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Mycoplasma pneumoniae large DNA repetitive elements RepMP1 show type specific organization among strains.

Musatovova O, Kannan TR, Baseman JB - PLoS ONE (2012)

Bottom Line: Recently, we described RepMP1-associated sequence variations between reference strain M129 and clinical isolate S1 that involved three RepMP1-genes (i.e. mpn130, mpn137 and mpn138).The only other detected difference was varying numbers of the 21-nucleotide tandem repeats within mpn127, mpn137, mpn501 and mpn524.Furthermore, typing of strains through analysis of large RepMPs localized within the adhesin P1 operon revealed that sequence divergence involving RepMP1-genes mpn130, mpn137 and mpn138 is strictly type-specific.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America. musatovova@gmail.com

ABSTRACT
Mycoplasma pneumoniae is the smallest self-replicating bacterium with a streamlined genome of 0.81 Mb. Complete genome analysis revealed the presence of multiple copies of four large repetitive elements (designated RepMP1, RepMP2/3, RepMP4 and RepMP5) that are implicated in creating sequence variations among individual strains. Recently, we described RepMP1-associated sequence variations between reference strain M129 and clinical isolate S1 that involved three RepMP1-genes (i.e. mpn130, mpn137 and mpn138). Using PCR and sequencing we analyze 28 additional M. pneumoniae strains and demonstrate the existence of S1-like sequence variants in nine strains and M129-like variants in the remaining nineteen strains. We propose a series of recombination steps that facilitates transition from M129- to S1-like sequence variants. Next we examined the remaining RepMP1-genes and observed no other rearrangements related to the repeat element. The only other detected difference was varying numbers of the 21-nucleotide tandem repeats within mpn127, mpn137, mpn501 and mpn524. Furthermore, typing of strains through analysis of large RepMPs localized within the adhesin P1 operon revealed that sequence divergence involving RepMP1-genes mpn130, mpn137 and mpn138 is strictly type-specific. Once more our analysis confirmed existence of two highly conserved groups of M. pneumoniae strains.

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Predicted secondary structure of modified RepMP1-proteins.A. Type-specific modification of Mpn130, Mpn137 and Mpn138 proteins. Three proteins (within grey box) are predicted in type 1 isolates. In type 2 strains, fused protein Mpn138/7 consists of Mpn138-N-terminal and Mpn137-C-terminal region that is shorter by one heptad repeat (*). Only the indicated 16-aa region of MPN130 (**) is retained in type 2 strains. Regions of coiled coils are shown (numbers represent start and end of region). Locations of leucine zipper (LZ) in Mpn138 and Mpn130 and of leucine repeats (LR) in Mpn138 and Mpn138/7 are indicated. B. Type-specific modification of Mpn524. The position of direct tandem heptad repeats (DR) and coiled coil region is presented for type 1 Mpn524. In all type 2 strains one heptad repeat is deleted (*). C. Mpn501 modification. The positions of direct tandem heptad repeats (DR) and coiled coil domains are indicated. The insertion of an additional heptad repeat (+1) is the only not type-specific modification identified among strains. Transmembrane domains (TM) were predicted by DAS analysis.
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pone-0047625-g004: Predicted secondary structure of modified RepMP1-proteins.A. Type-specific modification of Mpn130, Mpn137 and Mpn138 proteins. Three proteins (within grey box) are predicted in type 1 isolates. In type 2 strains, fused protein Mpn138/7 consists of Mpn138-N-terminal and Mpn137-C-terminal region that is shorter by one heptad repeat (*). Only the indicated 16-aa region of MPN130 (**) is retained in type 2 strains. Regions of coiled coils are shown (numbers represent start and end of region). Locations of leucine zipper (LZ) in Mpn138 and Mpn130 and of leucine repeats (LR) in Mpn138 and Mpn138/7 are indicated. B. Type-specific modification of Mpn524. The position of direct tandem heptad repeats (DR) and coiled coil region is presented for type 1 Mpn524. In all type 2 strains one heptad repeat is deleted (*). C. Mpn501 modification. The positions of direct tandem heptad repeats (DR) and coiled coil domains are indicated. The insertion of an additional heptad repeat (+1) is the only not type-specific modification identified among strains. Transmembrane domains (TM) were predicted by DAS analysis.

Mentions: Analyses and cross-comparison of RepMP1-genes/proteins lead us to the conclusion that RepMP1-core elements and sReps provide a network for intergenic domain exchanges. For example, as demonstrated in Figure 3D, sRepD and sRepE-mediated recombination among three genes leads to three novel genes/proteins with different combinations of conserved proximal regions with coiled-coil domains (Figure 3 and 4). It is predictable that the exchange of domains will provide proteins with modified function. Currently, function(s) of both conserved and DUF16 domains as well as the majority of RepMP1-proteins remain unknown. So far, it has been shown that transposon insertions within MPN104 and MPN524 resulted in M. pneumoniae mutants with altered satellite growth phenotype and altered gliding motility, possibly suggesting these proteins could play a role in cytoskeletal functions [26]. Recombination-mediated protein domain variations have been reported previously for the Arp protein (an immunoglobulin A receptor in the M protein family) of Streptococcus pyogenes[27]. Repeat-associated plasticity in the Helicobacter pylori RD gene family has been analyzed, and a mechanism leading to the exchange of domains was proposed [28]. In eukaryotes, these translocations often involve transcriptional factors [29], [30].


