, transport, regulation, transposition, and DNA modification. Most notably, p11163_1 bears an arsenical resistance operon inserted in a type II secretion locus, whereas p11163_2, otherwise homologous to the 41-kb ZM4 plasmid (GenBank accession number ), harbors a unique ca. 12-kb CRISPR insertion that interrupts nucleotide colinearity with the aforementioned replicon. AY057845相似文献
13.
Elucidating and Minimizing the Loss by Recombinant Vaccinia Virus of Human Immunodeficiency Virus Gene Expression Resulting from Spontaneous Mutations and Positive Selection
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Linda S. Wyatt Patricia L. Earl Wei Xiao Jeffrey L. Americo Catherine A. Cotter Jennifer Vogt Bernard Moss 《Journal of virology》2009,83(14):7176-7184
While characterizing modified vaccinia virus recombinants (rMVAs) containing human immunodeficiency virus env and gag-pol genes, we detected nonexpressing mutants by immunostaining individual plaques. In many cases, the numbers of mutants increased during successive passages, indicating strong selection pressure. This phenomenon provided an opportunity to investigate the formation of spontaneous mutations in vaccinia virus, which encodes its own cytoplasmic replication system, and a challenge to reduce the occurrence of mutations for vaccine production. Analysis of virus from individual plaques indicated that loss of expression was due to frameshift mutations, mostly by addition or deletion of a single nucleotide in runs of four to six Gs or Cs, and large deletions that included MVA DNA flanking the recombinant gene. Interruption of the runs of Gs and Cs by silent codon alterations and moving the recombinant gene to a site between essential, highly conserved MVA genes eliminated or reduced frameshifts and viable deletion mutants, respectively. The rapidity at which nonexpressing mutants accumulated depended on the individual env and gag-pol genes and their suppressive effects on virus replication. Both the extracellular and transmembrane domains contributed to the selection of nonexpressing Env mutants. Stability of an unstable Env was improved by swapping external or transmembrane domains with a more stable Env. Most dramatically, removal of the transmembrane and cytoplasmic domains stabilized even the most highly unstable Env. Understanding the causes of instability and taking preemptive actions will facilitate the development of rMVA and other poxviruses as human and veterinary recombinant vaccines.Vaccinia virus (VACV), the first recombinant virus shown to induce a protective immune response against an unrelated pathogen (21, 22), is being employed as a vector for veterinary and wildlife vaccines (19). Development of recombinant VACV for human use, however, has been impeded by safety concerns. For this reason, there is interest in modified VACV Ankara (MVA), a highly attenuated smallpox vaccine with an exemplary safety profile even in immunodeficient animals (17, 26, 27). MVA is severely host range restricted and propagates poorly or not at all in most mammalian cells because of a block in virion assembly (29). Initial experiments with recombinant MVA (rMVA) demonstrated its ability to robustly express foreign proteins (29) and induce protective humoral and cell-mediated immunity (30). Currently, rMVA candidate vaccines expressing genes from a wide variety of pathogens are undergoing animal and human testing (13).While developing candidate human immunodeficiency virus (HIV) and other vaccines, we encountered a tendency for mutant rMVA that had lost the ability to express foreign proteins to arise after tissue culture passage (28, 34, 37). This instability may initially go undetected, however, unless individual plaques are isolated and analyzed. Nevertheless, once established in the population, the nonexpressors can rapidly overgrow the original rMVA. These considerations are particularly important for production of large vaccine seed stocks of rMVA. The instability of cloned genes in MVA is surprising, since MVA had already undergone genetic changes during its adaptation through hundreds of passages in chicken embryo fibroblasts (CEFs) and is now quite stable. Indeed, identical 167,000-bp genome sequences have been reported for three independent plaque isolates, accession numbers , U94848, and AY603355, and by Antoine et al. ( DQ9832361). Although the cause of the instability of the gene inserts had not been previously investigated, harmful effects of the recombinant protein seem to play a role in the selective advantage of nonexpressing mutants. Thus, reducing the expression level of parainfluenza virus and measles virus transmembrane proteins and deleting part of the cytoplasmic tail of HIV Env improves the stability of rMVAs (28, 34, 37). Reducing expression, however, can also decrease immunogenicity and therefore may be undesirable (36).In view of the importance of understanding and overcoming this pernicious instability problem, we carried out a systematic study of HIV env and gag-pol genes that were unstable in rMVA. We also considered that the analysis would provide basic information regarding the kinds of errors that can occur during replication of the VACV genome, which encodes its own cytoplasmic replication system (20). The most common mutations, which led to loss of recombinant gene expression, were large deletions that extended deep into the MVA flanks and frameshift mutations within consecutive identical nucleotides in the insert. The frequency of viable mutations was minimized by introducing the recombinant gene between two essential, highly conserved MVA genes and by making silent codon alterations to interrupt the homonucleotide runs. In addition, we constructed a panel of recombinant viruses with chimeric and truncated env genes to determine the basis for the selection of nonexpressing mutants and to prevent their expansion during virus propagation. Understanding the causes of the instability and taking preemptive actions should facilitate the development of MVA and other poxviruses as human and veterinary vaccines. In addition, these insights may have application to other DNA expression vectors. 相似文献
14.
