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PubMed1998

The control of protein release from poly(DL-lactide co-glycolide) microparticles by variation of the external aqueous phase surfactant in the water-in oil-in water method.

Poly(DL-lactide co-glycolide) microparticles below 5 microm in size and containing ovalbumin (OVA), were prepared using the water-in oil-in water (w/o/w) technique with either polyvinyl alcohol (PVA) or polyvinylpyrrolidone (PVP) as stabilisers in the external aqueous phase. PVP-stabilised microparticles exhibited higher protein loading (8.2%, w/w relative to 4.0% for PVA stabilised microparticles) and increased core loading (encapsulation) of protein (70% vs. 30% for the PVA system). The use of PVP instead of PVA to prepare microparticles also resulted in reduction in the initial burst release of OVA, together with sustained protein release over 28 days and an increase in the protein delivery capacity from 35 to 45 microg/mg particles. The changes in protein loading and delivery characteristics are considered to arise in part from an increase in the viscosity of the droplets of polymer solution, constituting the primary water-in oil emulsion, by diffusion of PVP from the external aqueous phase. Variation of the external aqueous phase surfactant provides a promising approach for improving the loading of therapeutic proteins and vaccine antigens within biodegradable microparticles and for modulating their release pattern.

Drug Carriers↗
PubMed1997

k-Space detection and correction of physiological artifacts in fMRI.

Signal phase variations caused by physiology are a major source of instability in fMRI images produced by multiple RF pulses. k-Space phase variation maps show cyclic phase variations at the frequency of respiration combined with a cardiac variation of lower amplitude. The amplitude of the variation increases with gradient echo time and proximity to the chest, suggesting that the dominant cause of the phase variation is a B0 shift (approximately 0.01 ppm) produced by movement of organs in the chest. A simple k-space phase correction method is proposed and demonstrated for FLASH fMRI. The retrospective method requires no pulse sequence modification, and is more effective than navigator echo correction. Physiological noise is dramatically reduced, especially at inferior slice locations.

Artifacts↗
PubMed2000

Molecular cloning and mutagenesis of a DNA locus involved in lipooligosaccharide biosynthesis in Haemophilus somnus.

Haemophilus somnus undergoes antigenic and structural phase variation in its lipooligosaccharide (LOS). A gene (lob-1) containing repetitive 5'-CAAT-3' sequences that may, in part, contribute to phase variation was cloned and sequenced (T. J. Inzana et al., Infect. Immun. 65:4675-4681, 1997). We have now identified another putative gene (lob-2A) immediately upstream from lob-1. Lob-2A contained homology to several LOS biosynthesis proteins of the family Pasteurellaceae and the LgtB and LgtE galactosyltransferases of Neisseria meningitidis and N. gonorrhoeae. Unlike lob-1, lob-2A contained 18 to 20 5'-GA-3' repeats 141 bp upstream of the termination codon as determined by PCR amplification of DNA from individual colonies. Twenty repeats were most common, but when 19 5'-GA-3' repeats were present a stop codon would occur 1 bp after the last 5'-GA-3' repeat. A 630-bp SalI-BsgI fragment within lob-2A was deleted, and a kanamycin resistance (Km(r)) gene was inserted into this site to create pCAATDeltalob2A. Following electroporation of pCAATDeltalob2A into H. somnus 738, several allelic exchange mutants were isolated. The LOS electrophoretic profile of one mutant, strain 738-lob2A1::Km, was altered, and the phase variation rate was reduced but phase variation was not eliminated. A variant with 19 5'-GA-3' repeats in lob-2A had an LOS profile similar to that of 738-lob2A1::Km, suggesting that lob-2A was turned off in this phase. Nanoelectrospray mass spectrometry (nES-MS) and nuclear magnetic resonance spectroscopy showed that 738-lob2A1::Km was deficient in the terminal betaGal(1-3)betaGlcNAc residue present in parent strain 738. Mutant 738-lob2A1::Km was significantly more sensitive to the bactericidal action of normal bovine serum and was less virulent in mice than was parent strain 738. When H. somnus 129Pt was electrotransformed with shuttle vector pLS88 containing lob-2A, its LOS electrophoretic profile was modified and additional N-acetylhexosamine residues were present, as determined by nES-MS analysis. These results indicated that lob-2A may be an N-acetylglucosamine transferase involved in LOS biosynthesis and phase variation and that LOS structure is important to H. somnus virulence.

