Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Haft, Daniel H ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL DEHYDROGENASE; BACTERIOCIN; MYOFACTOCIN; N METHYL N NITROSOANILINE; NICOTINAMIDE ADENINE DINUCLEOTIDE PHOSPHATE; OXIDOREDUCTASE; PYRROLOQUINOLINEQUINONE; RNA; UNCLASSIFIED DRUG; BACTERIAL PROTEIN;

ACTINOBACTERIA; ARCHAEBACTERIUM; ARTICLE; BACTERIAL GENETICS; BINDING SITE; BIOINFORMATICS; CRYSTAL STRUCTURE; DELTAPROTEOBACTERIA; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME SUBSTRATE; FIRMICUTES; GENE CLUSTER; GENETIC CONSERVATION; IN VITRO STUDY; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; OXIDATION REDUCTION STATE; PHYLOGENY; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MODIFICATION; PROTEIN SYNTHESIS; RIBOSOME; SEQUENCE HOMOLOGY; AMINO ACID SEQUENCE; BACTERIUM; BIOLOGY; CHEMISTRY; ELECTRON TRANSPORT; GENETICS; METHODOLOGY; MOLECULAR GENETICS; MULTIGENE FAMILY; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT;

ACTINOBACTERIA; ARCHAEA; CHLOROFLEXI; CHLOROFLEXI (CLASS); DELTAPROTEOBACTERIA; FIRMICUTES; MYCOBACTERIUM TUBERCULOSIS;

AMINO ACID SEQUENCE; ARCHAEA; BACTERIA; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; ELECTRON TRANSPORT; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PROTEIN STRUCTURE, TERTIARY; RIBOSOMES; SEQUENCE ALIGNMENT;

EID: 78651081719     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-21     Document Type: Article

References (33)

