Origins of the mycoplasmas: sterol-nonrequiring mycoplasmas evolved from streptococci

A Phylogenetic Analysis of Lactobacilli, Pediococcus pentosaceus and Leuconostoc mesenteroides

Lactobacillus acidophilus, L. helveticus, L. lactis, L. brevis, L. plantarum, L. ruminis, L. casei, L. bifermentans, L. viridescens, L. fermentum, Pediococcus pentosaceus and Leuconostoc mesenteroides have been characterized by oligonucleotide cataloguing of their 16 S ribosomal RNAs. All Lactobacillus species investigated together with P. pentosaceus and L. mesenteroides form a phylogenetically coherent and ancient group. L. acidophilus and L. helveticus is the only closely related pair of species; all other species are only remotely related among each other, indicating that they are well-defined species. Lactobacillus, together with Streptococcus and Bacillus, constitute a super-cluster within the 'clostridium' sub-branch of Gram-positive eubacteria showing a low guanine plus cytosine content of their deoxyribonucleic acid.

Isolation and Identification of Acholeplasma sp. from the Mud Crab, Scylla serrata

For the first time, a mollicute-like organism (MLO) was cultured from moribund mud crabs (Scylla serrata) during an outbreak of clearwater disease in Zhejiang Province, China. The MLO displayed a fried-egg colony morphology in culture, did not possess a cell wall, and was not retained by 0.45 μm and 0.2 μm filters. It was able to ferment glucose, sucrose, lactose, and maltose, but it did not utilize arginine and urea. The MLO grew in the absence of bovine serum and was not susceptible to digitonin. Sequence analysis of the 16S rRNA gene revealed that this MLO had 99% identity with Acholeplasma laidlawii PG-8A, which indicates that the organism isolated from mud crabs is a member of the genus Acholeplasma.

Genetic analysis of housekeeping genes of members of the genus Acholeplasma: Phylogeny and complementary molecular markers to the 16S rRNA gene

The partial nucleotide sequences of the rpoB and gyrB genes as well as the complete sequence of the 16S-23S rRNA intergenic transcribed spacer (ITS) were determined for all known Acholeplasma species. The same genes of Mesoplasma and Entomoplasma species were also sequenced and used to infer phylogenetic relationships among the species within the orders Entomoplasmatales and Acholeplasmatales. The comparison of the ITS, rpoB, and gyrB phylogenetic trees with the 16S rRNA phylogenetic tree revealed a similar branch topology suggesting that the ITS, rpoB, and gyrB could be useful complementary phylogenetic markers for investigation of evolutionary relationships among Acholeplasma species. Thus, the multilocus phylogenetic analysis of Acholeplasma multilocale sequence data (ATCC 49900 (T) = PN525 (NCTC 11723)) strongly indicated that this organism is most closely related to the genera Mesoplasma and Entomoplasma (family Entomoplasmataceae) and form the branch with Mesoplasma seiffertii, Mesoplasma syrphidae, and Mesoplasma photuris. The closest genetic relatedness of this species to the order Entomoplasmatales was additionally supported by the finding that A. multilocale uses UGA as the tryptophan codon in its gyrB and gyrA sequences. Use of the UGA codon for encoding tryptophan was previously reported as a unique genetic feature of Entomoplasmatales and Mycoplasmatales but not of Acholeplasmatales. These data, as well as previously published data on metabolic features of A. multilocale, leads to the proposal to reclassify A. multilocale as a member of the family Entomoplasmataceae.

