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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

Phylogenetic tree of ArcA. The protein sequences of the two ArcA protein sequences from M. pneumoniae (MPN304 and MPN560), ArcA sequences from other Mycoplasma species, and the protein sequence of arginine deiminase from Streptococcus pneumoniae strain R6 (spr0822_Spn_R6) were aligned and a tree was generated from the alignment. Confidence values, represented as percent of supporting bootstrapping iterations are shown for each node. Scale, in differences per site, is indicated at the bottom
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Fig6: Phylogenetic tree of ArcA. The protein sequences of the two ArcA protein sequences from M. pneumoniae (MPN304 and MPN560), ArcA sequences from other Mycoplasma species, and the protein sequence of arginine deiminase from Streptococcus pneumoniae strain R6 (spr0822_Spn_R6) were aligned and a tree was generated from the alignment. Confidence values, represented as percent of supporting bootstrapping iterations are shown for each node. Scale, in differences per site, is indicated at the bottom

Mentions: Our attention was also drawn to the M. pneumoniae arcA gene, an essential component of the arginine deiminase pathway that is thought to be inactive in M. pneumoniae [49]. There are two copies of arcA in M. pneumoniae, MPN304 and MPN560. MPN304 is truncated by a frameshift yielding a premature stop codon and is contiguous to arcC. MPN560 is not truncated but is found in another part of the genome. There were no variants in the coding sequence of either gene (before premature stop for MPN304) in any of the 15 sequenced strains. We also aligned the amino acid sequence of both proteins against the amino acid sequence of ArcA of several other Mycoplasma species. The protein sequence of arginine deiminase from Streptococcus pneumoniae strain R6 (spr0822) was included as an outgroup. MPN304 and MPN560 were more similar to ArcA sequences from other species than they were to each other, with MPN304 being most similar to ArcA from Mycoplasma fermentans and MPN560 being most similar to ArcA from Mycoplasma gallisepticum (Fig. 6).Fig. 6


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)

Phylogenetic tree of ArcA. The protein sequences of the two ArcA protein sequences from M. pneumoniae (MPN304 and MPN560), ArcA sequences from other Mycoplasma species, and the protein sequence of arginine deiminase from Streptococcus pneumoniae strain R6 (spr0822_Spn_R6) were aligned and a tree was generated from the alignment. Confidence values, represented as percent of supporting bootstrapping iterations are shown for each node. Scale, in differences per site, is indicated at the bottom
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig6: Phylogenetic tree of ArcA. The protein sequences of the two ArcA protein sequences from M. pneumoniae (MPN304 and MPN560), ArcA sequences from other Mycoplasma species, and the protein sequence of arginine deiminase from Streptococcus pneumoniae strain R6 (spr0822_Spn_R6) were aligned and a tree was generated from the alignment. Confidence values, represented as percent of supporting bootstrapping iterations are shown for each node. Scale, in differences per site, is indicated at the bottom
Mentions: Our attention was also drawn to the M. pneumoniae arcA gene, an essential component of the arginine deiminase pathway that is thought to be inactive in M. pneumoniae [49]. There are two copies of arcA in M. pneumoniae, MPN304 and MPN560. MPN304 is truncated by a frameshift yielding a premature stop codon and is contiguous to arcC. MPN560 is not truncated but is found in another part of the genome. There were no variants in the coding sequence of either gene (before premature stop for MPN304) in any of the 15 sequenced strains. We also aligned the amino acid sequence of both proteins against the amino acid sequence of ArcA of several other Mycoplasma species. The protein sequence of arginine deiminase from Streptococcus pneumoniae strain R6 (spr0822) was included as an outgroup. MPN304 and MPN560 were more similar to ArcA sequences from other species than they were to each other, with MPN304 being most similar to ArcA from Mycoplasma fermentans and MPN560 being most similar to ArcA from Mycoplasma gallisepticum (Fig. 6).Fig. 6

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