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Comparative genome analysis of Mycoplasma pneumoniae.

Xiao L, Ptacek T, Osborne JD, Crabb DM, Simmons WL, Lefkowitz EJ, Waites KB, Atkinson TP, Dybvig K - BMC Genomics (2015)

Bottom Line: Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed.The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex.Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. lixiao@uab.edu.

ABSTRACT

Background: Mycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40% of community-acquired pneumonias. It also causes a wide array of extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the organism have been generally restricted to specific genes or regions of the genome, because whole genome sequencing has been completed for only 4 strains. To better understand the physiology and pathogenicity of this important human pathogen, we performed comparative genomic analysis of 15 strains of M. pneumoniae that were isolated between the 1940s to 2009 from respiratory specimens and cerebrospinal fluid originating from the USA, China and England.

Results: Illumina MiSeq whole genome sequencing was performed on the 15 strains and all genome sequences were completed. Results from the comparative genomic analysis indicate that although about 1500 SNP and indel variants exist between type1 and type 2 strains, there is an overall high degree of sequence similarity among the strains (>99% identical to each other). Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed. The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.

Conclusions: These data indicate that despite conclusions drawn from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is extraordinarily stable over time and geographic distance across the globe with a striking lack of evidence of horizontal gene transfer.

No MeSH data available.


Related in: MedlinePlus

Multiple protein sequence of the variable regions in the hsdS genes. Both copies of the hsdS gene had a repetitive region of varying length consisting of TELS and AELS units (highlighted in orange and yellow, respectively). Note that in both copies, the length and composition of the repeat does not correspond to strain subtype. Strain names are to the right and highlighted in blue for type 1 and green for type 2. a Repeat region in the MPN089 copy of the hsdS gene. This is part of the variation in the 108000–126000 region shown in Fig. 2c. b Repeat region in the MPN343 copy of the hsdS gene. This is the variation in the 409700–410900 region shown in Fig. 2c
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Fig7: Multiple protein sequence of the variable regions in the hsdS genes. Both copies of the hsdS gene had a repetitive region of varying length consisting of TELS and AELS units (highlighted in orange and yellow, respectively). Note that in both copies, the length and composition of the repeat does not correspond to strain subtype. Strain names are to the right and highlighted in blue for type 1 and green for type 2. a Repeat region in the MPN089 copy of the hsdS gene. This is part of the variation in the 108000–126000 region shown in Fig. 2c. b Repeat region in the MPN343 copy of the hsdS gene. This is the variation in the 409700–410900 region shown in Fig. 2c

Mentions: The 10 hsdS genes are found in all sequenced strains (Table 7). MPN289 and MPN290 appear to be two truncated subunits derived from an integral hsdS locus that was interrupted by a point mutation resulting in a stop codon. MPN365 and MPN615 in all sequenced type 2 strains are truncated due to a premature stop. MPN285 is also truncated in 3 strains (MAC, PO1, and 142.8) due to frameshifts. Interestingly, a 12-bp tandem repeat (TR) corresponding to a 4-amino acids repeat (AELS or TELS) within the first alpha helical dimerization domain was found in 7 out of the 10 hsdS genes (Table 6). The copy number of this TR varies in 6 out of the 7 hsdS genes among the 15 strains (Table 7). It also varies in the same strains from different passages/laboratory conditions, e.g. in published M129 and FH genomes and our resequenced M129 and FH genomes (Table 7). Because two copies of the hsdS gene (MPN089 and MPN343) are part of two of the strain specific genomic structure variants annotated by MAUVE, we aligned the sequences of these proteins to look at variations in these genes. In both copies of the hsdS, the main source of variation is the TR region of varying length with two different repetitive units (TELS and AELS). The repeat in MPN089 consists only of AELS units, although all strains have one TELS unit, like all other TR-containing hsdS genes (Fig. 7a). The copy number of the repeat varies from 2 to 6 and does not correspond to strain subtype. However, in MPN343, the repeats are much longer in type 1 strains (10 – 16 copies) compared to type 2 strains (1 – 2 copies). Three type 1 strains (51494, 54089, and 54524) have long repeats of mixed TELS and AELS unit (Fig. 7b and Table 7).Table 7


Comparative genome analysis of Mycoplasma pneumoniae.

