Biological systems discovery in silico: Radical S-adenosylmethionine protein families and their target peptides for posttranslational modification

Journal of Bacteriology

Volumn 193, Issue 11, 2011, Pages 2745-2755

  Haft, Daniel H ^a   Basu, Malay Kumar ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALBA PROTEIN; BACTERIAL ENZYME; BACTERIOCIN; CYCLODEHYDRATASE; CYSTEINE; HISTIDINE; LANTIBIOTIC SYNTHASE; MATURASE; MOLECULAR MARKER; MYCOFACTOCIN; NIF11 PROTEIN; OXIDOREDUCTASE; PQQE PROTEIN; QUINOHEMOPROTEIN AMINE DEHYDROGENASE; S ADENOSYLMETHIONINE; SELENIUM; SERINE; SULFATASE; UNCLASSIFIED DRUG;

ACIDAMINOCOCCUS; AEROMONAS SALMONICIDA; AMMONIFEX DEGENSII; ANAEROCOCCUS LACTOLYTICUS; ANAEROFUSTIS STERCORIHOMINIS; ARTICLE; AZOBACTEROIDES PSEUDOTRICHONYMPHAE; BACTERIUM; BACTEROIDES; BINDING SITE; BIOINFORMATICS; BLAUTIA HANSENII; CALDICELLULOSIRUPTOR SACCHAROLYTICUS; CANDIDATUS; CARBOXY TERMINAL SEQUENCE; CARBOXYDOTHERMUS HYDROGENOFORMANS; CHLOROBIUM PHAEOBACTEROIDES; CLOSTRIDIA; CLOSTRIDIUM HATHEWAYI; CLOSTRIDIUM NOVYI; CLOSTRIDIUM PERFRINGENS; CLOSTRIDIUM SCINDENS; COMPARATIVE STUDY; COMPUTER MODEL; CONTROLLED STUDY; CUPRIAVIDUS NECATOR; DESULFOCOCCUS OLEOVORANS; DESULFOHALOBIUM RETBAENSE; DESULFOMICROBIUM BACULATUM; DESULFONATRONOSPIRA THIODISMUTANS; DESULFOTOMACULUM ACETOXIDANS; DESULFOTOMACULUM REDUCENS; DESULFOVIBRIO VULGARIS; DESULFURIVIBRIO ALKALIPHILUS; DETHIOBACTER ALKALIPHILUS; DIALISTER INVISUS; EPULOPISCIUM; ETHANOLIGENENS HARBINENSE; EUBACTERIUM BIFORME; EUBACTERIUM SAPHENUM; FAECALIBACTERIUM PRAUSNITZII; FILIFACTOR ALOCIS; GENETIC CONSERVATION; GENOME; GENOMICS; GEOBACTER; GEOBACTER LOVLEYI; GEOBACTER SULFURREDUCENS; HIDDEN MARKOV MODEL; NATRANAEROBIUS THERMOPHILUS; NONHUMAN; OPITUTACEAE; PAENIBACILLUS LARVAE; PHENYLOBACTERIUM ZUCINEUM; PHYLOGENY; PREDICTIVE VALUE; PRIORITY JOURNAL; PROSTHECOCHLORIS AESTUARII; PROTEIN FAMILY; PROTEIN PROCESSING; PROTEIN TARGETING; PSEUDOMONAS FLUORESCENS; RHODOBACTER; SELENOMONAS FLUEGGEI; SHUTTLEWORTHIA SATELLES; STIGMATELLA AURANTIACA; SUBDOLIGRANULUM VARIABILE; THERMOANAEROBACTER ITALICUS; THERMOSINUS CARBOXYDIVORANS; VIBRIO PARAHAEMOLYTICUS; VICTIVALLIS VADENSIS;

BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; PROTEIN PROCESSING, POST-TRANSLATIONAL; S-ADENOSYLMETHIONINE;

CLOSTRIDIA;

EID: 79958173211     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00040-11     Document Type: Article

References (38)