Animals↗
PubMed2003

The precision of circadian clocks: assessment and analysis in Syrian hamsters.

Locomotor activity recordings of Syrian hamsters were systematically analyzed to estimate the precision of the overt circadian activity rhythm in constant darkness. Phase variation, i.e., the standard deviation of phase markers around the regression line, varied with the definition of phase. Smallest phase variation was found in the onset of wheel running activity defined by 1h running means of the raw data. Both lower and higher degrees of smoothing lead to decreased precision measured in the overt rhythm. With passive infrared recordings, the midpoint of activity defined by 3h running means was the least variable. This demonstrates that the choice of phase marker should vary between recording methods. Phase variation decreased with increasing activity and was larger in females than in males. By calculating the average cycle variation and serial covariance of consecutive cycles, we estimated the contribution of 'clock' and 'non-clock' related processes to the overt rhythm variability. Variance in precision between phase markers could be shown to be attributable mainly to nonclock processes. Variance in pacemaker cycle length appeared reduced in wheel running activity records compared with passive infrared sensing records, suggesting feedback from running activity onto pacemaker function.

Animals↗
PubMed2006

Automatic algorithm for correcting motion artifacts in time-resolved two-dimensional magnetic resonance angiography using convex projections.

Time-resolved contrast enhanced magnetic resonance angiography (MRA) may suffer from involuntary patient motion. It is noted that while MR signal change associated with motion is large in magnitude and has smooth phase variation in k-phase, signal change associated with vascular enhancement is small in magnitude and has rapid phase variation in k-space. Based upon this observation, a novel projection onto convex sets (POCS) algorithm is developed as an automatic iterative method to remove motion artifacts. The presented POCS algorithm consists of high-pass phase filtering and convex projections in both k-space and image space. Without input of detailed motion knowledge, motion effects are filtered out, while vasculature information is preserved. The proposed method can be effective for a large class of nonrigid motions, including through-plane motion. The algorithm is stable and converges quickly, usually within five iterations. A double-blind evaluation on a set of clinical MRA cases shows that a completely unsupervised version of the algorithm produces significantly better rank scores (P=0.038) when compared to angiograms produced manually by an experienced radiologist.

Algorithms↗
PubMed2001

Juxtaposition of an active promoter to vsp genes via site-specific DNA inversions generates antigenic variation in Mycoplasma bovis.

Mycoplasma bovis, the most important etiological agent of bovine mycoplasmosis, undergoes extensive antigenic variation of major and highly immunogenic surface lipoprotein antigens (Vsps). A family of 13 related but divergent vsp genes, which occur as single chromosomal copies, was recently found in the chromosome of M. bovis. In the present study, the molecular mechanism mediating the high-frequency phase variation of two Vsps (VspA and VspC) as representatives of the Vsp family was investigated. Analysis of clonal isolates exhibiting phase transitions of VspA or of VspC (i.e., ON-->OFF-->ON) has shown that DNA inversions occur during Vsp phase variation. The upstream region of each vsp gene contains two sequence cassettes. The first (cassette no. 1), a 71-bp region upstream of the ATG initiation codon, exhibits 98% homology among all vsp genes, while the second (cassette no. 2), upstream of cassette no. 1, ranges in size from 50 to 180 bp and is more divergent. Examination of the ends of the inverted fragments during VspA or VspC phase variation revealed that in both cases, a change in the organization of vsp upstream cassettes involving three vsp genes had occurred. Primer extension and Northern blot analysis have shown that a specific cassette no. 2, designated A(2), is an active promoter and that juxtaposition of this regulatory element to a silent vsp gene by DNA inversions allows transcription initiation of the recipient gene. Further genetic analysis revealed that phase variation of VspA or of VspC involves two site-specific DNA inversions occurring between inverted copies of a specific 35-bp sequence present within the conserved cassette no. 1. A model for the control of Vsp phase variation is proposed.

