High-throughput screen of essential gene modules in Mycobacterium tuberculosis: a bibliometric approach

BMC Infectious Diseases

Fan Li²  Guoqing Wang²  Jiyao Sheng²  Ying Zhang²  Chengguo Wei²  Fang Wang²  Bin Liu¹  Guangyu Xu² 

[1] The First Bethune Hospital of Jilin University, Changchun, Jilin, China;Key Laboratory of Zoonosis, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, China

关键词: Pathway;    Operon;    Essential gene modules;    Mycobacterium tuberculosis;   

Others  :  1148308
DOI  :  10.1186/1471-2334-13-227

 received in 2012-04-28, accepted in 2013-05-15,  发布年份 2013

【 摘 要 】

Background

Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis). The annotation of functional genome and signaling network in M. tuberculosis are still not systematic. Essential gene modules are a collection of functionally related essential genes in the same signaling or metabolic pathway. The determination of essential genes and essential gene modules at genomic level may be important for better understanding of the physiology and pathology of M. tuberculosis, and also helpful for the development of drugs against this pathogen. The establishment of genomic operon database (DOOR) and the annotation of gene pathways have felicitated the genomic analysis of the essential gene modules of M. tuberculosis.

Method

Bibliometric approach has been used to perform a High-throughput screen for essential genes of M. tuberculosis strain H37Rv. Ant colony algorithm were used to identify the essential genes in other M. tuberculosis reference strains. Essential gene modules were analyzed by operon database DOOR. The pathways of essential genes were assessed by Biocarta, KEGG, NCI-PID, HumanCyc and Reactome. The function prediction of essential genes was analyzed by Pfam.

Results

A total approximately 700 essential genes were identified in M. tuberculosis genome. 40% of operons are consisted of two or more essential genes. The essential genes were distributed in 92 pathways in M. tuberculosis. In function prediction, 61.79% of essential genes were categorized into virulence, intermediary metabolism/respiration,cell wall related and lipid metabolism, which are fundamental functions that exist in most bacteria species.

Conclusion

We have identified the essential genes of M. tuberculosis using bibliometric approach at genomic level. The essential gene modules were further identified and analyzed.

