DNA rearrangements and phenotypic switching in prokaryotes

Molecular basis of size and antigenic variation of a Mycoplasma hominis adhesin encoded by divergent vaa genes

The molecular basis for the size and antigenic diversity of the variable adherence-associated (Vaa) antigen, a major surface protein and a putative adhesin (of Mycoplasma hominis, is described. Size-variant alleles of the single-copy vaa gene encode abundant surface lipoproteins containing one to four nearly identical, tandem repetitive units of 121 amino acids in the central region of the mature Vaa product. Gain or loss of central repeats in vaa genes gives rise to distinct size-variant Vaa antigens in clonal populations of this organism. The N-terminal and repeat regions of Vaa contain highly conserved sequences, while the C-terminal region, implicated as the adherence-mediating module, is highly variable and divergent among different strains of this pathogen. Sequence variation in this region may underlie the strain-dependent binding of some monoclonal antibodies to Vaa products. The Vaa antigen is expressed in vivo during chronic, active arthritis associated with M. hominis infection and is highly immunogenic in the human host. Size variation and C-terminal antigenic divergence of Vaa could affect the adherence of M. hominis and evasion of antibody-mediated immunity, thereby contributing to the organism's adaptive capability in the human host. Variation in vaa genes reveals a distinct pattern of mutations generating mycoplasma surface variation.

Biofunctional domains of the Mycoplasma pneumoniae P30 adhesin

The P30 adhesin genes of spontaneous, hemadsorption-negative (HA-) class II Mycoplasma pneumoniae mutants that displayed P30 adhesin-deficient protein profiles were analyzed. One subclass of P30-deficient mutants possessed the entire p3O structural gene without alterations (825 nucleotides, encoding 275 amino acids with a predicted molecular mass of 29,743 Da [S. F. Dallo, A. Chavoya, and J. B. Baseman, Infect. Immun. 58:4163-4165, 1990]). However, the second mutant subclass contained a deletion in p3O resulting in the expression of a 25-kDa peptide (681 nucleotides, encoding 227 amino acids with a calculated molecular mass of 24,823 Da). This P25-truncated peptide lacked 8 of the 13 proline-rich amino acid repeat sequences at the carboxy terminus. Whole-cell radioimmunoprecipitation of M. pneumoniae with antibodies directed against the proline-rich repeat sequences located in the carboxy terminus demonstrated their surface accessibility. In contrast, antibodies generated against N-terminal amino acid sequences upstream of the repeats did not bind to intact mycoplasmas. The amino acid sequence homologies exhibited by the P30 adhesin and eucaryotic structural proteins were corroborated by cross-reactive epitopes shared between the P30 adhesin and fibrinogen, keratin, and myosin. These data reinforce the importance of the P30 protein in cytadherence and virulence and provide a molecular basis for postinfectious autoimmunity associated with M. pneumoniae-mediated pathologies.

Antigenic topology of the P29 surface lipoprotein of Mycoplasma fermentans: differential display of epitopes results in high-frequency phase variation

Antibodies to P29, a major lipid-modified surface protein of Mycoplasma fermentans, reveal phase variation of surface epitopes occurring with high frequency in clonal lineages of the organism. This occurs despite continuous expression of the entire epitope-bearing P29 product (detected by Western immunoblotting) and contrasts with phase variation of other surface antigens mediated by differential expression of proteins. To understand the structure and antigenic topology of P29, the single-copy p29 gene from strain PG18 was cloned and sequenced. The gene encodes a prolipoprotein containing a signal sequence predicted to be modified with lipid and cleaved at the N-terminal Cys-1 residue of the mature P29 lipoprotein. The remaining 218-residue hydrophilic sequence of P29 is predicted to be located external to the single plasma membrane. Additional Cys residues at positions 91 and 128 in the mature protein were shown to form a 36-residue disulfide loop by selectively labeling sulfhydryl groups that were liberated only after chemical reduction of monomeric P29. Two nearly identical charged amino acid sequences occurred in P29, within the disulfide loop and upstream of this structure. Two distinct epitopes binding different monoclonal antibodies were associated with opposite ends of the P29 protein, by mapping products expressed in Escherichia coli from PCR-generated 3' deletion mutations of the p29 gene. Each monoclonal antibody detected high-frequency and noncoordinate changes in accessibility of the corresponding epitopes in colony immunoblots of clonal variants, yet sequencing of the p29 gene from these variants and analysis of disulfide bonds revealed no associated changes in the primary sequence or disulfide loop structure of P29. These results suggest that P29 surface epitope variation may involve masking of selected regions of P29, possibly by other surface components undergoing phase variation by differential expression. Differential masking may be an important mechanism for altering the antigenic or functional surface topology of this mycoplasma and other wall-less mycoplasmas.