Mycoplasma ovis comb. nov. (formerly Eperythrozoon ovis), an epierythrocytic agent of haemolytic anaemia in sheep and goats

Eperythrozoon ovis, an erythrocytic agent that causes haemolytic anaemia in sheep and goats, occurs worldwide and is currently thought to be a rickettsia. To determine the relationship between this agent and other haemotrophic bacterial parasites, the 16S rRNA gene of this organism was sequenced. Phylogenetic analysis revealed that this wall-less bacterium is not a rickettsia, but a mycoplasma. This mycoplasma is related closely to several other uncultivated, epierythrocytic mycoplasmas that comprise a recently identified group, the haemotrophic mycoplasmas (haemoplasmas). The haemoplasma group is composed of former Eperythrozoon and Haemobartonella species, as well as newly identified epierythrocytic mycoplasmas. Haemoplasmas parasitize the surface of erythrocytes of a wide variety of vertebrate animal hosts and are transmitted mainly by blood-feeding arthropod vectors. Recognition that E. ovis is a mycoplasma provides a new approach to dealing with this bacterium. It is proposed that E. ovis should be reclassified as Mycoplasma ovis comb. nov.

Characterization of Acholeplasma laidlawii ftsZ gene and its gene product

The ftsZ gene was found among representatives of all bacterial groups. FtsZ protein is an essential component of cell division ring. Contraction of this cytoskeleton-like ring is believed to be the universal way of bacterial division. Acholeplasma laidlawii possesses all features of the minimal mycoplasma cell and some traits of cell-wall bacteria and seems to be a promising object for study of basic principles of the bacterial division process. We cloned an A. laidlawii chromosomal fragment containing ftsZ gene and two flanking orf which also were identified. A. laidlawii FtsZ protein has been determined with polyclonal antibodies raised in rabbit. It was demonstrated that ftsZ gene of A. laidlawii could be expressed in E. coli cells. We also revealed that A. laidlawii FtsZ had a low similarity to proteins of Mycoplasma genitalium and M. pneumoniae. The comparison of FtsZ structures may be used for investigation of bacterial phylogenetic relations.

The comparative metabolism of the mollicutes (Mycoplasmas): the utility for taxonomic classification and the relationship of putative gene annotation and phylogeny to enzymatic function in the smallest free-living cells

Mollicutes or mycoplasmas are a class of wall-less bacteria descended from low G + C% Gram-positive bacteria. Some are exceedingly small, about 0.2 micron in diameter, and are examples of the smallest free-living cells known. Their genomes are equally small; the smallest in Mycoplasma genitalium is sequenced and is 0.58 mb with 475 ORFs, compared with 4.639 mb and 4288 ORFs for Escherichia coli. Because of their size and apparently limited metabolic potential, Mollicutes are models for describing the minimal metabolism necessary to sustain independent life. Mollicutes have no cytochromes or the TCA cycle except for malate dehydrogenase activity. Some uniquely require cholesterol for growth, some require urea and some are anaerobic. They fix CO2 in anaplerotic or replenishing reactions. Some require pyrophosphate not ATP as an energy source for reactions, including the rate-limiting step of glycolysis: 6-phosphofructokinase. They scavenge for nucleic acid precursors and apparently do not synthesize pyrimidines or purines de novo. Some genera uniquely lack dUTPase activity and some species also lack uracil-DNA glycosylase. The absence of the latter two reactions that limit the incorporation of uracil or remove it from DNA may be related to the marked mutability of the Mollicutes and their tachytelic or rapid evolution. Approximately 150 cytoplasmic activities have been identified in these organisms, 225 to 250 are presumed to be present. About 100 of the core reactions are graphically linked in a metabolic map, including glycolysis, pentose phosphate pathway, arginine dihydrolase pathway, transamination, and purine, pyrimidine, and lipid metabolism. Reaction sequences or loci of particular importance are also described: phosphofructokinases, NADH oxidase, thioredoxin complex, deoxyribose-5-phosphate aldolase, and lactate, malate, and glutamate dehydrogenases. Enzymatic activities of the Mollicutes are grouped according to metabolic similarities that are taxonomically discriminating. The arrangements attempt to follow phylogenetic relationships. The relationships of putative gene assignments and enzymatic function in My. genitalium, My. pneumoniae, and My. capricolum subsp. capricolum are specially analyzed. The data are arranged in four tables. One associates gene annotations with congruent reports of the enzymatic activity in these same Mollicutes, and hence confirms the annotations. Another associates putative annotations with reports of the enzyme activity but from different Mollicutes. A third identifies the discrepancies represented by those enzymatic activities found in Mollicutes with sequenced genomes but without any similarly annotated ORF. This suggests that the gene sequence is significantly different from those already deposited in the databanks and putatively annotated with the same function. Another comparison lists those enzymatic activities that are both undetected in Mollicutes and not associated with any ORF. Evidence is presented supporting the theory that there are relatively small gene sequences that code for functional centers of multiple enzymatic activity. This property is seemingly advantageous for an organism with a small genome and perhaps under some coding restraint. The data suggest that a concept of "remnant" or "useless genes" or "useless enzymes" should be considered when examining the relationship of gene annotation and enzymatic function. It also suggests that genes in addition to representing what cells are doing or what they may do, may also identify what they once might have done and may never do again.