【 授权许可】

   
2013 Xu et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

【 参考文献 】

• [1]Dutta NK, Mehra S, Didier PJ, Roy CJ, Doyle LA, Alvarez X, Ratterree M, Be NA, Lamichhane G, Jain SK, et al.: Genetic requirements for the survival of tubercle bacilli in primates. J Infect Dis 2010, 201(11):1743-1752.
• [2]Meena LS: Rajni: Survival mechanisms of pathogenic Mycobacterium tuberculosis H37Rv. FEBS J 2010, 277(11):2416-2427.
• [3]Cavusoglu C, Durmaz R, Bilgic A, Gunal S: Genotyping of rifampin-resistant Mycobacterium tuberculosis isolates from western Turkey. Ann Saudi Med 2004, 24(2):102-105.
• [4]Cohn DL, Bustreo F, Raviglione MC: Drug-resistant tuberculosis: review of the worldwide situation and the WHO/IUATLD Global Surveillance Project. International Union Against Tuberculosis and Lung Disease. Clin Infect Dis 1997, 24(Suppl 1):S121-S130.
• [5]Wallengren K, Scano F, Nunn P, Margot B, Buthelezi SS, Williams B, Pym A, Samuel EY, Mirzayev F, Nkhoma W, et al.: Drug-Resistant tuberculosis, KwaZulu-Natal, South Africa, 2001-2007. Emerg Infect Dis 2011, 17(10):1913-1916.
• [6]Gerdes S, Edwards R, Kubal M, Fonstein M, Stevens R, Osterman A: Essential genes on metabolic maps. Curr Opin Biotechnol 2006, 17(5):448-456.
• [7]Koonin EV: Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 2003, 1(2):127-136.
• [8]Hong-Geller E, Micheva-Viteva SN: Functional gene discovery using RNA interference-based genomic screens to combat pathogen infection. Curr Drug Discov Technol 2010, 7(2):86-94.
• [9]Awasthy D, Bharath S, Subbulakshmi V, Sharma U: Alanine racemase mutants of Mycobacterium tuberculosis require D-alanine for growth and are defective for survival in macrophages and mice. Microbiology 2011, 158(Pt 2):319-327.
• [10]Ta P, Buchmeier N, Newton GL, Rawat M, Fahey RC: Organic hydroperoxide resistance protein and ergothioneine compensate for loss of mycothiol in Mycobacterium smegmatis mutants. J Bacteriol 2011, 193(8):1981-1990.
• [11]Warnecke T, Hurst LD: Error prevention and mitigation as forces in the evolution of genes and genomes. Nat Rev Genet 2011, 12(12):875-881.
• [12]Bannantine JP, Stabel JR, Bayles DO, Geisbrecht BV: Characteristics of an extensive Mycobacterium avium subspecies paratuberculosis recombinant protein set. Protein Expr Purif 2010, 72(2):223-233.
• [13]Mao F, Dam P, Chou J, Olman V, Xu Y: DOOR: a database for prokaryotic operons. Nucleic Acids Res 2009, 37(Database issue):D459-D463.
• [14]Yin Y, Zhang H, Olman V, Xu Y: Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome. Proc Natl Acad Sci U S A 2010, 107(14):6310-6315.
• [15]Zhang H, Yin Y, Olman V, Xu Y: Genomic arrangement of regulons in bacterial genomes. PLoS One 2012, 7(1):e29496.
• [16]Zhang XC, Huang DS, Li F: Cancer nursing research output and topics in the first decade of the 21st century: results of a bibliometric and co-word cluster analysis. Asian Pac J Cancer Prev 2012, 12(8):2055-2058.
• [17]Spangler ML, Robbins KR, Bertrand JK, Macneil M, Rekaya R: Ant colony optimization as a method for strategic genotype sampling. Anim Genet 2009, 40(3):308-314.
• [18]Chen W, Liao B, Zhu W, Xiang X: Multiple sequence alignment algorithm based on a dispersion graph and ant colony algorithm. J Comput Chem 2009, 30(13):2031-2038.
• [19]Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE III, et al.: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998, 393(6685):537-544.
• [20]Alonso H, Aguilo JI, Samper S, Caminero JA, Campos-Herrero MI, Gicquel B, Brosch R, Martin C, Otal I: Deciphering the role of IS6110 in a highly transmissible Mycobacterium tuberculosis Beijing strain, GC1237. Tuberculosis (Edinb) 2011, 91(2):117-126.
• [21]Due AV, Kuper J, Geerlof A, von Kries JP, Wilmanns M: Bisubstrate specificity in histidine/tryptophan biosynthesis isomerase from Mycobacterium tuberculosis by active site metamorphosis. Proc Natl Acad Sci U S A 2011, 108(9):3554-3559.
• [22]Carrey EA, Dietz C, Glubb DM, Loffler M, Lucocq JM, Watson PF: Detection and location of the enzymes of de novo pyrimidine biosynthesis in mammalian spermatozoa. Reproduction 2002, 123(6):757-768.
• [23]Hotter GS, Collins DM: Mycobacterium bovis lipids: virulence and vaccines. Vet Microbiol 2011, 151(1–2):91-98.
• [24]Salaemae W, Azhar A, Booker GW, Polyak SW: Biotin biosynthesis in Mycobacterium tuberculosis: physiology, biochemistry and molecular intervention. Protein Cell 2011, 2(9):691-695.
• [25]Sassetti CM, Boyd DH, Rubin EJ: Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 2003, 48(1):77-84.
• [26]Rahman MS, Ceraul SM, Dreher-Lesnick SM, Beier MS, Azad AF: The lspA gene, encoding the type II signal peptidase of Rickettsia typhi: transcriptional and functional analysis. J Bacteriol 2007, 189(2):336-341.
• [27]Gey van Pittius NC, Sampson SL, Lee H, Kim Y, van Helden PD, Warren RM: Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol Biol 2006, 6:95. BioMed Central Full Text