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Post a Comment 1 DOE Joint Genome Institute, Walnut Creek, California, USA
2 DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
3 Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico USA
4 Biological Data Management and Technology Center, Lawrence Berkeley National Laboratory, Berkeley, California, USA
5 Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
6 Lawrence Livermore National Laboratory, Livermore, California, USA
7 University of California Davis Genome Center, Davis, California, USA
Print publication date: July 20, 2009.
Abstract
Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
Keywords: Sulfate reducer, Gram-negative, free-living, non-pathogenic, freshwater, anaerobe, mesophile, Desulfomicrobiaceae.
This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Strain XT (DSM 4028 = CCUG 34229 = VKM B-1378) is the type strain of the species Desulfomicrobium baculatum, which is the type species of the genus Desulfomicrobium. Strain XT was first described as Desulfovibrio baculatus by Rozanova and Nazina [1,2], and later transferred to the novel genus Desulfomicrobium (currently containing seven species) [3] (Figure 1) because several phenotypic traits were not consistent with the definition of the genus Desulfovibrio. In 1998 the species epithet was corrected to D. baculatum [8]. Three accompanying strains have been described in addition to strain XT: Strain H.L21 (DSM 2555) was isolated from anoxic intertidal sediment at the Ems-Dollard Estuary, Netherlands (16S rRNA gene accession AJ277895) [9], strain 5174 (DSM 17142) was isolated from a forest pond near Braunschweig, Germany (16S rRNA gene accession AJ277896) [10], and strain 9974 (DSM 17143) was isolated as a contaminating chemotrophic bacterium from a culture of a green sulfur bacterium designated ’Chloropseudomonas ethylica’ N2 [10]. These strains were tentatively affiliated with the species D. baculatum based on some phenotypic traits. Although 16S rRNA gene sequence data are now available for two strains, a definitive affiliation of strains to the species Desulfomicrobium requires supplementary DNA-DNA hybridization experiments due to the observed high similarity values of 16S rRNA gene sequences among distinct species of this genus [11]. Other isolates and clones related to the species were isolated from production waters of a low-temperature biodegraded oil reservoir in Canada [12], and wastewater from penicillin G production in China (clone B19 EU234202). Screening of environmental genomic samples and surveys reported at the NCBI BLAST server indicated no closely related phylotypes that can be linked to the species. Here we present a summary classification and a set of features for D. baculatum strain XT (Table 1), together with the description of the complete genomic sequencing and annotation.
Figure 1 Phylogenetic tree of D. baculatum strain XT and all type strains of species within members of the family Desulfomicrobiaceae, inferred from 1,457 aligned characters [4,5] of the 16S rRNA gene sequence under the maximum likelihood criterion [6]. The tree was rooted with all members from the Desulfonatronaceae, another family in the order Desulfovibrionales. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates if larger than 60%. Strains with a genome-sequencing project registered in GOLD [7] are printed in blue; published genomes in bold. |
| MIGS ID | Property | Term | Evidence code |
|---|---|---|---|
| Current classification | Domain Bacteria Phylum Proteoobacteria Class Deltaproteobacteria Order Desulfovibrionales Family Desulfomicrobiaceae Genus Desulfomicrobium Species Desulfomicrobium baculatum Type strain X |
TAS [14] TAS [14] TAS [14] TAS [1] TAS [1] TAS [1] |
|
| Gram stain | negative | TAS [1] | |
| Cell shape | rod-shaped | TAS [1] | |
| Motility | motile, single polar flagellum | TAS [1] | |
| Sporulation | non-sporulating | TAS [1] | |
| Temperature range | mesophilic | TAS [1] | |
| Optimum temperature | 28-37°C | TAS [1] | |
| Salinity | 10 g NaCl/l | TAS [1] | |
| MIGS-22 | Oxygen requirement | strictly anerobic | TAS [1] |
| Carbon source | lactate, pyruvate, malate, fumarate | TAS [1,12] | |
| Energy source | formate, H2 | TAS [1] | |
| MIGS-6 | Habitat | freshwater to brackish anoxic sediments | TAS [1] |
| MIGS-15 | Biotic relationship | free-living | NAS |
| MIGS-14 | Pathogenicity | none | NAS |
| Biosafety level | 1 | TAS [15] | |
| Isolation | water-saturated manganese carbonate ore | TAS [1] | |
| MIGS-4 | Geographic location | not reported | |
| MIGS-5 | Sample collection time | 1975 or earlier | IDA |
| MIGS-4.1 MIGS-4.2 | Latitude – Longitude | not reported | |
| MIGS-4.3 | Depth | not reported | |
| MIGS-4.4 | Altitude | not reported |
Evidence codes – IDA: Inferred from Direct Assay (first time in publication); TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from the Gene Ontology project [16]. If the evidence code is IDA, then the property was directly observed for a live isolate by one of the authors or an expert mentioned in the acknowledgements.
