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Phylogeny of the Goat Mycoplasmas Mycoplasma Adleri, Mycoplasma Auris, Mycoplasma Cottewii and Mycoplasma Yeatsii

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Phylogeny of the Goat Mycoplasmas Mycoplasma Adleri, Mycoplasma Auris, Mycoplasma Cottewii and Mycoplasma Yeatsii International Journal of Systematic Bacteriology (1 998), 48, 263-268 Printed in Great Britain Sequences of the 16s rRNA genes and phylogeny of the goat mycoplasmas Mycoplasma adleri, Mycoplasma auris, Mycoplasma cottewii and Mycoplasma yeatsii Malin Heldtander,’ Bertil Pettersson,2 Joseph G. Tully3 and Karl-Erik Johansson’ Author for correspondence: Karl-Erik Johansson. Tel: +46 18 67 40 00. Fax: +46 18 30 91 62. e-mail : [email protected] 1 Department of The nucleotide sequences of the 16s rRNA genes from the type strains of four Bacteriology, National goat mycoplasmas, Mycoplasma adleri, Mycoplasma auris, Mycoplasma Veterinary Institute, PO BOX 7073,s-75007 cottewii and Mycoplasma yeatsii, were determined by direct solid-phase DNA Uppsala, Sweden sequencing. Polymorphisms were found in two of the 16s rRNA gene 2 Department of sequences, showing the existence of two different rRNA operons. Three Biochemistry and polymorphisms were found in M. adleri, and one was found in M. yeatsii. The Biotechnology, The Royal sequence information was used for the construction of phylogenetic trees. M. Institute of Technology, 5-100 44 Stockholm, adleri was included in the Mycoplasma lipophilum cluster within the hominis Sweden group. M. auris was comprised in the Mycoplasma hominis cluster of the 3 Mycoplasma Section, hominis group. M. cottewii and M. yeatsii were found to be very closely Frederick Cancer Research related with only four nucleotide differences, and they grouped with and Development Center, Mycoplasma putrefaciens in the Mycoplasma mycoides cluster within the National Institute of Allergy and Infectious spiroplasma group. Sequencing of two field isolates of M. coftewii and M. Diseases, Frederick, yeatsii, geographically distant from the type strains, showed that thel6S rRNA MD 21702, USA gene from the field isolate of M. cottewii was identical to the one from the type strain. The field isolate of M. yeafsii had only two nucleotide differences to the type strain and these were present in only one of the two rRNA operons. Sequencing of the 165 rRNA genes from two unidentified mycoplasma isolates from Nepal indicated that they should both be regarded as M. auris strains. Keywords : goat mycoplasmas, Mycoplasma adleri, Mycoplasma auris, Mycoplasma cottewii, Mycoplasma yeatsii INTRODUCTION 16s rRNA data because they are supposed to reflect phylogeny (19). By this method, the mycoplasmas Mycoplasmas (class Mollicutes) are wall-less, free- have been arranged in five phylogenetic groups : the living bacteria that have a low G+C content in the hominis, pneumoniae, spiroplasma, anaeroplasma and genome and they are closely related to Gram-positive asteroleplasma groups ; and several sub-groups (22, bacteria (23). They are often host-specific, and domes- 29). Mycoplasmas have one, two or three rRNA ticated animals usually harbour several mycoplasma operons and many mycoplasmas of ruminants have species. Thus far, about 150 different mycoplasma two rRNA operons (rmA and rrnB). Existence of two species have been described, many of which are rRNA operons has been established by restriction pathogenic, making the mycoplasmas and their phy- enzyme analysis and hybridization with rDNA probes logeny important in veterinary medicine (25, 27). (5) and by sequence analysis of the two operons (20, 2 1, 24). A nucleotide substitution (polymorphism) in Classification of micro-organisms is partly based on one of the operons will result in a double peak with a 1 : 1 ratio in the computerized on-line determination of The GenBank accession numbers for the sequences reported in this paper the sequence from the automated sequencer. Thus, are U67943-U67946. polymorphisms are easily identified and existence of 00628 0 1998 IUMS 263 M. Heldtander and others polymorphisms in a 1 : 1 ratio shows that two rRNA 1250 bp, respectively, with an overlap of about 600 bp. The operons (20, 21) are present. reactions were performed in 50 pl volumes with 10 pmol of each primer, 25 mM Tris/HCl buffer (pH %O), 50 mM KCl, We have determined the nucleotide sequences of the 2 mM MgCl,, 0.1 % Tween 20, 0.2 mM dNTP, 0.75 U 16s rRNA genes, and established the molecular AmpliTaq (Perkin-Elmer Cetus), and 1 pl lysed myco- phylogeny of four recently described goat myco- plasma1 suspension or diluted PCR product. Two of the plasmas. Three of these mycoplasmas, Mycoplasma primers (U5 and US) were biotinylated to make the PCR auris, Mycoplasma cottewii and Mycoplusmu yeatsii, products suitable for solid-phase DNA sequencing. were originally isolated from the external ear canal of Solid-phase DNA sequencing. Forty microlitres of bio- goats in Australia (6). The fourth