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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

Phylum Deinococcus-Thermus

Phylum Proteobacteria

Phylum Tenericutes

Phylum Firmicutes

Phylum Actinobacteria

Phylum Spirochaetes

Non-Bacterial genomes

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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 subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Non-Bacterial genomes

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3.
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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 this subsequent versions of this list are invited to provide the bibliometric data for such references to the SIGS editorial office.

Non-Bacterial genomes

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5.
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6.
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

Phylum Crenarchaeota

Phylum Deinococcus-Thermus

Phylum Proteobacteria

Phylum Tenericutes

Phylum Firmicutes

Phylum Actinobacteria

Non-Bacterial genomes

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7.
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8.
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9.
White spot syndrome virus (WSSV) is currently the most serious global threat for cultured shrimp production. Although its large, double-stranded DNA genome has been completely characterized, most putative protein functions remain obscure. To provide more informative knowledge about this virus, a proteomic-scale network of WSSV-WSSV protein interactions was carried out using a comprehensive yeast two-hybrid analysis. An array of yeast transformants containing each WSSV open reading frame fused with GAL4 DNA binding domain and GAL4 activation domain was constructed yielding 187 bait and 182 prey constructs, respectively. On screening of ∼28,000 pairwise combinations, 710 interactions were obtained from 143 baits. An independent coimmunoprecipitation assay (co-IP) was performed to validate the selected protein interaction pairs identified from the yeast two-hybrid approach. The program Cytoscape was employed to create a WSSV protein–protein interaction (PPI) network. The topology of the WSSV PPI network was based on the Barabási-Albert model and consisted of a scale-free network that resembled other established viral protein interaction networks. Using the RNA interference approach, knocking down either of two candidate hub proteins gave shrimp more protection against WSSV than knocking down a nonhub gene. The WSSV protein interaction map established in this study provides novel guidance for further studies on shrimp viral pathogenesis, host-viral protein interaction and potential targets for therapeutic and preventative antiviral strategies in shrimp aquaculture.White spot syndrome virus (WSSV)1 is the causative agent of white spot disease (WSD) and is one of the most serious viral pathogens that threaten the shrimp culture industry worldwide. Because WSD causes rapid and high mortality up to 100% within 3–10 days after viral infection (1), it causes dramatic economic losses on farms. WSSV is a large enveloped, ovoid to bacilliform, double-stranded DNA (dsDNA) virus with a genome of ∼300 kb (See reviews in (2, 3)). The WSSV genome has been completely characterized for isolates from Thailand (GenBank accession number AF369029), China (accession number AF332093) and Taiwan (accession number AF440570). To expand its basic genetic information, various genomic and proteomic approaches have been applied to gain more insight into the molecular mechanisms of WSSV pathogenesis (See reviews in (2, 3)). However, the roles of most of the WSSV proteins still remain to be elucidated. This is due to the fact that many of its putative open reading frames (ORFs) lack homology to known proteins in the database. Protein–protein interaction studies can provide a valuable framework for understanding the roles of protein functions. Interaction studies of WSSV proteins have particularly focused on viral structural proteins (4–15). However, so far there has been no report on a protein–protein interaction (PPI) network for WSSV or any other crustacean virus. By contrast, several PPI networks for cellular organisms such as Saccharomyces cerevisiae (16, 17), Helicobacter pylori (18), Drosophila melanogaster (19), Caenarhabitis elegans (20), Plasmodium falciparum (21), and Homo sapiens (22, 23) and pathogens such as bacteriophage T7 (24), vaccinia virus (25), hepatitis C virus (26), and herpesviruses (27–29) have already been established. Therefore, the present study aimed to obtain a more fundamental understanding of WSSV protein interactions. A comprehensive yeast two-hybrid assay was employed to generate viral fusion proteins with DNA binding (BD) and activation (AD) domains in an array format that effectively allowed searching every possible binary interaction in WSSV. The interaction results from the yeast two-hybrid assays were subsequently validated by coimmunoprecipitation (co-IP). Topological properties of the WSSV PPI network were assessed and compared with previously published viral networks. Candidate viral hub proteins with high numbers of interacting partners were identified in this study and their significance was investigated using an RNA interference approach.  相似文献   

10.
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 H10407, 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 (3, 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 H10407 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 (17).Here, we report the complete genome sequence and virulence factor repertoire of the prototypical ETEC strain H10407 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.  相似文献   

