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Mycoplasma genitalium is an important etiologic agent of non-gonococcal urethritis (NGU), known for chronicity and multidrug resistance, in which biofilms may play an integral role. In some bacterial species capable of forming biofilms, extracellular polymeric substances (EPS) composed of poly-N-acetylglucosamine (PNAG) are a crucial component of the matrix. Monosaccharide analysis of M. genitalium strains revealed high abundance of GlcNAc, suggesting a biofilm-specific EPS. Chromatograms also showed high concentrations of galactose and glucose as observed in other mycoplasma species. Fluorescence microscopy of M. genitalium biofilms utilizing fluor-coupled lectins revealed differential staining of biofilm structures. Scanning electron microscopy (SEM) showed increasing maturation over time of bacterial “towers” seen in biofilm development. As seen with Mycoplasma pneumoniae, organisms within fully mature M. genitalium biofilms exhibited loss of cell polarization. Bacteria associated with disrupted biofilms exhibited decreased dose-dependent viability after treatment with antibiotics compared to bacteria with intact biofilms. In addition, growth index analysis demonstrated decreases in metabolism in cultures with disrupted biofilms with antibiotic treatment. Taken together, these data suggest that M. genitalium biofilms are a contributing factor in antibiotic resistance.

Background Mycoplasma pneumoniae (Mpn), one of the smallest self-replicating prokaryotes, is known to readily adhere to host cells and to form aggregates in suspension. Having only one cell membrane and no cell wall, mycoplasmas present questions as to optimal aggregate disruption method while minimizing cell death in vitro. We compared conventional vortex mixing with other methods for disruption of bacterial aggregates and for its effect on cell viability. Methods Strain UAB PO1, a clinical Mpn isolate, was dispersed using a conventional vortex mixer with or without nonionic detergent (0.1% and 0.01% Tween-20), a probe-type ultrasonicator, or repeated passage through a 27-gauge needle. The resulting suspensions were assayed for recoverable colony-forming units (CFU). Flow cytometric assays were carried out to examine particle size and membrane integrity with the transmembrane potential dye DiBAC4. Wet Scanning Transmission Electron Microscopy (Wet-STEM) was performed for high resolution imaging of the resultant cell suspensions. Additional Mpn strains and other human mollicute species were assayed in a similar manner. Mice were infected with either vortexed or sonicated UAB PO1 and bacterial persistence was examined via Mpn-specific 16S qPCR. Results Comparison between dispersion methods showed a 10-fold enrichment of recoverable Mpn CFU with sonication compared to other methods. Time-course analysis showed significantly lower bacterial CFU with vortexing compared to sonication at all time points. Flow cytometric analysis showed increased cellular membrane damage via DiBAC4 staining in sonicated suspensions, but a decreased particle size. Wet-STEM imaging showed markedly improved dispersion with sonication compared to conventional vortex treatment, and surprisingly vortexing for 30 s produced up to a 100-fold drop in CFU. Results similar to UAB PO1 were obtained with three additional Mpn strains and other Mollicutes species, although they exhibited differential susceptibilities to disaggregation by sonication. Finally, increased persistence of the organism in a mouse model of infection was observed using sonicated suspensions for initial infection. Conclusions Sonication is superior to vortexing with or without nonionic detergent or repeated 27-gauge needle passage for dispersion of Mpn aggregates while preserving cell viability. Preparation of Mpn suspensions for in vivo experiments is best accomplished using brief sonication due to the dramatic increase in CFU produced by sonication. Dispersion methods may affect the final experimental results and should be an important consideration for future research involving mycoplasma species.

Summary Although mycoplasmas have a paucity of glycosyltransferases and nucleotidyltransferases recognizable by bioinformatics, these bacteria are known to produce polysaccharides and glycolipids. We show here that mycoplasmas also produce glycoproteins and hence have glycomes more complex than previously realized. Proteins from several species of Mycoplasma reacted with a glycoprotein stain, and the murine pathogen Mycoplasma arthritidis was chosen for further study. The presence of M. arthritidis glycoproteins was confirmed by high-resolution mass spectrometry. O-linked glycosylation was clearly identified at both serine and threonine residues. No consensus amino acid sequence was evident for the glycosylation sites of the glycoproteins. A single hexose was identified as the O-linked modification, and glucose was inferred by 13C-labelling to be the hexose at several of the glycosylation sites. This is the first study to conclusively identify sites of protein glycosylation in any of the mollicutes.

Here, we describe mutants of Mycoplasma pulmonis that were obtained using a minitransposon, Tn4001TF1, which actively transposes but is then unable to undergo subsequent excision events. Using Tn4001TF1, we disrupted 39 genes previously thought to be essential for growth. Thus, the number of genes required for growth has been overestimated. This study also revealed evidence of gene duplications in M. pulmonis and identified chromosome segregation proteins that are dispensable in mycoplasmas but essential in Bacillus subtilis.

