Genetic Variation in Mycoplasma genitalium

Gilho Lee

doi:10.14777/uti.2017.12.02.65

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Lee: Genetic Variation in Mycoplasma genitalium

Review

Urogenit Tract Infect 2017;12(2):65-76.

Published online: 19 August 2017

DOI: https://doi.org/10.14777/uti.2017.12.02.65

Genetic Variation in Mycoplasma genitalium

Gilho Lee

Department of Urology, Dankook University College of Medicine, Cheonan, Korea

Correspondence to: Gilho Lee http://orcid.org/0000-0002-9253-6245 Department of Urology, Dankook University College of Medicine, 119 Dandae-ro, Dongnam-gu, Cheonan 31116, Korea Tel: +82-41-550-6630, Fax: +82-41-550-3905 E-mail: multiorigins@yahoo.com

Received 14 July 2017 Revised 3 August 2017 Accepted 3 August 2017

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Mycoplasma genitalium (MG) is the smallest self-replicating bacterium. Although small in size, unique MG genome induces distinctive and often serious characteristics in the infected cells. Due to its small genome and chronic symptomatic characteristics in the infected host, it first appears as a weak, insignificant, and easily controllable microbe. However, it is not a monotonous chrysalis, but rather a multicolored butterfly with various capabilities. Repetitive DNA sequence in MG's immunodominant MgPa operon has been considered as an efficient strategy to evade the host immune surveillance and mediate MG's genetic flexibility. Because of MG's pathogenicity in multiple organs, various antimicrobials are prescribed, further exerting selection pressure on microbes. Consequently, a rapidly increasing drug resistance in macrolide and moxifloxacin has been frequently reported globally, radically decreasing the overall cure rate of infection. Re-infection can be defined as a new MG infection through antigenic variation, while persistent infection refers to recurrent infections caused by the same MG isolate through acquisition of antimicrobial resistance. Therefore, we must differentiate between re-infection and persistent MG infection, and approach them accordingly. The genetic mechanisms of DNA variation in the MgPa operon and antibiotic resistance must be considered for the management of multicolored infection. In this respect, the unique genetic characteristics of MG will be described in detail. We hope that with this manuscript, clinicians can expand their understanding of recurrent MG infections and better choose an appropriate treatment for the infection in clinical setting.

Keywords: Mycoplasma genitalium, Genetics, Recurrence

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Fig 1.

Phylogenetic tree of 16S rRNA gene sequences reveals that Mycoplasma pneumoniae M129 is closely related with Mycoplasma genitalium (MG). NR074611.1 is MG strain G37 (16S ribosomal RNA), NC000912.1 is M. pneumoniae M129 complete genome (16S ribosomal RNA), NC010503.1 is Ureaplasma parvum serotype 3 str. ATCC27815, complete genome (16S ribosomal RNA), NC011374 is Ureaplasma urealyticum serotype 10 str. ATCC33699, complete genome (16S ribosomal RNA), and AB680681.1 is Mycoplasma hominis gene for 16S ribosomal RNA, strain NBRC14850.

Fig. 2.

Schematic view of Mycoplasma genitalium (MG). It appears as a flask or pear-shaped cell with a narrow terminal structure (A). This structure is crucial for MG to attach onto the host cell surfaces.

Fig. 3.

Complete genome sequence in MgPa and MgPar genes of the Mycoplasma genitalium (MG) G37 strain. The expression sites for each of the three genes are present in only one copy; but there are nine repetitive elements in the form of truncated copies of MG191 and MG192 genes dispersed throughout the genome, designated as MgPa repeats or MgPar sequences [31,39,40].

Fig. 4.

Twenty mgpB DNA sequences from the National Center for Biotechnology Information (NCBI) (https://www.ncbi.nlm.nih.gov/nuccore/) are evaluated for their homology using the Clustal W alignment algorithm (http://www.genome.jp/tools/clustalw/). Locations in the MG191 gene are indicated in the upper area. There are three areas of hot genetic variety in the mgpB gene (520-1,040 bp for B area, 2,340-2,990 bp for EF area, 3,250-3,640 bp for G area). The gray colors represent matching, while the black colors represent mismatching (http://multalin.toulouse.inra.fr/). MG: Mycoplasma genitalium.

Fig. 5.

Sixty-four partial mgpC DNA sequences (Supplementary Table 2) from the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov/nuccore/) are collected and evaluated for their homology using the Clustal W alignment algorithm (http://www.genome.jp/tools/clustalw/). Locations in the mgpB gene are indicated in the upper area. The gray colors represent matching, while the black colors represent mismatching (http://multalin.toulouse.inra.fr).