11.
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12.
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13.
Angiogenesis requires the mobilization of progenitor cells from the bone marrow (BM) and homing of progenitor cells to ischemic tissue. The cholesterol lowering drug Statins can stimulate angiogenesis via mobilization of BM derived endothelial progenitor cells (EPCs), promoting EPC migration, and inhibiting EPC apoptosis. The chemokine stromal cell-derived factor-1 (SDF-1) augments EPC chemotaxis, facilitates EPC incorporation into the neovasculature. The combined use of a statin to mobilize EPCs and local overexpression of SDF-1 to augment EPC homing to ischemic muscle resulted in superior angiogenesis versus use of either agent alone. Their effects are through augmenting EPC mobilization, incorporation, proliferation, migration and tube formation while inhibiting EPC apoptosis. Statin and SDF-1 therefore display synergism in promoting neovascularization by improving reperfusion of ischemic muscle, increasing progenitor cell presentation and capillary density in ischemic muscle, and diminishing apoptosis. These results suggest that the combination of statin and SDF-1 may be a new therapeutic strategy in the treatment of limb ischemia.Key words: angiogenesis, endothelial progenitor cells, statin, SDF-1, migrationAngiogenesis is the process by which new vessels form in ischemic tissue. The cytokine Stromal Cell Derived Factor-1 (SDF-1) is released into the circulation in response to ischemia and is an initiating signal in the angiogenesis process. SDF-1 mobilizes bone marrow cells (BMC) by binding to the cell surface receptor CXCR4. BMCs then enter the circulation and migrate to the ischemic site following the SDF-1 gradient. On arrival, BMCs promote angiogenesis by providing cellular elements such as endothelial cells (EC) and perivascular cells and also by secreting signaling proteins that mature the angiogenesis process. BMC surface CXCR4 expression and the SDF-1/CXCR4 interaction are essential for BMC to home to the injured site.Cell-based strategies to improve neovascularization of ischemic tissue have been achieved by injecting mononuclear cells derived from either BM1 or peripheral blood, directly into ischemic muscle,2 or by mobilizing BM-MNC with cytokines3 or other drugs such as statins.4–6Statins are 3-hydroxy-3-methyl-glutaryl-CoA reductase inhibitors and are primarily used to lower circulating cholesterol levels. In addition to reducing cholesterol synthesis, inhibition of the mevalonate pathway prevents synthesis of isoprenoid intermediates including geranylgeranylpyrophosphate. Geranylgeranylation is important in the posttranslational modification of intracellular signaling proteins, including Rho GTPases. This mechanism underlies many of the pleiotropic effects including the ability of statins to stabilize endothelial nitric oxide synthase mRNA and increase nitric oxide biosynthesis. In fact, statins have been shown to protect against ischemic injury of the heart and stimulate angiogenesis in ischemic limbs of normocholesterolemic animals.7,8 The mechanism of action of statins has been demonstrated via mobilization of BM endothelial progenitor cells (EPCs) and facilitation of EPC incorporation into the neovasculature through a phosphoinositide-3 (PI-3) kinase-dependent pathway.4–6 Statins have also been reported to enhance EPC migration, augment EPC chemotaxis and inhibit EPC apoptosis both in vitro and in vivo.4,9,10SDF-1, an 89-amino acid polypeptide, is a member of the chemokine CXC subfamily originally isolated from murine bone marrow stromal cells.11 SDF-1 was initially identified as a potent chemoattractant for lymphocytes and monocytes, and as an enhancer of B cell proliferation. SDF-1 is considered to be a key regulator of hematopoietic stem cell trafficking between BM and the peripheral circulation. SDF-1 is highly expressed in ischemic tissues.12,13 Elevation of SDF-1 levels in peripheral blood results in BMC mobilization to the peripheral circulation with a concurrent decrease within the BM.14 SDF-1 not only mobilizes progenitor cells in BM but also directs them to the ischemic site by promoting cell migration and proliferation.3,15 SDF-1 may generate a gradient similar to developmental morphogens during ischemia that provides the cues and directions for progenitor cell mobilization into peripheral blood and homing to ischemic tissues.16,17 Furthermore, SDF-1 also reduces EPC apoptosis and enhances survival of the progenitor cells.3,18 SDF-1, either delivered locally in its protein form,3,19,20 or generated in situ via