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1.
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]
2.
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]
3.
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]
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 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]
5.
6.
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
7.
8.
9.
Abul Kalam Azad Yoshihiro Sawa Takahiro Ishikawa Hitoshi Shibata 《Applied and environmental microbiology》2009,75(9):2792-2797
Water channels formed by aquaporins (AQPs) play an important role in the control of water homeostasis in individual cells and in multicellular organisms. Plasma membrane intrinsic proteins (PIPs) constitute a subclass of plant AQPs. TgPIP2;1 and TgPIP2;2 from tulip petals are members of the PIP family. In this study, we overexpressed TgPIP2;1 and TgPIP2;2 in Pichia pastoris and monitored their water channel activity (WCA) either by an in vivo spheroplast-bursting assay performed after hypo-osmotic shock or by growth assay. Osmolarity, pH, and inhibitors of AQPs, protein kinases (PKs), and protein phosphatases (PPs) affect the WCA of heterologous AQPs in this expression system. The WCA of TgPIP2;2-expressing spheroplasts was affected by inhibitors of PKs and PPs, which indicates that the water channel of this homologue is regulated by phosphorylation in P. pastoris. From the results reported herein, we suggest that P. pastoris can be employed as a heterologous expression system to assay the WCA of PIPs and to monitor the AQP-mediated channel gating mechanism, and it can be developed to screen inhibitors/effectors of PIPs.The movement of water across cell membranes has long been thought to occur by free diffusion through the lipid bilayer. However, the discovery of the membrane protein CHIP28 in red blood cells has suggested the involvement of protein channels (29), and it is now well established that transmembrane water permeability is facilitated by aquaporins (AQPs), water channel proteins that are found in bacteria, fungi, plants, and animals (1, 7, 13, 24). AQPs contain six transmembrane α-helices and five connecting loops, and both the N and C termini are located in the cytosol. The monomers assemble into tetrameric complexes, with each monomer forming an individual water channel (11, 14, 24, 33). Apart from the exceptions of AQP11 and AQP12 from mice, as described by K. Ishibashi (15), AQPs have two signature Asn-Pro-Ala motifs, which are located in the second intracellular and the fifth extracellular loops, B and E.While 13 different AQPs have been identified in mammals (16), more than 33 AQP homologues have been discovered in plants (6, 17, 30). Plant AQPs fall into four subclasses: (i) the plasma membrane (PM) intrinsic proteins (PIPs), which are localized in the PM; (ii) the tonoplast intrinsic proteins (TIPs), which are localized in the vacuolar membranes; (iii) the nodulin-26-like intrinsic proteins; and (iv) the small basic intrinsic proteins (24). In Arabidopsis and maize, there are 13 PIPs, which can be divided further into two subfamilies, PIP1 and PIP2 (6, 17).The functions and mechanisms of regulation of plant AQPs have been extensively investigated (7, 13, 18, 24). There have been several reports on the water channel activity (WCA) of specific AQPs and their regulation by protein phosphorylation (3, 4, 8, 12, 18, 25, 32, 33). It has been shown that the WCA of the PIP2 member SoPIP2;1 from spinach is regulated by phosphorylation at two Ser residues (19, 33).The physiologically interesting temperature-dependent opening and closing of tulip (Tulipa gesneriana) petals occur concomitantly with water transport and are regulated by reversible phosphorylation of an undefined PIP (4, 5). Recently, four PIP homologues were isolated from tulip petals, and their WCAs have been analyzed by heterologous expression in Xenopus laevis oocytes (3). It has been shown that the tulip PIP TgPIP2;2 (DDBJ/EMBL/GenBank accession no. ) is ubiquitously expressed in all organs of the tulip and that TgPIP2;2 is the most likely of the TgPIP homologues to be modulated by the reversible phosphorylation that regulates transcellular water transport and mediates petal opening and closing ( AB3056173, 4). However, while the members of the PIP2 subfamily are characterized as water channels (6), TgPIP2;1 (DDBJ/EMBL/GenBank accession no. ) shows no significant WCA in the oocyte expression system ( AB3056163). There is growing interest in research on AQPs due to their crucial roles in the physiology of plants and animals (1, 16, 21-24, 26-28, 36). The assay of AQP channel activity is usually performed using either a X. laevis oocyte expression system (29) or a stopped-flow light-scattering spectrophotometer (35), both of which are not widely available. Furthermore, the complexity of these methods and requirement of expertise limit their high-throughput applications. In contrast, a Pichia pastoris expression system is simple to use, inexpensive, and feasible and can be used in high-throughput applications. Although a P. pastoris expression system has been shown to assay the WCA of a TIP (9), extensive research is necessary with other AQPs such as PIPs or AQPs present in intragranular membranes to establish whether this assay system can be used to characterize a water channel and study its regulation mechanisms. With this in view, in the study reported herein, TgPIP2;1 and TgPIP2;2 have been heterologously expressed in P. pastoris, and their WCAs have been assayed. The effects of several factors, such as osmolarity, pH, and inhibitors of protein kinases (PKs) and protein phosphatases (PPs), on the WCA of the recombinant P. pastoris have been investigated. Based on the results, we demonstrate that the P. pastoris heterologous expression system can be used to rapidly characterize PIP channels, to monitor the effects of mutations, and to score the effects of inhibitors and abiotic factors. 相似文献
10.