Generation of Campylobacter fetus S-layer protein diversity utilizes a single promoter on an invertible DNA segment

Wild-type strains of Campylobacter fetus contain a monomolecular array of surface layer proteins (SLPs) and vary the antigenicity of the predominant SLP expressed. Reciprocal recombination events among the eight genomic SLP gene cassettes, which encode 97- to 149 kDa SLPs, permit this variation. To explore whether SLP expression utilizes a single promoter, we created mutant bacterial strains using insertional mutagenesis by rescue of a marker from plasmids. Experimental analysis of the mutants created clearly indicates that SLP expression solely utilizes the single sapA promoter, and that for variation C. fetus uses a mechanism of DNA rearrangement involving inversion of a 6.2 kb segment of DNA containing this promoter. This DNA inversion positions the sapA promoter immediately upstream of one of two oppositely oriented SLP gene cassettes, leading to its expression. Additionally, a second mechanism of DNA rearrangement occurs to replace at least one of the two SLP gene cassettes bracketing the invertible element. As previously reported promoter inversions in prokaryotes, yeasts and viruses involve alternate expression of at most two structural genes, the ability of C. fetus to use this phenomenon to express one of multiple cassettes is novel.

Sequence analysis of the chromosomal region around and within the V-1-encoding gene of Mycoplasma pulmonis: evidence for DNA inversion as a mechanism for V-1 variation

Although the variation of V-1 antigens of Mycoplasma pulmonis has been correlated with variable expression of the cytadherence properties of this organism and has been implicated as a virulence determining factor in M. pulmonis-induced murine respiratory disease, the precise function of these antigens remains unknown. We have cloned and characterized genes encoding V-1 from two M. pulmonis UAB CT V-1 variants that differ in hemadsorption properties. A comparison of the nucleotide sequences revealed that these two variant genes were identical in the 5'-most 724 nucleotides. Regions of extensive divergence that contained repeated sequences were found 3' to this conserved region. On the basis of their deduced amino acid sequences, one variant expressed a V-1 protein of 94.2 kDa presumptively containing 40 repeats of 17 amino acids and the other expressed a protein of 27.4 kDa consisting 2 direct, noncontiguous 9-amino-acid repeats. These general properties, as well as the presence of a prokaryotic lipoprotein acylation sequence (L-X-Y-C), indicated that the genes encoding V-1 were similar in structure to genes encoding other mycoplasma surface lipoproteins. Further analysis of sequences flanking these genes revealed that these variants arose via an inversion event which provided an interchange of the two variable regions as well as for the conserved region of these genes and immunoblot analyses using rabbit polyclonal antibodies specific for synthetic peptides derived from the sequences of the different variable regions indicated that DNA inversion acted as a switch which allowed only one of the two different genes to be expressed at any given time. This inversion model clearly provides a mechanism by which M. pulmonis can alter its surface architecture and also strongly suggests that the as-yet-undefined function of V-1 residues in the variable carboxy region of these proteins.

Conservation and variability in Archaea: protein antigens with tandem repeats encoded by a cluster of genes with common motifs in Methanosarcina mazei S-6

Three open reading frames, orf492, orf375 and orf783, were identified in a 5.9-kb DNA fragment from the genome of Methanosarcina mazei S-6 that code for proteins recognized by antibodies against cell-surface antigens. The deduced amino-acid (aa) sequences of orfs492 and 375, i.e., ORF492 and ORF375, contain seven and four copies of an approx. 42-aa repeat, respectively. The aa sequence of ORF783 contains nine copies of an approx. 85-aa repeat, one of which is also present once in each of the first two ORFs. The organization of the repeats is similar to that of some Gram+ cell-wall-associated proteins. Comparative analyses of aa sequences, compositions and hydropathy profiles of the archaeal ORFs showed similarity with surface (S-) layer and outer-membrane proteins of Bacteria and Archaea.