plasmid and viral vector-mediated gene expression,10,21,22 enhances neovascularization by augmenting EPC recruitment into ischemic tissues.SDF-1 binding to its receptor CXCR4 on the cell surface provides essential signals for mobilization and homing of EPCs to the injured site.23–25 SDF-1 binding with CXCR4 triggers internalization of CXCR4. This SDF-1/CXCR4 interaction results in elevation of cytoplasmic Ca2+ levels26 and phosphorylation of PI-3 kinase and other protein kinases, e.g. Akt,21 MEK/ERK27,28 and Janus kinase (JAK)-2.29 Activation of Akt protein kinase further upregulates the activity of eNOS by increasing both eNOS expression and phosphorylation, which in turn catalyzes the production of nitric oxide (NO), an important signal molecule for vascular protection and remodeling.21,26 Disruption of SDF-1/CXCR4 interaction impaired incorporation of EPC into sites of ischemia, and disturbed ischemic limb neo-vascularization.30To explore if the combined use of a statin to mobilize BM EPCs and local overexpression of SDF-1 to augment EPC homing to ischemic muscle will result in superior angiogenesis versus use of either agent alone, we used the murine hindlimb ischemia model to determine the effects of Fluvastatin and SDF-1 on angiogenesis.10 Fluvastatin (5 mg/kg) was injected intra-peritoneally into the mice daily for 7 days to mobilize progenitor cells prior to ischemia-inducing surgery. NIH 3T3 cells transduced with the retroviral vector carrying SDF-1 gene were injected I.M. into the ischemic limb after surgery to locally deliver SDF-1 to ischemic muscle.22 The number of circulating EPCs increased 9–18 fold seven days post statin/SDF-1 treatment.Our data of single treatment with Fluvastatin are consistent with the previous reports that statins not only augment mobilization of progenitor cells by increasing circulating EPC originated from BM,4,31 but also modulate their differentiation. We further give a new insight view of the mechanism for statin induced EPC mobilization. We found that statin induced activation of matrix metalloproteinases (MMP)-2 and -9 in EPC. The increased MMP activity could result in degradation of extracellular matrix.17 Progenitor cells will be such mobilized into circulation when the cellular attachment is reduced within the bone marrow niches. We show that statin alone can enhance the phosphorylation of Akt, promote EPC proliferation, migration and inhibit cell apoptosis in vitro. The proangiogenic effects of statin are also illustrated in vivo using a murine hind-limb ischemia model. In this model, Fluvastatin treatment results in more EPC in circulation, more BM derived progenitor cells in ischemic muscle, more cell proliferation, enhanced capillary formation, and diminished cell apoptosis; these effects end up in improved reperfusion versus control. The beneficial effects of statin on angiogenesis are independent of cholesterol since the total serum cholesterol level is not changed by Fluvastatin treatment under these experimental conditions.To be noted, the effect of statins on EPCs was found to be concentration dependent. EPC proliferation, migration and the inhibition of apoptosis are enhanced at low statin concentrations (10 nM and 100 nM) but are significantly inhibited at a higher statin concentration (1,000 nM). The toxic effect of statin at high concentration cannot be compensated by addition of SDF-1, indicating that Statin causes apoptosis in a pathway different from the pathway that SDF-1 uses to prevent EPC apoptosis. Increased apoptosis at the higher statin concentration could explain the reversed effect of stain in angiogenesis. These findings are consistent with the reports in which statins were found to have proangiogenic effects at low therapeutic concentrations but angiostatic effects at high concentrations, the latter effect being reversible by geranylgeranyl pyrophosphate.32,33Combined statin and SDF-1 treatment significantly enhanced angiogenesis versus treatment with either reagent alone. More cell proliferation and less apoptosis were observed both in vitro and in vivo, along with increased cell migration and tube formation in vitro, and enhanced progenitor cell incorporation and higher capillary density in ischemic tissue in vivo. It is interesting to note that neither statin nor SDF-1 alone promotes EPC tube formation, but combined treatment results in significant EPC tube formation. These results suggest that SDF-1 and statin have different mechanisms of action with regards to the promotion of neovascularization. It is possible that each drug affects a specific subset of progenitor cells.The facilitative