one, Mycoplasma tinylated PCR product was immobilized onto 200 pg strep- adleri, was isolated from a goat's abscessed ankle in tavidin-coated paramagnetic beads (Dynabeads M280 ; DYNAL) diluted in 40 p1 2x binding/washing (B/W) Maryland, also determined USA (7). We have the buffer [2 x B/W buffer is 10 mM Tris/HCl buffer (pH 7.9, nucleotide sequences of the 16s rRNA genes of four 1 mM EDTA, 2.0 M NaCl] by incubation for 15 min at other mycoplasma isolates from goats. Two of them room temperature. The tube was placed in a magnetic tube were isolated and typed as M. cottewii and M. yeatsii rack, to sediment the beads while the supernatant was by F. Thiaucourt in France, and two were myco- removed. The beads were then washed in 1 x B/W buffer plasmas isolated in Nepal and sent to Europe (K. and incubated in 8 pl 0.1 M NaOH for 10 min at room Sachse & R. Nicholas) for identification. temperature to separate the strands of the PCR product. The tube was put in the magnetic tube rack, and the alkaline supernatant, containing the eluted single strand, was re- METHODS moved and transferred to a new tube and neutralized with 4 ~10.2M HC1 and 1 pl 1 M Tris/HCl buffer (pH 7.4). The Sample preparation. Strain designations, including indicated beads were washed first with 50 plO.1 M NaOH, then with type strains, of the mycoplasmas examined in the study are 40 pl B/W buffer and finally with 50 p1 TE buffer [lo mM given in Table 1 or in previously published reports (6,7). The Tris/HCl buffer (pH 7.5), 1 mM EDTA]. The washed beads two strains of M. yeatsii were grown in M medium, and all were diluted in 13 pl distilled water (1 1, 12). The sequences the other strains were grown in HA medium (2). One were determined by the dideoxynucleotide chain-termin- millilitre of the culture suspension was centrifuged for 15 min ation method with T7 DNA polymerase (Pharmacia Bio- at lOOOOg, washed in 1 ml PBS [0.14 M NaCl, 8.1 mM tech) and fluorescently labelled primers (20-22). The samples sodium phosphate buffer (pH 7.4)], centrifuged for another were then loaded onto a sequencing gel of the ALFexpress 15 min, suspended in 1 ml distilled water and heated in a automated laser fluorescent DNA sequencer (Amersham boiling water bath for 10 min. The suspensions were rapidly Pharmacia Biotech) followed by electrophoretic separation, chilled on ice and stored at -20 "C until used. on-line detection, and computerized sequence evaluation (20). In vitro amplification of the 16s rRNA genes. The 16s rRNA Phylogenetic analysis. Three different alignments, including genes were amplified by semi-nested PCR with four primers the 16s rRNA sequences from the four type strains of the complementary to the universal regions U1, U2, U5 and US, goat mycoplasmas determined in this work, were performed. as defined by Gray et al. (10). Primers complementary to the First, to determine which phylogenetic group they belong to, universal regions U1 and U8 (21, 22) were first used for the all four type strain sequences were aligned with a selection of amplification of the 16s rRNA genes of the four species. The 16s rRNA sequences from Acholeplasma, Anaeroplasma, PCR products were then diluted and amplified with one Asteroleplasma, Mycoplasma, Spiroplasma and Ureaplasma primer pair complementary to regions U1 and U5, and species retrieved from the database of the Ribosomal another primer pair complementary to regions U2 and US Database Project (1 5). Then, in two separate alignments, the (2 1,22). These reactions generated two fragments of 900 and sequences were compared with the respective members of the ~ ~___~ Table 1, Mycoplasma strains from which the 165 rRNA gene sequences were determined in this work 1 Species Strain Position of polymorphic sites* GenBank no.? 1 M. adleri G145T 120,/T, 420C/T,819.4/C U67943 M. auris UIAT Not found U67944 M. cottewii VIST Not found U67945 M. cottewii 950 13-218CP Not found Mycoplasma sp. Nepal 1 125C,T, l2l8G/T, 1255A/G Mycoplasma sp. Nepal 2 125,/,, 1218G/T9 1255A/(3 M. yeatsii GIHT 218G/T U67946 M. yeatsii 950 13- 106CG 808C,T * According to the numbering of the sequences in GenBank. Only the sequences of the type strains have been deposited in GenBank. The sequences of the other strains can be deduced from the information in this table. 264 International Journal of Systematic Bacteriology 48 16s rRNA from four goat mycoplasmas groups in which they were comprised. One of these align- Phylogenetic analysis of the type strains , ments was composed of representatives from the hominis 1 group and the other consisted ofmembers of the spiroplasma The first alignment, including the sequences of the four group. Gaps and ambiguities were removed from the final type strains and representatives from all five major data sets. The two latter data sets were corrected for multiple groups of the mycoplasma phylogenetic tree (29), base changes at single locations by the method of Jukes & resulted in a tree where M.
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