Antigenic Variation↗
PubMed2004

Modification of Helicobacter pylori outer membrane protein expression during experimental infection of rhesus macaques.

Clinical isolates of Helicobacter pylori show marked diversity, which may derive from genomic changes that occur during the often lifelong association of the bacterium with its human host. We used the rhesus macaque model, together with DNA microarrays, to examine genomic changes in H. pylori that occur early during experimental infection. Microarray analysis showed that H. pylori recovered from challenged macaques had deleted babA, a member of a large family of paralogous outer membrane proteins (OMPs) that mediates attachment of H. pylori to the Lewis B blood group antigen on gastric epithelium. In some cases the babA gene was replaced by babB, an uncharacterized OMP that is closely related to babA. In other cases the babA gene was present but was not expressed because of alteration in dinucleotide CT repeats in the 5' coding region. In either case, strains lacking babA did not adhere to Lewis B, which is expressed on macaque gastric epithelium. Absence of babA and duplication of babB was also seen in H. pylori isolates derived from human clinical samples, suggesting that this gene conversion event is not unique to experimentally infected rhesus monkeys. These results demonstrate in real time with a relevant animal model that H. pylori regulates OMP expression in vivo by using both antigenic variation and phase variation. We suggest that changes in babA and babB after experimental infection of macaques represent a dynamic response in the H. pylori outer membrane that facilitates adherence to the gastric epithelium and promotes chronic infection.

Adhesins, Bacterial↗
PubMed2005

Microsatellite instability regulates transcription factor binding and gene expression.

Microsatellites are tandemly repeated simple sequence DNA motifs widely prevalent in eukaryotic and prokaryotic genomes. In pathogenic bacteria, instability of these hypermutable loci through slipped-strand mispairing mediates the high-frequency reversible switching of phenotype expression, i.e., phase variation. Phase-variable expression of NadA, an outer membrane protein and adhesin of the pathogen Neisseria meningitidis, is mediated by changes in the number of TAAA repeats located upstream of the core promoter of nadA. Here we report that loss or gain of TAAA repeats affects the binding of the transcriptional regulatory protein IHF to the nadA promoter. Thus, phase-variable transcription of nadA potentially incorporates interplay between stochastic (mutational) and prescriptive (classical) mechanisms of gene regulation.

Amino Acid Sequence↗
PubMed2001

The regulation of pap and type 1 fimbriation in Escherichia coli.

The ability of bacterial pathogens to bind to the host mucosa is a critical step in the pathogenesis of many bacterial infections and, for Escherichia coli, a large number of different fimbrial adhesins have been implicated as virulence factors. In this chapter, our current understanding of the regulatory mechanisms that control the expression of two of the best characterized fimbrial adhesins, pyelonephritis-associated pilus (encoded by pap) and the type 1 fimbria (encoded by fim), will be described. The expression of both fimbrial adhesins is controlled by phase variation (the reversible and apparently random switching between expressing ('on') and non-expressing ('off') states), and is regulated in response to environmental conditions. The phase variation of pap (and of some other fimbriae in Escherichia coli) is determined by the formation of alternative nucleoprotein complexes that either activate (phase 'on') or suppress (phase 'off') transcription of the fimbria genes. Formation of each complex protects a single Dam methylation site (5' GATC) from modification (GATCdist in phase 'on' cells and GATCprox in phase 'off' cells). Furthermore, complex formation is inhibited by methylation of the two 5' GATC sites. Both the phase variation of pap and the transcription of the pap genes in phase 'on' cells, are regulated and expression is subject to both positive and negative feedback control. In contrast to pap, the phase variation of fim is determined by the site-specific inversion of a short element of DNA (the fim switch). In phase 'on' cells, a promoter within the invertible element directs the transcription of the fim structural genes, whereas in phase 'off' cells transcription of the fimbrial genes is silenced. Despite the very different molecular mechanisms controlling the expression of pap and fim, the two systems share many features in common and have probably evolved to fulfill the same function. In addition to details about the molecular mechanisms that control pap and fim, the possible physiological significance of the observed regulation will be discussed.