1. Altschul, S. F., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-402.
2. Benjdia, A., et al. 2010. Anaerobic sulfatase-maturating enzyme-a mechanistic link with glycyl radical-activating enzymes? FEBS J. 277:1906-1920.
3. Bierbaum, G., and H. G. Sahl. 2009. Lantibiotics: mode of action, biosynthesis and bioengineering. Curr. Pharm. Biotechnol. 10:2-18.
4. Brindley, A. A., R. Zajicek, M. J. Warren, S. J. Ferguson, and S. E. Rigby. 2010. NirJ, a radical SAM family member of the d1 heme biogenesis luster. FEBS Lett. 584:2461-2466.
5. Butcher, B. G., Y. P. Lin, and J. D. Helmann. 2007. The yydFGHIJ operon of Bacillus subtilis encodes a peptide that induces the LiaRS two-omponent system. J. Bacteriol. 189:8616-8625.
6. Challand, M. R., et al. 2009. Product inhibition in the radical S-adenosylmethionine family. FEBS Lett. 583:1358-1362.
7. Dall'Acqua, W., and P. Carter. 2000. Substrate-assisted catalysis: molecular basis and biological significance. Protein Sci. 9:1-9.
8. Eddy, S. R. 2009. A new generation of homology search tools based on probabilistic inference. Genome Inform. 23:205-211.
9. Finn, R. D., et al. 2008. The Pfam protein families database. Nucleic Acids Res. 36:D281-D288.
10. Frey, P. A., A. D. Hegeman, and F. J. Ruzicka. 2008. The radical SAM superfamily. Crit. Rev. Biochem. Mol. Biol. 43:63-88.
11. Graham, D. E., H. Xu, and R. H. White. 2003. Identification of the 7,8-didemethyl-8-hydroxy-5-deazariboflavin synthase required for coenzyme (420) biosynthesis. Arch. Microbiol. 180:455-464.
12. Haft, D. 2011. Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its icotinoprotein redox partners. BMC Genomics 12:21.
13. Haft, D. H. 2009. A strain-variable bacteriocin in Bacillus anthracis and Bacillus cereus with repeated Cys-Xaa-Xaa motifs. Biol. Direct 4:15.
14. Haft, D. H., M. K. Basu, and D. A. Mitchell. 2010. Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related recursor family. BMC Biol. 8:70.
15. Haft, D. H., I. T. Paulsen, N. Ward, and J. D. Selengut. 2006. Exopolysaccharide-associated protein sorting in environmental organisms: the PEPCTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. BMC Biol. 4:29.
16. Hiratsuka, T., et al. 2008. An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321:1670-1673.
17. Ibrahim, M., et al. 2007. Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing ystem? J. Bacteriol. 189:8844-8854.
18. Kawulka, K. E., et al. 2004. 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 43:3385-3395.
19. Krentz, B. D., et al. 2010. A comparison of methanobactins from Methylo-sinus trichosporium OB3b and Methylocystis strain Sb2 predicts methanobactins are synthesized from diverse peptide precursors modified to create a common core for binding and reducing copper ions. Biochemistry 9:10117-10130.
20. Lee, K. H., et al. 2009. Characterization of RimO, a new member of the methylthiotransferase subclass of the radical SAM superfamily. Biochemistry 8:10162-10174.
21. Lee, S. W., et al. 2008. Discovery of a widely distributed toxin biosynthetic gene cluster. Proc. Natl. Acad. Sci. U. S. A. 105:5879-5884.
22. Lippi, M., A. Passerini, M. Punta, B. Rost, and P. Frasconi. 2008. Metal-Detector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence. Bioinformatics 24:2094-2095.
23. McIntosh, J. A., M. S. Donia, and E. W. Schmidt. 2009. Ribosomal peptide natural products: bridging the ribosomal and nonribosomal worlds. Nat. rod. Rep. 26:537-559.
24. Mondot, S., et al. 2011. Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm. Bowel Dis. 17:185-192.
25. Posewitz, M. C., et al. 2004. Discovery of two novel radical S-adenosylmethionine proteins required for the assembly of an active [Fe] hydrogenase. J. iol. Chem. 279:25711-25720.
26. Rea, M. C., et al. 2010. Thuricin CD, a posttranslationally modified bacteriocin with a narrow spectrum of activity against Clostridium difficile. Proc. atl. Acad. Sci. U. S. A. 107:9352-9357.
27. Rebeil, R., and W. L. Nicholson. 2001. The subunit structure and catalytic mechanism of the Bacillus subtilis DNA repair enzyme spore photoproduct yase. Proc. Natl. Acad. Sci. U. S. A. 98:9038-9043.
28. Schmidt, E. W. 2010. The hidden diversity of ribosomal peptide natural products. BMC Biol. 8:83.
29. Selengut, J. D., et al. 2007. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic enomes. Nucleic Acids Res. 35:D260-D264.
30. Sofia, H. J., G. Chen, B. G. Hetzler, J. F. Reyes-Spindola, and N. E. Miller. 2001. 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 es. 29:1097-1106.
31. Tatusov, R. L., M. Y. Galperin, D. A. Natale, and E. V. Koonin. 2000. The COG database: a tool for genome-scale analysis of protein functions nd evolution. Nucleic Acids Res. 28:33-36.
32. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 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.
33. Toh, S. M., L. Xiong, T. Bae, and A. S. Mankin. 2008. The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S RNA. RNA 14:98-106.
34. Ward, J. H. 1963. Hierachical grouping to optimize an objective function. J. Am. Stat. Assoc. 58:236-244.
35. Wecksler, S. R., et al. 2009. Pyrroloquinoline quinone biogenesis: demonstration that PqqE from Klebsiella pneumoniae is a radical S-adenosyl-methionine enzyme. Biochemistry 48:10151-10161.
36. Yokoyama, K., M. Numakura, F. Kudo, D. Ohmori, and T. Eguchi. 2007. Characterization and mechanistic study of a radical SAM dehydrogenase in the biosynthesis of butirosin. J. Am. Chem. Soc. 129:15147-15155.
37. Zhang, Y., and V. N. Gladyshev. 2005. An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes. ioinformatics 21:2580-2589.
38. Zhang, Y., and V. N. Gladyshev. 2008. Trends in selenium utilization in marine microbial world revealed through the analysis of the global ocean ampling (GOS) project. PLoS Genet. 4:e1000095.