Hyun-Myung Oh Ilnam Kang Steve Ferriera Stephen J. Giovannoni Jang-Cheon Cho 《Journal of bacteriology》2010,192(17):4530-4531
Strain HTCC2143 was isolated from Oregon Coast surface waters using dilution-to-extinction culturing. Here we present the genome of strain HTCC2143 from the BD1-7 clade of the oligotrophic marine Gammaproteobacteria group. The genome of HTCC2143 contains genes for carotenoid biosynthesis and proteorhodopsin and for proteins that have potential biotechnological significance: epoxide hydrolases, Baeyer-Villiger monooxygenases, and polyketide synthases.Strain HTCC2143 was sampled and isolated from surface waters (depth, 10 m) off the Coastal Pacific Ocean, Newport, OR (44°36′0"N, 124°6′0"W). In the course of dilution-to-extinction culture studies on coastal microbial communities, strain HTCC2143 was isolated in a pristine seawater-based medium (2). Phylogenetic analysis of 16S rRNA gene sequences placed strain HTCC2143 in the BD1-7 clade of the oligotrophic marine Gammaproteobacteria (OMG) group (2) and indicated that it is related to Dasania marina, isolated from Arctic marine sediment (3, 8). The HTCC2143 16S rRNA gene sequence is 95.3% similar to that of D. marina () and is 96.6% similar to that of environmental gene clone 20m-45 ( AY771747), taken from intertidal beach seawater of the Yellow Sea, South Korea. Other closer relatives of HTCC2143 included uncultured gammaproteobacterial clones from seafloor lava (clone P0X3b5B06 from Hawaii South Point X3, GU061297; 96.3%) ( EU4913839), deep-sea sediment (Ucp1554 from the South Atlantic Ocean, Cape Basin, ; 95.9%) ( AM99764510), Yellow Sea sediment (95.8%; D8S-33, ), and Arctic sediment (from Kings Bay, Svalbard, Norway; clone SS1_B_07_55, EU652559; 95.7%).Genomic DNA was prepared at Oregon State University and sequenced by the J. Craig Venter Institute. The finished contigs were automatically annotated with a system based on the program GenDB ( EU0508255) and manually annotated as described in previous reports (7, 12). The annotation is available at http://bioinfo.cgrb.oregonstate.edu/microbes/. The draft genome of strain HTCC2143 comprises 3,925,629 bases and 3,662 predicted coding sequences with a G+C content of 47.0%. The genome of HTCC2143 was predicted to contain 40 tRNAs, 1 16S rRNA, 2 5S rRNAs, and 2 23S rRNA genes. Four genes for selenocysteine metabolism were found, including a selenophosphate-dependent tRNA 2-selenouridine synthase and an l-seryl-tRNA(Sec) selenium transferase (EC 2.9.1.1).Strain HTCC2143 had genes for a complete tricarboxylic acid cycle, glycolysis, a pentose phosphate pathway, and an Entner-Doudoroff pathway. Genes were present for a high-affinity phosphate transporter and a pho regulon for sensing of environmental inorganic phosphate availability, as well as genes from the NUDIX (nucleoside diphosphate linked to some other moiety X) hydrolase domain family (1) that reflects the metabolic complexity of prokaryotes (4). Genes for ammonium transporters, nitrate reductase, and sulfate reductase were also present in the HTCC2143 genome.Carotenoid and proteorhodopsin genes were also found in the genome, as well as genes for polyketide synthase modules and related proteins. Carotenoid and proteorhodopsin genes were reported previously from another member of the OMG group, strain HTCC2207, a SAR92 clade isolate (11). HTCC2143 also encoded two epoxide hydrolases, two cyclohexanone monooxygenases (CHMOs) and a cyclododecanone monooxygenase (CDMO). CDMOs and CHMOs are members of the Baeyer-Villiger monooxygenase (BVMO) family. BVMOs are “green” alternatives to the chemically mediated Baeyer-Villiger reactions that allow the conversion of ketones into esters or of cyclic ketones into lactones (6).This genome provides further evidence that dilution-to-extinction culturing methods that make use of low-nutrient media that are similar to the conditions of the natural environment can result in the isolation of novel, environmentally significant organisms with potential biotechnological value (13). 相似文献
15.