Ichthyophthirius multi¢liis(Ich), a ciliated protozoanparasite of ¢sh, expresses surface antigens (i-anti-gens), which react with host antibodies that renderthemimmobile.Thenucleotidesequenceofani-anti-gen gene of I. multi¢liis strain ARS-6 was deduced.The predicted protein of 47493Da is comprised of460 amino acids (aa’s) arranged into ¢ve imperfectrepeats with periodic cysteine residues with thestructure: CX (19)20 CX 2 CX 16 27 CX 2 CX 20(21) CX 3 . TheN-terminal aa’s typify a signal peptide motif whilea stretch of C-terminal aa’s resemble a glycosyl^phosphatidyl^inositol (GPI)-anchor addition site.Thedegreeofdeducedi-antigenaasequenceidentityof strain ARS-6 (GenBank accession # ACH87654and # ACH95659) with other I. multi¢liis i-antigensequences present in GenBank ranges from 99% to36% identity with 52kDa i-antigens of I. multi¢liisstrain G5 (accession #s AAK94941and AAK01661respectively). Immunoblot analysis of i-antigens fol-lowing exposure of I. multi¢liis theronts to cat¢shanti-I. multi¢liis immune serum did not show anyappreciable alteration in i-antigen expression. Themechanism that regulates i-antigen expression inI.multi¢liisremainsapuzzlingquestion.Keywords: immobilization antigen, gene, nucleo-tidesequence,Ichthyophthiriusmulti¢liisIntroductionIchthyophthiriusmulti¢liis(Ich) is a hymenostomatidparasitic ciliate that causes ‘white spot’ disease inmany species of freshwater cultured and/or free liv-ing ¢sh. Fish that recover from I. multi¢liis infectionareknowntopossessbothserumandcutaneousmu-cus antibodies that are capable of immobilizing theparasite in vitro (Clark & Dickerson 1997). The anti-gens on the parasite surface that are involved in theantibody-mediatedimmobilizationarecomprisedofaclass of abundant glycosyl^phosphatidyl^inositol(GPI)-anchoredmembraneproteinsthatareaptlyde-signated as immobilization antigens (i-antigens)(Clark, Gao, Gaertig, Wang & Cheng 2001; Clark FHatanka,Umeda,YamashitaH Swennes, Findly DLee & Kim 2008).Tetrahymena and Paramecium spe-cies are free-living ciliated protists that have servedas model systems, in which i-antigens have been ex-tensively studied (Doerder 2000; Simon & Schmidt2005). Both Tetrahymena and Paramecium possess arepertoire of paralogous genes that encode alterna-tive forms of i-antigens, the expression of which isunder the in£uence of certain environmental cuessuch as temperature and medium, in which they

Summary The presence of capsular exopolysaccharide (EPS) in Mollicutes has been inferred from electron micrographs for over 50 years without conclusive data to support the production of complex carbohydrates by the organism. Mycoplasma pulmonis binds the lectin Griffonia simplicifolia I (GS-I), which is specific for terminal β-linked galactose residues. Mutants that failed to produce the EPS bound by GS-I were isolated from a transposon library. All of the mutants had the transposon located in open reading frame MYPU_7410 or MYPU_7420. These overlapping genes are predicted to code for a heterodimeric pair of ABC transporter permeases and may code for part of a new pathway for synthesis of EPS. Analysis by lectin-affinity chromatography in conjunction with gas chromatography demonstrated that the wild-type mycoplasma produced an EPS (EPS-I) composed of equimolar amounts of glucose and galactose that was lacking in the mutants. Phenotypic analysis revealed that the mutants had an increased propensity to form a biofilm on glass surfaces, colonized mouse lung and trachea efficiently, but had a decreased association with the A549 lung cell line. Confounding the interpretation of these results is the observation that the mutants missing EPS-I had an eightfold overproduction of an apparent second EPS (EPS-II) containing N-acetylglucosamine.

Even though free-living, mycoplasmas depend on their hosts for key nutrients, including purines, pyrimidines, several amino acids, and sterols, which are incorporated into the membranes of these wall-less bacteria. These requirements reflect their relative genomic simplicity. The 580-kb genome of Mycoplasma genitalium, for example, is comparable in size to that of a large virus.

The length of the tandem repeat region of the Vsa protein of Mycoplasma pulmonis has previously been shown to modulate the susceptibility of mycoplasmas to killing by complement: cells that produce a short form of the Vsa protein are highly sensitive, and cells producing the long Vsa protein are resistant. In contrast to their differing susceptibilities to complement, the mycoplasmas were highly sensitive to gramicidin irrespective of the length of the Vsa protein produced. We show here that when encased within a biofilm, cells of M. pulmonis producing a short form of the Vsa protein were more resistant to complement and gramicidin than mycoplasmas that were dispersed. The resistance appeared to be localized to those mycoplasmas within tower structures of the biofilms. Biofilm formation may be a mechanism that protects mycoplasmas from host immunity.

Bacterial biofilms are communities of bacteria that are enclosed in an extracellular matrix. Within a biofilm the bacteria are protected from antimicrobials, environmental stresses, and immune responses from the host. Biofilms are often believed to have a highly developed organization that is derived from differential regulation of the genes that direct the synthesis of the extracellular matrix and the attachment to surfaces. The mycoplasmas have the smallest of the prokaryotic genomes and apparently lack complex gene-regulatory systems. We examined biofilm formation by Mycoplasma pulmonis and found it to be dependent on the length of the tandem repeat region of the variable surface antigen (Vsa) protein. Mycoplasmas that produced a short Vsa protein with few tandem repeats formed biofilms that attached to polystyrene and glass. Mycoplasmas that produced a long Vsa protein with many tandem repeats formed microcolonies that floated freely in the medium. The biofilms and the microcolonies contained an extracellular matrix which contained Vsa protein, lipid, DNA, and saccharide. As variation in the number of Vsa tandem repeats occurs by slipped-strand mispairing, the ability of the mycoplasmas to form a biofilm switches stochastically.