Fig. 6.

Twenty-four partial mgpC DNA sequences (Supplementary Table 3) from patient no. 126 are evaluated from the National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov/nuccore/) to investigate the homology using the Clustal W alignment algorithm (http://www.genome.jp/ tools/clustalw/). Ma et al. [50] serially examined the DNA sequence changes in the mgpC gene in serial culturing periods (from the starting point to 4th subculturing period). The DNA sequences of MG192 changed rapidly in vitro within a short period of time. The gray colors represent matching, while the black colors represent mismatching (http://multalin.toulouse.inra.fr/multalin/multalin.html). MG: Mycoplasma genitalium.

Fig. 7.

Phylogenetic analysis of the MG192 variable sequences from serially cultured in vitro samples from MG infected patients no. 61 and no. 126. Time intervals are described in Table 4. There are greater variations in the MG192 gene during sequential cultures, but the variances are more closely related within an individual patient than between the patients. MG: Mycoplasma genitalium.

Fig. 8.

Ma et al. [51] intraurethrally inoculated a single cloned Mycoplasma genitalium (MG) strain G37 into one male chimpanzee's urethra. Urethral swabs were obtained at different time points (5 weeks, 9 weeks, and 11 weeks). Phylogenetic analysis in the MG192 gene revealed several MG192 sequences variants during an in vivo study.

Fig. 9.

JX857899.1(61.0a) is the partial DNA sequences of MG192 gene at the starting point (11/20/2000) obtained from patient no. 61, as presented in Fig. 7. The JX857903.1(61.2e) is the partial DNA sequences of MG192 gene obtained from the same patient post 6 months (05/07/2001). EF117289.1 is the partial DNA sequences of MG strain G37 MgPar 8 region genomic sequence, FJ872575.1 is the partial DNA sequences of MG strain M2321 MgPar 2 region genomic sequence, and FJ872582.1 is the partial DNA sequences of MG strain M2321 MgPar 9 region genomic sequence. JX857903.1(61.2e) may get some AGT repeats in the original MG192 gene (JX857899.1), and newly mutated isolate (JX857903.1) is closely related to the partial DNA sequences of MG strain G37 MgPar 8 region genomic sequence (EF117289.1) (dotted box). MG: Mycoplasma genitalium.

Fig. 10.

A schematic view of homologous recombination between MG192 and MgPar 8 in the MG type strain G37 during in vitro passage. A presents the alignment of a portion of the MG192 variable region and MgPar 8 in G37-P1, while B demonstrates the alignment of a portion of the recombined MG192 variable region and MgPar 8 in G37-P35, clearly depicting the sequence exchange at the recombination sites. Arrows indicate where sequence exchanges took place, with the reciprocal exchange (gene cross-over) shown by two arrows (area II) and gene conversion shown by one arrow (area I). MG: Mycoplasma genitalium.

Table 1.

Taxonomical classification of Mycoplasmataceae family

Bacteria

Terrabacteria group

Tenericutes

Mollicutes

Mycoplasmataceae

Candidatus Hepatoplasma

Candidatus Marinoplasma

Candidatus Moeniiplasma

Mycoplasma (329 species)

Mycoplasma genitalium

Mycoplasma hominis

Mycoplasma pneumoniae

Ureaplasma (24 species)

Ureaplasma pavum

Ureaplasma urealyticum

Table 2.

Structural characteristics of Mycoplasma genitalium

Organisms	Size (m)	Genome size (base pair)	Protein coding gene (no)
Escherichia coli	2.0-6.0	5,000,000-4,000,000	5,400-4,300
Neisseria	0.6-1.0	2,232,025 (NCCP11945)	2,662
gonorrhoeae
Chlamydia	0.3	1,044,282 (FM872307)	2,032-1,052
trachomatis
M. genitalium	0.3	580,070	480
Eukaryotic cell	10-100	3,000,000,000	19,000-20,000

Table 3.

Tissue tropisms of Mycoplasmas

Species	Primary site of colonization		Pathogenicity
Species	Oropharynx	Urogenital tract	Pathogenicity
Mycoplasma hominis	Y	Y	Y
Ureaplasma urealyticum	Y	Y	Y
Mycoplasma pneumonia	Y	N	Y
Mycoplasma genitalium	?Y	Y	Y

Table 4.

