Putative essential and core-essential genes in Mycoplasma genomes

Scientific Reports

Volumn 1, Issue , 2011, Pages

  Lin, Yan ^a   Zhang, Randy Ren ^b  

^a TIANJIN UNIVERSITY   (China)

^b WAYNE STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENOME; CHROMOSOME MAP; ESSENTIAL GENE; GENETICS; METHODOLOGY; MYCOPLASMA; PHYSIOLOGY;

BACTERIAL PROTEINS; CHROMOSOME MAPPING; GENES, ESSENTIAL; GENOME, BACTERIAL; MYCOPLASMA;

EID: 84860112417     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep00053     Document Type: Article

References (38)

1. Gibson, D. G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52-6 (2010).
2. Pennisi, E. Synthetic genome brings new life to bacterium. Science 328, 958-9 (2010).
3. Itaya, M. An estimation of minimal genome size required for life. FEBS Lett 362, 257-60 (1995).
4. Koonin, E. V. How many genes can make a cell: the minimal-gene-set concept. Annu Rev Genomics Hum Genet 1, 99-116 (2000).
5. Editorial. Unbottling the genes. Nat Biotechnol 27, 1059 (2009).
6. Henkel, J. & Maurer, S. M. Parts, property and sharing. Nat Biotechnol 27, 1095-8 (2009).
7. Koonin, E. V. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 1, 127-36 (2003).
8. Hutchison, C. A. et al. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286, 2165-9 (1999).
9. Zhang, R. & Lin, Y. DEG 5. 0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res 37, D455-8 (2009).
10. Jeong, H. & Barabasi, A. L. Prediction of proteni essentiality based on genomic data. ComPlexUs 1, 19-28 (2003).
11. Chen, Y. & Xu, D. Understanding protein dispensability through machinelearning analysis of high-throughput data. Bioinformatics 21, 575-81 (2005). (Pubitemid 40424781)
12. Saha, S. & Heber, S. In silico prediction of yeast deletion phenotypes. Genet Mol Res 5, 224-32 (2006).
13. Seringhaus, M., Paccanaro, A., Borneman, A., Snyder, M. & Gerstein, M. Predicting essential genes in fungal genomes. Genome Res 16, 1126-35 (2006). (Pubitemid 44320400)
14. Gustafson, A. M., Snitkin, E. S., Parker, S. C., DeLisi, C. & Kasif, S. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics 7, 265 (2006).
15. Plaimas, K., Eils, R. & Konig, R. Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC Syst Biol 4, 56 (2010).
16. Deng, J. et al. Investigating the predictability of essential genes across distantly related organisms using an integrative approach. Nucleic Acids Res 39, 795-807 (2011).
17. Zhang, R., Ou, H. Y. & Zhang, C. T. DEG: a database of essential genes. Nucleic Acids Res 32, D271-2 (2004). (Pubitemid 38081654)
18. Sakharkar, K. R., Sakharkar, M. K. & Chow, V. T. A novel genomics approach for the identification of drug targets in pathogens, with special reference to Pseudomonas aeruginosa. In Silico Biol 4, 355-60 (2004). (Pubitemid 39600481)
19. Chong, C. E., Lim, B. S., Nathan, S. & Mohamed, R. In silico analysis of Burkholderia pseudomallei genome sequence for potential drug targets. In Silico Biol 6, 341-6 (2006). (Pubitemid 44430622)
20. Dutta, A. et al. In silico identification of potential therapeutic targets in the human pathogen Helicobacter pylori. In Silico Biol 6, 43-7 (2006). (Pubitemid 43905155)
21. Sharma, V., Gupta, P. & Dixit, A. In silico identification of putative drug targets from different metabolic pathways of Aeromonas hydrophila. In Silico Biol 8, 331-8 (2008).
22. Barh, D. & Kumar, A. In silico identification of candidate drug and vaccine targets from various pathways in Neisseria gonorrhoeae. In Silico Biol 9, 225-31 (2009).
23. Barh, D., Kumar, A. & Misra, A. N. Genomic Target Database (GTD): a database of potential targets in human pathogenic bacteria. Bioinformation 4, 50-1 (2010).
24. Holman, A. G., Davis, P. J., Foster, J. M., Carlow, C. K. & Kumar, S. Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi. BMC Microbiol 9, 243 (2009).
25. Duffield, M. et al. Predicting conserved essential genes in bacteria: in silico identification of putative drug targets. Mol Biosyst 6, 2482-9 (2010).
26. Rocha, E. P. & Danchin, A. Essentiality, not expressiveness, drives gene-strand bias in bacteria. Nat Genet 34, 377-8 (2003). (Pubitemid 36935329)
27. Lin, Y., Gao, F. & Zhang, C. T. Functionality of essential genes drives gene strandbias in bacterial genomes. Biochem Biophys Res Commun 396, 472-6 (2010).
28. Gao, F. & Zhang, C. T. DoriC: a database of oriC regions in bacterial genomes. Bioinformatics 23, 1866-7 (2007). (Pubitemid 47250330)
29. Kobayashi, K. et al. Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100, 4678-83 (2003). (Pubitemid 36457789)
30. Forsyth, R. A. et al. Agenome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol 43, 1387-400 (2002). (Pubitemid 34595533)
31. Ji, Y. et al. Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science 293, 2266-9 (2001). (Pubitemid 32900238)
32. Ogata, H. et al. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 27, 29-34 (1999). (Pubitemid 29209394)
33. Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003).
34. Even, S. et al. Ribonucleases J1 and J2: two novel endoribonucleases in B. subtilis with functional homology to E. coli RNase E. Nucleic Acids Res 33, 2141-52 (2005). (Pubitemid 41439882)
35. Camacho, C. et al. BLAST1: architecture and applications. BMC Bioinformatics 10, 421 (2009).
36. Glass, J. I. et al. Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 103, 425-30 (2006). (Pubitemid 43122417)
37. French, C. T. et al. Large-scale transposon mutagenesis of Mycoplasma pulmonis. Mol Microbiol 69, 67-76 (2008). (Pubitemid 351832755)
38. Gerdes, S. et al. Essential genes on metabolic maps. Curr Opin Biotechnol 17, 448-56 (2006). (Pubitemid 44442929)