11.
Patrick D. Scheu Yun-Feng Liao Julia Bauer Holger Kneuper Thomas Basché Gottfried Unden Wolfgang Erker 《Journal of bacteriology》2010,192(13):3474-3483
DcuS is the membrane-integral sensor histidine kinase of the DcuSR two-component system in Escherichia coli that responds to extracellular C4-dicarboxylates. The oligomeric state of full-length DcuS was investigated in vitro and in living cells by chemical cross-linking and by fluorescence resonance energy transfer (FRET) spectroscopy. The FRET results were quantified by an improved method using background-free spectra of living cells for determining FRET efficiency (E) and donor fraction {fD = (donor)/[(donor) + (acceptor)]}. Functional fusions of cyan fluorescent protein (CFP) and yellow fluorescent protein (YFP) variants of green fluorescent protein to DcuS were used for in vivo FRET measurements. Based on noninteracting membrane proteins and perfectly interacting proteins (a CFP-YFP fusion), the results of FRET of cells coexpressing DcuS-CFP and DcuS-YFP were quantitatively evaluated. In living cells and after reconstitution of purified recombinant DcuS in proteoliposomes, DcuS was found as a dimer or higher oligomer, independent of the presence of an effector. Chemical cross-linking with disuccinimidyl suberate showed tetrameric, in addition to dimeric, DcuS in proteoliposomes and in membranes of bacteria, whereas purified DcuS in nondenaturing detergent was mainly monomeric. The presence and amount of tetrameric DcuS in vivo and in proteoliposomes was not dependent on the concentration of DcuS. Only membrane-embedded DcuS (present in the oligomeric state) is active in (auto)phosphorylation. Overall, the FRET and cross-linking data demonstrate the presence in living cells, in bacterial membranes, and in proteoliposomes of full-length DcuS protein in an oligomeric state, including a tetramer.The DcuSR (dicarboxylate uptake sensor and regulator) system of Escherichia coli is a typical two-component system consisting of a membranous sensor kinase (DcuS) and a cytoplasmic response regulator (DcuR) (11, 26, 48). DcuS responds to C4-dicarboxylates like fumarate, malate, or succinate (19). In the presence of the C4-dicarboxlates, the expression of the genes of anaerobic fumarate respiration (dcuB, fumB, and frdABCD) and of aerobic C4-dicarboxylate uptake (dctA) is activated. DcuS is a histidine protein kinase composed of two transmembrane helices with an intermittent sensory PAS domain in the periplasm (PASP) that was also termed the PDC domain (for PhoQ/DcuS/DctB/CitA domain or fold) (7, 20, 32, 48). The second transmembrane helix is followed by a cytoplasmic PAS domain (PASC) and the C-terminal transmitter domain. PASC functions in signal transfer from transmembrane helix 2 (TM2) to the kinase domain (9). The C-terminal part of the transmitter domain consists of a catalytic or HATPase (histidine kinase/ATPase) subdomain for autophosphorylation of DcuS (16). The N-terminal part of the transmitter contains two conserved α-helical regions, including a conserved His residue which is the site for autophosphorylation. The α-helices serve in dimerization and form a four-helix bundle in the kinase dimer (dimerization and histidine phosphotransfer [DHp] domain) (25, 35, 42, 44).The dimeric sensor kinases have been supposed to phosphorylate mutually, by the catalytic domain of one monomer, the His residue of the partner monomer (10). The oligomeric state of the membrane-bound sensor kinases EnvZ and VirA was also deduced from in vivo complementation studies (31, 46). In addition, signal transduction across the membrane and along cytoplasmic PAS domains appears to be a mechanical process requiring oligomeric proteins (9, 40). Therefore, His kinases are supposed to be dimeric in the functional state, but a higher oligomeric state has not been tested and is conceivable. Only a limited number of membrane-bound sensor kinases have been studied for their oligomerization in their membrane-bound state. Thus, the oligomeric state of the KdpD and TorS sensor kinases of E. coli have been shown to prevail in the detergent-solubilized state as oligomers, presumably dimers (14, 29). There was indirect information that functional DcuS is a dimer as well. Purified DcuS shows kinase activity only after reconstitution into liposomes, and phosphorylation is stimulated by C4-dicarboxylates (16, 19). Detergent-solubilized DcuS, on the other hand, shows no kinase activity, and it was assumed that reconstituted DcuS prevails as a dimer, whereas the inactivation of the detergent-solubilized form is due to monomerization. Recently, it was suggested that autophosphorylation in a sensor kinase of Thermotoga maritima proceeds by a cis mechanism on DHp and catalytic kinase domains within the same monomer (6). The sensor kinase is supposed to prevail as a dimer for reasons of signal transfer to the sensor domain, but the presence of cis phosphorylation principally brings into question the need for dimers for sensor kinase function.Overall, it appears that sensor kinases are oligomers for functional reasons. There is, however, no clear evidence for an oligomeric state of full-length sensor kinases in their membrane-embedded state. Moreover, the studies do not address the question of whether the sensor kinases are dimers or higher oligomers. Therefore, several aspects of the oligomeric state of sensor kinases in vivo in bacterial membranes, that is, before solubilization by detergent, are not clear. In this study, the oligomerization of full-length DcuS was examined in vivo in growing bacteria and in bacterial membranes and in vitro after isolation and reconstitution in liposomes by chemical cross-linking and fluorescence resonance energy transfer (FRET) spectroscopy. FRET techniques have been used widely to study intermolecular interactions of biological molecules (1, 4, 18, 21, 23, 34). The sensitivity of fluorescence allows experiments at low concentrations of native proteins, and genetically generated fusions of DcuS with fluorescent proteins ensure site-specific labeling of DcuS for noninvasive and nondestructive measurements in living cells. In particular, it was investigated whether dimers or higher oligomeric states can be detected for DcuS and whether the oligomerization state depends on function-related parameters. 相似文献