Adhesins, Escherichia coli↗
PubMed1996

The clp (CS31A) operon is negatively controlled by Lrp, ClpB, and L-alanine at the transcriptional level.

Biosynthesis of the Escherichia coli CS31A surface antigen was subject to phase-variation control and repressed by L-alanine. Nucleotide sequence analysis of the clp operon, encoding the biosynthesis of CS31A, revealed the presence of a regulatory gene, clpB. The amino acid sequence of the regulatory protein ClpB showed similarity to the primary structure of PapB, FaeB and AfaA, involved in the regulation of expression of Pap, K88, and Afa-3 fimbriae, respectively. The clp regulatory region contained two deoxyadenosine methylase sites (GATC-I and GATC-II). The leucine-responsive regulatory protein (Lrp) was required for specific methylation inhibition of the GATC-II site. The activity of the clp promoter was monitored in a clp-lacZYA single-copy fusion. The cloned DNA used in this study did not contain a related papl gene. In these conditions, we showed, as expected, that phase variation did not occur. However, transcription of the clp operon was negatively controlled by ClpB and Lrp, and was maximal in the absence of Dam methylase. In the presence of AfaF, a Papl equivalent, the phase-variation control was restored. We concluded that two regulatory mechanisms were superimposed to control the clp expression. Phase variation, mediated by Lrp and a Papl equivalent, controlled the number of cells producing CS31A in a single colony. The second mechanism, described in this report, was mediated by ClpB and Lrp and controls the level of CS31A produced by a single cell. Furthermore, we showed that L-alanine reduced, by about twofold, the clp promoter activity independently of a Papl equivalent, ClpB, Lrp or Dam methylase. In addition, the presence of L-alanine prevented the phase-variation control mediated by AfaF.

Alanine↗
PubMed2006

A phase-variable mechanism controlling the Campylobacter jejuni FlgR response regulator influences commensalism.

Phase variation of genes in bacteria enables phenotypic alteration to modulate interactions within a host as conditions change. To promote commensalism in animals and disease in humans, Campylobacter jejuni produces a flagellar organelle for motility. In addition to tight transcriptional regulation of flagellar genes, C. jejuni also controls flagellar biosynthesis by phase variation. In this study, an unusual phase-variable mechanism controlling production of FlgR, the response regulator of the FlgSR two-component system required for transcription of sigma54-dependent flagellar genes, is identified. Phase variation of FlgR production is due to loss or gain of a nucleotide in homopolymeric adenine or thymine tracts within flgR. This mechanism occurs during commensalism in poultry to alter the colonization capacity of C. jejuni, presumably by influencing the motility phenotype of the bacterium. These findings provide more understanding into the genetic and colonization strategies C. jejuni employs to achieve commensalism in a natural host. Second, due to the richness of the C. jejuni genome in adenine or thymine residues and the apparent lack of the normal set of mismatch repair enzymes, the results from this study may suggest that the C. jejuni genome is more unstable and variable than previously realized. Furthermore, phase variation of flagellar motility by targeting flgR may be a phenomenon specific to C. jejuni that is absent in other Campylobacter species and contribute to reasons why C. jejuni is more frequently found as a commensal organism in poultry and as the cause of disease in humans.

Amino Acid Sequence↗
PubMed1995

Leucine-responsive regulatory protein plays dual roles as both an activator and a repressor of the Escherichia coli pap fimbrial operon.