The variable surface antigens (Vsa) of the murine respiratory pathogen Mycoplasma pulmonis are associated with the virulence of the microorganism in the lung. In strain UAB CT, the antigens consist of an N-terminal region that is combined with one of seven different C-terminal variable regions comprised of tandem repeats. M. pulmonis producing a VsaA protein with about 40 tandem repeats (R40) does not adhere to red blood cells or polystyrene. Strains that produce VsaH contain a short C-terminal region that lacks tandem repeats and adhere to red blood cells and plastic. We isolated and analyzed M. pulmonis strain CT variants (CT182 and derivatives) that produced a VsaA protein with only three tandem repeats (R3). These variants adhered to plastic and red blood cells similarly to the VsaH-producing strain. When the R3-producing CT182 strain or the VsaH-producing strains were incubated with normal guinea pig serum, they were efficiently killed. Killing was abolished when the serum was heat inactivated. In contrast, the M. pulmonis strains that produced VsaA R40 were highly resistant to complement killing. CT182R3 variants that survived the complement killing reactions all produced the R40 form of VsaA and were resistant to complement killing. VsaA R40 is the first mycoplasmal protein shown to be associated with resistance to complement. As both VsaH and VsaA can mediate adherence to plastic, cytadherence, and susceptibility to complement, we propose that Vsa modulates these phenotypes by nonspecific interactions.

The lysogenic bacteriophage MAV1 has been shown to be a virulence factor for the development of arthritis in rats infected with Mycoplasma arthritidis. In the present study, arthritis was evaluated by histopathologic examination to demonstrate that MAV1 is a virulence factor not only in the rat but also in the mouse. Specifically, the MAV1 lysogen 158L3-1 was more virulent than the nonlysogen strain 158 in DBA/2NCr, C3H/HeNCr, C3H/HeJ, and C3Smn.CB17-Prkdc(scid)/J mice, as well as in LEW rats.

Restriction and modification (R-M) systems are generally thought to protect bacteria from invasion by foreign DNA. This paper proposes the existence of an alternative role for the phase-variable R-M systems encoded by the hsd loci of Mycoplasma pulmonis. Populations of M. pulmonis cells that arose during growth in different environments were compared with respect to R-M activity and surface antigen production. When M. pulmonis strain X1048 was propagated in laboratory culture medium, > 95% of colony-forming units (cfu) lacked R-M activity and produced the variable surface protein VsaA. Mycoplasmas isolated from the nose of experimentally infected rats also lacked R-M activity and produced VsaA. In contrast, the cell population of mycoplasmas isolated from the lower respiratory tract of the infected rats was more complex. The most dramatic results were obtained for mycoplasmas isolated from the trachea. At 14 days postinfection, 38% of mycoplasma isolates produced a Vsa protein other than VsaA, and 34% of isolates had active restriction systems. These data suggest that differences in selection pressures in animal tissues affect the surface proteins and the R-M activity of the mycoplasmal cell population. We propose that variations in the production of R-M activity and cell surface proteins are important for the survival of the mycoplasma within the host.

To improve the detection of Mycoplasma pulmonis contamination of isolates of cilia-associated respiratory (CAR) bacillus, we developed a nested PCR method using primers for 16S rRNA gene sequences. Of 140 samples of 16 different CAR bacillus isolates, 73 (52%) were inhibitory in the first PCR, as indicated by the absence of amplicons of the internal control, but only 11 of 140 (7.9%) were inhibitory in the second PCR. Of 27 samples known to contain M. pulmonis, only 12 (44%) were positive in the first PCR, but 25 of 27 (93%) were positive in the second PCR. Nested PCR also detected M. pulmonis in 21 of 61 (34%) CAR bacillus samples from which M. pulmonis could not be cultured and identified 2 additional M. pulmonis-contaminated CAR bacillus isolates. Of 359 respiratory and reproductive tract lavage samples from rats and mice, 35 (9.8%) were inhibitory in the first PCR, but only 15 (4.2%) were inhibitory in the second PCR. Of 72 lavage specimens from rats inoculated with an avirulent, poorly infective M. pulmonis strain, 14 (19%) were positive by nested PCR, but only 2 of 72 (2.8%) were positive by culture. Nested PCR also detected M. pulmonis in 14 of 20 (70%) paraffin sections of lung and trachea from rats and mice inoculated with CAR bacillus isolates known to contain M. pulmonis, whereas single PCR gave no positive results. We conclude that nested PCR is superior to single PCR or culture for detecting M. pulmonis, and that M. pulmonis is present in all but four CAR bacillus isolates in our collection that were from naturally infected rats; the four isolates that were exceptions were obtained from rats from a single colony.

The RecA protein has a central role in DNA repair and is essential for homologous recombination in most eubacteria. Little is known about these critical processes in mycoplasmas. By using standard and inverse polymerase chain reactions (PCR) coupled with conventional cloning techniques, a series of overlapping fragments comprising the entire recA genes of Mycoplasma mycoides subsp. mycoides (Mm) and Mycoplasma pulmonis (Mp) were generated. Each gene was sequenced in its entirety. The recA genes of Mm and Mp would encode proteins of 345 amino acids (aa) and 339 aa, respectively. The mycoplasmal RecA proteins revealed strong conservation when compared with RecA sequences from other bacterial species.

Only two plasmids have been isolated and characterized from the entire genus Mycoplasma, which includes over 90 recognized species. Both of these plasmids were obtained from the same species, Mycoplasma mycoides subsp. mycoides. We have previously characterized one of these plasmids, pKMK1, as a preliminary step in developing mycoplasmal cloning vectors. In the present study, we have separately combined pKMK1 with two different Escherichia coli replicons and a tetracycline resistance (tetM) gene. One of the constructs, plasmid p2D4, was shuttled from E. coli to M. mycoides subsp. mycoides and back to E. coli with no deletions or rearrangements occurring in the plasmid. In the second construct, the E. coli replicon was deleted when the plasmid was transformed into M. mycoides subsp. mycoides. This derivative, designated plasmid pIK delta, is noteworthy in that it could be transformed into M. mycoides subsp. mycoides at a much higher frequency than the parental plasmid. A gram-positive bacterial erythromycin resistance determinant (erm) was cloned into both p2D4 and pIK delta. Resistance to erythromycin was stably maintained using both constructs, even in the absence of erythromycin selection, indicating that these plasmids will be useful mycoplasmal cloning vectors.