Cells of D. baculatum strain XT are short rods with rounded ends of 0.6 x 1-2 µm (Figure 2). Cells stain Gram-negative, are motile by a single polar flagellum, and do not form endospores. The metabolism is strictly anaerobic and can be respiratory or fermentative [3,17]. Temperature range for growth is 2-41°C (optimum 28-37°C) and NaCl concentrations of 0-6% (w/v) are tolerated (optimum 1% w/v). Sulfate, sulfite and thiosulfate are used as electron acceptors and are reduced to H2S. Nitrate is not reduced. Simple organic compounds are incompletely oxidized to acetate [3]. Malate, fumarate and pyruvate can be fermented with succinate and acetate as end products. Carbohydrates are not fermented. Vitamins are not required for growth [3]. D. baculatum strain 9974 (DSM 1743) is also able to use ethanol as a substrate [18] and sulfur as an electron acceptor [10]. The use of ethanol as an electron donor for sulfate respiration depends on supplementing the medium with the trace elements tungstate or molybdate [18]. Sulfate uptake in symport with sodium ions has been shown in strain 9974, unlike in other fresh water sulfate reducers which use protons [19]. Distinctive features of D. baculatum strain XT are: (i) NaCl is not required for growth [3], (ii) fermentation of fumarate and malate to succinate and acetate is preferred against utilization of these substrates as electron donors for sulfate reduction [17], (iii) sulfur is not used as an electron acceptor and (IV) molecular nitrogen can be assimilated [3].
Figure 2 Scanning electron micrograph of D. baculatum XT (Manfred Rohde, Helmholtz Centre for Infection Biology, Braunschweig) |
A desulfoviridin-type dissimilatory sulfite reductase, which is a hallmark feature of the genus Desulfovibrio, is absent in strain XT, however a sulfite reductase of the desulforubidin-type was reported for strain 9974 [20]. Cells of D. baculatum strain XT contain c- and b-type cytochromes [3]. The tetraheme cytochrome c3 of strain 9974, which is thought to play a role in sulfur reduction and the coupling of electron transfer to hydrogenases, has been analyzed in some detail using advanced biophysical methods [21-23]. Strain 9974 also contains several distinct [NiFeSe] hydrogenases that are located in different cellular compartments [24]. The crystal structure of the periplasmic [NiFeSe] hydrogenase of this strain has been determined [25] and it is proposed that the selenium ion in the active center plays a role in the oxygen-tolerant hydrogen production of this enzyme, which distinguishes it from most [NiFe] hydrogenases [26]. An active selenocysteine system for usage of the 21st amino acid has been studied in detail for D. baculatum strain 9974 [27-29]. Pyridoxal-5’-phosphate, the prosthetic group of selenocysteine synthases, is bound to a distinct lysine residue (Lys295) within the active site of the enzyme of this strain [28].
Figure 1 shows the phylogenetic neighborhood of D. baculatum strain XT in a 16S rRNA based tree. Analysis of the two 16S rRNA gene sequences in the genome of strain XT indicated that the two genes are almost identical (1 bp difference), and that both genes differed by one nucleotide from the previously published 16S rRNA sequence generated from DSM 4028 (AJ277894).