Sequential cultures of Mycoplasma genitalium (MG) from two infected parents and unique MG192 variants

Patient no.	Date	Clonesʼ no.	Unique MG192 sequences variant(s)
61	11/20/2000	8	61.0a^a)
	5/7/2001	6	61.2b, 61.2c, 61.2d, 61.2e, 61.2f
126	10/23/2001	10	126.0a, 126.0b, 126.0c, 126.0d^a)
	1/15/2002	10	126.1e, 126.1f, 126.1g, 126.1h, 126.1i, 126.1j, 126.1k
	6/26/2002	10	126.2l, 126.2m, 126.2n, 126.2o, 126.2p
	9/17/2002	10	126.3q, 126.3r, 126.3s, 126.3t, 126.3u, 126.3v, 126.3w, 126.3x
	12/3/2002	10	126.4.1, 126.4.2, 126.4.3, 126.4.4, 126.4.5, 126.4.6, 126.4.7, 126.4.8, 126.4.9

All unique variants in table reveal different sequences. Modified from the article of Ma et al. Infect Immun 2014:82:1326-34 [50].

^a) Indicate the starting points in serial MG cultures.

Table 5.

Topoisomerase IIA family in Mycoplasma genitalium

Enzyme	Type	Structure	Genes	Annotations	Location^a)	Gene name
Gyrase	Topoisomerase IIA	Heterodimer	gyrA	DNA gyrase subunit A	4812..7322	AFQ04307.1
		(AB/AB)	gyrB	DNA gyrase subunit B	2845..4797	AFQ04306.1
Topo IV	Topoisomerase IIA	Heterodimer	ParC	DNA topoisomerase IV, A subunit	242059..244404	AFQ04524.1
		(AB/AB)	ParE	DNA topoisomerase IV, B subunit	240158..242059	AFQ04523.1

^a) CP003773; Mycoplasma genitalium M2288, complete genome from https://www.ncbi.nlm.nih.gov/nuccore/CP003773.

Table 6.

List of common DNA mutations in toposiomerase IIA genes that change their amino acid sequences, which may inactivate moxifloxacin treatment in Mycoplasma genitalium infection [67-69]

Gene	Position	Mutation	AA change
ParC	234	C to T	No change
	241	G to T	Glt to Cys
	244	G to A	Asp to Asn
	247	G to T	Ser to Arg
	248	G to A	Ser to Ile
	259	G to A	Asp to Asn
		G to C	Asp to His
		G to T	Asp to Tyr
	260	A to G	Asp to Gly
	290	A to G	Lys to Met
	307	G to A	Val to Ile
	351	T to C	No change
	356	C to A	Ala to Val
GyrA	237	G to T	No change
	267	C to T	No change
	270	C to T	No change
	285	G to A	No change
		G to C	Met to Ile

AA: amino acid.

Supplementary Table 1.

Mycoplasma genitalium mgpB sequences from the National Center for Biotechnology Information

> CP003773.1:221365-225744 Mycoplasma genitalium M2288,complete genome

>GU226203.1:1247-5599 Mycoplasma genitalium isolate 6286 MgPa operon, complete sequence

>GU226202.1:1247-5569 Mycoplasma genitalium isolate M6285 MgPa operon, complete sequence

>GU226200.1:1250-5593 Mycoplasma genitalium isolate M6283 MgPa operon, complete sequence

>GU226201.1:1250-5578 Mycoplasma genitalium isolate M6284 MgPa operon, complete sequence

>FJ872591.1:1152-5510 Mycoplasma genitalium strain New Orleans 64 MgPa operon, complete sequence

>FJ872584.1:1206-5537 Mycoplasma genitalium strain M2282 MgPa operon, complete sequence

>KP318806.1 Mycoplasma genitalium strain Seattle2 MgpB adhesin gene, complete cds

>FJ872588.1:1257-5615 Mycoplasma genitalium strain M2341 MgPa operon, complete sequence

>FJ872592.1:1152-5501 Mycoplasma genitalium strain New Orleans 64 MgPa operon, complete sequence

>FJ872586.1:1260-5585 Mycoplasma genitalium strain M2300 MgPa operon, complete sequence

>FJ872589.1:1143-5465 Mycoplasma genitalium strain New Orleans 199 MgPa operon, complete sequence

>GU226196.1:1250-5581 Mycoplasma genitalium isolate M30 MgPa operon, complete sequence

>FJ872587.1:1245-5588 Mycoplasma genitalium strain M2321 MgPa operon, complete sequence

>M31431.1:1066-5400 M.genitalium attachment protein (MgPa) gene, complete cds

>FJ872590.1:1143-5465 Mycoplasma genitalium strain New Orleans 199 MgPa operon, complete sequence

>GU226199.1:1250-5593 Mycoplasma genitalium isolate M6282 MgPa operon, complete sequence

>GU226197.1:1063-5388 Mycoplasma genitalium isolate M6257 MgPa operon, complete sequence

>GU226198.1:1250-5584 Mycoplasma genitalium isolate M6280 MgPa operon, complete sequence

>KP318805.1 Mycoplasma genitalium strain Seattle1 MgpB adhesin gene, complete cds

Supplementary Table 2.