The expression of the pap pilus operon of Escherichia coli is under a phase-variation control mechanism in which cells undergo a reversible transition between transcriptionally active (phase ON) and inactive (phase OFF) states. In this study, we explore the roles of leucine-responsive regulatory protein (Lrp) and the histone-like protein H-NS in the regulation of pap phase variation. Our data indicate that the phase OFF state results from repression of the intrinsically active papBA promoter by Lrp and H-NS, each of which can act independently as transcriptional repressors. Lrp requires pap DNA sequences upstream of the papBA promoter for its repressor activity whereas H-NS does not. In contrast, in the ON state, Lrp, in conjunction with PapI, activates pap transcription. This activation is not merely a result of alleviating the H-NS mediated repression, but induces a level of transcription that is eightfold higher than the basal level of transcription from the papBA promoter measured in the absence of both H-NS and Lrp. Analysis of Lrp activation mutants indicates that binding of Lrp to pap DNA sequences is not sufficient for transcription activation, consistent with a model in which an additional domain of Lrp interacts with the transcriptional apparatus. Together, our results show that Lrp functions as a transcriptional activator in phase-ON cells and as a repressor of basal transcription in phase-OFF cells. Because pap phase variation occurs in the absence of H-NS, it is not clear what role this regulatory protein plays in pap gene regulation.

Bacterial Outer Membrane Proteins↗
PubMed1975

Integration, at hag or elsewhere, of H2 (phase-2 flagellin) genes transduced from Salmonella to Escherichia coli.

A fla mutant of E. coli K12 was given fla+ and H1-i by phage P1kc cotransduction from S. typhimurium, then made Fla- by transduction of ah1 from S. typhimurium. Motile clones expressing a Salmonella phase-2 antigen, e,n,x or 1,2, were obtained from the K12 i ah1 (therefore Fla-) line by P1kc transduction of flagellin-specifying genes, H2-e,n,x or H2-1,2, from Salmonella donors. Of eighteen such transductants sixteen failed to show phase variation, and on transduction back to Salmonella each structural gene for a phase-2 flagellin (or at least for its antigenically determinant part) now behaved as an allele of H1, presumably in consequence of incorporation in the hag region of the K12 recipient, in place of H1-i ah1. The e,n,x- and 1,2-specifying genes were shown to have been integrated in the K12 chromosome without the linked H1-repressor gene or the adjacent vh2 gene (controlling rate of phase-variation) and they responded to the repressing activity of an H2 allele elsewhere in the cell, in this respect resembling H1 alleles of Salmonella or hag alleles of E. coli. Two K12 e,n,x transductants had flagellin-specifying genes which when transduced back to Salmonella were integrated at H2; they are inferred to have resulted from integration of H2-e,n,x in the K12 chromosome elsewhere than the hag region. These two clones showed phase variation, between a Fla+ phase, with antigen e,n,x, and a Fla- phase (with e,n,x determinant in the nonactive state and the determinant of antigen i inactivated by ah1). The two integrated e,n,x genes when in the "active" state retained the ability to repress expression of exogenote H1 alleles, which indicates that the closely linked H1-repressor gene also was integrated. One of the two exceptional transductants derived its e,n,x gene from a Salmonella donor with the linked vh2- gene, which in Salmonella almost entirely prevents change of phase, and transduction of this e,n,x gene back to Salmonella recipients proved that vh2- had been incorporated into the E. coli chromosome along with the e,n,x determinant and the H1-repressor gene. The high frequency of change of phase (Fla+ in equilibrium Fla-) in the K12 e,n,x vh2- transductant concerned suggests that vh2- fails to prevent frequent change of state of the phase-determined part of H2 when vh2- and H2 are incorporated in the E. coli chromosome.

Bacterial Proteins↗
PubMed1993

Cisplatin induced cell killing and chromosomal aberrations in CHO cells: treated during G1 or S phase.

