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Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

Ma L, Jensen JS, Myers L, Burnett J, Welch M, Jia Q, Martin DH - Mol. Microbiol. (2007)

Bottom Line: In order to establish the origin of the MG192 variants, we examined nine genomic loci containing partial copies of the MgPa operon, known as MgPar sequences.Our analysis suggests that the MG192 sequence variation is achieved by recombination between the MG192 expression site and MgPar sequences via gene cross-over and, possibly, also by gene conversion.It appears plausible that M. genitalium has the ability to generate unlimited variants from its minimized genome, which presumably allows the organism to adapt to diverse environments and/or to evade host defences by antigenic variation.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA. lma1@lsuhsc.edu

ABSTRACT
Mycoplasma genitalium, a human pathogen associated with sexually transmitted diseases, is unique in that it has smallest genome of any known free-living organism. The goal of this study was to investigate if and how M. genitalium uses a minimal genome to generate genetic variations. We analysed the sequence variability of the third gene (MG192 or mgpC) of the M. genitalium MgPa adhesion operon, demonstrated that the MG192 gene is highly variable among and within M. genitalium strains in vitro and in vivo, and identified MG192 sequence shifts in the course of in vitro passage of the G37 type strain and in sequential specimens from an M. genitalium-infected patient. In order to establish the origin of the MG192 variants, we examined nine genomic loci containing partial copies of the MgPa operon, known as MgPar sequences. Our analysis suggests that the MG192 sequence variation is achieved by recombination between the MG192 expression site and MgPar sequences via gene cross-over and, possibly, also by gene conversion. It appears plausible that M. genitalium has the ability to generate unlimited variants from its minimized genome, which presumably allows the organism to adapt to diverse environments and/or to evade host defences by antigenic variation.

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representation of MG192 sequence variation and rapid shift identified in two sequential samples (No. 199.0 and 199.1) obtained 10 days apart from an M. genitalium-infected patient. A total of six MG192 variants (a to f) were identified from these two specimens, with three variants present in each specimen. The sequence of the variant a, which is the most predominant variant from the first specimen, is considered the prototype. Various patterns in other five variants represent regions that are different from the variant a and instead have homology to MgPars identified in this patient, as indicated by the key. The diamond indicates single-nucleotide substitutions, which can be traced to a specific MgPar sequence, whereas the star indicates single-nucleotide substitutions, which are not present in any other MG192 variants or MgPars. Numbers above each region refer to the nucleotide positions in the full-length MG192 of the variant a. Detailed nucleotide sequences for the regions included in the box with dashed lines are given in Fig. 6. The number of plasmid clones analysed for MgPars in the patient specimens is listed in Table 3. All clones analysed for each MgPar showed the same sequence except for the triplet repeat number variation in MgPars 2 and 8. The sequences of MG192 variants a to f and MgPars 1 through 9 identified from this patient's strain have been submitted to GenBank under Accession No. EF117283 to EF117288 and EF117293 to EF117301 respectively.
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fig04: representation of MG192 sequence variation and rapid shift identified in two sequential samples (No. 199.0 and 199.1) obtained 10 days apart from an M. genitalium-infected patient. A total of six MG192 variants (a to f) were identified from these two specimens, with three variants present in each specimen. The sequence of the variant a, which is the most predominant variant from the first specimen, is considered the prototype. Various patterns in other five variants represent regions that are different from the variant a and instead have homology to MgPars identified in this patient, as indicated by the key. The diamond indicates single-nucleotide substitutions, which can be traced to a specific MgPar sequence, whereas the star indicates single-nucleotide substitutions, which are not present in any other MG192 variants or MgPars. Numbers above each region refer to the nucleotide positions in the full-length MG192 of the variant a. Detailed nucleotide sequences for the regions included in the box with dashed lines are given in Fig. 6. The number of plasmid clones analysed for MgPars in the patient specimens is listed in Table 3. All clones analysed for each MgPar showed the same sequence except for the triplet repeat number variation in MgPars 2 and 8. The sequences of MG192 variants a to f and MgPars 1 through 9 identified from this patient's strain have been submitted to GenBank under Accession No. EF117283 to EF117288 and EF117293 to EF117301 respectively.

Mentions: To test the hypothesis that MG192 variation occurs in vivo, we examined two sequential specimens (199.0 and 199.1) obtained 10 days apart from an M. genitalium-infected man (Table 1). These two specimens were previously studied for the variable numbers of tandem repeats (VNTR) in the putative lipoprotein gene, MG309, and single-nucleotide polymorphisms in both the rRNA operon (Ma and Martin, 2004) and the MG191 conserved AB region (Hjorth et al., 2006). All of these loci are present in a single copy in the genome (Fraser et al., 1995). It has been well documented that molecular typing based on these loci, particularly the MG309 VNTR and the MG191 conserved AB region, provides excellent discriminatory power for unrelated M. genitalium strains (Ma and Martin, 2004; Hjorth et al., 2006). The two sequential specimens showed identical genotypes at all three loci, thus demonstrating that this patient was infected with a single M. genitalium strain. Direct sequencing of the MG192 PCR products from both specimens showed a mixture of two or more different sequences. In order to obtain the individual sequences, we studied plasmid clones of the PCR products from two independent assays for each specimen. Three MG192 variant sequences were identified in each specimen (Fig. 4). Remarkably, none of these variant sequences were shared between the two specimens. In silico translation analysis showed that all these six variant sequences remained in the correct reading frame and are predicted to encode divergent amino acid sequences. Comparison of the entire variable region sequence (nt 126–1548) of the G37T MG192 gene to the patient MG192 sequences showed a 14–15% difference at the nucleotide level and a 15–17% difference at the deduced amino acid level.


Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

Ma L, Jensen JS, Myers L, Burnett J, Welch M, Jia Q, Martin DH - Mol. Microbiol. (2007)

representation of MG192 sequence variation and rapid shift identified in two sequential samples (No. 199.0 and 199.1) obtained 10 days apart from an M. genitalium-infected patient. A total of six MG192 variants (a to f) were identified from these two specimens, with three variants present in each specimen. The sequence of the variant a, which is the most predominant variant from the first specimen, is considered the prototype. Various patterns in other five variants represent regions that are different from the variant a and instead have homology to MgPars identified in this patient, as indicated by the key. The diamond indicates single-nucleotide substitutions, which can be traced to a specific MgPar sequence, whereas the star indicates single-nucleotide substitutions, which are not present in any other MG192 variants or MgPars. Numbers above each region refer to the nucleotide positions in the full-length MG192 of the variant a. Detailed nucleotide sequences for the regions included in the box with dashed lines are given in Fig. 6. The number of plasmid clones analysed for MgPars in the patient specimens is listed in Table 3. All clones analysed for each MgPar showed the same sequence except for the triplet repeat number variation in MgPars 2 and 8. The sequences of MG192 variants a to f and MgPars 1 through 9 identified from this patient's strain have been submitted to GenBank under Accession No. EF117283 to EF117288 and EF117293 to EF117301 respectively.
© Copyright Policy
Related In: Results  -  Collection

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fig04: representation of MG192 sequence variation and rapid shift identified in two sequential samples (No. 199.0 and 199.1) obtained 10 days apart from an M. genitalium-infected patient. A total of six MG192 variants (a to f) were identified from these two specimens, with three variants present in each specimen. The sequence of the variant a, which is the most predominant variant from the first specimen, is considered the prototype. Various patterns in other five variants represent regions that are different from the variant a and instead have homology to MgPars identified in this patient, as indicated by the key. The diamond indicates single-nucleotide substitutions, which can be traced to a specific MgPar sequence, whereas the star indicates single-nucleotide substitutions, which are not present in any other MG192 variants or MgPars. Numbers above each region refer to the nucleotide positions in the full-length MG192 of the variant a. Detailed nucleotide sequences for the regions included in the box with dashed lines are given in Fig. 6. The number of plasmid clones analysed for MgPars in the patient specimens is listed in Table 3. All clones analysed for each MgPar showed the same sequence except for the triplet repeat number variation in MgPars 2 and 8. The sequences of MG192 variants a to f and MgPars 1 through 9 identified from this patient's strain have been submitted to GenBank under Accession No. EF117283 to EF117288 and EF117293 to EF117301 respectively.
Mentions: To test the hypothesis that MG192 variation occurs in vivo, we examined two sequential specimens (199.0 and 199.1) obtained 10 days apart from an M. genitalium-infected man (Table 1). These two specimens were previously studied for the variable numbers of tandem repeats (VNTR) in the putative lipoprotein gene, MG309, and single-nucleotide polymorphisms in both the rRNA operon (Ma and Martin, 2004) and the MG191 conserved AB region (Hjorth et al., 2006). All of these loci are present in a single copy in the genome (Fraser et al., 1995). It has been well documented that molecular typing based on these loci, particularly the MG309 VNTR and the MG191 conserved AB region, provides excellent discriminatory power for unrelated M. genitalium strains (Ma and Martin, 2004; Hjorth et al., 2006). The two sequential specimens showed identical genotypes at all three loci, thus demonstrating that this patient was infected with a single M. genitalium strain. Direct sequencing of the MG192 PCR products from both specimens showed a mixture of two or more different sequences. In order to obtain the individual sequences, we studied plasmid clones of the PCR products from two independent assays for each specimen. Three MG192 variant sequences were identified in each specimen (Fig. 4). Remarkably, none of these variant sequences were shared between the two specimens. In silico translation analysis showed that all these six variant sequences remained in the correct reading frame and are predicted to encode divergent amino acid sequences. Comparison of the entire variable region sequence (nt 126–1548) of the G37T MG192 gene to the patient MG192 sequences showed a 14–15% difference at the nucleotide level and a 15–17% difference at the deduced amino acid level.

Bottom Line: In order to establish the origin of the MG192 variants, we examined nine genomic loci containing partial copies of the MgPa operon, known as MgPar sequences.Our analysis suggests that the MG192 sequence variation is achieved by recombination between the MG192 expression site and MgPar sequences via gene cross-over and, possibly, also by gene conversion.It appears plausible that M. genitalium has the ability to generate unlimited variants from its minimized genome, which presumably allows the organism to adapt to diverse environments and/or to evade host defences by antigenic variation.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA. lma1@lsuhsc.edu

ABSTRACT
Mycoplasma genitalium, a human pathogen associated with sexually transmitted diseases, is unique in that it has smallest genome of any known free-living organism. The goal of this study was to investigate if and how M. genitalium uses a minimal genome to generate genetic variations. We analysed the sequence variability of the third gene (MG192 or mgpC) of the M. genitalium MgPa adhesion operon, demonstrated that the MG192 gene is highly variable among and within M. genitalium strains in vitro and in vivo, and identified MG192 sequence shifts in the course of in vitro passage of the G37 type strain and in sequential specimens from an M. genitalium-infected patient. In order to establish the origin of the MG192 variants, we examined nine genomic loci containing partial copies of the MgPa operon, known as MgPar sequences. Our analysis suggests that the MG192 sequence variation is achieved by recombination between the MG192 expression site and MgPar sequences via gene cross-over and, possibly, also by gene conversion. It appears plausible that M. genitalium has the ability to generate unlimited variants from its minimized genome, which presumably allows the organism to adapt to diverse environments and/or to evade host defences by antigenic variation.

Show MeSH
Related in: MedlinePlus