Comparative genomics reveals new candidate genes involved in selenium metabolism in prokaryotes

Genome Biology and Evolution

Volumn 7, Issue 3, 2015, Pages 664-676

  Lin, Jie ^a,b   Peng, Ting ^b   Jiang, Liang ^c   Ni, Jia Zuan ^c   Liu, Qiong ^c   Chen, Luonan ^a   Zhang, Yan ^b  

^a INSTITUTE OF BIOCHEMISTRY AND CELL BIOLOGY   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c SHENZHEN UNIVERSITY   (China)

Author keywords

Comparative genomics; Prokaryotes; SelD; Selenium metabolism

Indexed keywords

ARCHAEAL PROTEIN; BACTERIAL PROTEIN; SELENIUM;

ARCHAEAL GENE; ARCHAEAL GENOME; ARCHAEON; BACTERIAL GENE; BACTERIAL GENOME; BACTERIUM; GENETICS; GENOMICS; METABOLISM;

ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; GENES, ARCHAEAL; GENES, BACTERIAL; GENOME, ARCHAEAL; GENOME, BACTERIAL; GENOMICS; SELENIUM;

EID: 84942098584     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evv022     Document Type: Article

References (56)

1. Aguilar-Barajas E, Diaz-Perez C, Ramirez-Diaz MI, Riveros-Rosas H, Cervantes C. 2011. Bacterial transport of sulfate, molybdate, and related oxyanions. Biometals 24:687-707.
2. Allmang C, Wurth L, Krol A. 2009. The selenium to selenoprotein pathway in eukaryotes: more molecular partners than anticipated. Biochim Biophys Acta. 1790:1415-1423.
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol. 215:403-410.
4. Bock A. 2000. Biosynthesis of selenoproteins-an overview. Biofactors 11:77-78.
5. Bock A, et al. 1991. Selenocysteine: the 21st amino acid. Mol Microbiol. 5:515-520.
6. Brouwer RW, Kuipers OP, Van Hijum SA. 2008. The relative value of operon predictions. Brief Bioinform. 9:367-375.
7. Ching WM, Alzner-De Weerd B, Stadtman TC. 1985. A seleniumcontaining nucleoside at the first position of the anticodon in seleno-tRNAGlu from Clostridium sticklandii. Proc Natl Acad Sci U S A. 82:347-350.
8. Ciccarelli FD, et al. 2006. Toward automatic reconstruction of a highly resolved tree of life. Science 311:1283-1287.
9. Copeland PR, Driscoll DM. 2001. RNA binding proteins and selenocysteine. Biofactors 14:11-16.
10. Donovan J, Copeland PR. 2010. Threading the needle: getting selenocysteine into proteins. Antioxid Redox Signal. 12:881-892.
11. Driscoll DM, Copeland PR. 2003. Mechanism and regulation of selenoprotein synthesis. Annu Rev Nutr. 23:17-40.
12. Felsenstein J. 1989. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166.
13. Fersch J, Stock T, Rother M. 2013. Analysis of selenoprotein gene regulation in Methanococcus maripaludis. Paper presented at the 10th International Symposium on Selenium in Biology and Medicine 2013;2013 Sep. 14-18; Berlin, Germany.
14. Franceschini A, et al. 2013. STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 41:D808-D815.
15. Gristwood T, McNeil MB, Clulow JS, Salmond GP, Fineran PC. 2011. PigS and PigP regulate prodigiosin biosynthesis in Serratia via differential control of divergent operons, which include predicted transporters of sulfur-containing molecules. J Bacteriol. 193:1076-1085.
16. Guillouard I, et al. 2002. Identification of Bacillus subtilis CysL, a regulator of the cysJI operon, which encodes sulfite reductase. J Bacteriol. 184:4681-4689.
17. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52:696-704.
18. Gyaneshwar P, et al. 2005. Lessons from Escherichia coli genes similarly regulated in response to nitrogen and sulfur limitation. Proc Natl Acad Sci U S A. 102:3453-3458.
19. Haft DH, Self WT. 2008. Orphan SelD proteins and selenium-dependent molybdenum hydroxylases. Biol Direct. 3:4.
20. Hatfield DL, Gladyshev VN. 2002. How selenium has altered our understanding of the genetic code. Mol Cell Biol. 22:3565-3576.
21. Henikoff S, Haughn GW, Calvo JM, Wallace JC. 1988. A large family of bacterial activator proteins. Proc Natl Acad Sci U S A. 85:6602-6606.
22. Hohn MJ, Palioura S, Su D, Yuan J, Soll D. 2011. Genetic analysis of selenocysteine biosynthesis in the archaeon Methanococcus maripaludis. Mol Microbiol. 81:249-258.
23. Katoh E, et al. 2000. High precision NMR structure of YhhP, a novel Escherichia coli protein implicated in cell division. J Mol Biol. 304:219-229.
24. Katoh K, Toh H. 2008. Recent developments in the MAFFT multiple sequence alignment program. Brief Bioinform. 9:286-298.
25. Kryukov GV, et al. 2003. Characterization of mammalian selenoproteomes. Science 300:1439-1443.
26. Kurokawa S, et al. 2011. Mammalian selenocysteine lyase is involved in selenoprotein biosynthesis. J Nutr Sci Vitaminol (Tokyo). 57:298-305.