The cellular fatty acid patterns of D. baculatum strain XT and the accompanying strains 5174, 9974 and H.L21 [30] were found to be dominated by anteiso- (ai) and iso-methyl branched unsaturated and saturated fatty acids. The most abundant fatty acid is iso-17:1 cis7 (24.2-28.6%), followed by 18:1 cis11 (6.4-12.2%), iso-15:0 (8.2-11.6%), ai-17:0 (4.5-8.3%), ai-15:0 (5.2-7.7%), 18:0 (3.9-7.1%) and 16:0 (3.6-5.7%). Less abundant fatty acids are iso-15:1 (3.1–4.0%), 16:1 cis7 (2.2–5.0%), ai-17:1 (2.4–4.1%), 18:1 cis9 (2.6–4.3%), iso-16:1 (0.5–2.2%), and 17:0 (0.2-0.3%). Branched chain, hydroxylated fatty acids are also present, 3-OH iso-15:0 (1.4–2.4%), 3-OH ai-15:0 (0.7–1.2%), and 3-OH iso-17:0 (1.2–2.2%), which may be derived from a lipopolysaccharide. The polar lipid composition of D. baculatum strain XT has not been investigated. The respiratory quinone composition of D. baculatum strain XT has also not been investigated, but the presence of MK-6 has been reported in D. macestii and D. norvegicum [11,31].
This organism was selected for sequencing on the basis of its phylogenetic position, and is part of the Genomic Encyclopedia of Bacteria and Archaea project. The genome project is deposited in the Genomes OnLine Database [7] and the complete genome sequence (CP001629) is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.
| MIGS ID | Property | Term |
|---|---|---|
| MIGS-31 | Finishing quality | Finished |
| MIGS-28 | Libraries used | Two genomic libraries: one 8 kb Sanger pMCL200 library and one 454 pyrosequence standard library |
| MIGS-29 | Sequencing platforms | ABI3730, 454 GS FLX |
| MIGS-31.2 | Sequencing coverage | 6.8x Sanger; 30.4x pyrosequence |
| MIGS-20 | Assemblers | Newbler version 1.1.02.15, phrap |
| MIGS-32 | Gene calling method | Prodigal |
| INSDC / Genbank ID | CP001629 | |
| Genbank Date of Release | not yet | |
| GOLD ID | Gc01026 | |
| NCBI project ID | 29527 | |
| Database: IMG-GEBA | 2501416908 | |
| MIGS -13 | Source material identifier | DSM 4028 |
| Project relevance | Tree of Life, GEBA |
D. baculatum strain XT (DSM 4028) was grown in DSMZ medium 63 at 30°C. DNA was isolated from 1-1.5 g of cell paste using Qiagen Genomic 500 DNA Kit (Qiagen, Hilden, Germany) with a modified protocol for cell lysis, adding 100 µl lysozyme; 500 µl achromopeptidase, lysostaphin, mutanolysin, each, to standard lysis solution, but reducing proteinase K to 160µl, only. Incubation over night at 35°C.
The genome was sequenced using a combination of Sanger and 454 sequencing platforms. All general aspects of library construction and sequencing performed at the JGI can be found at the JGI website. 454 Pyrosequencing reads were assembled using the Newbler assembler version 1.1.02.15 (Roche). Large Newbler contigs were broken into 4,375 overlapping fragments of 1,000 bp and entered into assembly as pseudo-reads. The sequences were assigned quality scores based on Newbler consensus q-scores with modifications to account for overlap redundancy and to adjust inflated q-scores. A hybrid 454/Sanger assembly was made using the parallel phrap assembler (High Performance Software, LLC). Possible mis-assemblies were corrected with Dupfinisher or transposon bombing of bridging clones [32]. Gaps between contigs were closed by editing in Consed, custom primer walk or PCR amplification. 731 Sanger finishing reads were produced to close gaps, to resolve repetitive regions, and to raise the quality of the finished sequence. The error rate of the completed genome sequence is less than 1 in 100,000. Together all sequence types provided 37.2 x coverage of the genome.