Cilia-associated respiratory (CAR) bacillus, an unclassified gliding bacterium associated with respiratory disease in rats, mice, and rabbits, has previously been cultivated only in embryonated chicken eggs, cell culture, or cell culture medium supplemented with conditioned medium from cultured tracheas. A reference strain of CAR bacillus, originally isolated in eggs, grew in cell culture flasks as adherent individual bacilli and ropy, whorled fascicles in cell culture media supplemented only with fetal calf serum. Using Dulbecco's minimal essential medium, we isolated CAR bacillus from naturally infected rats and a naturally infected rabbit and from experimentally inoculated mice and rats. Isolates were maintained for up to 20 passages. Isolates from rats were similar in morphology to the reference strain, but most were more actively motile and formed pincushion-like aggregates. The rabbit bacilli were smaller and formed fewer aggregates. DNAs of rat isolates differed only slightly in restriction fragment patterns from that of the reference strain, whereas that of the rabbit isolate was distinctly different. Cultures of CAR bacilli of all strains from rats contained Mycoplasma fermentans, Mycoplasma pulmonis, or both, and cultures of the CAR bacillus from the rabbit contained an unidentified arginine-utilizing mycoplasma. The sequence of the 16S rRNA gene of the reference strain was determined by amplification by polymerase chain reaction, cloning of the product, and sequencing by the dideoxynucleotide chain termination method. Comparison of the sequence with sequences in the GenBank data base indicated that CAR bacillus is a unique organism most closely related to Flavobacterium ferrugineum and Flexibacter sancti.

Summary Fourteen established serovars of Ureaplasma urealyticum were examined by restriction endonuclease cleavage patterns of genomic DNA, Southern blot hybridization and DNA-DNA hybridization. The restriction endonuclease cleavage patterns and the Southern blot hybridization both revealed that the 14 serovars are divided into two clusters. The DNA-DNA hybridization data further confirmed that these two clusters are genetically distinct of each other.

Mycoplasma arthritidisinduces an acute to chronic arthritis in rodents. Arthritis induced in mice histologically resembles human rheumatoid arthritis and can be associated with lethal toxicity following systemic injection. TheM. arthritidismitogen (MAM) superantigen has long been implicated as having a role in pathogenesis, but its significance with respect to toxicity and arthritogenicity in mycoplasma-induced disease is unclear. To study the pathogenic significance of MAM,M. arthritidismutants that overproduced or failed to produce MAM were developed. MAM overproduction and knockout mutants were more and less mitogenic, respectively, than the wild-type strain. The degree of mitogenic activity correlated with lethal toxicity in DBA/2J mice. In contrast, histopathological studies detected no correlation between MAM production and the severity of arthritis induced in DBA/2J and CBA/J mice.

The genomes of several species of mycoplasma have been sequenced. Most of these species rely on the glycolytic pathway for energy production, with the one exception of Ureaplasma , a species that breaks down urea as its principle source of acquiring energy. Several species, including as Mycoplasma arthritidis , are nonglycolytic and can use arginine as their source of energy. Described here are the genome sequence and a transposon library of M. arthritidis . The genome of 820,453 bp is typical in size for a mycoplasma and contains two large families of genes that are predicted to code for phase-variable proteins. The transposon library was constructed using a minitransposon that inserts stably into the mycoplasma genome. Of the 635 predicted coding regions, 218 were disrupted in a library of 1,100 members. Dispensable genes included the gene coding for the MAM superantigen and genes coding for ribosomal proteins S15, S18, and L15.

To obtain mutants for the study of the basic biology and pathogenic mechanisms of mycoplasmas, the insertion site of transposon Tn4001T was determined for 1700 members of a library of Mycoplasma pulmonis mutants. After evaluating several criteria for gene disruption, we concluded that 321 of the 782 protein coding regions were inactivated. The dispensable and essential genes of M. pulmonis were compared with those reported for Mycoplasma genitalium and Bacillus subtilis. Perhaps the most surprising result of the current study was that unlike other bacteria, ribosomal proteins S18 and L28 were dispensable. Carbohydrate transport and the susceptibility of selected mutants to UV irradiation were examined to assess whether active transposition of Tn4001T within the genome would confound phenotypic analysis. In contrast to earlier reports suggesting that mycoplasmas were limited in their DNA repair machinery, mutations in recA, uvrA, uvrB and uvrC resulted in a DNA-repair deficient phenotype. A mutant with a defect in transport of N-acetylglucosamine was identified.

A multiplex PCR (m-PCR) method was developed for simultaneous detection of 3 important fish pathogens in warm water aquaculture. The m-PCR to amplify target DNA fragments from Flavobacterium columnare (504 bp), Edwardsiella ictaluri (407 bp) and Aeromonas hydrophila (209 bp) was optimized by adjustment of reaction buffers and a touchdown protocol. The lower detection limit for each of the 3 bacteria was 20 pg of nucleic acid template from each bacteria per m-PCR reaction mixture. The sensitivity threshold for detection of the 3 bacteria in tissues ranged between 3.4 x 10(2) and 2.5 x 10(5) cells g(-1) of tissue (channel catfish Ictalurus punctatus Rafinesque). The diagnostic sensitivity and specificity of the m-PCR was evaluated with 10 representative isolates of each of the 3 bacteria and 11 other Gram-negative and 2 Gram-positive bacteria that are taxonomically related or ubiquitous in the aquatic environment. Except for a single species (A. salmonicida subsp. salmonicida), each set of primers specifically amplified the target DNA of the cognate species of bacteria. m-PCR was compared with bacteriological culture for identification of bacteria in experimentally infected fish. The m-PCR appears promising for the rapid, sensitive and simultaneous detection of Flavobacterium columnare, E. ictaluri and A. hydrophila in infected fish compared to the time-consuming traditional bacteriological culture techniques.

