Limits...
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.

Show MeSH

Related in: MedlinePlus

Model of two proposed recombination events.A and B. Chromosomal region MPN129-MPN140 in M. pneumoniae M129. Position, length and orientation of all genes are presented and color-coded as above (arrows). C. Identification of sReps within MPN130, MPN137 and MPN138. Short repeats B (green arrows labeled B) were identified within both intergenic regions surrounding MPN130. Analyses revealed copies of sRepD and sRepE (red and blue arrows labeled D and E, respectively). Corresponding sReps involved in homologous recombination are connected by dotted lines. A diagram illustrates exchange of chromosomal regions during homologous recombination. D. Chromosomal regions after homologous recombination. Coding regions of three RepMP1-genes with rearranged domains are shown. sRepBs presumably involved in sequence deletion are indicated (asterisks). E. Deletion of two RepMP1-genes. Deleted region containing two RepMP1-genes (dotted loop) and implicated sRepB (green arrow) are represented. F. Chromosomal region MPN129-MPN140 in S1. Detailed depiction of MPN129-MPN131 and MPN138/7 regions and organization of the chromosomal region are presented.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3472980&req=5

pone-0047625-g003: Model of two proposed recombination events.A and B. Chromosomal region MPN129-MPN140 in M. pneumoniae M129. Position, length and orientation of all genes are presented and color-coded as above (arrows). C. Identification of sReps within MPN130, MPN137 and MPN138. Short repeats B (green arrows labeled B) were identified within both intergenic regions surrounding MPN130. Analyses revealed copies of sRepD and sRepE (red and blue arrows labeled D and E, respectively). Corresponding sReps involved in homologous recombination are connected by dotted lines. A diagram illustrates exchange of chromosomal regions during homologous recombination. D. Chromosomal regions after homologous recombination. Coding regions of three RepMP1-genes with rearranged domains are shown. sRepBs presumably involved in sequence deletion are indicated (asterisks). E. Deletion of two RepMP1-genes. Deleted region containing two RepMP1-genes (dotted loop) and implicated sRepB (green arrow) are represented. F. Chromosomal region MPN129-MPN140 in S1. Detailed depiction of MPN129-MPN131 and MPN138/7 regions and organization of the chromosomal region are presented.

Mentions: Since we detected major identical sequence rearrangements involving mpn130, mpn137 and mpn138 genes in all S1-like strains, we analyzed these genes and their immediate surroundings for the presence of recombination favoring short repeats (both direct and inverted, Table 3, Figure 3A and 3B). Analysis of the chromosomal region between genes mpn129 and mpn140 in M129 strains revealed copies of short repeats sRepA, sRepB and sRepC that were previously associated with RepMP1-core elements [17]. As indicated in Figures 1B and 2B, due to deletion, S1-like strains lack several of these short repeats. In particular, M129-mpn130 is flanked by two direct sRepB repeats (72-nt and 69-nt, Table 3, Figure 2B, 3C and 3D). In the corresponding chromosomal region in S1 contains only one sRepB repeat (Figure 2B and 3E; Table 3). Further examination of M129-mpn130, mpn138 and mpn137 sequences led to the identification of two additional short repeats designated sRepD (46-nt) and sRepE (41-nt). In M129, inverted sRepD is present within mpn130 and mpn138 and inverted sRepE is identified within mpn130 and mpn137 (Table 3, Figure 3C). Notably, the region of M129-mpn130 enclosed between sRepD and sRepE is the 49-nucleotide linker of mpn138 and mpn137 in S1-mpn138/7 (Figure 3E).


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

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

Model of two proposed recombination events.A and B. Chromosomal region MPN129-MPN140 in M. pneumoniae M129. Position, length and orientation of all genes are presented and color-coded as above (arrows). C. Identification of sReps within MPN130, MPN137 and MPN138. Short repeats B (green arrows labeled B) were identified within both intergenic regions surrounding MPN130. Analyses revealed copies of sRepD and sRepE (red and blue arrows labeled D and E, respectively). Corresponding sReps involved in homologous recombination are connected by dotted lines. A diagram illustrates exchange of chromosomal regions during homologous recombination. D. Chromosomal regions after homologous recombination. Coding regions of three RepMP1-genes with rearranged domains are shown. sRepBs presumably involved in sequence deletion are indicated (asterisks). E. Deletion of two RepMP1-genes. Deleted region containing two RepMP1-genes (dotted loop) and implicated sRepB (green arrow) are represented. F. Chromosomal region MPN129-MPN140 in S1. Detailed depiction of MPN129-MPN131 and MPN138/7 regions and organization of the chromosomal region are presented.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3472980&req=5

pone-0047625-g003: Model of two proposed recombination events.A and B. Chromosomal region MPN129-MPN140 in M. pneumoniae M129. Position, length and orientation of all genes are presented and color-coded as above (arrows). C. Identification of sReps within MPN130, MPN137 and MPN138. Short repeats B (green arrows labeled B) were identified within both intergenic regions surrounding MPN130. Analyses revealed copies of sRepD and sRepE (red and blue arrows labeled D and E, respectively). Corresponding sReps involved in homologous recombination are connected by dotted lines. A diagram illustrates exchange of chromosomal regions during homologous recombination. D. Chromosomal regions after homologous recombination. Coding regions of three RepMP1-genes with rearranged domains are shown. sRepBs presumably involved in sequence deletion are indicated (asterisks). E. Deletion of two RepMP1-genes. Deleted region containing two RepMP1-genes (dotted loop) and implicated sRepB (green arrow) are represented. F. Chromosomal region MPN129-MPN140 in S1. Detailed depiction of MPN129-MPN131 and MPN138/7 regions and organization of the chromosomal region are presented.
Mentions: Since we detected major identical sequence rearrangements involving mpn130, mpn137 and mpn138 genes in all S1-like strains, we analyzed these genes and their immediate surroundings for the presence of recombination favoring short repeats (both direct and inverted, Table 3, Figure 3A and 3B). Analysis of the chromosomal region between genes mpn129 and mpn140 in M129 strains revealed copies of short repeats sRepA, sRepB and sRepC that were previously associated with RepMP1-core elements [17]. As indicated in Figures 1B and 2B, due to deletion, S1-like strains lack several of these short repeats. In particular, M129-mpn130 is flanked by two direct sRepB repeats (72-nt and 69-nt, Table 3, Figure 2B, 3C and 3D). In the corresponding chromosomal region in S1 contains only one sRepB repeat (Figure 2B and 3E; Table 3). Further examination of M129-mpn130, mpn138 and mpn137 sequences led to the identification of two additional short repeats designated sRepD (46-nt) and sRepE (41-nt). In M129, inverted sRepD is present within mpn130 and mpn138 and inverted sRepE is identified within mpn130 and mpn137 (Table 3, Figure 3C). Notably, the region of M129-mpn130 enclosed between sRepD and sRepE is the 49-nucleotide linker of mpn138 and mpn137 in S1-mpn138/7 (Figure 3E).

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