Genes were identified using Prodigal [33] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using JGI’s GenePRIMP pipeline [34]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGRFam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation were performed within the Integrated Microbial Genomes (IMG-ER) platform.
The genome is 3,942,657 bp long and comprises one circular chromosome with a 58.7% GC content (Table 3 and Figure 3). Of the 3,565 genes predicted, 3,494 were protein coding genes, and 71 RNAs; 58 pseudogenes were also identified. 74.9% of the genes were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The properties and the statistics of the genome are summarized in Table 3. The distribution of genes into COGs functional categories is presented in Table 4.
| Attribute | Value | % of Total |
|---|---|---|
| Genome size (bp) | 3,942,657 | |
| DNA Coding region (bp) | 3,572,336 | 90.61% |
| DNA G+C content (bp) | 2,312,250 | 58.65% |
| Number of replicons | 1 | |
| Extrachromosomal elements | 0 | |
| Total genes | 3565 | |
| RNA genes | 71 | 2.02% |
| rRNA operons | 2 | |
| Protein-coding genes | 3494 | 97.98% |
| Pseudo genes | 58 | 1.63% |
| Genes with function prediction | 2675 | 75.01% |
| Genes in paralog clusters | 357 | 12.82% |
| Genes assigned to COGs | 2689 | 75.41% |
| Genes assigned Pfam domains | 2688 | 75.38% |
| Genes with signal peptides | 723 | 20.27% |
| Genes with transmembrane helices | 897 | 25.15% |
| CRISPR repeats | 0 |
Figure 3 Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew. |
| Code | Value | % | Description |
|---|---|---|---|
| J | 166 | 4.8 | Translation, ribosomal structure and biogenesis |
| A | 0 | 0.0 | RNA processing and modification |
| K | 154 | 4.4 | Transcription |
| L | 116 | 3.3 | Replication, recombination and repair |
| B | 3 | 0.1 | Chromatin structure and dynamics |
| D | 35 | 1.0 | Cell cycle control, mitosis and meiosis |
| Y | 0 | 0.0 | Nuclear structure |
| V | 38 | 1.1 | Defense mechanisms |
| T | 325 | 9.3 | Signal transduction mechanisms |
| M | 221 | 6.3 | Cell wall/membrane biogenesis |
| N | 108 | 3.1 | Cell motility |
| Z | 0 | 0.0 | Cytoskeleton |
| Code | Value | % | Description |
|---|---|---|---|
| W | 0 | 0.0 | Extracellular structures |
| U | 82 | 2.3 | Intracellular trafficking and secretion |
| O | 122 | 3.5 | Posttranslational modification, protein turnover, chaperones |
| C | 241 | 6.9 | Energy production and conversion |
| G | 126 | 3.6 | Carbohydrate transport and metabolism |
| E | 266 | 7.6 | Amino acid transport and metabolism |
| F | 68 | 1.9 | Nucleotide transport and metabolism |
| H | 135 | 3.9 | Coenzyme transport and metabolism |
| I | 52 | 1.5 | Lipid transport and metabolism |
| P | 137 | 3.9 | Inorganic ion transport and metabolism |
| Q | 34 | 1.0 | Secondary metabolites biosynthesis, transport and catabolism |
| R | 319 | 9.1 | General function prediction only |
| S | 221 | 6.3 | Function unknown |
| - | 805 | 23.0 | Not in COGs |
We would like to gratefully acknowledge the help of Maren Schroeder (DSMZ) for growing D. baculatum cultures. This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396 as well as German Research Foundation (DFG) INST 599/1-1.