Mycoplasma pulmonis possesses a cassette of genes that are predicted to code for type III restriction and modification (R-M) enzymes. Transposon disruption of a gene predicted to code for the endonuclease subunit of the enzyme resulted in loss of R-M activity. Genomic data indicate that the cassette was acquired by horizontal gene transfer and possibly located on a mobile element.

Previous studies demonstrated that Mycoplasma arthritidis strain 158 acquired a high degree of virulence upon lysogenization with bacteriophage MAV1. In the present study, the association between MAV1 and virulence was reexamined by creating new lysogens of 158 and of a relatively avirulent mutant, strain 158-1. In the absence of lysogenization, 158 was more virulent than expected. The virulence of 158 and 158-1 did not increase upon lysogenization. A major antigenic difference between 158 and 158-1 was identified that is unrelated to MAV1 and could account for the difference in virulence.

The Vsa proteins are associated with the virulence of the murine respiratory pathogenMycoplasma pulmonis. The antigens consist of a conserved N-terminal region that is combined with one of several different variable C-terminal regions comprised of tandem repeats.M. pulmonisstrains that produce VsaA with about 40 tandem repeats do not adhere to polystyrene or erythrocytes and are highly resistant to complement killing. Strains that produce VsaA with three tandem repeats adhere strongly to polystyrene and erythrocytes and are highly susceptible to complement killing. We report here that the resistance to complement lysis was not due to a lack of activation of the complement cascade. Isolation and analysis ofM. pulmonisstrains that produced Vsa proteins other than VsaA (VsaG and VsaI) with either long or short repeat regions indicated that adherence to polystyrene and resistance to complement were dependent on the length of the repeat region but not on the Vsa type. Furthermore,M. pulmonisVsa variants were susceptible to the polypeptide pore-forming molecule gramicidin D, independent of the Vsa type and length. Collectively, the data indicate the Vsa proteins nonspecifically mediateM. pulmonissurface interactions and function to sterically hinder access of complement to the mycoplasma cell membrane while permitting access of smaller molecules.

Lysogenization of Mycoplasma arthritidis with the MAV1 bacteriophage increases the virulence of the mycoplasma in rats. The MAV1 vir gene is one of only two constitutively transcribed phage genes in the lysogen. We show here that Vir is a lipoprotein and is located on the outer surface of the cell membrane. To investigate whether Vir is a virulence factor, the vir gene was cloned into the transposon vector Tn 4001T and inserted in the genome of the nonlysogen strain 158. The virulence of the resulting transformants was no different from that of the parent strain. Interestingly, all vir -containing transformants were resistant to infection by MAV1. Vir had no effect on MAV1 adsorption. We conclude that Vir is not a virulence factor but functions to exclude superinfecting phage, possibly by blocking the injection of phage DNA into the bacterial cytoplasm.

Microsatellites (short tandem polynucleotide repeats) are found throughout eukaryotic genomes at frequencies many orders of magnitude higher than the frequencies predicted to occur by chance. Most of these microsatellites appear to have evolved in a generally neutral manner. In contrast, microsatellites are generally absent from bacterial genomes except in locations where they provide adaptive functional variability, and these appear to have evolved under selection. We demonstrate a mutational bias towards deletion (repeat contraction) in a native chromosomal microsatellite of the bacterium Mycoplasma gallisepticum, through the collection and analysis of independent mutations in the absence of natural selection. Using this and similar existing data from two other bacterial species and four eukaryotic species, we find strong evidence that deletion biases resulting in repeat contraction are common in bacteria, while eukaryotic microsatellites generally experience unbiased mutation or a bias towards insertion (repeat expansion). This difference in mutational bias suggests that eukaryotic microsatellites should generally expand wherever selection does not exclude them, whereas bacterial microsatellites should be driven to extinction by mutational pressure wherever they are not maintained by selection. This is consistent with observed bacterial and eukaryotic microsatellite distributions. Hence, mutational biases that differ between eukaryotes and bacteria can account for many of the observed differences in microsatellite DNA content and distribution found in these two groups of organisms.

The pMGA genes of the avian respiratory pathogen Mycoplasma gallisepticum encode a family of hemagglutinins that are subject to phase variation. A trinucleotide GAA repeat region is located upstream of the pMGA transcription start site. The length of the repeat region varies at a high frequency due to changes in the number of repeat units. Previous studies have shown that pMGA genes are transcribed when 12 GAA repeats are present but are not transcribed when the number of repeats is not 12. To further analyze the mechanism of gene regulation, the pMGA promoter region was modified either by deleting the nucleotides 5" of the GAA repeats or by inserting linkers of 10 or 12 bp at a position 3" of the repeats. The modified promoter region was fused to a promoterless lacZ gene and transformed into M. gallisepticum by using transposon Tn 4001 as a vector. Transformants and successive generations of progeny were analyzed with 5-bromo-4-chloro-3-indolyl-β- d -galactopyranoside (X-Gal) to monitor β-galactosidase activity. For the transformants of M. gallisepticum containing the reporter with deletion of nucleotides 5" of the GAA repeats, GAA-dependent pMGA gene regulation was abolished. For the transformants containing the reporter with an addition of 10- or 12-bp linkers, lacZ was expressed only when eight GAA repeats were present. These data indicate that the nucleotides 5" of the GAA repeats as well as the spacing between the GAA repeats and sequences downstream (3") of the repeats are important for pMGA gene expression.