Bacterial persistence and expression of disease

A considerable body of experimental and clinical evidence supports the concept that difficult-to-culture and dormant bacteria are involved in latency of infection and that these persistent bacteria may be pathogenic. This review includes details on the diverse forms and functions of individual bacteria and attempts to make this information relevant to the care of patients. A series of experimental studies involving host-bacterium interactions illustrates the probability that most bacteria exposed to a deleterious host environment can assume a form quite different from that of a free-living bacterium. A hypothesis is offered for a kind of reproductive cycle of morphologically aberrant bacteria as a means to relate their diverse tissue forms to each other. Data on the basic biology of persistent bacteria are correlated with expression of disease and particularly the mechanisms of both latency and chronicity that typify certain infections. For example, in certain streptococcal and nocardial infections, it has been clearly established that wall-defective forms can be induced in a suitable host. These organisms can survive and persist in a latent state within the host, and they can cause pathologic responses compatible with disease. A series of cases illustrating idiopathic conditions in which cryptic bacteria have been implicated in the expression of disease is presented. These conditions include nephritis, rheumatic fever, aphthous stomatitis, idiopathic hematuria, Crohn's disease, and mycobacterial infections. By utilizing PCR, previously nonculturable bacilli have been identified in patients with Whipple's disease and bacillary angiomatosis. Koch's postulates may have to be redefined in terms of molecular data when dormant and nonculturable bacteria are implicated as causative agents of mysterious diseases.

Nucleotide sequence of the Streptococcus gordonii PK488 coaggregation adhesin gene, scaA, and ATP-binding cassette

Human oral viridans group streptococci that coaggregate with Actinomyces naeslundii PK606 express surface proteins related to ScaA, the coaggregation-mediating adhesin of Streptococcus gordonii PK488 (R. N. Andersen, N. Ganeshkumar, and P. E. Kolenbrander, Infect. Immun. 61:981-987, 1993). The nucleotide sequence of the 6,125-bp EcoRI insert of pRA1, containing scaA, the gene encoding ScaA, was determined. Six open reading frames (ORFs) were identified. The orientation of four ORFs, two upstream (ORF 1 and ORF 2) and one downstream (ORF 4) of scaA (ORF 3), indicated transcription in one direction, whereas ORF 5 and ORF 6 were transcribed divergently. Computer analysis of the deduced amino acid sequences identified a consensus binding site for ATP (GxxGxGKS) in the putative 28,054-Da protein encoded by ORF 1. ORF 2 potentially encoded a hydrophobic protein of 29,705 Da with six potential membrane-spanning regions. ScaA was 310 amino acids, 34,787 Da, and contained the lipoprotein consensus sequence LxxC, also reported for the ScaA-related proteins SsaB, FimA, and PsaA from Streptococcus sanguis 12, Streptococcus parasanguis FW213, and Streptococcus pneumoniae R36A, respectively. ORF 4 potentially encoded a 163-amino-acid protein of 17,912 Da, which was nearly identical to the downstream adjacent gene products of ssaB, fimA, and psaA. No significant homology with other proteins was found with the putative ORF 5 gene product, a 229-amino-acid protein of 25,107 Da. ORF 6 was incomplete and encoded a protein larger than 564 amino acids. This putative protein had a consensus Zn2+ binding motif, HExxH, found among bacterial thermolysins and mammalian neutral endopeptidases and was 40% identical to a homologous 210-amino-acid region of human enkephalinase. The genetic organization of ORFs 1, 2, and 3 was similar to those of the bacterial periplasmic-binding protein-dependent transport systems of gram-negative bacteria and binding-lipoprotein-dependent transport systems of gram-positive bacteria, and these genes appeared to encode ABC (ATP-binding cassette) proteins. This report describes a cell-to-cell adherence function associated with an ATP-binding cassette.