Fabio Rezzonico Guido Vogel Brion Duffy Mauro Tonolla 《Applied and environmental microbiology》2010,76(13):4497-4509
Pantoea agglomerans is an ecologically diverse taxon that includes commercially important plant-beneficial strains and opportunistic clinical isolates. Standard biochemical identification methods in diagnostic laboratories were repeatedly shown to run into false-positive identifications of P. agglomerans, a fact which is also reflected by the high number of 16S rRNA gene sequences in public databases that are incorrectly assigned to this species. More reliable methods for rapid identification are required to ascertain the prevalence of this species in clinical samples and to evaluate the biosafety of beneficial isolates. Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) methods and reference spectra (SuperSpectrum) were developed for accurate identification of P. agglomerans and related bacteria and used to detect differences in the protein profile within variants of the same strain, including a ribosomal point mutation conferring streptomycin resistance. MALDI-TOF MS-based clustering was shown to generally agree with classification based on gyrB sequencing, allowing rapid and reliable identification at the species level.Pantoea agglomerans (20) is a ubiquitous plant-epiphytic bacterium that belongs to the family Enterobacteriaceae. While several strains are commercialized for biological control of plant diseases (23), the species also includes two phytopathogenic pathovars that carry distinctive virulence plasmids (32). P. agglomerans has a Jekyll-Hyde nature, being described also as an opportunistic human pathogen (30), which raises biosafety regulatory issues for the utilization of beneficial isolates (45). Clinical reports predominantly involve septicemia following penetrating trauma (16, 56) or nosocomial infections (14, 55). Clinical pathogenicity of this species has not been confidently confirmed (unfulfilled Koch''s postulates). Infections attributed to P. agglomerans are typically of a polymicrobial nature involving patients affected by other diseases (14) and may represent secondary contamination of wounds. Standard clinical diagnostics and identification rely mainly on biochemical profiling analysis or alternatively on 16S rRNA gene sequencing, despite the inadequacy of these techniques for precise discrimination within the Enterobacter and Pantoea genera (5, 20, 39). Problems with correct identification have been observed for automated systems such as the API 20E (24, 39) and Vitek-2/GNI+ (39, 40) (both from bioMerieux) or the Phoenix (11, 38) and Crystal identification systems (40, 48) (both from BD Diagnostic Systems).P. agglomerans is a composite taxon conglomerating former Enterobacter agglomerans, Erwinia milletiae, and Erwinia herbicola strains. Accurate identification is complicated by the unsettled taxonomy of the “P. agglomerans-E. herbicola-E. agglomerans” complex (45). Recent analyses based on gyrB sequencing, multilocus sequence analysis (MLSA) (4), and fluorescent amplified fragment length polymorphisms (fAFLP) (45) indicate that strains belonging to Enterobacter or Erwinia archived in culture collections are often erroneously assigned to P. agglomerans and are likely also misidentified in clinical diagnostics. False classifications of environmental P. agglomerans strains as related Pantoea species, including human- or plant-pathogenic P. ananatis, are also common (45). Inadequate biochemical identification methods and uncertainty regarding current taxonomy are revealed also by the excessive number of 16S rRNA gene sequences incorrectly assigned to P. agglomerans that can be retrieved from GenBank (Fig. (Fig.1).1). Sequencing of housekeeping genes, MLSA, and fAFLP are labor-intensive, time-consuming, and impractical approaches as routine diagnostic tools.Open in a separate windowFIG. 1.Taxonomy of putative P. agglomerans isolates based on 16S rRNA gene sequences retrieved from GenBank under the currently accepted species name or under the old basonyms Enterobacter agglomerans and Erwinia herbicola. Out of a total of 331 complete or partial sequences found, 263 could be aligned over their 1,240-bp central region resulting in a minimum evolution tree. For the analysis, gaps and missing data were eliminated only in pairwise sequence comparisons, resulting in a total of 1,114 positions. Nodal supports were assessed by 1,000 bootstrap replicates. Only bootstrap values greater than 50% are shown. The scale bar represents the number of base substitutions per site. The number of “P. agglomerans” sequences clustering with a given reference strain in shown in parentheses. Reference strains and clades containing reference strains are marked in bold, and the corresponding accession numbers are indicated between brackets. For the genus Erwinia the following reference strains were used: E. persicina HK204 [], E. rhapontici 2OP2 [ NR_026049.1], E. billingiae Eb661 [ FJ595873], E. tasmaniensis Et2/99 [ AM055711], and E. amylovora FAW 23482 [ AM292080].Whole-cell matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) ( AY45671131) is an emerging technology for identification of bacteria (26, 46), fungi (17, 33), viruses (29, 51), insects (41), and helminths (42). MALDI-TOF MS-based identification can accurately resolve bacterial identity at the genus, species, and in some taxa subspecies levels (e.g., Salmonella enterica serovars, Listeria genotypes) (1, 18). Identity is based on unique mass/charge ratio (m/z) fingerprints of proteins, which are ionized using short laser pulses directed to bacterial cells obtained from a single colony embedded in a matrix. After desorption, ions are accelerated in vacuum by a high electric potential and separated on the basis of the time taken to reach a detector, which is directly proportional to the mass-to-charge ratio of an ion. This technique has been shown to deliver reproducible protein mass fingerprints starting from an aliquot of a single bacterial colony within minutes and without any prior separation, purification, or concentration of samples. Whole-cell MALDI-TOF MS is a reliable technique across broad conditions (e.g., different growth media, cell growth states), with limited variability in mass-peak signatures within a selected mass range (2,000 < m/z < 20,000) that does not affect reliability of identification (28, 31). MALDI-TOF MS profiles primarily represent ribosomal proteins, which are the most abundant cellular proteins and are synthesized under all growth conditions (47). MALDI-TOF MS identification profiles derived from several characterized strains for a given species are used to develop reference spectra (e.g., SuperSpectrum; AnagnosTec GmbH, Potsdam, Germany), and they include a subset of characteristic and reproducible markers. MALDI-TOF MS identification databases are currently available for a relatively wide range of clinical bacteria, and this method has become an accepted tool for routine clinical diagnostics due to enhanced simplicity, rapidity, and reliability. However, environmental bacteria, such as Pantoea, have not been widely evaluated using MALDI-TOF MS and are largely absent from identification databases, limiting the practical reach of this new technology.Our objectives were to develop a robust method for rapid identification of P. agglomerans and related bacteria based on MALDI-TOF MS and to compare MALDI-TOF MS results against those obtained from a phylogenetic analysis based on gyrB sequencing as well as against biochemical identification methods. 相似文献
16.
Zhuo-Yang Zhang Chang Liu Yong-Zhang Zhu Yi Zhong Yong-Qiang Zhu Hua-Jun Zheng Guo-Ping Zhao Sheng-Yue Wang Xiao-Kui Guo 《Journal of bacteriology》2009,191(15):5020-5021
Lactobacillus plantarum is a lactic acid bacterium (LAB) species commonly used as a probiotic. We have sequenced the genome of Lactobacillus plantarum JDM1, which is a Chinese commercial LAB with several probiotic functions, using a GS 20 system. We recommend that each commercial probiotic strain should undergo complete genome sequencing to ensure safety and stability.Lactic acid bacteria (LAB) play a prominent role in the world food supply, performing the main bioconversions in fermented food, and are also used as probiotic supplements in dairy products and other foods. Lactobacillus plantarum is a LAB species commonly used as a probiotic. We have sequenced the genome of Lactobacillus plantarum JDM1, which is a widely used Chinese commercial LAB with several probiotic functions, using a GS 20 system (454 Life Science Corporation) (11). Two hundred thirty-six thousand, five hundred sixty-three high-quality reads were assembled with the 454 assembly tool, which had an average depth of 18.6-fold coverage of the genome and yielded 367 contigs. Among these, 225 large contigs represented 99.17% of the draft sequence. In the finishing process, the order of the selected large contigs was determined by BLAST analysis with the originally published genome sequence of strain WCFS1 (GenBank accession number ) ( AL9352638). Physical gaps were filled through sequencing of PCR products that spanned these regions using ABI 3730 xl DNA sequencers. Sequence assembly was accomplished by using the Phred/Phrap/Consed software package (4, 7). To ensure final accuracy, the errors in homopolymer sites that arose from the pyrosequencing method were solved via comparison with the corresponding sites on WCFS1 and then resequencing of the ambiguous bases using the ABI 3730 xl DNA sequencer.The complete genome of Lactobacillus plantarum JDM1 contains a single, circular chromosome of 3,197,759 bp and two plasmids (pLP2000 [2,062 bp] and pLP9000 [9,254 bp]). The two plasmids have been sequenced and published, with GenBank accession numbers and AY096004 ( AY0960053). The overall GC content of the chromosome is 44.66%, whereas the plasmids have a GC content slightly lower than that of the chromosome. The entire