The restriction-modification (R-M) systems are so named because of their ability to degrade foreign DNA (restrict viral infection) and to methylate (modify) unmethylated and hemimethylated DNA. They were discovered as genetic elements that determined the susceptibility of E. coli and S. typhimurium to phage infection in a strain-dependent manner, with bacteriophage plaquing efficiency being reduced upon infection of a heterologous host strain (2). At the time of writing, 3154 R-M enzymes, many with overlapping DNA recognition specificities, have been catalogued in the restriction enzyme database (REBASE) (65). R-M systems are ubiquitous and arose early in prokaryotic evolution

International audience; Mycoplasma pulmonis is a wall-less eubacterium belonging to the Mollicutes (trivial name, mycoplasmas) and responsible for murine respiratory diseases. The genome of strain UAB CTIP is composed of a single circular 963 879 bp chromosome with a G + C content of 26.6 mol%, i.e. the lowest reported among bacteria, Ureaplasma urealyticum apart. This genome contains 782 putative coding sequences (CDSs) covering 91.4% of its length and a function could be assigned to 486 CDSs whilst 92 matched the gene sequences of hypothetical proteins, leaving 204 CDSs without significant database match. The genome contains a single set of rRNA genes and only 29 tRNAs genes. The replication origin oriC was localized by sequence analysis and by using the G + C skew method. Sequence polymorphisms within stretches of repeated nucleotides generate phase-variable protein antigens whilst a recombinase gene is likely to catalyse the site-specific DNA inversions in major M.pulmonis surface antigens. Furthermore, a hemolysin, secreted nucleases and a glyco-protease are predicted virulence factors. Surprisingly, several of the genes previously reported to be essential for a self-replicating minimal cell are missing in the M.pulmonis genome although this one is larger than the other mycoplasma genomes fully sequenced until now.

Few genetic systems for studying mycoplasmas exist, but transposon Tn916 has been shown to transpose into the genomes of some species and can be used as an insertional mutagen. In the current study, the ability of Enterococcus faecalis to serve as a donor for the conjugative transfer of transposon Tn916 into the genome of the avian pathogen Mycoplasma gallisepticum strain PG31 was examined. Transconjugants were obtained at a frequency of ≥6 × 10−8 per recipient CFU. To determine the transposon insertion site, an oligonucleotide primer corresponding to the 3′ end of Tn916 was designed for the purpose of directly sequencing genomic DNA without PCR amplification. Using the direct sequencing approach, Tn916 was shown to insert into any of numerous sites in the M. gallisepticum genome. This is the first report of conjugal transposition of Tn916 into the M. gallisepticum genome. The ability to determine transposon insertion sites in mycoplasmas by genomic sequencing has not been previously described and allows rapid sequence analysis of transposon-generated mutants.

Mycoplasma gallisepticum , the cause of chronic respiratory infections in the avian host, possesses a family of M9/pMGA genes encoding an adhesin(s) associated with hemagglutination. Nucleotide sequences of M9/pMGA gene family members indicate extensive sequence similarity in the promoter regions of both the transcribed and silent genes. The mechanism that regulates M9/pMGA gene expression is unknown, but studies have revealed an apparent correlation between gene expression and the number of tandem GAA repeat motifs located upstream of the putative promoter. In this study, transposon Tn 4001 was used as a vector with the Escherichia coli lacZ gene as the reporter system to examine the role of the GAA repeats in M9/pMGA gene expression in M. gallisepticum . A 336-bp M9 gene fragment (containing the GAA repeat region, the promoter, and the translation start codon) was amplified by PCR, ligated with a lacZ gene from E. coli , and inserted into the Tn 4001 -containing plasmid pISM2062. This construct was transformed into M. gallisepticum PG31. Transformants were filter cloned on agar supplemented with 5-bromo-4-chloro-3-indolyl-β- d -galactopyranoside (X-Gal) to monitor lacZ gene expression on the basis of blue/white color selection. Several cycles of filter cloning resulted in cell lineages in which lacZ gene expression alternated between the On and Off states in successive generations of progeny clones. The promoter regions of the M9- lacZ hybrid genes of individual progeny clones were amplified by PCR and sequenced. The only differences between the promoter regions of the blue and white colonies were in the number of GAA repeats. Clones that expressed lacZ had exactly 12 tandem copies of the GAA repeat. Clones that did not express lacZ invariably had either more than 12 (14 to 16) or fewer than 12 (5 to 11) GAA repeats. Southern analysis of M. gallisepticum chromosomal DNA confirmed that the phase-variable expression of the lacZ reporter gene was not caused by Tn 4001 transposition. These data strongly indicate that changes in the length of the GAA repeat region are responsible for regulating M9/pMGA gene expression.

The bacteriophage MAV1 is required for the development of arthritis in rats after infection with its host Mycoplasma arthritidis . To identify the phage-encoded virulence factor for this arthritis, the complete nucleotide sequence of MAV1 was determined. The linear double-stranded genome of MAV1 is 15 644 bp and contains 15 ORFs. Putative protein products from these ORFs were identified by comparison of the deduced amino acid sequences to known proteins and comprise DNA replication, restriction–modification, structural, regulatory, and integration/excision proteins. Eight putative promoters were identified; four of these would produce polycistronic transcripts. Translation of each ORF appears to be initiated independently, with each having its own RBS. A single ORF, vir , was identified on the minus strand of the phage genome. The putative protein product of vir contains a classic prokaryotic lipoprotein signal sequence and is a strong candidate for the MAV1-encoded virulence determinant.