Isolation and characterization of full-length chromosomes from non-culturable plant-pathogenic Mycoplasma-like organisms

We describe the isolation and characterization of full-length chromosomes from non-culturable plant-pathogenic, mycoplasma-like organisms (MLOs). MLO chromosomes are circular and their sizes (640 to 1185 kbp) are heterogeneous. Divergence in the range of chromosome sizes is apparent between MLOs in the two major MLO disease groups, and chromosome size polymorphism occurs among some related agents. MLO chromosome sizes overlap those of culturable mycoplasmas; consequently, small genome size alone cannot explain MLO non-culturability. Hybridization with cloned MLO-specific chromosomal and 16S rRNA probes detected two separate chromosomes in some MLO 'type' strains. Large DNA molecules that appear to be MLO megaplasmids were also demonstrated. The ability to characterize full-length chromosomes from virtually any non-culturable prokaryote should greatly facilitate the molecular and genetic analysis of these difficult bacteria.

Pulse-field electrophoresis indicates full-length Mycoplasma chromosomes range widely in size

Full-size linear chromosomes were prepared from mycoplasmas by using gamma-irradiation to introduce one (on average) double-strand break in their circular chromosomes. Chromosome sizes were estimated by pulsed-field gel electrophoresis (PFGE) from the mobilities of these full-length molecules relative to DNA size references. Sizes estimated for Ureaplasma urealyticum T960 and 16 Mycoplasma species ranged from 684 kbp (M. hominis) to 1315 kbp (M. iowae). Using this sample, we found no correlation between the mobility of the full-size linear chromosomes and their G + C content. Sizes for A. laidlawii and A. hippikon were within the range expected from renaturation kinetics. PFGE size estimates are in good agreement with sizes determined by other methods, including electron microscopy, an ordered clone library, and summation of restriction fragments. Our estimates also agree with those from renaturation kinetics for both the largest and some of the smallest chromosomes, but in the intermediate size range, renaturation kinetics consistently provides lower values than PFGE or electron microscopy. Our PFGE estimates show that mycoplasma chromosomes span a continual range of sizes, with several intermediate values falling between the previously recognized large and small chromosome size clusters.

A phylogenetic analysis of the mycoplasmas: basis for their classification

Small-subunit rRNA sequences were determined for almost 50 species of mycoplasmas and their walled relatives, providing the basis for a phylogenetic systematic analysis of these organisms. Five groups of mycoplasmas per se were recognized (provisional names are given): the hominis group (which included species such as Mycoplasma hominis, Mycoplasma lipophilum, Mycoplasma pulmonis, and Mycoplasma neurolyticum), the pneumoniae group (which included species such as Mycoplasma pneumoniae and Mycoplasma muris), the spiroplasma group (which included species such as Mycoplasma mycoides, Spiroplasma citri, and Spiroplasma apis), the anaeroplasma group (which encompassed the anaeroplasmas and acholeplasmas), and a group known to contain only the isolated species Asteroleplasma anaerobium. In addition to these five mycoplasma groups, a sixth group of variously named gram-positive, walled organisms (which included lactobacilli, clostridia, and other organisms) was also included in the overall phylogenetic unit. In each of these six primary groups, subgroups were readily recognized and defined. Although the phylogenetic units identified by rRNA comparisons are difficult to recognize on the basis of mutually exclusive phenotypic characters alone, phenotypic justification can be given a posteriori for a number of them.