Molecular cloning and characterization of an adherence-related operon of Mycoplasma genitalium

Adhesins and adhesin-related accessory proteins of pathogenic mycoplasmas are required for cytadherence and the subsequent development of disease pathology. The classic example has been Mycoplasma pneumoniae, which causes primary atypical pneumonia in humans. Mutants of M. pneumoniae defective in adhesins (P1 and P30) or in adherence-accessory proteins (HMW1 through HMW4) are unable to colonize host tissues and are avirulent. Mycoplasma genitalium, implicated in nongonococcal, nonchlamydial urethritis, pneumonia, arthritis, and AIDS progression, was found to encode a 140-kDa adhesin that shared both DNA and protein sequence similarities with P1, a major adhesin of M. pneumoniae. In this report, we show that M. genitalium possesses additional homolog sequences to well-characterized adherence-related genes and proteins of M. pneumoniae. The M. genitalium homologs are designated P32 and P69 and correspond to P30 and HMW3 of M. pneumoniae, respectively (J. B. Baseman, p. 243-259, in S. Rottem and I. Kahane, ed., Subcellular biochemistry, vol. 20. Mycoplasma cell membranes, 1993, and D. C. Krause, D. K. Leith, R. M. Wilson, and J. B. Baseman, Infect. Immun. 35:809-817, 1982). Interestingly, the operon-like organizations of P32 and P69 in the M. genitalium genome are similar to the organizations of P30 and HMW3 genes of M. pneumoniae, suggesting that the conservation of these adherence-related genes and proteins might have occurred through horizontal gene transfer events originating from an ancestral gene family.

Increased structural and combinatorial diversity in an extended family of genes encoding Vlp surface proteins of Mycoplasma hyorhinis

Variable lipoproteins (Vlp) constitute the major coat protein of Mycoplasma hyorhinis. They are products of multiple, divergent, single-copy genes organized in a chromosomal cluster. Three genes, vlpA, vlpB, and vlpC, have been previously identified in clonal isolates of M. hyorhinis SK76. Each is linked to a characteristic promoter region containing a homopolymeric tract of adenine residues [poly(A) tract], subject to hypermutation, that transcriptionally controls phase variation of vlp genes and leads to combinatorial surface mosaics of distinct Vlp products. The size of the natural vlp gene repertoire is unknown but may critically determine the degree of structural and combinatorial diversity available in this species. In this study, the vlp repertoire of M. hyorhinis GDL-1 was characterized and shown to contain three additional genes, vlpD, vlpE, and vlpF, clustered with other known vlp genes in the order 5'-vlpD-vlpE-vlpF-IS-vlpA-IS-vlpB-vlpC+ ++-3', where IS represents copies of the IS1221 element of M. hyorhinis. The 5' boundary of this expanded family was identical to that of the more limited family 5'-vlpA-IS-vlpB-vlpC-3' previously described in a clonal isolate of strain SK76. A recombinant construct containing vlpD, vlpE, and vlpF expressed antigenically distinguishable products corresponding to each gene. These genes encode characteristic C-terminal repetitive regions that are subject to size variation by insertion or deletion of intragenic repeats but maintain an extended, charged structure. Each vlp gene also contained characteristic alternative open reading frames, which provide a potential reservoir of coding sequence for Vlp diversity, possibly recruited through insertion and/or deletion mutations. These findings demonstrate a vastly expanded potential for structural diversity and combinatorial display of surface mosaics on this organism and suggest that modulation of the vlp repertoire, possibly in conjunction with mobile elements, may determine the capacity for surface variation in natural populations and laboratory strains of this mycoplasma species.

Two genes involved in the phase-variable phi C31 resistance mechanism of Streptomyces coelicolor A3(2)

The phage growth limitation (Pgl) system of Streptomyces coelicolor confers resistance to phi C31 and its homoimmune phages. The positions of the pgl genes within a 16-kb clone of S. coelicolor DNA were defined by subcloning, insertional inactivation, and deletion mapping. Nucleotide sequencing and functional analysis identified two genes, pglY and pglZ, required for the Pgl+ (phage-resistant) phenotype. pglY and pglZ, which may be translationally coupled, are predicted to encode proteins with M(r)S of 141,000 and 104,000, respectively. Neither protein shows significant similarity to other known proteins, but PglY has a putative ATP/GTP binding motif. The pglY and pglZ genes are cotranscribed from a single promoter which appears to be constitutive and is not induced by phage infection.