A 62-kDa cell surface antigen (M9) of Mycoplasma gallisepticum PG31 that mediates antibody-induced agglutination of the organism was purified and subjected to N-terminal amino-acid sequencing. A 999-bp region of the cDNA encoding the M9 protein was generated by reverse transcription-PCR, and its nucleotide sequence was determined. PCR primers based on this sequence were used to screen a genomic DNA library of PG31. A full-length M9 protein-encoding gene was isolated and sequenced, revealing 96% nucleotide identity with the pMGA1.1 gene of M. gallisepticum S6. Sequence analyses of the M9 gene and flanking open reading frames that encode other pMGA family members suggest that a tandemly repeated GAA sequence may influence pMGA gene expression.

This chapter provides an overview of identification and characterization of genome rearrangements. Gene rearrangements occur in Mycoplasma pulmonis at a high frequency. Some of these rearrangements apparently regulate the expression of surface antigens and generate heterogeneous cell populations with varied phenotypes. Phenotypic changes mediated by high-frequency chromosomal rearrangements affect the ability of the mycoplasma to respond to environmental changes, likely playing a significant role in the pathogenic potential of the organism. The purpose of the method described is to identify chromosomal sequences that undergo high-frequency rearrangement, with the view that these sequences will likely be key determinants to cell survival. Mycoplasmas generally grow as aggregates that contain heterogeneous populations with varied phenotypes and genotypes. Restriction endonuclease digestion of the small mycoplasmal chromosome results in fewer fragments relative to most bacterial genomes. For mycoplasmas it is easy to detect restriction fragment length polymorphism on routine agarose gels stained with ethidium bromide. Genome rearrangements have been described in transposon Tn916- containing strains of Mycoplasma mycoides subspecies mycoides.

This chapter discusses the artificial transformation of mollicutes via polyethylene glycol (PEG)- and electroporation-mediated methods. The principle behind electroporation is the use of high-voltage electric field pulses to transiently disrupt the cell membrane allowing for the uptake of exogenous DNA. This technique is useful in the transformation of both prokaryotes and eukaryotes. The method of choice for transformation of mycoplasmas, PEG-mediated versus electroporation, depends on the species in question and on the nature of the DNA molecule to be used. Electroporation and the PEG-mediated method usually work about equally well for transformation of Acholiplasmalaidlawii and Spiroplasma citri. In the case of A. laidlawii , the most efficient transformation method depends on the DNA molecule being employed. For transfection with mycoplasma virus L1 DNA, the PEG method is about 10 times more efficient than electroporation. Several factors are considered for optimal transformation using the PEG method. These include the PEG concentration, choice of buffers, concentration of the transforming DNA molecule, host cell concentration, presence of CaCl 2 , and presence of carrier DNA or RNA.

Plasmids pIKΔ and pIKΔ-erm have recently been developed as mycoplasmal cloning vectors. In this report, we demonstrate that these plasmids can replicate in Mycoplasma capricolum , a mycoplasmal species for which transformation had not previously been characterized. Both plasmids are stably maintained at a higher copy number than in their parental species, Mycoplasma mycoides subsp. mycoides . We have also examined the possibility of one or more restriction-modification systems affecting transformation frequencies in both species.

Mycoplasma hominis is a heterogeneous species with DNA-DNA hybridization values ranging from 51 to 100%. We report here the sequencing of the 16S rRNA gene of a strain (183) that greatly differs from the type strain (PG21) of this species. Comparison of 16S rDNA sequences from these two strains showed limited differences, indicating that the two strains belong to the same rRNA species complex. Using these nucleotide sequence data, we established a rapid method for the detection of M. hominis by using polymerase chain reaction. This method was shown to be sensitive and specific when tested with reference strains and clinical isolates.

To facilitate the development of mycoplasmal cloning vectors, we have determined the nucleotide sequence of pKMK1, a cryptic plasmid isolated from Mycoplasma mycoides subsp. mycoides. It is 1875 bp in length and contains two open reading frames (ORFs) that share homology with ORFs from members of a large family of gram-positive bacterial plasmids which replicate via a single-stranded DNA intermediate. Putative origins of replication and candidate cloning sites have been identified.

Summary Mycoplasma pulmonis is a murine pathogen that causes chronic respiratory disease in laboratory rats and mice. Several examples of high-frequency phenotypic switching have been reported for M. pulmonis, the molecular basis of which is unknown. We report here that during growth the M. pulmonis chromosome undergoes DNA rearrangements at a high frequency. Some of the rearrangements we examined correlated with changes in the susceptibility of the cells to mycoplasma virus P1, an example of phenotypic switching involving changes in surface antigen structure. Other rearrangements, unrelated to phenotypic switching, involved a DNA element present in the chromosome in multiple copies. The high level of DNA recombination that occurred in M. pulmonis indicates that this may be one of the most variable genomes studied to date. High levels of DNA recombination may contribute to the unusually high rate of evolution that mycoplasmas are thought to be undergoing. Understanding the molecular basis for this phenomenon may provide an insight into the chronic nature of many mycoplasmal infections.

