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Journal of Bacteriology, May 2009, p. 3321-3327, Vol. 191, No. 10
0021-9193/09/$08.00+0     doi:10.1128/JB.00120-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Whole-Genome Tiling Array Analysis of Mycobacterium leprae RNA Reveals High Expression of Pseudogenes and Noncoding Regions{triangledown} ,{dagger}

Takeshi Akama,1 Koichi Suzuki,1* Kazunari Tanigawa,1 Akira Kawashima,1 Huhehasi Wu,1 Noboru Nakata,2 Yasunori Osana,3 Yasubumi Sakakibara,3 and Norihisa Ishii1

Department of Bioregulation, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan,1 Department of Microbiology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan,2 Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Japan3

Received 29 January 2009/ Accepted 6 March 2009

Whole-genome sequence analysis of Mycobacterium leprae has revealed a limited number of protein-coding genes, with half of the genome composed of pseudogenes and noncoding regions. We previously showed that some M. leprae pseudogenes are transcribed at high levels and that their expression levels change following infection. In order to clarify the RNA expression profile of the M. leprae genome, a tiling array in which overlapping 60-mer probes cover the entire 3.3-Mbp genome was designed. The array was hybridized with M. leprae RNA from the SHR/NCrj-rnu nude rat, and the results were compared to results from an open reading frame array and confirmed by reverse transcription-PCR. RNA expression was detected from genes, pseudogenes, and noncoding regions. The signal intensities obtained from noncoding regions were higher than those from pseudogenes. Expressed noncoding regions include the M. leprae unique repetitive sequence RLEP and other sequences without any homology to known functional noncoding RNAs. Although the biological functions of RNA transcribed from M. leprae pseudogenes and noncoding regions are not known, RNA expression analysis will provide insights into the bacteriological significance of the species. In addition, our study suggests that M. leprae will be a useful model organism for the study of the molecular mechanism underlying the creation of pseudogenes and the role of microRNAs derived from noncoding regions.

* Corresponding author. Mailing address: Department of Bioregulation, Leprosy Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama-shi, Tokyo 189-0002, Japan. Phone: 81-42-391-8211. Fax: 81-42-394-9092. E-mail: koichis{at}nih.go.jp

{triangledown} Published ahead of print on 13 March 2009.

{dagger} Supplemental material for this article may be found at http://jb.asm.org/.

Journal of Bacteriology, May 2009, p. 3321-3327, Vol. 191, No. 10
0021-9193/09/$08.00+0     doi:10.1128/JB.00120-09
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



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