Single nucleotide polymorphism in the genes of mce1 and mce4 operons of Mycobacterium tuberculosis: Analysis of clinical isolates and standard reference strains

Rashmi Pasricha, Amita Chandolia, Prija Ponnan, Neeraj K. Saini, Sangeeta Sharma, Madhu Chopra, Mandira Varma Basil, Vani Brahmachari, Mridula Bose

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Abstract

Background: The presence of four mammalian cell entry (mce) operons in Mycobacterium tuberculosis suggests the essentiality of the functions of the genes in these operons. The differential expression of the four mce operons in different phases of in vitro growth and in infected animals reported earlier from our laboratory further justifies the apparent redundancy for these genes in the genome. Here we investigate the extent of polymorphism in eight genes in the mce1 and mce4 operons of M. tuberculosis from four standard reference strains (H37Rv, H37Ra, LVS (Low Virulent Strain) and BCG) and 112 clinical isolates varying in their drug susceptibility profile, analysed by direct sequencing and Sequenom MassARRAY platform. Results: We discovered 20 single nucleotide polymorphisms (SNPs) in the two operons. The comparative analysis of the genes of mce1 and mce4 operons revealed that yrbE1A [Rv0167] was most polymorphic in mce1 operon while yrbE4A [Rv3501c] and lprN [Rv3495c] had the highest number of SNPs in the mce4 operon. Of 20 SNPs, 12 were found to be nonsynonymous and were further analysed for their pathological relevance to M. tuberculosis using web servers PolyPhen and PMut, which predicted five deleterious nonsynonymous SNPs. A mutation from proline to serine at position 359 of the native Mce1A protein was most deleterious as predicted by both PolyPhen and PMut servers. Energy minimization of the structure of native Mce1A protein and mutated protein was performed using InsightII. The mutated Mce1A protein showed structural changes that could account for the effects of this mutation. Conclusions: Our results show that SNPs in the coding sequences of mce1 and mce4 operons in clinical isolates can be significantly high. Moreover, mce4 operon is significantly more polymorphic than mce1 operon (p <0.001). However, the frequency of nonsynonymous substitutions is higher in mce1 operon and synonymous substitutions are more in mce4 operon. In silico modeling predict that nonsynonymous SNP at mce1A [Rv0169], a virulence gene could play a pivotal role in causing functional changes in M. tuberculosis that may reflect upon the biology of the bacteria.

Original languageEnglish (US)
Article number41
JournalBMC Microbiology
Volume11
DOIs
StatePublished - 2011
Externally publishedYes

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Operon
Mycobacterium tuberculosis
Single Nucleotide Polymorphism
Genes
Proteins
Mutation
Mycobacterium bovis
Proline
Computer Simulation
Serine
Virulence
Genome

ASJC Scopus subject areas

  • Microbiology (medical)
  • Microbiology

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Single nucleotide polymorphism in the genes of mce1 and mce4 operons of Mycobacterium tuberculosis : Analysis of clinical isolates and standard reference strains. / Pasricha, Rashmi; Chandolia, Amita; Ponnan, Prija; Saini, Neeraj K.; Sharma, Sangeeta; Chopra, Madhu; Basil, Mandira Varma; Brahmachari, Vani; Bose, Mridula.

In: BMC Microbiology, Vol. 11, 41, 2011.

Research output: Contribution to journalArticle

Pasricha, Rashmi ; Chandolia, Amita ; Ponnan, Prija ; Saini, Neeraj K. ; Sharma, Sangeeta ; Chopra, Madhu ; Basil, Mandira Varma ; Brahmachari, Vani ; Bose, Mridula. / Single nucleotide polymorphism in the genes of mce1 and mce4 operons of Mycobacterium tuberculosis : Analysis of clinical isolates and standard reference strains. In: BMC Microbiology. 2011 ; Vol. 11.
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author = "Rashmi Pasricha and Amita Chandolia and Prija Ponnan and Saini, {Neeraj K.} and Sangeeta Sharma and Madhu Chopra and Basil, {Mandira Varma} and Vani Brahmachari and Mridula Bose",
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T1 - Single nucleotide polymorphism in the genes of mce1 and mce4 operons of Mycobacterium tuberculosis

T2 - Analysis of clinical isolates and standard reference strains

AU - Pasricha, Rashmi

AU - Chandolia, Amita

AU - Ponnan, Prija

AU - Saini, Neeraj K.