Variation in sensitivity to cisplatin during the cell cycle was studied in synchronous CHO cells treated during G1 or late S phase. The cells were assayed for cell killing, cell-cycle delay, and chromosomal aberrations after they were treated with cisplatin (1-12 micrograms/ml) for 1 h at 37 degrees C. They were either plated for colony survival, or colcemid was added from 12 to 40 h after plating followed by fixation 4 h later for analysis of chromosomal aberrations after the cells completed 1 or 2 cycles (i.e. first or second mitosis). Cells treated with 6 micrograms/ml exhibited about a 10-h delay during the first cycle after treatment during G1 compared with about 3 h during the first cycle and 6 h during the second cycle after treatment during late S. In both cases, cells entering metaphase exhibited predominantly chromatid-type breaks and exchanges. For both cell killing and chromosomal aberrations, the cells in G1 were 1.5-1.6 times more sensitive than those treated in late S, with 1 aberration per cell corresponding to about 37% survival. However, the exchanges and breaks were observed primarily in the first mitosis when cells were treated in G1 compared with the second mitosis when cells were treated in late S. These results suggest that DNA replication opposite cisplatin cross-links in the DNA results in lethal chromosomal aberrations.

Animals↗
PubMed2003

Leucine-responsive regulatory protein-mediated repression of clp (encoding CS31A) expression by L-leucine and L-alanine in Escherichia coli.

CS31A produced by septicemic and diarrheic Escherichia coli belongs to the Pap-regulatory family of adhesive factors, which are under methylation-dependent transcriptional regulation. Common features of operons encoding members of this family include two conserved GATC sites in the upstream regulatory region, and transcriptional regulators homologue to the PapB and PapI proteins. Methylation protection of GATC sites was previously shown to be dependent on the leucine-responsive regulatory protein (Lrp). Lrp and ClpB, the PapB equivalent, repressed clp basal transcription. A PapI homologue (AfaF) was required together with Lrp to establish the phase variation control, which gave rise to phase-ON cells that expressed CS31A and phase-OFF cells that did not express CS31A. In phase-OFF cells, the GATC(dist) site was methylated and the GATC(prox) site was protected from methylation, whereas in phase-ON cells, the inverse situation was found. Unlike Pap fimbriae, CS31A synthesis was dramatically reduced in media containing L-alanine or L-leucine. L-Alanine prevented the OFF-to-ON switch, locking clp expression in the OFF phase, whereas L-leucine repressed transcription without obvious effect on the switch frequency of phase variation. In phase-variable cells, leucine and alanine promoted methylation of GATC(dist) and methylation protection of GATC(prox), increasing the methylation pattern characteristic of repressed cells. Furthermore, alanine prevented the AfaF-dependent methylation protection of GATC(dist) and thus the appearance of phase-ON cells. In addition, analysis of clp expression in a Lrp-negative background indicated that alanine and leucine also repressed clp transcription by a methylation-independent mechanism.

Adenosine Triphosphatases↗
PubMed2001

Salmonella enterica serotype typhimurium elicits cross-immunity against a Salmonella enterica serotype enteritidis strain expressing LP fimbriae from the lac promoter.

The biological significance of fimbrial phase variation in Salmonella serotypes is currently unknown. Exposure to long polar (LP) fimbriae of Salmonella enterica serotype Typhimurium results in selection against lpf phase ON cells of serotype Enteritidis during a subsequent challenge, suggesting that fimbrial phase variation may be a mechanism to evade cross-immunity between Salmonella serotypes. This notion was tested by assessing the effect of an immune response against serotype Typhimurium LP fimbriae on colonization of mice with a serotype Enteritidis mutant in which the lpf promoter region was replaced with the Escherichia coli lac promoter. During a challenge with a serotype Enteritidis mutant carrying the lac promoter in front of the lpf operon, significantly lower numbers were recovered from organs and feces of mice previously immunized with an lpf phase ON culture of serotype Typhimurium than from mice not previously exposed to LP fimbriae. Immunization with the lpf phase ON culture of serotype Typhimurium elicited antibodies that cross-reacted with a purified gluthathione-S-transferase-LpfA fusion protein of serotype Enteritidis. These data suggested that cross-immunity against LP fimbrial proteins cannot be evaded if phase variation on the transcriptional level is prevented by expressing the lpf operon from the lac promoter. These data hence support the idea that phase variation of LP fimbriae is a mechanism to evade cross-immunity between serotypes Enteritidis and Typhimurium.

