Structural features and the persistence of acquired proteins

Proteomics

Volumn 8, Issue 22, 2008, Pages 4772-4781

  Narra, Hema Prasad ^a   Cordes, Matthew H J ^a   Ochman, Howard ^a  

^a UNIVERSITY OF ARIZONA   (United States)

Author keywords

E. coli; Genome evolution; Lateral gene transfer; ORFans; Protein folding

Indexed keywords

ALPHA HELIX; ARTICLE; BACTERIAL GENE; BETA SHEET; CIRCULAR DICHROISM; ESCHERICHIA COLI; GENE EXPRESSION; GENETIC ANALYSIS; HOP GENE; MOLECULAR CLONING; NONHUMAN; ORFAN GENE; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN PURIFICATION; STRUCTURE ANALYSIS;

CIRCULAR DICHROISM; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; OPEN READING FRAMES; PHYLOGENY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; HUMULUS; PROKARYOTA;

EID: 55849108484     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800061     Document Type: Article

References (65)

1. Hayashi, T., Makino, K., Kurokawa, K., Ishii, K. et al., Complete sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 2001, 8, 11-22.
2. Lerat, E., Daubin, V., Ochman, H., Moran, N. A., Evolutionary origins of genomic repertoires in bacteria. PLoS Biol. 2005, 3, e130.
3. Koonin, E. V., Makarova, K. S., Aravind, L., Horizontal gene transfer in prokaryotes: Quantification and classification. Annu. Rev. Microbiol. 2001, 55, 709-742.
4. Daubin, V., Moran, N. A., Ochman, H., Phylogenetics and the cohesion of bacterial genomes. Science 2003, 301, 829-832.
5. Fischer, D., Eisenberg, D., Finding families for genomic ORFans. Bioinformatics 1999, 15, 759-762.
6. Daubin, V., Ochman, H., Bacterial genomes as new gene homes: The genealogy of ORFans in E. coli. Genome Res. 2004, 14, 1036-1042.
7. Welch, R. A., Burland, V., Plunkett, G., III, Redford, P. et al., Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 2002, 99, 17020-17024.
8. Yin, Y., Fischer, D., On the origin of microbial ORFans: Quantifying the strength of the evidence for viral lateral transfer. BMC Evol. Biol. 2006, 6, 63.
9. Siew, N., Fischer, D., Twenty thousand ORFan microbial protein families for the biologists? Structure 2003, 11, 7-9.
10. Amiri, H., Davids, W., Andersson, S. G., Birth and death of orphan genes in rickettsia. Mol. Biol. Evol. 2003, 20, 1575-1587.
11. Charlebois, R. L., Clarke, G. D., Beiko, R. G., St Jean, A., Characterization of species-specific genes using a flexible, web-based querying system. FEMS Microbiol. Lett. 2003, 225, 213-220.
12. Domazet-Loso, T., Tautz, D., An evolutionary analysis of orphan genes in Drosophila. Genome Res. 2003, 13, 2213-2219.
13. Russell, R. B., Domain insertion. Protein Eng. 1994, 7, 1407-1410.
14. Claverie, J. M., Ogata, H., The insertion of palindromic repeats in the evolution of proteins. Trends Biochem. Sci. 2003, 28, 75-80.
15. Pedulla, M. L., Ford, M. E., Houtz, J. M., Karthikeyan, T. et al., Origins of highly mosaic mycobacteriophage genomes. Cell 2003, 113, 171-182.
16. Alimi, J. P., Poirot, O., lopez, F., Claverie, J. M., Reverse transcriptase-polymerase chain reaction validation of 25 "orphan" genes from Escherichia coli. Genome Res. 2000, 10, 959-966.
17. Shimomura, S., Shigenobu, S., Morioka, M., Ishikawa H., An experimental validation of orphan genes of Buchnera, a symbiont of aphids. Biochem. Biophys. Res. Commun. 2002, 292, 263-267.
18. Shmuely, H., Dinitz, E., Dahan, I., Eichler, J. et al., Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins. Bioinformatics 2004, 20, 1248-1253.
19. Renesto, P., Abergel, C., Decloquement, P., Moinier, D. et al., Mimivirus giant particles incorporate a large fraction of anonymous and unique gene products. J. Virol. 2006, 80, 11678-11685.
20. Ogata, H., Claverie, J. M., Unique genes in giant viruses: Regular substitution pattern and anomalously short size. Genome Res. 2007, 17, 1353-1361.
