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Genome-Wide Analysis of Intergenic Regions of Mycobacterium tuberculosis H37Rv Using Affymetrix GeneChips

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Abstract

Sequencing the complete genome of Mycobacterium tuberculosis H37Rv is a major milestone in the genome project and it sheds new light in our fight with tuberculosis. The genome contains around 4000 genes (protein-coding sequences) in the original genome annotation. A subsequent reannotation of the genome has added 80 more genes. However, we have found that the intergenic regions can exhibit expression signals, as evidenced by microarray hybridization. It is then reasonable to suspect that there are unidentified genes in these regions. We conducted a genome-wide analysis using the Affymetrix GeneChip to explore genes contained in the intergenic sequences of the M. tuberculosis H37Rv genome. A working criterion for potential protein-coding genes was based on bioinformatics, consisting of the gene structure, protein coding potential, and presence of ortholog evidence. The bioinformatics criteria in conjunction with transcriptional evidence revealed potential genes with a specific function, such as a DNA-binding protein in the CopG family and a nickle binding GTPase, as well as hypothetical proteins that had not been reported in the H37Rv genome. This study further demonstrated that microarray-based transcriptional evidence would facilitate genome-wide gene finding, and is also the first report concerning intergenic expression in M. tuberculosis genome.

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References

  1. 1.

    Cole ST, Brosch R, Parkhill J, et al.: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 1998, 393(6685):537-544. 10.1038/31159

  2. 2.

    Overbeek R, Begley T, Butler RM, et al.: The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research 2005, 33(17):5691-5702. 10.1093/nar/gki866

  3. 3.

    Van Domselaar GH, Stothard P, Shrivastava S, et al.: BASys: a web server for automated bacterial genome annotation. Nucleic Acids Research 2005, 33(Web Server):W455-W459. 10.1093/nar/gki593

  4. 4.

    Stothard P, Wishart DS: Automated bacterial genome analysis and annotation. Current Opinion in Microbiology 2006, 9(5):505-510. 10.1016/j.mib.2006.08.002

  5. 5.

    Nielsen P, Krogh A: Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics 2005, 21(24):4322-4329. 10.1093/bioinformatics/bti701

  6. 6.

    Lee J-M, Zhang S, Saha S, Santa Anna S, Jiang C, Perkins J: RNA expression analysis using an antisense Bacillus subtilis genome array. Journal of Bacteriology 2001, 183(24):7371-7380. 10.1128/JB.183.24.7371-7380.2001

  7. 7.

    Zheng D, Zhang Z, Harrison PM, Karro J, Carriero N, Gerstein M: Integrated pseudogene annotation for human chromosome 22: evidence for transcription. Journal of Molecular Biology 2005, 349(1):27-45. 10.1016/j.jmb.2005.02.072

  8. 8.

    Lukashin AV, Borodovsky M: GeneMark.hmm: new solutions for gene finding. Nucleic Acids Research 1998, 26(4):1107-1115. 10.1093/nar/26.4.1107

  9. 9.

    Besemer J, Borodovsky M: GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Research 2005, 33(Web Server):W451-W454. 10.1093/nar/gki487

  10. 10.

    Fisher MA, Plikaytis BB, Shinnick TM: Microarray analysis of the Mycobacterium tuberculosis transcriptional response to the acidic conditions found in phagosomes. Journal of Bacteriology 2002, 184(14):4025-4032. 10.1128/JB.184.14.4025-4032.2002

  11. 11.

    Finn RD, Mistry J, Schuster-Böckler B, et al.: Pfam: clans, web tools and services. Nucleic Acids Research 2006, 34(Database):D247-D251.

  12. 12.

    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. Journal of Molecular Biology 1990, 215(3):403-410.

  13. 13.

    Burge C, Karlin S: Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology 1997, 268(1):78-94. 10.1006/jmbi.1997.0951

  14. 14.

    Erdmann VA, Barciszewska MZ, Hochberg A, de Groot N, Barciszewski J: Regulatory RNAs. Cellular and Molecular Life Sciences 2001, 58(7):960-977. 10.1007/PL00000913

  15. 15.

    Pickford AS, Cogoni C: RNA-mediated gene silencing. Cellular and Molecular Life Sciences 2003, 60(5):871-882.

  16. 16.

    Camus J-C, Pryor MJ, Médigue C, Cole ST: Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 2002, 148(10):2967-2973.

  17. 17.

    Li J, Pankratz M, Johnson JA: Differential gene expression patterns revealed by oligonucleotide versus long cDNA arrays. Toxicological Sciences 2002, 69(2):383-390. 10.1093/toxsci/69.2.383

  18. 18.

    DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278(5338):680-686. 10.1126/science.278.5338.680

  19. 19.

    Fu LM: Exploring drug action on Mycobacterium tuberculosis using affymetrix oligonucleotide genechips. Tuberculosis 2006, 86(2):134-143. 10.1016/j.tube.2005.07.004

  20. 20.

    Fu LM, Shinnick TM: Genome-wide exploration of the drug action of capreomycin on Mycobacterium tuberculosis using Affymetrix oligonucleotide GeneChips. Journal of Infection 2007, 54(3):277-284. 10.1016/j.jinf.2006.05.012

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Correspondence to Li M Fu.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License (https://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fu, L.M., Shinnick, T.M. Genome-Wide Analysis of Intergenic Regions of Mycobacterium tuberculosis H37Rv Using Affymetrix GeneChips. J Bioinform Sys Biology 2007, 23054 (2007) doi:10.1155/2007/23054

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Keywords

  • Tuberculosis
  • Intergenic Region
  • Hypothetical Protein
  • Genome Annotation
  • Microarray Hybridization