Characterization of a major Mycoplasma penetrans lipoprotein and of its gene

A novel mycoplasmal species designated as Mycoplasma penetrans has been isolated recently from patients infected with human immunodeficiency virus. p35, a major antigen extracted from the membrane of this mycoplasma using Triton X-114 has been found to be a lipoprotein. After proteolytic treatment of p35, the sequence of one of the resulting peptides was determined and a corresponding oligonucleotide was deduced. Using this oligonucleotide as a probe the p35 gene was cloned and sequenced. Sequence analysis revealed an amino-terminal signal peptide with a potential acylation site which would result in a 35.3 kDa mature product. In addition, the p35 gene was followed by an open reading frame with a corresponding polypeptide partially homologous to p35, in particular to the N-terminus region.

Interspecies recombination in nature: a meningococcus that has acquired a gonococcal PIB porin

A vaginal isolate of Neisseria has been reported to resemble Neisseria meningitidis in biochemical characteristics but to react with serological reagents that are specific to the PI porin from Neisseria gonorrhoeae. We have confirmed that this isolate has the biochemical attributes of a meningococcus and have shown that it clusters among meningococcal isolates on a dendrogram based on isoenzyme variation within housekeeping enzymes from populations of N. meningitidis and N. gonorrhoeae. Furthermore, the sequences of the fbp and adk genes were typical of those of N. meningitidis and were distinct from those of N. gonorrhoeae. However, the porB gene was very similar to the por genes of N. gonorrhoeae isolates that express the PIB class of outer-membrane porin (differing from one gonococcal por allele at only a single nucleotide site), and was clearly distinct from the porB genes of N. meningitidis. The isolate therefore appears to be a typical meningococcus, except that its porB gene has been replaced with the por gene from a gonococcus.

An archaeal S-layer gene homolog with repetitive subunits

An S-layer protein gene homolog of the slgA gene of two Methanothermus species was found in the genome of another methanogenic archaeon of a different family, Methanosarcina mazei S-6. The new gene (slgB) encodes a molecule (SlpB) with the characteristics of S-layer proteins. The N-terminal half of SlpB is 44% identical to that encoded by SlgA, but the other half shows distinctive features: four 56 amino acid long tandem repeats, and Trp-Xaa-Trp clusters located six amino acids from the N-terminus of each repeat.

High-frequency S-layer protein variation in Campylobacter fetus revealed by sapA mutagenesis

Campylobacter fetus utilizes paracrystalline surface (S-) layer proteins that confer complement resistance and that undergo antigenic variation to facilitate persistent mucosal colonization in ungulates. C. fetus possesses multiple homologues of sapA, each of which encode full-length S-layer proteins. Disruption of sapA by a gene targeting method (insertion of kanamycin (km) resistance) caused the loss of C. fetus cells bearing full-length S-layer proteins and their replacement by cells bearing a 50 kDa truncated protein that was not exported to the cell surface. After incubation of the mutants with serum, the survival rate was approximately 2 x 10(-2). Immunoblots of survivors showed that phenotypic reversion involving high-level production of full-length (98, 127 or 149 kDa) S-layer proteins had occurred. Revertants were serum resistant but caused approximately 10-fold less bacteraemia in orally challenged mice than did the wild-type strain. Southern hybridizations of the revertants showed rearrangement of sapA homologues and retention of the km marker. These results indicate that there exists high-frequency generation of C. fetus sapA antigenic variants, and that intracellular mechanisms acting at the level of DNA reciprocal recombination play key roles in this phenomenon.

Regulation of a restriction and modification system via DNA inversion in Mycoplasma pulmonis

An invertible DNA element of 6.8 kb, designated the hsd1 locus, was identified in the chromosome of Mycoplasma pulmonis. Infection of host cells with mycoplasma virus P1 revealed that the organism's restriction and modification (R-M) properties are controlled by inversion of hsd1. The nucleotide sequence of hsd1 revealed several genes, the predicted amino acids of which bear striking similarity to the subunits of the type I R-M enzymes previously found only in enteric bacteria.