genome of JDM1 contains 2,948 protein-coding genes, 62 tRNA-encoding genes, and 16 rRNA-encoding genes. Several repeated sequences, designated ISP2, were found in the chromosome which were almost the same as those in WCSF1, identified as a class of transposase-encoding regions representing mobile genetic elements. The other repeated sequence, ISP1 of WCSF1, was absent in JDM1.The entire genomic sequence of L. plantarum JDM1 was a little shorter than that of L. plantarum WCSF1 (3.3 Mb). The two genomes were highly similar (>90% by BLASTN analysis) with respect to genome structure and gene order. Intraspecies diversity may be required for successful adaptation in a complex ecological habitat (2). L. plantarum JDM1 has been grown as a probiotic in rich nutritional medium for so long that the genome may have gradually contracted. As supporting evidence, many sugar transport and metabolism genes in WCFS1 were absent in JDM1.The prophage sequences and locations of JDM1 and WCFS1 are highly variable. L. plantarum JDM1 contains three prophage elements in its genome. R-Pg1, representing a short prophage remnant, is about 14 kb in size, which is similar to R-Lp3 in WCFS1. Pg2 and Pg3 are two ∼39-kb-long prophages that are closely related to Listeria phage B025 (accession no. ) and the phage Pediococcus pentosaceus ATCC 25745 (accession no. DQ003639), respectively.The genomes of LAB evolve actively to adapt to nutritionally rich environments. Even for two strains of the same species, differences obviously exist. The degradation of the genome appears to be an ongoing process not only in all species of Lactobacillus ( CP00042210) but also in different strains of the same species(2).With the development of better living conditions, the biosafety of food and medicine has received more attention. Lactobacillus bacteria have been supposed to have a “generally accepted as safe” status, but they still have been associated with negative reports (1, 6, 9). More about the functional mechanisms of JDM1 and potential side effects would be explored by complete genome sequencing and data mining. Furthermore, comparative genomics analysis could be carried out with Chinese and European strains. We believe the complete genome of each probiotic strain should be sequenced to ensure safety and stability. At the end of the day, we will get what we pay for in terms of microbial genome sequencing projects (5). 相似文献
17.
Bovine Coronavirus Nonstructural Protein 1 (p28) Is an RNA Binding Protein That Binds Terminal Genomic cis-Replication Elements
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Kortney M. Gustin Bo-Jhih Guan Agnieszka Dziduszko David A. Brian 《Journal of virology》2009,83(12):6087-6097
Nonstructural protein 1 (nsp1), a 28-kDa protein in the bovine coronavirus (BCoV) and closely related mouse hepatitis coronavirus, is the first protein cleaved from the open reading frame 1 (ORF 1) polyprotein product of genome translation. Recently, a 30-nucleotide (nt) cis-replication stem-loop VI (SLVI) has been mapped at nt 101 to 130 within a 288-nt 5′-terminal segment of the 738-nt nsp1 cistron in a BCoV defective interfering (DI) RNA. Since a similar nsp1 coding region appears in all characterized groups 1 and 2 coronavirus DI RNAs and must be translated in cis for BCoV DI RNA replication, we hypothesized that nsp1 might regulate ORF 1 expression by binding this intra-nsp1 cistronic element. Here, we (i) establish by mutation analysis that the 72-nt intracistronic SLV immediately upstream of SLVI is also a DI RNA cis-replication signal, (ii) show by gel shift and UV-cross-linking analyses that cellular proteins of ∼60 and 100 kDa, but not viral proteins, bind SLV and SLVI, (SLV-VI) and (iii) demonstrate by gel shift analysis that nsp1 purified from Escherichia coli does not bind SLV-VI but does bind three 5′ untranslated region (UTR)- and one 3′ UTR-located cis-replication SLs. Notably, nsp1 specifically binds SLIII and its flanking sequences in the 5′ UTR with ∼2.5 μM affinity. Additionally, under conditions enabling expression of nsp1 from DI RNA-encoded subgenomic mRNA, DI RNA levels were greatly reduced, but there was only a slight transient reduction in viral RNA levels. These results together indicate that nsp1 is an RNA-binding protein that may function to regulate viral genome translation or replication but not by binding SLV-VI within its own coding region.Coronaviruses (CoVs) (59) cause primarily respiratory and gastroenteric diseases in birds and mammals (35, 71). In humans, they most commonly cause mild upper respiratory disease, but the recently discovered human CoVs (HCoVs), HCoV-NL63 (65), HCoV-HKU1 (73), and severe acute respiratory syndrome (SARS)-CoV (40) cause serious diseases in the upper and lower respiratory tracts. The SARS-CoV causes pneumonia with an accompanying high (∼10%) mortality rate (69). The ∼30-kb positive-strand CoV genome, the largest known among RNA viruses, is 5′ capped and 3′ polyadenylated and