1. Bernal A, Ear U, Kyrpides N. Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res 2001, 29(1):126-127. 10.1093/nar/29.1.126, 29859, 11125068.
2. Kensche PR, van Noort V, Dutilh BE, Huynen MA. Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface 2008, 5(19):151-170. 10.1098/rsif.2007.1047, 2405902, 17535793.
3. Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, et al. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res 2005, 33(17):5691-5702. 10.1093/nar/gki866, 1251668, 16214803.
4. Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, et al. STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res 2009, (37 Database):D412-416. 10.1093/nar/gkn760, 2686466, 18940858.
5. Mavromatis K, Chu K, Ivanova N, Hooper SD, Markowitz VM, Kyrpides NC. Gene context analysis in the Integrated Microbial Genomes (IMG) data management system. PLoS One 2009, 4(11):e7979. 10.1371/journal.pone.0007979, 2776528, 19956731.
6. Haft DH, Basu MK, Mitchell DA. Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. BMC Biol 2010, 8(1):70. 10.1186/1741-7007-8-70, 2887384, 20500830.
7. Selengut JD, Haft DH. Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. J Bacteriol 2010, 192(21):5788-5798. 10.1128/JB.00425-10, 20675471.
8. Haft DH, Paulsen IT, Ward N, Selengut JD. Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC Biol 2006, 4:29. 10.1186/1741-7007-4-29, 1569441, 16930487.
9. Selengut JD, Rusch DB, Haft DH. Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. BMC Bioinformatics 2010, 11(1):52. 10.1186/1471-2105-11-52, 20102603.
10. Taylor MC, Jackson CJ, Tattersall DB, French N, Peat TS, Newman J, Briggs LJ, Lapalikar GV, Campbell PM, Scott C, et al. Identification and characterization of two families of F420 H2-dependent reductases from Mycobacteria that catalyse aflatoxin degradation. Mol Microbiol 2010, 78(3):561-575. 10.1111/j.1365-2958.2010.07356.x, 20807200.
11. Sofia HJ, Chen G, Hetzler BG, Reyes-Spindola JF, Miller NE. Radical SAM, a novel protein superfamily linking unresolved steps in familiar biosynthetic pathways with radical mechanisms: functional characterization using new analysis and information visualization methods. Nucleic Acids Res 2001, 29(5):1097-1106. 10.1093/nar/29.5.1097, 29726, 11222759.
12. Kawulka KE, Sprules T, Diaper CM, Whittal RM, McKay RT, Mercier P, Zuber P, Vederas JC. Structure of subtilosin A, a cyclic antimicrobial peptide from Bacillus subtilis with unusual sulfur to alpha-carbon cross-links: formation and reduction of alpha-thio-alpha-amino acid derivatives. Biochemistry 2004, 43(12):3385-3395. 10.1021/bi0359527, 15035610.
13. Meulenberg JJ, Sellink E, Riegman NH, Postma PW. Nucleotide sequence and structure of the Klebsiella pneumoniae pqq operon. Mol Gen Genet 1992, 232(2):284-294.
14. Benjdia A, Subramanian S, Leprince J, Vaudry H, Johnson MK, Berteau O. Anaerobic sulfatase-maturating enzyme--a mechanistic link with glycyl radical-activating enzymes?. Febs J 2010, 277(8):1906-1920. 10.1111/j.1742-4658.2010.07613.x, 20218986.
15. Ibrahim M, Guillot A, Wessner F, Algaron F, Besset C, Courtin P, Gardan R, Monnet V. Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?. J Bacteriol 2007, 189(24):8844-8854. 10.1128/JB.01057-07, 2168622, 17921293.
16. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, et al. The Pfam protein families database. Nucleic Acids Res 2008, (36 Database):D281-288. 2238907, 18039703.
17. Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, Richter AR, White O. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res 2007, (35 Database):D260-264. 10.1093/nar/gkl1043, 1781115, 17151080.
18. Wecksler SR, Stoll S, Tran H, Magnusson OT, Wu SP, King D, Britt RD, Klinman JP. Pyrroloquinoline quinone biogenesis: demonstration that PqqE from Klebsiella pneumoniae is a radical S-adenosyl-L-methionine enzyme. Biochemistry 2009, 48(42):10151-10161. 10.1021/bi900918b, 2814799, 19746930.
19. Kuchenreuther JM, Stapleton JA, Swartz JR. Tyrosine, cysteine, and S-adenosyl methionine stimulate in vitro [FeFe] hydrogenase activation. PLoS One 2009, 4(10):e7565. 10.1371/journal.pone.0007565, 2762031, 19855833.
20. Lotierzo M, Tse Sum Bui B, Florentin D, Escalettes F, Marquet A. Biotin synthase mechanism: an overview. Biochem Soc Trans 2005, 33(Pt 4):820-823.
21. Perzl M, Reipen IG, Schmitz S, Poralla K, Sahm H, Sprenger GA, Kannenberg EL. Cloning of conserved genes from Zymomonas mobilis and Bradyrhizobium japonicum that function in the biosynthesis of hopanoid lipids. Biochim Biophys Acta 1998, 1393(1):108-118.
22. Benjdia A, Leprince J, Guillot A, Vaudry H, Rabot S, Berteau O. Anaerobic sulfatase-maturating enzymes: radical SAM enzymes able to catalyze in vitro sulfatase post-translational modification. J Am Chem Soc 2007, 129(12):3462-3463. 10.1021/ja067175e, 17335281.
23. Dischinger J, Josten M, Szekat C, Sahl HG, Bierbaum G. Production of the novel two-peptide lantibiotic lichenicidin by Bacillus licheniformis DSM 13. PLoS One 2009, 4(8):e6788. 10.1371/journal.pone.0006788, 2727956, 19707558.
24. Lee SW, Mitchell DA, Markley AL, Hensler ME, Gonzalez D, Wohlrab A, Dorrestein PC, Nizet V, Dixon JE. Discovery of a widely distributed toxin biosynthetic gene cluster. Proc Natl Acad Sci USA 2008, 105(15):5879-5884. 10.1073/pnas.0801338105, 2311365, 18375757.
25. Haft DH, Selengut JD, Brinkac LM, Zafar N, White O. Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics. Bioinformatics 2005, 21(3):293-306. 10.1093/bioinformatics/bti015, 15347579.
26. van der Werf MJ, van der Ven C, Barbirato F, Eppink MH, de Bont JA, van Berkel WJ. Stereoselective carveol dehydrogenase from Rhodococcus erythropolis DCL14. A novel nicotinoprotein belonging to the short chain dehydrogenase/reductase superfamily. J Biol Chem 1999, 274(37):26296-26304. 10.1074/jbc.274.37.26296, 10473585.
27. Yang JK, Park MS, Waldo GS, Suh SW. Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis. Proc Natl Acad Sci USA 2003, 100(2):455-460. 10.1073/pnas.0137017100, 141016, 12524453.
28. Norin A, Van Ophem PW, Piersma SR, Persson B, Duine JA, Jornvall H. Mycothiol-dependent formaldehyde dehydrogenase, a prokaryotic medium-chain dehydrogenase/reductase, phylogenetically links different eukaroytic alcohol dehydrogenases--primary structure, conformational modelling and functional correlations. Eur J Biochem 1997, 248(2):282-289. 10.1111/j.1432-1033.1997.00282.x, 9346279.
29. Piersma SR, Visser AJ, de Vries S, Duine JA. Optical spectroscopy of nicotinoprotein alcohol dehydrogenase from Amycolatopsis methanolica: a comparison with horse liver alcohol dehydrogenase and UDP-galactose epimerase. Biochemistry 1998, 37(9):3068-3077. 10.1021/bi972115u, 9485460.
30. Van Ophem PW, Van Beeumen J, Duine JA. Nicotinoprotein [NAD(P)-containing] alcohol/aldehyde oxidoreductases. Purification and characterization of a novel type from Amycolatopsis methanolica. Eur J Biochem 1993, 212(3):819-826. 10.1111/j.1432-1033.1993.tb17723.x, 8385013.
31. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
32. Basu MK, Selengut JD, Haft DH. PhyloProf: a software framework and dataset for iterative search of sequence similarity space using phylogenetic profiles. , ftp://ftp.jcvi.org/pub/data/ppp/
33. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004, 5:113. 10.1186/1471-2105-5-113, 517706, 15318951.