Functional analysis of an intergenic non-coding sequence within mce1 operon of M.tuberculosis

Monika Joon,Shipra Bhatia,Rashmi Pasricha,Mridula Bose,Vani Brahmachari

doi:10.1186/1471-2180-10-128

Abstract

BackgroundThe mce operons play an important role in the entry of M. tuberculosis into macrophages and non-phagocytic cells. Their non-redundant function as well as complex regulation is implied by the phenotype of mce mutants. Recently, mce1 operon was found to extend over 13 genes, fadD5 (Rv0166) being the first gene of the operon. The presence of a non-coding sequence of 200 base pairs between Rv0166 and Rv0167 is peculiar to mce1 among the four mce operons of M.tuberculosis. We have examined the function of this region.ResultsWe predicted putative promoter activity of the 200 base pairs of non-coding, intergenic region between Rv0166 and Rv0167 in silico using MEME software and designate it as intergenic promoter, IGPr. We demonstrate both promoter activity and a putative negative regulatory function of this fragment by reporter assays carried out in the surrogate host M.smegmatis. We find that the repressive elements not only control the native promoter but also repress a heterologous promoter of M.smegmatis. The higher activity of the intergenic promoter in a clinical isolate in comparison with the wild type sequence from M.tuberculosis H37Rv could be correlated with a point mutation within the negative element. We have mapped two transcription start sites for mce1 operon both of which are utilized in M.tuberculosis H37Rv as well as the clinical isolate VPCI591. Our studies show that the promoter activity in the non-coding region is relevant not only in reporter gene expression but also in the expression of mce1 operon in M. tuberculosis cells grown in synthetic medium.ConclusionThe mce operon of M.tuberculosis H37Rv potentially can be transcribed from two promoters P1 and P2, former mapping upstream of Rv0166 and the latter in the non-coding intergenic region between Rv0166 and Rv0167. The transcription initiation from P1 results in a transcript with Rv0166 while that from P2 will be without it. The sequences between the translation start site of Rv0167 and the promoter P2 have a negative regulatory role, as point mutation within the sequence leads to enhanced activity of P2 as well as a heterologous promoter from M.smegmatis. The mutation detected in the clinical isolate VPCI591 therefore behaves like a gain-of-function mutation.

Highlights

The mce operons play an important role in the entry of M. tuberculosis into macrophages and nonphagocytic cells
Detection of a putative promoter in intergenic region of mce1 operon ORF analysis on sequences extending from Rv0166 across Rv0167 revealed the expected stop codon for Rv0166 at 196655 and the initiator codon for Rv0167 at 196861
Since we detect landmarks of promoters known in M.tuberculosis within this region, we refer to it, as intergenic promoter (IGPr)

Summary

Introduction

The mce operons play an important role in the entry of M. tuberculosis into macrophages and nonphagocytic cells. Their non-redundant function as well as complex regulation is implied by the phenotype of mce mutants. The conservation of most of the mce operons in all members of the Mycobacterium tuberculosis complex, and the presence of orthologous mce genes throughout the genus Mycobacteria, including the non-pathogenic species M.smegmatis suggests their functional importance in processes besides pathogenicity [6,7,9,10,11,12,13]. In tune with the proposed functional diversity it has been suggested that mce operon could be under the control of a global stress regulator or multiple negative regulators [4,14]. Given the importance of mce operon and evidences from knock-out studies, any alteration in the expression or genetic polymorphism in mce operons would have significant consequence on the pathogenicity and the severity of infection [6,7,8,16,17]

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