effect of both statin and SDF-1 on EPC proliferation and migration is involved with Akt phosphorylation and endothelial nitric oxide synthase (eNOS) activation. The mechanism by which statins promote angiogenesis is through, at least partly, improved nitric oxide bioavailability. Statins have been reported to induce eNOS mRNA stability34 and eNOS activity through a PI3k/Akt dependent pathway.31,35–37 However, neither eNOS mRNA/protein expression nor EPCs are reported to be essential for the therapeutic effect of Fluvastatin on hypoxia-induced pulmonary hypertension; Fluvastatin improved eNOS phosphorylation by a mechanism independent of Akt activation.38 Our data favor a mechanism involving Akt phosphorylation since phosphorylated Akt is increased when EPCs are cultured in the presence of statin, and statin-enhanced EPC proliferation and migration were inhibited by the PI3K/Akt inhibitor LY294002.The angiogenic effects of SDF-1 also involve increased production of NO26 as NO is essential for EC migration and angiogenesis. SDF-1α gene transfer has been shown to enhance eNOS activity.21 Our in vitro data confirmed the involvement of Akt and eNOS in SDF-1 mediated cell migration.10 Phosphorylated Akt is increased when EPCs are cultured in the presence of SDF-1. The facilitative effect of SDF-1 on EPC migration is blocked by both the Akt inhibitor LY294002 and the eNOS inhibitor L-NMMA. In contrast, L-NMMA does not reverse the inhibitory effect of SDF-1 on apoptosis, indicating that the inhibitory effect of SDF-1 on apoptosis is not mediated through NO.22We also show that the expression of MMP-2 and MMP-9 was increased when EPCs were cultured in the presence of statin or SDF-1. MMPs are a family of proteolytic enzymes that degrade components of the extracellular matrix (ECM). Degradation of ECM is an essential step for cell mobilization and migration. Our data indicate that the novel effect of statin and SDF-1 on migration is through enhancement of MMP-2 and MMP-9 activity, resulting in ECM degradation, thus promoting progenitor cell mobilization and migration. Both Akt phosphorylation and expression of MMP-2 and MMP-9 in EPCs are further enhanced by combined treatment with statin and SDF-1. This result indicates that treatment of EPCs with either statin or SDF-1 as monotherapy results in a sub-maximal angiogenic response. The effects of statin partially overlap with that of SDF-1; and the combined use of two factors appears to have an optimal effect on progenitor cells (Fig. 1).Open in a separate windowFigure 1Effect of statins and SDF-1 on promoting angiogenesis. Statin enhances the phosphorylation of Akt with a yet undefined mechanism. SDF-1 binding with the G-protein coupled membrane receptor CXCR4 results in phosphorylation of protein kinases like PI3 kinase and Akt. Activation of Akt then upregulates the activities of MMPs and eNOS. NOS catalyze the synthesis of NO which is essential for the EPC migration. MMPs degrade extracellular matrix to initiate cell migration. Activation of Akt also prevents cell apoptosis. These reactions promote cell migration and proliferation and enhance EPC survival. EPCs from bone marrow are thus mobilized into circulation. The circulating EPC are homed into ischemia area in lure of SDF-1. EPCs contribute to neovascularisation, either directly by incorporation into endothelium and differentiation into endothelial cells or indirectly by differentiating into perivascular cells that provide physical support and secrete signaling proteins and structural enzymes enabling the angiogenesis process. The effects of statin partially overlap with that of SDF-1; and the combined use of two factors appears to have an additive/synergistic effect on progenitor cells.In summary, the combination of progenitor cell mobilization with statin and targeted recruitment into the ischemic bed by SDF-1 leads to improved blood flow in the ischemic limb versus treatment with either agent alone. Statin and SDF-1 therefore display synergism in promoting neovascularization. This result suggests that the combination of statin and SDF-1 may be a new therapeutic strategy in the treatment of limb ischemia. However, the use of statins as a clinical modifier of angiogenesis is still unproven. A great number of patients have been treated with these drugs and if they were potently proangiogenic, one might expect to see an increased risk of tumors. However, there is no evidence that these drugs encourage tumor development. Likewise, there is no definitive evidence for an antiangiogenic, tumor-modulating action of statins. We await further studies with interest.  相似文献   