A hypothesis for the mechanism of mycoplasma evolution

Mycoplasmas are wall-less prokaryotes which have small genomes and are known to have evolved from ancestors of Gram-positive bacteria. A model is proposed to explain how mycoplasmas may have evolved from these ancestors which had cell walls and large genomes. It is proposed that the initial step in this process was loss of the cell wall and conversion of the ancestral bacterium to an L-form. Fusion of L-forms would have resulted in a single cell that contained two or more complete genomes. It is thought that this bringing together of multiple genomes by cell fusion resulted in genetic recombination between genomes and loss of DNA segments from the cell. Data from bacterial systems are cited in support of this model.

Molecular biology and genetics of mycoplasmas (Mollicutes)

Images

Purification and properties of an FAD-containing NADH oxidase from Mycoplasma capricolum

From the prokaryotic microorganism Mycoplasma capricolum an FAD-containing NADH oxidase has been purified by preparative FPLC to homogeneity, as judged by polyacrylamide gel electrophoresis. The apparent molecular mass of the enzyme was found to be 72.5 kDa, with an isoelectric point of 5.2, and no detectable subunits. No iron, copper, manganese or molybdenium could be detected. On the basis of a minimum molecular mass of 72.5 kDa a ratio of FAD/protein of 1:1 could be derived. Its amino-acid composition, the light absorption and the fluorescence spectra are presented.

Antigenic mimicry of mammalian intermediate filaments by mycoplasmas

A murine monoclonal antibody raised against Mycoplasma hyorhinis specifically reacted by indirect immunofluorescence with mammalian intermediate filaments. The antibody recognized a related epitope on a 74,000-molecular-weight protein of M. hyorhinis and on components of similar size from other pathogenic mycoplasmas. This defines a shared antigenic structure of interest in autoantibody development during mycoplasmal diseases.

Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data

The 5S rRNA sequences of eubacteria and mycoplasmas have been analyzed and a phylogenetic tree constructed. We determined the sequences of 5S rRNA from Clostridium innocuum, Acholeplasma laidlawii, Acholeplasma modicum, Anaeroplasma bactoclasticum, Anaeroplasma abactoclasticum, Ureaplasma urealyticum, Mycoplasma mycoides mycoides, Mycoplasma pneumoniae, and Mycoplasma gallisepticum. Analysis of these and published sequences shows that mycoplasmas form a coherent phylogenetic group that, with C. innocuum, arose as a branch of the low G+C Gram-positive tree, near the lactobacilli and streptococci. The initial event in mycoplasma phylogeny was formation of the Acholeplasma branch; hence, loss of cell wall probably occurred at the time of genome reduction to approximately to 1000 MDa. A subsequent branch produced the Spiroplasma. This branch appears to have been the origin of sterol-requiring mycoplasmas. During development of the Spiroplasma branch there were several independent genome reductions, each to approximately 500 MDa, resulting in Mycoplasma and Ureaplasma species. Mycoplasmas, particularly species with the smallest genomes, have high mutation rates, suggesting that they are in a state of rapid evolution.