21. Pascal, G., Médigue, C., Danchin, A., Universal biases in protein composition of model prokaryotes. Proteins 2005, 60, 27-35.
22. Clark, E. H., East, J. M., Lee, A. G., The role of tryptophan residues in an integral membrane protein: Diacylglycerol kinase. Biochemistry 2003, 42, 11065-11073.
23. Pascal, G., Médigue, C., Danchin, A., Persistent biases in the amino acid composition of prokaryotic proteins. Bioessays 2006, 28, 726-738.
24. Zhu, K., Jutila, A., Tuominen, E. K., Patkar, S. A. et al., Impact of the tryptophan residues of Humicola lanuginosa lipase on its thermal stability. Biochem. Biophys. Acta 2001, 1547, 329-338.
25. Koshi, J. M., Bruno, W. J., Major structural determinants of transmembrane proteins identified by principal component analysis. Proteins 1999, 34, 333-340.
26. Tang, C. M., Moxon, E. R., The impact ofmicrobial genomics on antimicrobial drug development. Annu. Rev. Genomics. Hum. Genet. 2001, 2, 259-269.
27. Siew, N., Saini, H. K., Fischer, D., A putative novel alpha/beta hydrolase family in bacillus. FEBS Lett. 2005, 579, 3175-3182.
28. Saini, H. K., Fischer, D., Structural and functional insights into mimivirus ORFans. BMC Genomics 2007, 8, 115.
29. Al-Shahib, A., Breitling, R., Gilbert, D., Predicting protein function by machine learning on amino acid sequences - a critical evaluation. BMC Genomics 2007, 8, 78.
30. Xu, Q., Krishna, S. S., McMullan, D., Schwarzenbacher, R. et al., Crystal structure of an ORFan protein (TM1622) from Thermotoga maritima at 1.75 A resolution reveals a fold similar to the Ran-binding protein Mog1p. Proteins 2006, 15, 777-782.
31. Chin, K. H., Ruan, S. K., Wang, A. H. J., Chou, S. H., XC5848, an ORFan protein from Xanthomonas campestris, adopts a novel variant of Sm-like motif. Proteins 2007, 68, 1006-1010.
32. Portugaly, E., Linial, M., Estimating the probability for a protein to have a new fold: A statistical computational model. Proc. Natl. Acad. Sci. USA 2000, 97, 5161-5166.
33. Siew, N., Fischer, D., Structural biology sheds light on the puzzle of genomic ORFans. J. Mol. Biol. 2004, 342, 369-373.
34. Shin, D. H., Hou, J., Chandonia, J. M., Das, D. et al., Structure-based inference of molecular functions of proteins of unknown function from berkeley structural genomics center. J. Struct. Funct. Genomics 2007, 8, 99-105.
35. Chen, Y. H., Yang, J. T., Martinez, H. M., Determination of the secondary structures of proteins by circular dichroism and optical rotary dispersion. Biochemistry 1972, 11, 4120-4131.
36. May, G., Dersch, P., Haardt, M., Middendorf, A., Bremer, E., The osmZ (bglY) gene encodes the DNA-binding protein HNS (H1a), a component of the Escherichia coli K-12 nucleoid. Mol. Gen. Genet. 1990, 224, 81-90.
37. Boyd, D., Weiss, D. S., Chen, J. C., Beckwith, J., Towards single-copy gene expression systems making gene cloning physiologically relevant: Lambda InCh, a simple Escherichia coli plasmid-chromosome shuttle system. J. Bacteriol. 2000, 182, 842-847.
38. Sorek, R., Zhu, Y. W., Creevey, C. J., Francino, M. P. et al., Genome-wide experimental determination of barriers to horizontal gene transfer. Science 2007, 318, 1449-1452.
39. Selinger, D. W., Cheung, K. J., Mei, R., Johansson, E. M. et al., RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat. Biotechnol. 2000, 18, 1262-1268.
40. Osterhout, R. E., Figueroa, I. A., Keasling, J. D., Arkin, A. P., Global analysis of host response to induction of a latent bacteriophage. BMC Microbiol. 2007, 7, 82.
41. Franchini, A. G., Egli, T., Global gene expression in Escherichia coli K-12 during short-term and long-term adaptation to glucose-limited continuous culture conditions. Microbiology 2006, 152, 2111-2127.
42. Bergholz, T. M., Wick, L. M., Weihong, Qi., Riordan, J. T. et al., Global transcriptional response of Escherichia coli O157:H7 to growth in glucose minimal medium. BMC Microbiol. 2007, 7, 97.