14.
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15.
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16.
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17.
The prion hypothesis1–3 states that the prion and non-prion form of a protein differ only in their 3D conformation and that different strains of a prion differ by their 3D structure.4,5 Recent technical developments have enabled solid-state NMR to address the atomic-resolution structures of full-length prions, and a first comparative study of two of them, HET-s and Ure2p, in fibrillar form, has recently appeared as a pair of companion papers.6,7 Interestingly, the two structures are rather different: HET-s features an exceedingly well-ordered prion domain and a partially disordered globular domain. Ure2p in contrast features a very well ordered globular domain with a conserved fold, and—most probably—a partially ordered prion domain.6 For HET-s, the structure of the prion domain is characterized at atomic-resolution. For Ure2p, structure determination is under way, but the highly resolved spectra clearly show that information at atomic resolution should be achievable.Key words: prion, NMR, solid-state NMR, MAS, structure, Ure2p, HET-sDespite the large interest in the basic mechanisms of fibril formation and prion propagation, little is known about the molecular structure of prions at atomic resolution and the mechanism of propagation. Prions with related properties to the ones responsible for mammalian diseases were also discovered in yeast and funghi8,9 which provide convenient model system for their studies. Prion proteins described include the mammalian prion protein PrP, Ure2p,10 Rnq1p,11 Sup35,12 Swi1,13 and Cyc8,14 from bakers yeast (S. cervisiae) and HET-s from the filamentous fungus P. anserina. The soluble non-prion form of the proteins characterized in vitro is a globular protein with an unfolded, dynamically disordered N- or C-terminal tail.15–18 In the prion form, the proteins form fibrillar aggregates, in which the tail adopts a different conformation and is thought to be the dominant structural element for fibril formation.Fibrills are difficult to structurally characterize at atomic resolution, as X-ray diffraction and liquid-state NMR cannot be applied because of the non-crystallinity and the mass of the fibrils. Solid-state NMR, in contrast, is nowadays well suited for this purpose. The size of the monomer, between 230 and 685 amino-acid residues for the prions of Figure 1, and therefore the number of resonances in the spectrum—that used to be large for structure determination—is now becoming tractable by this method.Open in a separate windowFigure 1Prions identified today and characterized as consisting of a prion domain (blue) and a globular domain (red).Prion proteins characterized so far were found to be usually constituted of two domains, namely the prion domain and the globular domain (see Fig. 1). This architecture suggests a divide-and-conquer approach to structure determination, in which the globular and prion domain are investigated separately. In isolation, the latter, or fragments thereof, were found to form β-sheet rich structures (e.g., Ure2p(1-89),6,19 Rnq1p(153-405)20 and HET-s(218-289)21). The same conclusion was reached by investigating Sup35(1-254).22 All these fragements have been characterized as amyloids, which we define in the sense that a significant part of the protein is involved in a cross-beta motif.23 An atomic resolution structure however is available presently only for the HET-s prion domain, and was obtained from solid-state NMR24 (vide infra). It contains mainly β-sheets, which form a triangular hydrophobic core. While this cross-beta structure can be classified as an amyloid, its triangular shape does deviate significantly from amyloid-like structures of smaller peptides.23Regarding the globular domains, structures have been determined by x-ray crystallography (Ure2p25,26 and HET-s27), as well as NMR (mammal prions15,28–30). All reveal a protein fold rich in α-helices, and dimeric structures for the Ure2 and HET-s proteins. The Ure2p fold resembles that of the β-class glutathione S-transferases (GST), but lacks GST activity.25It is a central question for the structural biology of prions if the divide-and-conquer approach imposed by limitations in current structural approaches is valid. Or in other words: can the assembly of full-length prions simply be derived from the sum of the two folds observed for the isolated domains?  相似文献   