AU - Sharma, Sangeeta

AU - Chopra, Madhu

AU - Basil, Mandira Varma

AU - Brahmachari, Vani

AU - Bose, Mridula

PY - 2011

Y1 - 2011

N2 - Background: The presence of four mammalian cell entry (mce) operons in Mycobacterium tuberculosis suggests the essentiality of the functions of the genes in these operons. The differential expression of the four mce operons in different phases of in vitro growth and in infected animals reported earlier from our laboratory further justifies the apparent redundancy for these genes in the genome. Here we investigate the extent of polymorphism in eight genes in the mce1 and mce4 operons of M. tuberculosis from four standard reference strains (H37Rv, H37Ra, LVS (Low Virulent Strain) and BCG) and 112 clinical isolates varying in their drug susceptibility profile, analysed by direct sequencing and Sequenom MassARRAY platform. Results: We discovered 20 single nucleotide polymorphisms (SNPs) in the two operons. The comparative analysis of the genes of mce1 and mce4 operons revealed that yrbE1A [Rv0167] was most polymorphic in mce1 operon while yrbE4A [Rv3501c] and lprN [Rv3495c] had the highest number of SNPs in the mce4 operon. Of 20 SNPs, 12 were found to be nonsynonymous and were further analysed for their pathological relevance to M. tuberculosis using web servers PolyPhen and PMut, which predicted five deleterious nonsynonymous SNPs. A mutation from proline to serine at position 359 of the native Mce1A protein was most deleterious as predicted by both PolyPhen and PMut servers. Energy minimization of the structure of native Mce1A protein and mutated protein was performed using InsightII. The mutated Mce1A protein showed structural changes that could account for the effects of this mutation. Conclusions: Our results show that SNPs in the coding sequences of mce1 and mce4 operons in clinical isolates can be significantly high. Moreover, mce4 operon is significantly more polymorphic than mce1 operon (p <0.001). However, the frequency of nonsynonymous substitutions is higher in mce1 operon and synonymous substitutions are more in mce4 operon. In silico modeling predict that nonsynonymous SNP at mce1A [Rv0169], a virulence gene could play a pivotal role in causing functional changes in M. tuberculosis that may reflect upon the biology of the bacteria.

AB - Background: The presence of four mammalian cell entry (mce) operons in Mycobacterium tuberculosis suggests the essentiality of the functions of the genes in these operons. The differential expression of the four mce operons in different phases of in vitro growth and in infected animals reported earlier from our laboratory further justifies the apparent redundancy for these genes in the genome. Here we investigate the extent of polymorphism in eight genes in the mce1 and mce4 operons of M. tuberculosis from four standard reference strains (H37Rv, H37Ra, LVS (Low Virulent Strain) and BCG) and 112 clinical isolates varying in their drug susceptibility profile, analysed by direct sequencing and Sequenom MassARRAY platform. Results: We discovered 20 single nucleotide polymorphisms (SNPs) in the two operons. The comparative analysis of the genes of mce1 and mce4 operons revealed that yrbE1A [Rv0167] was most polymorphic in mce1 operon while yrbE4A [Rv3501c] and lprN [Rv3495c] had the highest number of SNPs in the mce4 operon. Of 20 SNPs, 12 were found to be nonsynonymous and were further analysed for their pathological relevance to M. tuberculosis using web servers PolyPhen and PMut, which predicted five deleterious nonsynonymous SNPs. A mutation from proline to serine at position 359 of the native Mce1A protein was most deleterious as predicted by both PolyPhen and PMut servers. Energy minimization of the structure of native Mce1A protein and mutated protein was performed using InsightII. The mutated Mce1A protein showed structural changes that could account for the effects of this mutation. Conclusions: Our results show that SNPs in the coding sequences of mce1 and mce4 operons in clinical isolates can be significantly high. Moreover, mce4 operon is significantly more polymorphic than mce1 operon (p <0.001). However, the frequency of nonsynonymous substitutions is higher in mce1 operon and synonymous substitutions are more in mce4 operon. In silico modeling predict that nonsynonymous SNP at mce1A [Rv0169], a virulence gene could play a pivotal role in causing functional changes in M. tuberculosis that may reflect upon the biology of the bacteria.

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