Molecular and biological features of mollicutes (mycoplasmas)

The small size of the mollicute genome considerably restricts the amount of genetic information available to the organisms. This is reflected in the relatively small number of cell proteins synthesized, the lack of many biosynthetic pathways and the marked dependence on exogenous nutrients for growth. The protein synthesizing machinery of mollicutes resembles that of eubacteria and is sensitive to the same antibiotics, except for rifampicin, to which RNA polymerases of mollicutes appear resistant. The mollicute ribosomes are built of 50 S and 30 S subunits and contain about 50 different proteins and 5 S, 16 S and 23 S rRNA, as in eubacteria. However, the 5 S rRNA in mollicutes appears shorter (107-112 nucleotides) than in eubacteria (116-120 nucleotides). We hybridized restriction endonuclease-digested DNA from a variety of Mycoplasma, Ureaplasma, Acholeplasma and Spiroplasma species with nick-translated probes consisting of defined portions of the rrnB rRNA operon of Escherichia coli and the rRNA operon of M. capricolum. The results suggest the presence of only one or two sets (operons) of rRNA genes in the genome of Mollicutes, a number falling considerably below that of the eubacteria examined so far but resembling that found in archaebacteria. Our data also indicate a marked nucleotide sequence homology along the rrnB rRNA operon of E. coli and the rRNA operons of the various mollicutes, indicating that the rRNA genes in mollicutes are linked in the classical prokaryotic fashion 16 S-23 S-5 S. Each mollicute appeared to possess, on its genome, different flanking sequences adjacent to the rRNA operon(s), resulting in species-specific hybridization patterns.(ABSTRACT TRUNCATED AT 250 WORDS)

Unusual structural features of the 5S ribosomal RNA from Streptococcus cremoris

The nucleotide sequence of the 5S ribosomal RNA of Streptococcus cremoris has been determined. The sequence is 5' (sequence in text) 3'. Comparison of the S. cremoris 5S RNA sequence to an updated prokaryotic generalized 5S RNA structural model shows that this 5S RNA contains some unusual structural features. These features result largely from uncommon base substitutions in helices I, II and IV. Some of these unusual structural features are shared by several of the known 5S RNA sequences from mycoplasmas. However, the characteristic bloc of deletions found in helix V of these mycoplasma 5S RNAs is not present in the 5S RNA of S. cremoris.

Cloned genomic DNA sequences from Mycoplasma hyorhinis encoding antigens expressed in Escherichia coli

A library of cloned Mycoplasma hyorhinis genomic sequences was constructed by incorporation of EcoRI digestion fragments of mycoplasma DNA into the lambda Charon 4A bacteriophage vector. Immunological screening of recombinant phage plaques identified clones containing genes encoding mycoplasma antigenic structures expressed in an Escherichia coli host. Two such recombinant phage isolates, lambda Ch4A-MhrG1 and lambda Ch4A-MhrG28, were defined and found to contain distinct genomic sequences by analysis of restriction endonuclease fragments. Inoculation of mice with recombinant gene products from lambda Ch4A-MhrG1 yielded antiserum selectively recognizing a Mr 29,500 trypsin-sensitive mycoplasma constituent. This established a means for producing selected immunogenic mycoplasma component in a bacterial host. The cloned genomic sequences of M. hyorhinis encoding expressed mycoplasma antigens represent molecular probes that can be characterized both by specific DNA sequences and by the antigenic structure of corresponding gene products. These genomic fragments define initial physical markers of the M. hyorhinis genome and may be useful in assessing antigenic and molecular genetic relationships within the genus Mycoplasma and among other members of the class Mollicutes.

Evolution of mycoplasmas and genome losses

Streptococci and acholeplasmas have a close evolutionary relationship. We examined their genomes to determine what chromosomal losses occurred to produce the smaller acholeplasma genomes and found by RNA-DNA hybridization that Streptococcus cremoris and S. lactis possess at least five or at least six ribosomal RNA gene sets, respectively, while acholeplasmas have only two rRNA gene sets. Other important deficiencies identified in mycoplasmas are associated with envelope or RNA genes, and analysis of these chromosomal deletions may lead to an understanding of how mycoplasmas evolved from walled bacteria.