The recent isolation and characterization of two plasmids from Mycoplasma mycoides subspecies mycoides has opened up new possibilities for studying mycoplasmal genetics. In order to facilitate the development of a genetic system in M. mycoides subsp. mycoides, parameters of polyethylene glycol (PEG)-mediated transformation were examined, as existing protocols prove very inefficient in this organism. The effects of PEG concentration, DNA concentration, presence of Ca2+ ions, and choice of buffers on the transformation of the Tn916-containing plasmid pAM120 into M. mycoides subsp. mycoides were examined. The stability of Tn916 in the M. mycoides subsp. mycoides chromosome was also evaluated. The optimal PEG concentration (53-62% (w/v)) in the transformation mixture was substantially higher than the PEG concentration reported to be optimal for transformation of other mycoplasmas (36% (w/v)). The PEG concentrations used here were also higher than the concentration used to promote transformation or fusion of gram-positive bacterial protoplasts. A necessity for the presence of Ca2+ ions for optimal transformation was shown, as was the possible involvement of cell culture growth stage. Our results demonstrate the need for expanding current transformation techniques for mycoplasmas. Studies also indicate that once Tn916 inserts into the M. mycoides subsp. mycoides chromosome, it can transpose to other sites at a relatively high frequency.

Plasmids have rarely been detected in organisms constituting the genusMycoplasma. Recently, the isolation of a cryptic plasmid fromMycoplasma mycoides subsp.mycoides has been described, and we report here the isolation of a second cryptic plasmid from this species. Restriction map and Southern blot analyses show that the second plasmid is distinct from the previously described plasmid, although a limited region of homology was detected. The availability of mycoplasmal cryptic plasmids may lead to the development of cloning vectors that replicate in these organisms.

One limitation with studying mycoplasma genetics is the lack of cloning vectors. Studies were undertaken to determine whether streptococcal plasmids could replicate in Acholeplasma laidlawii, for the purpose of identifying potential vectors. Plasmids pVA868 and pVA920 contain the same origin of replication and tetracycline resistance determinant. pVA920 also contains an erythromycin resistance determinant not present in pVA868. A. laidlawii was transformed with plasmids pVA868 (13.7 kb) and pVA920 (12.2 kb), and isolated from the transformants were deletion derivatives of the parent plasmids having sizes of 3.7 and 10.3 kb, respectively. The tetracycline and erythromycin resistance markers functioned in A. laidlawii, and the deletion derivatives may be useful for development of mycoplasma vectors. However, difficulties may arise due to plasmid instability.

The proteins of Mycoplasma pulmonis were examined by two-dimensional polyacrylamide gel electrophoresis and immunoblotting. Comparison of profiles from silver-stained two-dimensional polyacrylamide gel electrophoresis of 18 strains of M. pulmonis allowed identification of five proteins that were strain variable. These variable proteins were not dependent on the medium used to grow the organisms and were shown by reaction with serum samples from naturally infected rats and mice to be produced in vivo and not to be medium components. Identification of strain-variable proteins may lead to an explanation of the differences in properties found among M. pulmonis strains.

The adsorption of mycoplasma virus P1, a virus which infects some strains of Mycoplasma pulmonis, to host cells was examined. Mutants of M. pulmonis to which P1 virus did not adsorb were isolated. Proteins from the mutants and from wild-type cells were compared by two-dimensional polyacrylamide gel electrophoresis, and the only observed difference was in the surface antigen V-1. The electrophoretic properties of V-1 also correlated with the host range of the virus. These data strongly suggest that the V-1 antigen affects adsorption of P1 virus to host cells.

A DNA sequence consisting of the 5-mer AGAGG repeated tandemly 32 times has been detected in a chicken genomic clone and found to be present in about 2000 copies per chicken genome. This sequence was highly susceptible to single-strand specific endonucleases isolated from Aspergillus oryzae (S1) and mung bean, but cleavage by a single-strand specific endonuclease isolated from Neurospora crassa occurred only at a pH below 5.5. Endonucleolytic cutting of the AGAGG sequence by the single-strand specific enzymes required a supercoiled substrate and was independent of ionic strength.

A procedure for transformation of the murine pathogen Mycoplasma pulmonis with plasmid pAM120 was developed. This plasmid replicates in Escherichia coli and contains the gram-positive transposon Tn916. The transformation protocol also proved effective for the swine pathogen Mycoplasma hyorhinis. The tetracycline resistance determinant of Tn916 was expressed in transformed myocoplasma cells, and Tn916 was found inserted into numerous sites in the recipient chromosomes of M. pulmonis and M. hyorhinis, indicating that transposition had occurred. Interestingly, some transformants of M. pulmonis and M. hyorhinis contained cointegrate structures which apparently had a complete copy of the entire donor plasmid (pAM120) inserted into the recipient chromosome. Subsequent transposition of inserted Tn916 was observed in passaged clones of transformed M. pulmonis.

Mycoplasma genetics has been limited by a lack of genetic tools such as selectable markers, methods to transfer DNA, and suitable vectors for cloning. Studies were undertaken to examine the potential of using the streptococcal transposon Tn916 as a mycoplasma genetic tool. The Escherichia coli plasmid pAM120, which contains Tn916, was transformed into Acholeplasma laidlawii and Mycoplasma pulmonis. Transposition of Tn916 into the mycoplasma chromosome apparently occurred by an excision-insertion mechanism. This example shows that newly introduced DNA from other bacteria can be successfully expressed in mycoplasma and that Tn916 should serve as a powerful genetic tool for the study of mycoplasmas.

Heterogeneity in colony size of the murine pathogen Mycoplasma pulmonis was examined. Subcloning experiments showed that colony size variation resulted from high-frequency genetic changes. About 3% of the colonies from any given subclone were variants, with as much as a fourfold change in colony diameter. When the variants were propagated in liquid broth, their doubling times in logarithmic growth phase reflected the colony sizes obtained on agar. Colony size variation correlated with changes in the electrophoretic properties of the V-1 surface antigen.