replicates in the cytoplasm (41). As with other characterized cytoplasmically replicating positive-strand RNA viruses (3), translation of the CoV genome is an early step in replication, and terminally located cis-acting RNA signals regulate translation and direct genome replication (41). How these happen mechanistically in CoVs is only beginning to be understood.In the highly studied group 2 mouse hepatitis coronavirus model (MHV A59 strain) and its close relative the bovine CoV (BCoV Mebus strain), five higher-order cis-replication signals have been identified in the 5′ and 3′ untranslated regions (UTRs). These include two in the 5′ UTR required for BCoV defective interfering (DI) RNA replication (Fig. (Fig.1A)1A) described as stem-loop III (SLIII) (50) and SLIV (51). Recently, the SLI region in BCoV (15) has been reanalyzed along with the homologous region in MHV and is now described as comprising SL1 and SL2 (Fig. (Fig.1A),1A), of which SL2 has been shown to be a cis-replication structure in the context of the MHV genome (38). In the 3′ UTR, two higher-order cis-replication structures have been identified that function in both DI RNA and the MHV genome. These are a 5′-proximal bulged SL and adjacent pseudoknot that potentially act together as a unit (23, 27, 28, 72) and a 3′-proximal octamer-associated bulged SL (39, 76) (Fig. (Fig.1A).1A). In addition, the 5′-terminal 65-nucleotide (nt) leader and the 3′-terminal poly(A) tail have been shown to be cis-replication signals for BCoV DI RNA (15, 60).Open in a separate windowFIG. 1.RNA structures in the BCoV genome tested for nsp1 binding. (A) BCoV 5′-terminal and 3′-terminal cis-acting RNA SL structures and flanking sequences identified for BCoV DI RNA replication. Regions of the genome are identified and SL cis-replication elements are identified schematically. Open boxes at nt 100 and 211 identify AUG start codons for the short upstream ORF and ORF 1, respectively. A closed box at nt 124 identifies the UAG stop codon for the short upstream ORF. Shown below the SL structures are the RNA segments used as 32P-labeled probes in the gel shift assays. BSL-PK, bulged SL-pseudoknot; 8mer-BSL, octamer-associated bulged SL. (B) Gel shift assays for probes when used with purified nsp1. Protein-RNA complexes identifying a shifted probe are labeled C.In CoVs, the 5′-proximal open reading frame (ORF) of ∼20 kb (called ORF 1) comprising the 5′ two-thirds of the genome is translated to overlapping polyproteins of ∼500 and ∼700 kDa, named pp1a and pp1ab (41). pp1ab is formed by a −1 ribosomal frameshift event at the ORF1a-ORF1b junction during translation (41). pp1a and pp1ab are proteolytically processed into potentially 16 nonstructural protein (nsp) end products or partial end products that are proposed to function together as the replicase (24). ORF 1a encodes nsps 1 to 11 which include papain-like proteases (nsp3), a 3C-like main protease (nsp5), membrane-anchoring proteins (nsps 4 and 6), a potential primase (nsp8), and RNA-binding proteins (nsp 7/nsp 8 complex and nsps 9 and 10) of imprecisely understood function (19, 20, 24, 25, 29, 43, 49, 77). ORF 1b encodes nsps 12 to 16 which function as an RNA-dependent RNA polymerase, a helicase, an exonuclease, an endonuclease, and a 2′-O-methyltransferase, respectively (6, 17, 24, 44). 3′ Proximal genomic ORFs encoding structural and accessory proteins are translated from a 3′-nested set of subgenomic mRNAs (sgmRNAs) (41).The N-terminal ORF 1a protein, nsp1, in the case of BCoV and MHV is also named p28 to identify the cleaved 28-kDa product (18). The precise role of nsp1 in virus replication has not been determined, but it is known that a sequence encoding an N-proximal nsp1 region in MHV (nt 255 to 369 in the 738-nt coding sequence) cannot be deleted from the genome without loss of productive infection (10). nsp1 also directly binds nsp7 and nsp10 (11) and by confocal microscopy is found associated with the membranous replication complex (10, 66) and virus assembly sites (11). The amino acid sequence of nsp1 is poorly conserved among CoVs, indicating that it may be a protein that interacts with cellular components (1, 58). In the absence of other viral proteins, MHV nsp1 induces general host mRNA degradation (79) and cell cycle arrest (16). The SARS-CoV nsp1 homolog, a 20-kDa protein, has been reported to cause mRNA degradation (30, 45), inhibition of host protein synthesis (30, 45, 70), inhibition of interferon signaling (70, 79), and cytokine dysregulation in lung cells (36).In this study, we examine the RNA-binding properties of BCoV nsp1 with the hypothesis that it is a potential regulator of translation or replication through its binding of SLVI mapping within its coding region. The rationale for this hypothesis stems from five observations. (i) In the BCoV DI RNA, the 5′-terminal one-third (approximately) of the nsp1 cistron and the entire nucleocapsid (N) protein cistron together comprise the single contiguous