18.
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_006526) (19) 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 CP000489.1), Xanthobacter autotrophicus Py2 (GenBank accession number CP000781.1), and Gluconacetobacter diazotrophicus PAl 5 (GenBank accession number CP001189.1). 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 (4), 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 AY057845), harbors a unique ca. 12-kb CRISPR insertion that interrupts nucleotide colinearity with the aforementioned replicon.  相似文献   

19.
A multilocus sequence typing (MLST) analysis was used to examine the genetic structure and diversity within the two large extrachromosomal replicons in Medicago-nodulating rhizobia (Sinorhizobium meliloti and Sinorhizobium medicae). The allelic diversity within these replicons was high compared to the reported diversity within the corresponding chromosomes of the same strains (P. van Berkum et al., J. Bacteriol. 188:5570-5577, 2006). Also, there was strong localized linkage disequilibrium (LD) between certain pSymA loci: e.g., nodC and nifD. Although both of these observations could be explained by positive (or diversifying) selection by plant hosts, results of tests for positive selection did not provide consistent support for this hypothesis. The strong LD observed between the nodC and nifD genes could also be explained by their close proximity on the pSymA replicon. Evidence was obtained that some nodC alleles had a history of intragenic recombination, while other alleles of this locus had a history of intergenic recombination. Both types of recombination were associated with a decline in symbiotic competence with Medicago sativa as the host plant. The combined observations of LD between the nodC and nifD genes and intragenic recombination within one of these loci indicate that the symbiotic gene region on the pSymA plasmid has evolved as a clonal segment, which has been laterally transferred within the natural populations.Plants of the genus Medicago are legumes that often benefit from a mutualistic symbiosis with rhizobia. The most agriculturally significant species of rhizobia that nodulate these plants are Sinorhizobium meliloti (9) and Sinorhizobium medicae (22). Previously reported population genetic analyses of these bacteria have focused on the study of how allelic variants at multiple loci are distributed within and among natural populations (2, 3, 10, 26, 31, 32). This was also the focus of the present study, but it was extended by examining more loci in many more strains of both species of Sinorhizobium coupled with an analysis having a range of symbiotic genotypes. One goal was to determine if there were any obvious correlations between the megaplasmid genotypes observed and their symbiotic competence. A second goal was to determine if selection by their host plants may have influenced the evolution of their symbiotic relationships.The genes for symbiosis reside on the extrachromosomal replicons pSymA (1,354,226 nucleotides [nt]) and pSMED02 (1,245,408 nt) in the genomes of S. meliloti Rm1021 and S. medicae WSM419, respectively (GenBank accession no. AE006469 and CP000740, respectively). Besides these two plasmids, these two strains each harbor one other large extrachromosomal replicon, pSymB (1,683,333 nt) and pSMED01 (1,570,951 nt), respectively (GenBank accession no. AL591985 and CP000739, respectively).Multilocus sequence typing (MLST) (16) is a form of genomic indexing that is commonly used to study the population genetic structure and phylogenetic relatedness within diverse groups of bacteria. In this method, nucleotide sequences of a fixed set of common loci are obtained from a collection of strains, and polymorphic sites among these sequences are used to derive an allelic profile or sequence type (ST) for each genome. Comparisons of the resulting data can be used to infer phylogenetic relationships among the organisms in the sample population, and they also can be used to infer how evolutionary processes, such as recombination and selection, have shaped the genetic structure of the population. For example, levels of intergenic recombination among chromosomal genes in natural populations of Neisseria meningitidis reportedly are relatively high, while corresponding levels within populations of Staphylococcus aureus were low (28). Depending on the specific pairs of loci examined, the levels of linkage disequilibrium (LD) (a lack of intergenic recombination) among several chromosomally carried core genes of S. meliloti were reported to be generally moderate to high (26).The MLST approach has been used to confirm that the chromosomes of S. meliloti and S. medicae are sexually isolated (2, 3, 31) and to provide evidence that horizontal gene transfer (HGT) does occur between the symbiotic megaplasmids of these species (3, 32). It has also been used to demonstrate that levels of intergenic recombination, as indicated by linkage disequilibrium, differ between the three replicons of S. meliloti (26). Levels of intergenic recombination within the pSymB replicons of these strains are generally high, unlike the chromosomes and pSymA replicons within the same strains (26). Bailly et al. (3) hypothesized that the region of the pSymA plasmid that contains the nodulation (nod) genes is frequently transferred in natural populations. They also suggested that selective pressures from the host plant may have influenced both nod gene diversity and patterns of polymorphism across the entire nod gene region.In the present study, multilocus allelic variation of the two megaplasmids was examined among 231 Medicago-nodulating rhizobia that originated primarily from southwest Asia (10). Previously, 91 different chromosomal sequence types (STs) were identified among the same strains from sequence variation in 10 loci (31). This collection of strains had earlier been divided into two closely related groups based on results of multilocus enzyme electrophoresis (10), and this result was subsequently cited in support of separating the Medicago-nodulating rhizobia into the two species S. meliloti and S. medicae (22).The objectives of this study were (i) to use MLST to examine the genetic relationships within and among the large extrachromosomal replicons in S. meliloti and S. medicae, (ii) to estimate levels of intergenic and intragenic recombination in these replicons, (iii) to evaluate the nitrogen-fixing competence of representative symbiotic genotypes with Medicago sativa, and (iv) to determine whether positive (or diversifying) selection may have influenced the genetic structure of the megaplasmids.  相似文献   

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