Animals↗
PubMed1997

Molecular analysis of representative Streptococcus gordonii Spp phase variants reveals no differences in the glucosyltransferase structural gene, gtfG.

Streptococcus gordonii glucosyltransferase polymerizes sucrose to form glucans, which confer a hard, sucrose-promoted phenotype (Spp+) to colonies on sucrose agar plates. The glucosyltransferase structural gene, gtfG, is positively regulated by the upstream determinant, rgg. Strain Challis undergoes a spontaneous, reversible phase variation between high (Spp+) and low (Spp-) levels of glucosyltransferase activity. Representative strains were examined to gain insights into the basis of glucosyltransferase phase variation. Western blots indicated that the level of glucosyltransferase activity was related to the amount of extracellular glucosyltransferase protein produced by Spp- and Spp+ strains. The nucleotide sequence of rgg and gtfG of the Spp- strain CH97 was found to be identical to that of the Spp+ parent, indicating that DNA differences in these regions are not the basis for glucosyltransferase phase variation. Indeed, 13C-NMR spectroscopy suggested that glucans synthesized by strain CH97 glucosyltransferase were similar to those synthesized by glucosyltransferase of the Spp+ parental strain, indicating a quantitative rather than qualitative change. However, one Spp- strain, CH1C1, had a point mutation in rgg; replacement of the parent rgg with the CH1C1 allele resulted in decreased levels of glucosyltransferase protein and activity. The results indicate that glucosyltransferase phase variation can occur in more than one way, and suggest that glucosyltransferase regulation may involve distally located regulatory gene(s) that affect rgg and/or gtfG expression.

Alleles↗
PubMed2000

Repeat-associated phase variable genes in the complete genome sequence of Neisseria meningitidis strain MC58.

Phase variation, mediated through variation in the length of simple sequence repeats, is recognized as an important mechanism for controlling the expression of factors involved in bacterial virulence. Phase variation is associated with most of the currently recognized virulence determinants of Neisseria meningitidis. Based upon the complete genome sequence of the N. meningitidis serogroup B strain MC58, we have identified tracts of potentially unstable simple sequence repeats and their potential functional significance determined on the basis of sequence context. Of the 65 potentially phase variable genes identified, only 13 were previously recognized. Comparison with the sequences from the other two pathogenic Neisseria sequencing projects shows differences in the length of the repeats in 36 of the 65 genes identified, including 25 of those not previously known to be phase variable. Six genes that did not have differences in the length of the repeat instead had polymorphisms such that the gene would not be expected to be phase variable in at least one of the other strains. A further 12 candidates did not have homologues in either of the other two genome sequences. The large proportion of these genes that are associated with frameshifts and with differences in repeat length between the neisserial genome sequences is further corroborative evidence that they are phase variable. The number of potentially phase variable genes is substantially greater than for any other species studied to date, and would allow N. meningitidis to generate a very large repertoire of phenotypes through expression of these genes in different combinations. Novel phase variable candidates identified in the strain MC58 genome sequence include a spectrum of genes encoding glycosyltransferases, toxin related products, and metabolic activities as well as several restriction/modification and bacteriocin-related genes and a number of open reading frames (ORFs) for which the function is currently unknown. This suggests that the potential role of phase variation in mediating bacterium-host interactions is much greater than has been appreciated to date. Analysis of the distribution of homopolymeric tract lengths indicates that this species has sequence-specific mutational biases that favour the instability of sequences associated with phase variation.

Bacterial Proteins↗