12.
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
13.
Lisa C. Crossman Roy R. Chaudhuri Scott A. Beatson Timothy J. Wells Mickael Desvaux Adam F. Cunningham Nicola K. Petty Vivienne Mahon Carl Brinkley Jon L. Hobman Stephen J. Savarino Susan M. Turner Mark J. Pallen Charles W. Penn Julian Parkhill A. Keith Turner Timothy J. Johnson Nicholas R. Thomson Stephen G. J. Smith Ian R. Henderson 《Journal of bacteriology》2010,192(21):5822-5831
In most cases, Escherichia coli exists as a harmless commensal organism, but it may on occasion cause intestinal and/or extraintestinal disease. Enterotoxigenic E. coli (ETEC) is the predominant cause of E. coli-mediated diarrhea in the developing world and is responsible for a significant portion of pediatric deaths. In this study, we determined the complete genomic sequence of E. coli , a prototypical strain of enterotoxigenic E. coli, which reproducibly elicits diarrhea in human volunteer studies. We performed genomic and phylogenetic comparisons with other E. coli strains, revealing that the chromosome is closely related to that of the nonpathogenic commensal strain E. coli HS and to those of the laboratory strains E. coli K-12 and C. Furthermore, these analyses demonstrated that there were no chromosomally encoded factors unique to any sequenced ETEC strains. Comparison of the E. coli H10407 plasmids with those from several ETEC strains revealed that the plasmids had a mosaic structure but that several loci were conserved among ETEC strains. This study provides a genetic context for the vast amount of experimental and epidemiological data that have been published.Current dogma suggests the Gram-negative motile bacterium Escherichia coli colonizes the infant gut within hours of birth and establishes itself as the predominant facultative anaerobe of the colon for the remainder of life ( H104073, 59). While the majority of E. coli strains maintain this harmless existence, some strains have adopted a pathogenic lifestyle. Contemporary tenets suggest that pathogenic strains of E. coli have acquired genetic elements that encode virulence factors and enable the organism to cause disease (12). The large repertoire of virulence factors enables E. coli to cause a variety of clinical manifestations, including intestinal infections mediating diarrhea and extraintestinal infections, such as urinary tract infections, septicemia, and meningitis. Based on clinical manifestation of disease, the repertoire of virulence factors, epidemiology, and phylogenetic profiles, the strains causing intestinal infections can be divided into six separate pathotypes, viz., enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC), enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC), diffuse adhering E. coli (DAEC), and enterotoxigenic E. coli (ETEC) (33, 35, 39).ETEC is responsible for the majority of E. coli-mediated cases of human diarrhea worldwide. It is particularly prevalent among children in developing countries, where sanitation and clean supplies of drinking water are inadequate, and in travelers to such regions. It is estimated that there are 200 million incidences of ETEC infection annually, resulting in hundreds of thousands of deaths in children under the age of 5 (55, 64). The essential determinants of ETEC virulence are traditionally considered to be colonization of the host small-intestinal epithelium via plasmid-encoded colonization factors (CFs) and subsequent release of plasmid-encoded heat-stable (ST) and/or heat-labile (LT) enterotoxins that induce a net secretory state leading to profuse watery diarrhea (20, 62). More recently, additional plasmid-encoded factors have been implicated in the pathogenesis of ETEC, namely, the EatA serine protease autotransporter (SPATE) and the EtpA protein, which acts as an intermediate in the adhesion between bacterial flagella and host cells (23, 32, 42, 46). Furthermore, a number of chromosomal factors are thought to be involved in virulence, e.g., the invasin Tia; the TibA adhesin/invasin; and LeoA, a GTPase with unknown function (14, 21, 22). E. coli is considered a prototypical ETEC strain; it expresses colonization factor antigen 1 (CFA/I) and the heat-stable and heat labile toxins. Loss of a 94.8-kb plasmid encoding CFA/I and a gene for ST enterotoxin from E. coli strain H10407 leads to reduced ability to cause diarrhea ( H1040717).Here, we report the complete genome sequence and virulence factor repertoire of the prototypical ETEC strain and the nucleotide sequence and gene repertoire of the plasmids from ETEC strain E1392/75, and we describe a novel conserved secretion system associated with the sequenced ETEC strains. H10407相似文献
14.