| 1. | Rozanova EP, Nazina TN. A mesophilic, sulfate-reducing, rod-shaped, nonsporeforming bacterium. Mikrobiologiya 1976; 45:825-830. |
| 2. | List Editor. Validation of the publication of new names and new combinations previously effectively published outside the ISJB. Int J Syst Bacteriol 1984; 34:355-357. |
| 3. | Rozanova EP, Nazina TN, Galushko AS. Isolation of a new genus of sulfate-reducing bacteria and description of a new species of this genus, Desulfomicrobium apsheronum gen. nov., sp. nov. Mikrobiologiya 1988; 57:634-641. |
| 4. | Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics 2002; 18:452-464. [doi:10.1093/bioinformatics/18.3.452] [pmid:11934745] |
| 5. | Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. [pmid:10742046] |
| 6. | Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758-771. [doi:10.1080/10635150802429642] [pmid:18853362] |
| 7. | Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2008; 36:D475-D479. [doi:10.1093/nar/gkm884] [pmid:17981842] |
| 8. | Euzeby JP. Taxonomic note: necessary correction of specific and subspecific epithets according to Rules 12c and 13b of the International Code of Nomenclature of Bacteria (1990 Revision). Int J Syst Bacteriol 1998; 48:1073-1075. |
| 9. | Laanbroek HJ, Pfennig N. Oxidation of short-chain fatty acids by sulfate-reducing bacteria in freshwater and in marine sediments. Arch Microbiol 1981; 128:330-335. [doi:10.1007/BF00422540] [pmid:7212933] |
| 10. | Biebl H, Pfennig N. Growth of sulfate-reducing bacteria with sulfur as electron acceptor. Arch Microbiol 1977; 112:115-117. [doi:10.1007/BF00446664] [pmid:843165] |
| 11. | Grabowski A, Nercessian O, Fayolle F, Blanchet D, Jeanthon C. Microbial diversity in production waters of a low-temperature biodegraded oil reservoir. FEMS Microbiol Ecol 2005; 54:427-443. [doi:10.1016/j.femsec.2005.05.007] [pmid:16332340] |
| 12. | Hippe H, Vainshtein M, Gogotova GI, Stackebrandt E. Reclassification of Desulfobacterium macestii as Desulfomicrobium macestii comb. nov. Int J Syst Evol Microbiol 2003; 53:1127-1130. [doi:10.1099/ijs.0.02574-0] [pmid:12892138] |
| 13. | Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. [doi:10.1038/nbt1360] [pmid:18464787] |
| 14. | Kuever J, Rainey FA, Widdel F. Family II Desulfomicrobiaceae fam. nov. NR Krieg JS, GM Garrity, editor. New York: Springer; 2005. 944 |
| 15. | Anonymous. Biological Agents: Technical rules for biological agents. www.baua.de. |
| 16. | Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29. [doi:10.1038/75556] [pmid:10802651] |
| 17. | Sharak-Genthner BR, Friedman SD, Devereux R. Reclassification of Desulfovibrio desulfuricans Norway 4 as Desulfomicrobium norvegicum comb. nov. and confirmation of Desulfomicrobium escambiense (corrig., formerly "escambium") as a new species in the genus Desulfomicrobium. Int J Syst Bacteriol 1997; 47:889-892. |
| 18. | Hensgens CMH, Nienhuis-Kuiper ME, Hansen TA. Effect of tungstate on the growth of Desulfovibrio gigas NCIMB 9332 and other sulfate-reducing bacteria with ethanol as a substrate. Arch Microbiol 1994; 162:143-147. [doi:10.1007/BF00264388] |
| 19. | Kreke B, , Cypionka H. Energetics of sulfate transport in Desulfomicrobium baculatum. Arch Microbiol 1995; 163:307-309. [doi:10.1007/BF00393385] |
| 20. | Lee JP, Yi CS, LeGall J, Peck HD. Isolation of a new pigment, desulforubidin, from Desulfovibrio desulfuricans (Norway strain) and its role in sulfite reduction. J Bacteriol 1973; 115:453-455. [pmid:4717523] |