27. Lobanov AV, et al. 2007. Evolutionary dynamics of eukaryotic selenoproteomes: large selenoproteomes may associate with aquatic life and small with terrestrial life. Genome Biol. 8:R198.
28. Low SC, Berry MJ. 1996. Knowing when not to stop: selenocysteine incorporation in eukaryotes. Trends Biochem Sci. 21:203-208.
29. Pott AS, Dahl C. 1998. Sirohaem sulfite reductase and other proteins encoded by genes at the dsr locus of Chromatium vinosum are involved in the oxidation of intracellular sulfur. Microbiology 144:1881-1894.
30. Pryjma M, Apel D, Huynh S, Parker CT, Gaynor EC. 2012. FdhTU-modulated formate dehydrogenase expression and electron donor availability enhance recovery of Campylobacter jejuni following host cell infection. J Bacteriol. 194:3803-3813.
31. Romero H, Zhang Y, Gladyshev VN, Salinas G. 2005. Evolution of selenium utilization traits. Genome Biol. 6:R66.
32. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
33. Shaw FL, et al. 2012. Selenium-dependent biogenesis of formate dehydrogenase in Campylobacter jejuni is controlled by the fdhTU accessory genes. J Bacteriol. 194:3814-3823.
34. Sonnhammer EL, Von Heijne G, Krogh A. 1998. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol. 6:175-182.
35. Squires JE, Berry MJ. 2008. Eukaryotic selenoprotein synthesis: mechanistic insight incorporating new factors and new functions for old factors. IUBMB Life 60:232-235.
36. Stadtman TC. 1996. Selenocysteine. Annu Rev Biochem. 65:83-100.
37. Stec E, et al. 2006. Structural basis of the sulphate starvation response in E. coli: crystal structure and mutational analysis of the cofactorbinding domain of the Cbl transcriptional regulator. J Mol Biol. 364:309-322.
38. Sun J, Klein A. 2004. A lysR-type regulator is involved in the negative regulation of genes encoding selenium-free hydrogenases in the archaeon Methanococcus voltae. Mol Microbiol. 52:563-571.
39. Tatusov RL, Galperin MY, Natale DA, Koonin EV. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28:33-36.
40. Thanbichler M, Bock A. 2002. Selenoprotein biosynthesis: purification and assay of components involved in selenocysteine biosynthesis and insertion in Escherichia coli. Methods Enzymol. 347:3-16.
41. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
42. Vasak M. 2005. Advances in metallothionein structure and functions. J Trace Elem Med Biol. 19:13-17.
43. Wittwer AJ, Ching WM. 1989. Selenium-containing tRNA (Glu) and tRNA (Lys) from Escherichia coli: purification, codon specificity and translational activity. Biofactors 2:27-34.
44. Wolf YI, Koonin EV. 2012. A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes. Genome Biol Evol. 4:1286-1294.
45. Wolfe MD, et al. 2004. Functional diversity of the rhodanese homology domain: the Escherichia coli ybbB gene encodes a selenophosphatedependent tRNA 2-selenouridine synthase. J Biol Chem. 279:1801-1809.
46. Xu XM, et al. 2007. New developments in selenium biochemistry: selenocysteine biosynthesis in eukaryotes and archaea. Biol Trace Elem Res. 119:234-241.
47. Yoshizawa S, Bock A. 2009. The many levels of control on bacterial selenoprotein synthesis. Biochim Biophys Acta. 1790:1404-1414.
48. Zhang Y, Fomenko DE, Gladyshev VN. 2005. The microbial selenoproteome of the Sargasso Sea. Genome Biol. 6:R37.
49. Zhang Y, Gladyshev VN. 2008a. Molybdoproteomes and evolution of molybdenum utilization. J Mol Biol. 379:881-899.
50. Zhang Y, Gladyshev VN. 2008b. Trends in selenium utilization in marine microbial world revealed through the analysis of the global ocean sampling (GOS) project. PLoS Genet. 4:e1000095.
51. Zhang Y, Gladyshev VN. 2009. Comparative genomics of trace elements: emerging dynamic view of trace element utilization and function. Chem Rev. 109:4828-4861.
52. Zhang Y, Gladyshev VN. 2010. General trends in trace element utilization revealed by comparative genomic analyses of Co, Cu, Mo, Ni, and Se. J Biol Chem. 285:3393-3405.
53. Zhang Y, Rodionov DA, Gelfand MS, Gladyshev VN. 2009. Comparative genomic analyses of nickel, cobalt and vitamin B12 utilization. BMC Genomics 10:78.
54. Zhang Y, Romero H, Salinas G, Gladyshev VN. 2006. Dynamic evolution of selenocysteine utilization in bacteria: a balance between selenoprotein loss and evolution of selenocysteine from redox active cysteine residues. Genome Biol. 7:R94.
55. Zhang Y, Turanov AA, Hatfield DL, Gladyshev VN. 2008. In silico identification of genes involved in selenium metabolism: evidence for a third selenium utilization trait. BMC Genomics 9:251.
56. Zwolak I, Zaporowska H. 2012. Selenium interactions and toxicity: a review. Selenium interactions and toxicity. Cell Biol Toxicol. 28:31-46.