43. Yee, A., Chang, X., Pineda-Lucena, A., Wu, B. et al., An NMR approach to structural proteomics. Proc. Natl. Acad. Sci. USA 2002, 99, 1825-1830.
44. Maxwell, K. L., Bona, D., Liu, C., Arrowsmith, C. H., Edwards, A. M., Refolding out of guanidine hydrochloride is an effective approach for high-throughput structural studies of small proteins. Protein Sci. 2003, 12, 2073-2080.
45. Vogt, J., Schulz, G. E., The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence. Structure 1999, 7, 1301-1309.
46. Otto, K., Hermansson, M., Inactivation of ompX causes increased interactions of type I fimbriated Escherichia coli with abiotic surfaces. J. Bacteriol. 2004, 186, 226-234.
47. Motiejunaite, R., Armalyte, J., Markuckas, A., Suziedeliene, E., Escherichia coli dinJ-yafO genes acts as toxin-antitoxin module. FEMS Microbiol. Lett. 2007, 268, 112-119.
48. Rinas, U., Bailey, J. E., Overexpression of bacterial hemoglobin causes incorporation of preb-lactamase into cytoplasmic inclusion bodies. Appl. Environ. Microbiol. 1993, 59, 561-566.
49. Carrio, M. M., Villaverde, A., Construction and deconstruction of bacterial inclusion bodies. J. Biotechnol. 2002, 96, 3-12.
50. Baneyx, F., Mujacic, M., Recombinant protein folding and misfolding in Escherichia coli. Nature Biotechnol. 2004, 22, 1399-1408.
51. Gonzalez-Montalban, N., Carrio, M. M., Cuatrecasas, S., Aris, A. et al., Bacterial inclusion bodies are cytotoxic in vivo in absence of functional chaperones DnaK or GroEL. J. Biotechnol. 2005, 118, 406-412.
52. Ventura, S., Villaverde, A., Protein quality in bacterial inclusion bodies. Trends Biotechnol. 2006, 24, 179-185.
53. Worrall, D. M., Gross, N. H., The formation of biologically active beta-galactoside inclusion bodies in Escherichia coli. Aust. J. Biotechnol. 1989, 3, 28-32.
54. Tokatlidis, K., Dhurjati, P., Millet, J., Beguin, P. et al., High activity of inclusion bodies formed in Escherichia coli over-producing Clostridium thermocellum endoglucanase D. FEBS Lett. 1991, 282, 205-208.
55. Lees, J. G., Miles, A. J., Wien, F., Wallace, B. A., A reference database for circular dichroism spectroscopy covering fold and secondary structure space. Bioinformatics 2006, 22, 1955-1962.
56. Wolf, Y. L., Brenner, S. E., Bash, P. A., Koonin, E. V., Distribution of protein folds in the three superkingdoms of life. Genome Res. 1999, 9, 17-26.
57. Hegyi, H., Lin, J., Greenbaum, D., Gerstein, M., Structural genomics analysis: Ch aracteristics of atypical, common, and horizontally transferred folds. Proteins: Struct. Funct. Genet. 2002, 47, 126-141.
58. Jackson, S. E., How do small single-domain proteins fold? Fold Des. 1998, 3, R81-R91.
59. Raymond, S., Tocili, A., Ajamian, E., Li, Y. et al., Crystal structure of ureidoglycolate hydrolase (AllA) from Escherichia coli O157:H7. Proteins 2005, 61, 454-459.
60. Mira, A. H., Ochman, H., Moran, N. A., Deletional bias and the evolution of bacterial genomes. Trends Genet. 2001, 10, 589-596.
61. Pallen, M. J., Wren, B. W., Bacterial pathogenomics. Nature 2007, 449, 835-842.
62. Yin, Y., Fischer, D., Identification and investigation of ORFans in the viral world. BMC Genomics 2008, 9, 24.
63. Kim, S. H., Shin, D. H., Liu, J., Oganesyan, V. et al., Structural genomics of minimal organisms and protein fold space. J. Struct. Funct. Genomics 2005, 6, 63-70.
64. Bartlam, M., Xu, Y., Rao, Z., Structural proteomics of the SARS coronavirus: A model response to emerging infectious diseases. J. Struct. Funct. Genomics 2007, 8, 85-97.
65. Almeida, M. S., Johnson, M. A., Herrmann, T., Geralt, M., Wuthrich, K., Novel b-barrel fold in the nuclear magnetic resonance structure of the replicase nonstructural protein 1 from the severe acute respiratory syndrome coronavirus. J. Virol. 2007, 81, 3151-3161.