| 21. | Fauque G, Herve D, Le Gall J. Structure-function relationship in hemoproteins: the role of cytochrome c3 in the reduction of colloidal sulfur by sulfate-reducing bacteria. Arch Microbiol 1979; 121:261-264. [doi:10.1007/BF00425065] [pmid:229785] |
| 22. | Coutinho IB, Turner DL, Legall J, Xavier AV. NMR studies and redox titration of the tetraheme cytochrome c3 from Desulfomicrobium baculatum. Identification of the low-potential heme. Eur J Biochem 1995; 230:1007-1013. [doi:10.1111/j.1432-1033.1995.tb20649.x] [pmid:7601130] |
| 23. | Correia IJ, Paquete CM, Coelho A, Almeida CC, Catarino T, Louro RO, Frazao C, Saraiva LM, Carrondo MA, Turner DL, et al. Proton-assisted two-electron transfer in natural variants of tetraheme cytochromes from Desulfomicrobium sp. J Biol Chem 2004; 279:52227-52237. [doi:10.1074/jbc.M408763200] [pmid:15456779] |
| 24. | Teixeira M, Fauque G, Moura I, Lespinat PA, Berlier Y, Prickril B, Peck HD, Xavier AV, Le Gall J, Moura JJ. Nickel-[iron-sulfur]-selenium-containing hydrogenases from Desulfovibrio baculatus (DSM 1743). Redox centers and catalytic properties. Eur J Biochem 1987; 167:47-58. [doi:10.1111/j.1432-1033.1987.tb13302.x] [pmid:3040402] |
| 25. | Garcin E, Vernede X, Hatchikian EC, Volbeda A, Frey M, Fontecilla-Camps JC. The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center. Structure 1999; 7:557-566. [doi:10.1016/S0969-2126(99)80072-0] [pmid:10378275] |
| 26. | Parkin A, Goldet G, Cavazza C, Fontecilla-Camps JC, Armstrong FA. The difference a Se makes? Oxygen-tolerant hydrogen production by the [NiFeSe]-hydrogenase from Desulfomicrobium baculatum. J Am Chem Soc 2008; 130:13410-13416. [doi:10.1021/ja803657d] [pmid:18781742] |
| 27. | Tormay P, Wilting R, Heider J, Bock A. Genes coding for the selenocysteine-inserting tRNA species from Desulfomicrobium baculatum and Clostridium thermoaceticum: structural and evolutionary implications. J Bacteriol 1994; 176:1268-1274. [pmid:8113164] |
| 28. | Tormay P, Wilting R, Lottspeich F, Mehta PK, Christen P, Bock A. Bacterial selenocysteine synthase - structural and functional properties. Eur J Biochem 1998; 254:655-661. [doi:10.1046/j.1432-1327.1998.2540655.x] [pmid:9688279] |
| 29. | Kromayer M, Wilting R, Tormay P, Bock A. Domain structure of the prokaryotic selenocysteine-specific elongation factor SelB. J Mol Biol 1996; 262:413-420. [doi:10.1006/jmbi.1996.0525] [pmid:8893853] |
| 30. | Vainshtein M, Hippe H, Kroppenstedt RM. Cellular fatty acid composition of Desulfovibrio species and its use in classification of sulfate-reducing bacteria. Syst Appl Microbiol 1992; 15:554-566. |
| 31. | Collins MD, Widdel F. Respiratory quinones of sulphate-reducing and sulphur-reducing bacteria: a systematic investigation. Syst Appl Microbiol 1986; 8:8-18. |
| 32. | Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Del Rio TG, Nolan M, Chen F, Lucas S, et al. Complete genome of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12-20. [doi:10.4056/sigs.761] |
| 33. | Anonymous. Prodigal Prokaryotic Dynamic Programming Genefinding Algorithm. Oak Ridge National Laboratory and University of Tennessee 2009 http://compbio.ornl.gov/prodigal |
| 34. | Pati A. GenePRIMP: A Gene Prediction Improvement Pipeline for microbial genomes;(In press) |
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Acknowledgements
We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.
Funding for SIGS is provided by a grant from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707.
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