Xiao L, Ptacek T, Osborne JD, Crabb DM, Simmons WL, Lefkowitz EJ, Waites KB, Atkinson TP, Dybvig K - BMC Genomics (2015)

Multiple protein sequence of the variable regions in the hsdS genes. Both copies of the hsdS gene had a repetitive region of varying length consisting of TELS and AELS units (highlighted in orange and yellow, respectively). Note that in both copies, the length and composition of the repeat does not correspond to strain subtype. Strain names are to the right and highlighted in blue for type 1 and green for type 2. a Repeat region in the MPN089 copy of the hsdS gene. This is part of the variation in the 108000–126000 region shown in Fig. 2c. b Repeat region in the MPN343 copy of the hsdS gene. This is the variation in the 409700–410900 region shown in Fig. 2c
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4537597&req=5

Fig7: Multiple protein sequence of the variable regions in the hsdS genes. Both copies of the hsdS gene had a repetitive region of varying length consisting of TELS and AELS units (highlighted in orange and yellow, respectively). Note that in both copies, the length and composition of the repeat does not correspond to strain subtype. Strain names are to the right and highlighted in blue for type 1 and green for type 2. a Repeat region in the MPN089 copy of the hsdS gene. This is part of the variation in the 108000–126000 region shown in Fig. 2c. b Repeat region in the MPN343 copy of the hsdS gene. This is the variation in the 409700–410900 region shown in Fig. 2c
Mentions: The 10 hsdS genes are found in all sequenced strains (Table 7). MPN289 and MPN290 appear to be two truncated subunits derived from an integral hsdS locus that was interrupted by a point mutation resulting in a stop codon. MPN365 and MPN615 in all sequenced type 2 strains are truncated due to a premature stop. MPN285 is also truncated in 3 strains (MAC, PO1, and 142.8) due to frameshifts. Interestingly, a 12-bp tandem repeat (TR) corresponding to a 4-amino acids repeat (AELS or TELS) within the first alpha helical dimerization domain was found in 7 out of the 10 hsdS genes (Table 6). The copy number of this TR varies in 6 out of the 7 hsdS genes among the 15 strains (Table 7). It also varies in the same strains from different passages/laboratory conditions, e.g. in published M129 and FH genomes and our resequenced M129 and FH genomes (Table 7). Because two copies of the hsdS gene (MPN089 and MPN343) are part of two of the strain specific genomic structure variants annotated by MAUVE, we aligned the sequences of these proteins to look at variations in these genes. In both copies of the hsdS, the main source of variation is the TR region of varying length with two different repetitive units (TELS and AELS). The repeat in MPN089 consists only of AELS units, although all strains have one TELS unit, like all other TR-containing hsdS genes (Fig. 7a). The copy number of the repeat varies from 2 to 6 and does not correspond to strain subtype. However, in MPN343, the repeats are much longer in type 1 strains (10 – 16 copies) compared to type 2 strains (1 – 2 copies). Three type 1 strains (51494, 54089, and 54524) have long repeats of mixed TELS and AELS unit (Fig. 7b and Table 7).Table 7

Bottom Line: Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed.The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex.Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, 35294, USA. lixiao@uab.edu.

ABSTRACT

Background: Mycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40% of community-acquired pneumonias. It also causes a wide array of extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the organism have been generally restricted to specific genes or regions of the genome, because whole genome sequencing has been completed for only 4 strains. To better understand the physiology and pathogenicity of this important human pathogen, we performed comparative genomic analysis of 15 strains of M. pneumoniae that were isolated between the 1940s to 2009 from respiratory specimens and cerebrospinal fluid originating from the USA, China and England.

Results: Illumina MiSeq whole genome sequencing was performed on the 15 strains and all genome sequences were completed. Results from the comparative genomic analysis indicate that although about 1500 SNP and indel variants exist between type1 and type 2 strains, there is an overall high degree of sequence similarity among the strains (>99% identical to each other). Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed. The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.

Conclusions: These data indicate that despite conclusions drawn from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is extraordinarily stable over time and geographic distance across the globe with a striking lack of evidence of horizontal gene transfer.

No MeSH data available.


Related in: MedlinePlus