ORF in the DI RNA, and most of both coding regions appear required for DI RNA replication (15). (ii) The partial nsp1 cistron in the DI RNA must be translated in cis for DI RNA replication in helper virus-infected cells (12, 14). (iii) A similar part of the nsp1 cistron is found in the genome of all characterized naturally occurring group 1 and 2 CoV DI RNAs described to date (7, 8). (iv) A cis-acting SL named SLVI is found within the partial nsp1 cistron in the BCoV DI RNA (12). (v) Translation, which involves a 5′→3′ transit of ribosomes, and negative-strand synthesis, which involves a 3′→5′ transit of the RNA-dependent RNA polymerase, cannot simultaneously occur on the same molecule with a single ORF (4, 31). Thus, to enable genome replication an inhibition of translation at least early in infection for cytoplasmically replicating positive-strand RNA viruses is required (4, 5, 22, 32). Mechanisms of translation inhibition have been described for the Qβ viral genome, wherein the viral replicase autoregulates translation by binding an intracistronic cis-replication element (32), and for the polio virus genome, wherein genome circularization inhibits the early translation step (5, 22). Therefore, since nsp1 is synthesized early and also contains an intracistronic cis-replication element, we postulated that it is autoregulatory with RNA binding properties.Here, we do the following: (i) demonstrate by mutagenesis analysis that the 72-nt SLV, mapping immediately upstream of SLVI and within the partial nsp1 cistron, is also a cis-acting DI RNA replication element; (ii) show by gel shift and UV cross-linking analyses that there is likely no binding of an intracellular viral protein to SLV and SLVI (SLV-VI), but there is binding of unidentified cellular proteins of ∼60 and 100 kDa; and (iii) show by gel shift analysis that recombinant nsp1 purified from Escherichia coli does not bind SLV-VI but does bind SLs I to IV in the 5′ UTR and also the 3′-terminal bulged SL in the 3′ UTR, suggesting a possible regulatory role at these sites. Notably, specific binding with ∼2.5 μM affinity of nsp1 to SLIII and its flanking regions in the 5′ UTR was observed. Additionally, we show that, under conditions that would express nsp1 from a DI RNA-encoded sgmRNA, DI RNA levels are greatly reduced; viral RNA species levels, however, are reduced only slightly, and this reduction is transient. These results together indicate that nsp1 is an RNA-binding protein that may function as a regulator of viral translation or replication but not through its binding of cis-acting SLs V and VI within its own cistron. 相似文献
18.
Agrobacterium tumefaciens VirB proteins assemble a type IV secretion apparatus and a T-pilus for secretion of DNA and proteins into plant cells. The pilin-like protein VirB3, a membrane protein of unknown topology, is required for the assembly of the T-pilus and for T-DNA secretion. Using PhoA and green fluorescent protein (GFP) as periplasmic and cytoplasmic reporters, respectively, we demonstrate that VirB3 contains two membrane-spanning domains and that both the N and C termini of the protein reside in the cytoplasm. Fusion proteins with GFP at the N or C terminus of VirB3 were fluorescent and, like VirB3, localized to a cell pole. Biochemical fractionation studies demonstrated that VirB3 proteins encoded by three Ti plasmids, the octopine Ti plasmid pTiA6NC, the supervirulent plasmid pTiBo542, and the nopaline Ti plasmid pTiC58, are inner membrane proteins and that VirB4 has no effect on membrane localization of pTiA6NC-encoded VirB3 (pTiA6NC VirB3). The pTiA6NC and pTiBo542 VirB2 pilins, like VirB3, localized to the inner membrane. The pTiC58 VirB4 protein was earlier found to be essential for stabilization of VirB3. Stabilization of pTiA6NC VirB3 requires not only VirB4 but also two additional VirB proteins, VirB7 and VirB8. A binary interaction between VirB3 and VirB4/VirB7/VirB8 is not sufficient for VirB3 stabilization. We hypothesize that bacteria use selective proteolysis as a mechanism to prevent assembly of unproductive precursor complexes under conditions that do not favor assembly of large macromolecular structures.Bacteria use type IV secretion (T4S) to deliver macromolecules to prokaryotes and eukaryotes (12). Animal and human pathogens deliver proteins to their eukaryotic hosts to affect cellular processes causing disease. The plant-pathogenic bacterium Agrobacterium tumefaciens delivers both proteins and DNA to plants and other eukaryotes. DNA delivered by Agrobacterium directs constitutive synthesis of phytohormones in a transformed plant cell, promoting cancerous growth (56). The Ptl toxin of Bordetella pertussis modifies G proteins by ADP-ribosylation, affecting intracellular cell signaling, and CagA of Helicobacter pylori disrupts epithelial cell polarity by inhibiting PAR1 kinase activity (37, 44, 47). T4S is ancestrally related to bacterial conjugation, a mechanism used by bacteria for interbacterial