Mycoplasma genitalium mgpC sequences from the National Center for Biotechnology Information

>EF117280.1 Mycoplasma genitalium strain G37 adhesion protein (mgpC) gene, partial cds

>EF117281.1 Mycoplasma genitalium strain TW10-5 adhesion protein (mgpC) gene, partial cds

>JX869102.1 Mycoplasma genitalium strain A52.0A adhesion protein MG192 (mgpC) gene, partial cds

>JX869118.1 Mycoplasma genitalium strain 1125.5b adhesion protein MG192 (mgpC) gene,

>JX869119.1 Mycoplasma genitalium strain 1125.5c adhesion protein MG192 (mgpC) gene, partial cds

>JX869103.1 Mycoplasma genitalium strain A52.5B adhesion protein MG192 (mgpC) gene, partial cds

>EF117282.1 Mycoplasma genitalium strain TW48-5 adhesion protein (mgpC) gene, partial cds

>JX869120.1 Mycoplasma genitalium strain 1125.5d adhesion protein MG192 (mgpC) gene, partial cds

>JX869104.1 Mycoplasma genitalium strain A52.5C adhesion protein MG192 (mgpC) gene, partial cds

>JX869122.1 Mycoplasma genitalium strain 1125.5f adhesion protein MG192 (mgpC) gene, partial cds

>JX869123.1 Mycoplasma genitalium strain 1125.5g adhesion protein MG192 (mgpC) gene, partial cds

>JX869105.1 Mycoplasma genitalium strain A52.5D adhesion protein MG192 (mgpC) gene, partial cds

>JX869124.1 Mycoplasma genitalium strain 1125.5h adhesion protein MG192 (mgpC) gene, partial cds

>AY679761.1 Mycoplasma genitalium strain TW10-5 cytadherence-related protein p110 gene, partial cds

>JX869114.1 Mycoplasma genitalium strain A52.13M adhesion protein MG192 (mgpC) gene, partial cds

>JX869126.1 Mycoplasma genitalium strain 1125.11j adhesion protein MG192 (mgpC) gene, partial cds

>JX869128.1 Mycoplasma genitalium strain 1125.11l adhesion protein MG192 (mgpC) gene, partial cds

>JX869127.1 Mycoplasma genitalium strain 1125.11k adhesion protein MG192 (mgpC) gene, partial cds

>JX869116.1 Mycoplasma genitalium strain A52.13O adhesion protein MG192 (mgpC) gene, partial cds

>JX857935.1 Mycoplasma genitalium isolate 126.4.1 adhesion protein MG192 (mgpC) gene, partial cds

>JX869129.1 Mycoplasma genitalium strain 1125.1m adhesion protein MG192 (mgpC) gene, partial cds

>JX857936.1 Mycoplasma genitalium isolate 126.4.2 adhesion protein MG192 (mgpC) gene, partial cds

>JX869115.1 Mycoplasma genitalium strain A52.13N adhesion protein MG192 (mgpC) gene, partial cds

>JX857927.1 Mycoplasma genitalium isolate 126.3q adhesion protein MG192 (mgpC) gene, partial cds

>JX857922.1 Mycoplasma genitalium isolate 126.2l adhesion protein MG192 (mgpC) gene, partial cds

>JX857929.1 Mycoplasma genitalium isolate 126.3s adhesion protein MG192 (mgpC) gene, partial cds

>JX869131.1 Mycoplasma genitalium strain 1125.1o adhesion protein MG192 (mgpC) gene, partial cds

>JX869108.1 Mycoplasma genitalium strain A52.10G adhesion protein MG192 (mgpC) gene, partial cds

>JX869125.1 Mycoplasma genitalium strain 1125.9i adhesion protein MG192 (mgpC) gene, partial cds

>JX857901.1 Mycoplasma genitalium isolate 61.2c adhesion protein MG192 (mgpC) gene, partial cds

