Research article

Implications of high level pseudogene transcription in Mycobacterium leprae

Diana L Williams¹ , Richard A Slayden² , Amol Amin^{2^} , Alejandra N Martinez^1,3 , Tana L Pittman¹ , Alex Mira⁴ , Anirban Mitra⁵ , Valakunja Nagaraja⁵ , Norman E Morrison⁶ , Milton Moraes³ and Thomas P Gillis¹

¹  HRSA, BPHC, Division of National Hansen's Disease Programs, Laboratory Research Branch, Molecular Biology Research Department @ School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA

²  Rocky Mountain Regional Center of Excellence, Department of Microbiology, Immunology & Pathology, Colorado State University, Fort Collins, CO, USA

³  Leprosy Laboratory, Department, Tropical Medicine Institute Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, RJ, Brazil

⁴  Center for Advanced Research in Public Health, CSISP, Area de Genomica y Salud, Valencia, Spain

⁵  Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India

⁶  Center for Tuberculosis Research, Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA

author email corresponding author email^Deceased

BMC Genomics 2009, 10:397doi:10.1186/1471-2164-10-397

Published:	25 August 2009

Abstract

Background

The Mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. Preliminary evidence suggests that some pseudogenes are expressed. Therefore, defining pseudogene transcriptional and translational potentials of this genome should increase our understanding of their impact on M. leprae physiology.

Results

Gene expression analysis identified transcripts from 49% of all M. leprae genes including 57% of all ORFs and 43% of all pseudogenes in the genome. Transcribed pseudogenes were randomly distributed throughout the chromosome. Factors resulting in pseudogene transcription included: 1) co-orientation of transcribed pseudogenes with transcribed ORFs within or exclusive of operon-like structures; 2) the paucity of intrinsic stem-loop transcriptional terminators between transcribed ORFs and downstream pseudogenes; and 3) predicted pseudogene promoters. Mechanisms for translational "silencing" of pseudogene transcripts included the lack of both translational start codons and strong Shine-Dalgarno (SD) sequences. Transcribed pseudogenes also contained multiple "in-frame" stop codons and high Ka/Ks ratios, compared to that of homologs in M. tuberculosis and ORFs in M. leprae. A pseudogene transcript containing an active promoter, strong SD site, a start codon, but containing two in frame stop codons yielded a protein product when expressed in E. coli.

Conclusion

Approximately half of M. leprae's transcriptome consists of inactive gene products consuming energy and resources without potential benefit to M. leprae. Presently it is unclear what additional detrimental affect(s) this large number of inactive mRNAs has on the functional capability of this organism. Translation of these pseudogenes may play an important role in overall energy consumption and resultant pathophysiological characteristics of M. leprae. However, this study also demonstrated that multiple translational "silencing" mechanisms are present, reducing additional energy and resource expenditure required for protein production from the vast majority of these transcripts.