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
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.
Enrico Lavezzo Stefano Toppo Luisa Barzon Claudio Cobelli Barbara Di Camillo Francesca Finotello Elisa Franchin Denis Peruzzo Gianna Maria Toffolo Marta Trevisan Giorgio Palù 《Journal of bacteriology》2010,192(19):5270-5271
Neisseria meningitidis is a human-specific pathogen known for its capability to cause sepsis and meningitis. Here we report the availability of 2 draft genome sequences obtained from patients infected during the same epidemic outbreak. Both bacterial isolates belong to serogroup C, but their genome sequences show local and remarkable differences compared with each other or with the reference genome of strain FAM18.Neisseria meningitidis is found as a commensal organism of the human nasopharynx in 8 to 25% of the adult population (9), but sporadically, it is able to cross the mucosa and reach the bloodstream, causing severe septicemia and meningitis. Even though the reasons triggering these pathogenic outbreaks are not well understood, several factors related either to the host or the bacterium have been proposed 3, 8).So far, complete genome sequences for N. meningitidis serogroups A (strain Z2491 [GenBank accession no. ]) ( AL1579594), B (strain MC58 [GenBank accession no. ]) ( AE00209810), and C (strains FAM18, 8013, and 053442 [GenBank accession no. , AM421808, and FM999788, respectively]) ( CP0003811, 5, 6) have been reported, together with the unencapsulated strain α14 (GenBank accession no. ) ( AM8891367). Here we announce the availability of 2 draft genome sequences for N. meningitidis serogroup C, strains K1207 and S0108, isolated from the same epidemic cluster which occurred in the Veneto region in northern Italy during the 2007-2008 winter (2).The genomes were sequenced using 454 pyrosequencing (Roche), combining shotgun and 30-kb paired-end strategies, according to the manufacturer''s recommendations. The coverage was nearly 27×, and assemblies were performed with Newbler. We obtained 223 and 226 contigs for the 2 genomes, which were finally mapped in 17 and 16 scaffolds, respectively. From both samples, we also isolated a 7-kb plasmid, whose sequence was nearly identical to that of pJS-B, already available in GenBank (accession no. ).The first analysis was performed by comparing sequences of the two isolates with the most similar complete genome available, strain FAM18. This analysis showed that the genome lengths were almost identical (about 2.2 Mb) and GC contents were comparable (51.91% in both isolates versus 51.62% of strain FAM18). Then, to identify potential differences in coding sequence content, the contigs obtained for both isolates were aligned with those for strain FAM18 using MEGABLAST ( NC_00475811) and LASTZ tools, which showed that in the genomes of the two N. meningitidis isolates, several genes were missing or nonfunctional because of the presence of insertions or deletions. For example, a couple of FAM18 outer membrane proteins (NMC0214 and NMC0215) were completely missing in both genomes, due to a 3-kb deletion, and no homologues were present in other genomic regions.Sequences that did not map on the genome of strain FAM18 were investigated by performing a BLAST analysis on a nonredundant database. Interestingly, besides genes or partial genes belonging to the other completely sequenced N. meningitidis serogroup C strain 053442, the genomes of our isolates contained coding sequences from N. meningitidis serogroups A and B, from other Neisseria species, such as N. gonorrhoeae, N. cinerea, and N. mucosa, and even from other bacterial species, such as cobyrinic acid ac-diamide synthase from Shewanella baltica, attesting once more to the great capability of horizontal gene transfer, which is peculiar to this microorganism.A detailed report of our two isolates will be included in a future publication, with the results of a full comparative analysis between the genomes. 相似文献
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20.
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