>JX869110.1 Mycoplasma genitalium strain A52.10I adhesion protein MG192 (mgpC) gene, partial cds

>JX869109.1 Mycoplasma genitalium strain A52.10H adhesion protein MG192 (mgpC) gene, partial cds

>JX857925.1 Mycoplasma genitalium isolate 126.2o adhesion protein MG192 (mgpC) gene, partial cds

>JX857939.1 Mycoplasma genitalium isolate 126.4.5 adhesion protein MG192 (mgpC) gene, partial cds

>JX869111.1 Mycoplasma genitalium strain A52.10J adhesion protein MG192 (mgpC) gene, partial cds

>JX857899.1 Mycoplasma genitalium isolate 61.0a adhesion protein MG192 (mgpC) gene, partial cds

>JX857928.1 Mycoplasma genitalium isolate 126.3r adhesion protein MG192 (mgpC) gene, partial cds

>JX869112.1 Mycoplasma genitalium strain A52.10K adhesion protein MG192 (mgpC) gene, partial cds

>JX857921.1 Mycoplasma genitalium isolate 126.1k adhesion protein MG192 (mgpC) gene, partial cds

>JX857904.1 Mycoplasma genitalium isolate 61.2f adhesion protein MG192 (mgpC) gene, partial cds

>JX857914.1 Mycoplasma genitalium isolate 126.0d adhesion protein MG192 (mgpC) gene, partial cds

>JX857900.1 Mycoplasma genitalium isolate 61.2b adhesion protein MG192 (mgpC) gene, partial cds

>JX857934.1 Mycoplasma genitalium isolate 126.3x adhesion protein MG192 (mgpC) gene, partial cds

>JX857932.1 Mycoplasma genitalium isolate 126.3v adhesion protein MG192 (mgpC) gene, partial cds

>JX857903.1 Mycoplasma genitalium isolate 61.2e adhesion protein MG192 (mgpC) gene, partial cds

>JX857926.1 Mycoplasma genitalium isolate 126.2p adhesion protein MG192 (mgpC) gene, partial cds

>JX857881.1 Mycoplasma genitalium isolate 64.0a adhesion protein MG192 (mgpC) gene, partial cds

>JX857924.1 Mycoplasma genitalium isolate 126.2n adhesion protein MG192 (mgpC) gene, partial cds

>JX857915.1 Mycoplasma genitalium isolate 126.1e adhesion protein MG192 (mgpC) gene, partial cds

>JX857946.1 Mycoplasma genitalium isolate 136.0c adhesion protein MG192 (mgpC) gene, partial cds

>JX857941.1 Mycoplasma genitalium isolate 126.4.7 adhesion protein MG192 (mgpC) gene, partial cds

>JX857923.1 Mycoplasma genitalium isolate 126.2m adhesion protein MG192 (mgpC) gene, partial cds

>JX857920.1 Mycoplasma genitalium isolate 126.1j adhesion protein MG192 (mgpC) gene, partial cds

>JX857912.1 Mycoplasma genitalium isolate 126.0b adhesion protein MG192 (mgpC) gene, partial cds

>JX857902.1 Mycoplasma genitalium isolate 61.2d adhesion protein MG192 (mgpC) gene, partial cds

>JX857913.1 Mycoplasma genitalium isolate 126.0c adhesion protein MG192 (mgpC) gene, partial cds

>JX857908.1 Mycoplasma genitalium isolate 105.2d adhesion protein MG192 (mgpC) gene, partial cds

>JX857882.1 Mycoplasma genitalium isolate 64.1b adhesion protein MG192 (mgpC) gene, partial cds

>JX869113.1 Mycoplasma genitalium strain A52.10L adhesion protein MG192 (mgpC) gene, partial cds

>JX857943.1 Mycoplasma genitalium isolate 126.4.9 adhesion protein MG192 (mgpC) gene, partial cds

>JX857933.1 Mycoplasma genitalium isolate 126.3w adhesion protein MG192 (mgpC) gene, partial cds

>JX857916.1 Mycoplasma genitalium isolate 126.1f adhesion protein MG192 (mgpC) gene, partial cds

>JX857964.1 Mycoplasma genitalium isolate 172.2e adhesion protein MG192 (mgpC) gene, partial cds

>JX857954.1 Mycoplasma genitalium isolate 165.0b adhesion protein MG192 (mgpC) gene, partial cds

Supplementary Table 3.

Mycoplasma genitalium mgpC sequences from patient No. 126 from the National Center for Biotechnology Information