plasmid transfer, enabling them to acquire novel genes for antibiotic resistance, degradation of organic molecules, toxin production, and other virulence traits (29).The VirD4/VirB family of proteins, found conserved in many alphaproteobacteria, mediates T4S (12). The Ti plasmid-encoded Agrobacterium T4S system requires VirD4 and 11 VirB proteins, VirB1 to VirB11, for efficient DNA transfer (7, 54). The membrane and membrane-associated VirB proteins assemble a macromolecular structure at the cell membrane to promote substrate transfer (12). The octopine Ti plasmid pTiA6NC-encoded VirB6 to VirB11 proteins assemble the T4S apparatus at a cell pole (34, 35, 39). The VirD4 coupling protein targets the VirE2 substrate protein to the cell pole (4). A recent study found that the nopaline Ti plasmid pTiC58 T4S system (T4SS) and its substrates form a helical array around the cell circumference (1). Structural studies using Escherichia coli conjugative plasmid pKM101-encoded VirB homologues showed that TraN (VirB7), TraO (VirB9), and TraF (VirB10) form the core complex and that TraF forms a channel at the outer membrane (11, 23). The Agrobacterium VirB proteins assemble a T-pilus, an appendage composed primarily of VirB2, with VirB5 and VirB7 as its minor constituents (38, 40, 41, 48, 50, 55). VirB3, a homolog of the pilin-like TraL protein encoded in E. coli plasmids, is postulated to function in T-pilus assembly (52). Three ATP-utilizing proteins, VirB4, VirB11, and VirD4, supply energy for substrate translocation (3, 9, 34).The membrane topology of all the VirB proteins, except for VirB3, was determined by analyses of random phoA insertion mutants, targeted phoA fusions, and targeted bla fusions (6, 14, 15, 21, 22, 31, 35, 53). phoA and bla, which encode alkaline phosphatase and β-lactamase, respectively, serve as excellent markers for periplasmic proteins, as they are enzymatically active only when targeted to the cell periplasm (8, 30). Green fluorescent protein (GFP) is an ideal cytoplasmic marker because it fluoresces only when located in the cytoplasm (19, 20). When GFP is targeted to the periplasm through fusion with a membrane-spanning domain (MSD), it fails to fold properly and does not fluoresce.The prevailing view, based on in silico analysis, is that VirB3 is a bitopic membrane protein with a periplasmic C terminus. No phoA-positive insertions in virB3, however, were identified in two random mutagenesis studies of the virB operon (6, 15). The small size of VirB3, a polypeptide of 108 amino acids (aa), could be a contributing factor to the negative findings. Yet several PhoA-positive insertions in two smaller VirB proteins, VirB2 (74-aa mature peptide) and VirB7 (41-aa mature peptide), were successfully obtained in both studies. Therefore, the negative findings may also be indicative of the presence of a small periplasmic domain in VirB3. Biochemical studies showed that the nopaline Ti plasmid pTiC58-encoded VirB3 protein (pTiC58 VirB3) associates with the bacterial outer membrane, while VirB2 associates with both the inner and outer membranes (52). The pTiC58 VirB4 protein is required for localization of VirB3 to the outer membrane (33). VirB4 is also required for VirB3 stability (33, 55). A low level of VirB3 accumulated in a nonpolar pTiC58 virB6 deletion mutant; however, addition of virB6 in trans did not restore the level of the protein, even though it restored tumorigenicity (27). VirB3 participates in the formation of protein complexes with the T-pilus proteins VirB2 and VirB5 (55).Homologues of VirB3 are found in many alphaproteobacteria with a T4SS. While most VirB3 homologues are small proteins, several recently identified homologues are fusions of VirB3 and the immediate downstream protein VirB4 (5, 10, 24). These fusion homologs, which include Actinobacillus MagB03 (GenBank accession no. ), Campylobacter CmgB3/4 ( AAG24434), Yersinia pseudotuberculosis TriC ( EAQ71805), Citrobacter koseri PilX3-4 ( CAF25448), and Klebsiella pneumoniae PilX3-4 ( ABV12046), have VirB3 at the N terminus and VirB4 at the C terminus. Agrobacterium VirB4 is an integral membrane protein with a cytoplasmic N terminus ( BAF4949014). Its homologues are expected to have a similar topology. The prevailing view that pTi VirB3 has a periplasmic C terminus is inconsistent with the cytoplasmic location of the N terminus of VirB4 in the VirB3-VirB4 fusion protein homologues.In this study, we report the membrane topology of Agrobacterium VirB3 and demonstrate that the C terminus of the protein resides in the cytoplasm. We also demonstrate that VirB3 is an inner membrane protein, not an outer membrane protein as previously reported (52). The octopine Ti plasmid pTiA6NC VirB4 protein does not affect membrane localization of VirB3 but does stabilize VirB3. VirB4, however, is not sufficient for pTiA6NC VirB3 stabilization. Two additional proteins, VirB7 and VirB8, are required for the stabilization of pTiA6NC VirB3. 相似文献
19.