Mycoplasma pneumoniae large DNA repetitive elements RepMP1 show type specific organization among strains.

Musatovova O, Kannan TR, Baseman JB - PLoS ONE (2012)

Predicted secondary structure of modified RepMP1-proteins.A. Type-specific modification of Mpn130, Mpn137 and Mpn138 proteins. Three proteins (within grey box) are predicted in type 1 isolates. In type 2 strains, fused protein Mpn138/7 consists of Mpn138-N-terminal and Mpn137-C-terminal region that is shorter by one heptad repeat (*). Only the indicated 16-aa region of MPN130 (**) is retained in type 2 strains. Regions of coiled coils are shown (numbers represent start and end of region). Locations of leucine zipper (LZ) in Mpn138 and Mpn130 and of leucine repeats (LR) in Mpn138 and Mpn138/7 are indicated. B. Type-specific modification of Mpn524. The position of direct tandem heptad repeats (DR) and coiled coil region is presented for type 1 Mpn524. In all type 2 strains one heptad repeat is deleted (*). C. Mpn501 modification. The positions of direct tandem heptad repeats (DR) and coiled coil domains are indicated. The insertion of an additional heptad repeat (+1) is the only not type-specific modification identified among strains. Transmembrane domains (TM) were predicted by DAS analysis.
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Related In: Results  -  Collection

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pone-0047625-g004: Predicted secondary structure of modified RepMP1-proteins.A. Type-specific modification of Mpn130, Mpn137 and Mpn138 proteins. Three proteins (within grey box) are predicted in type 1 isolates. In type 2 strains, fused protein Mpn138/7 consists of Mpn138-N-terminal and Mpn137-C-terminal region that is shorter by one heptad repeat (*). Only the indicated 16-aa region of MPN130 (**) is retained in type 2 strains. Regions of coiled coils are shown (numbers represent start and end of region). Locations of leucine zipper (LZ) in Mpn138 and Mpn130 and of leucine repeats (LR) in Mpn138 and Mpn138/7 are indicated. B. Type-specific modification of Mpn524. The position of direct tandem heptad repeats (DR) and coiled coil region is presented for type 1 Mpn524. In all type 2 strains one heptad repeat is deleted (*). C. Mpn501 modification. The positions of direct tandem heptad repeats (DR) and coiled coil domains are indicated. The insertion of an additional heptad repeat (+1) is the only not type-specific modification identified among strains. Transmembrane domains (TM) were predicted by DAS analysis.
Mentions: Analyses and cross-comparison of RepMP1-genes/proteins lead us to the conclusion that RepMP1-core elements and sReps provide a network for intergenic domain exchanges. For example, as demonstrated in Figure 3D, sRepD and sRepE-mediated recombination among three genes leads to three novel genes/proteins with different combinations of conserved proximal regions with coiled-coil domains (Figure 3 and 4). It is predictable that the exchange of domains will provide proteins with modified function. Currently, function(s) of both conserved and DUF16 domains as well as the majority of RepMP1-proteins remain unknown. So far, it has been shown that transposon insertions within MPN104 and MPN524 resulted in M. pneumoniae mutants with altered satellite growth phenotype and altered gliding motility, possibly suggesting these proteins could play a role in cytoskeletal functions [26]. Recombination-mediated protein domain variations have been reported previously for the Arp protein (an immunoglobulin A receptor in the M protein family) of Streptococcus pyogenes[27]. Repeat-associated plasticity in the Helicobacter pylori RD gene family has been analyzed, and a mechanism leading to the exchange of domains was proposed [28]. In eukaryotes, these translocations often involve transcriptional factors [29], [30].

Bottom Line: Recently, we described RepMP1-associated sequence variations between reference strain M129 and clinical isolate S1 that involved three RepMP1-genes (i.e. mpn130, mpn137 and mpn138).The only other detected difference was varying numbers of the 21-nucleotide tandem repeats within mpn127, mpn137, mpn501 and mpn524.Furthermore, typing of strains through analysis of large RepMPs localized within the adhesin P1 operon revealed that sequence divergence involving RepMP1-genes mpn130, mpn137 and mpn138 is strictly type-specific.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology and Immunology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America. musatovova@gmail.com

ABSTRACT
Mycoplasma pneumoniae is the smallest self-replicating bacterium with a streamlined genome of 0.81 Mb. Complete genome analysis revealed the presence of multiple copies of four large repetitive elements (designated RepMP1, RepMP2/3, RepMP4 and RepMP5) that are implicated in creating sequence variations among individual strains. Recently, we described RepMP1-associated sequence variations between reference strain M129 and clinical isolate S1 that involved three RepMP1-genes (i.e. mpn130, mpn137 and mpn138). Using PCR and sequencing we analyze 28 additional M. pneumoniae strains and demonstrate the existence of S1-like sequence variants in nine strains and M129-like variants in the remaining nineteen strains. We propose a series of recombination steps that facilitates transition from M129- to S1-like sequence variants. Next we examined the remaining RepMP1-genes and observed no other rearrangements related to the repeat element. The only other detected difference was varying numbers of the 21-nucleotide tandem repeats within mpn127, mpn137, mpn501 and mpn524. Furthermore, typing of strains through analysis of large RepMPs localized within the adhesin P1 operon revealed that sequence divergence involving RepMP1-genes mpn130, mpn137 and mpn138 is strictly type-specific. Once more our analysis confirmed existence of two highly conserved groups of M. pneumoniae strains.

Show MeSH
Related in: MedlinePlus