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PubMed1997

Recent emergence of new variants of Yersinia pestis in Madagascar.

Yersinia pestis, the causative agent of plague, has been responsible for at least three pandemics. During the last pandemic, which started in Hong Kong in 1894, the microorganism colonized new, previously unscathed geographical areas where it has become well established. The aim of this longitudinal study was to investigate the genetic stability of Y. pestis strains introduced into a new environment just under a century ago and to follow the epidemiology of any new genetic variant detected. In the present study, 187 strains of Y. pestis isolated between 1939 and 1996 from different regions of Madagascar and responsible mainly for human cases of bubonic and pneumonic plague were studied. Our principal genotyping method was rRNA gene profiling (ribotyping), which has previously been shown to be an effective scheme for typing Y. pestis strains of different geographical origins. We report that all studied Y. pestis strains isolated in Madagascar before 1982 were of classical ribotype B, the ribotype attributed to the Y. pestis clone that spread around the world during the third pandemic. In 1982, 1983, and 1994, strains with new ribotypes, designated R, Q, and T, respectively, were isolated on the high-plateau region of the island. Analysis of other genotypic traits such as the NotI genomic restriction profiles and the EcoRV plasmid restriction profiles revealed that the new variants could also be distinguished by specific genomic and/or plasmid profiles. A follow-up of these new variants indicated that strains of ribotypes Q and R have become well established in their ecosystem and have a tendency to spread to new geographical areas and supplant the original classical strain.

Animals↗

PubMed1992

The human enamel protein gene amelogenin is expressed from both the X and the Y chromosomes.

Amelogenins, a family of extracellular matrix proteins of the dental enamel, are transiently but abundantly expressed by ameloblasts during tooth development. Amelogenins seem to regulate the formation of crystallites during the secretory stage of enamel development, while they are specifically degraded during tooth-bud maturation. In this paper we report the characterization of the AMGX and AMGY genes on the short arms of the human X and Y chromosomes which encode the amelogenins. Our studies on the expression of the amelogenin genes in male developing tooth buds showed that both the AMGX and AMGY genes are transcriptionally active and encode potentially functional proteins. We have isolated genomic and cDNA clones from both the AMGX and AMGY loci and have studied the sequence organization of these two genes. Reverse transcriptase (RT)PCR amplification of the 5' portion of the amelogenin transcripts revealed several alternatively spliced products. The splicing pattern observed in the Y-derived mRNA varies from that of the X-derived mRNA. The promoter regions from both genes and the predicted amelogenin protein sequences are presented. This information will be useful for studying the molecular basis of X-linked amelogenesis imperfecta, for understanding the evolution and regulation of gene expression on the mammalian sex chromosomes, and for investigating the role of amelogenin genes during tooth development.

Amelogenin↗

PubMed1991

Typing of methicillin resistant and susceptible Staphylococcus aureus strains by ribosomal RNA gene restriction patterns using a biotinylated probe.

Nine methicillin-sensitive (MSSA) and 37 methicillin-resistant (MRSA) Staphylococcus aureus isolates of various phage types and resistotypes from seven countries were investigated. Chromosomal DNA was restricted with HindIII or EcoRI, Southern blotted and hybridised with a cDNA probe to 16S+23S rRNA derived from MRSA NCTC 10442. Resulting rDNA profiles could be differentiated on the basis of 22 patterns which were unaffected by changes in plasmid, transposon, enterotoxin A or phage content. Percentage similarity values were calculated using the Dice coefficient and UPGA clustering. Australian and epidemic (EMRSA-1) isolates from the UK showed a high degree of similarity, but the pattern was not unique and was also found in MSSA and other MRSA, e.g. NCTC 10442. An MSSA of phage group II was the most distinct isolate. The method shows potential as an additional tool in a complex typing system, types non-phage typable strains and may provide clues to the clonal evolution of MRSA and MSSA.

Bacterial Typing Techniques↗

PubMed1990

Antimicrobial resistance in the intensive care unit.

Antimicrobial resistance remains a major clinical problem in the intensive care unit despite the introduction of potent new antibiotics and the application of infection control measures. Impaired antibiotic permeability, antibiotic inactivation and alteration of antibiotic target sites, typically in concert, are mechanisms by which this resistance occurs. Resistance traits may be chromosomally mediated, in which case they may be expressed constitutively or inducibly, or may be mediated by plasmids and/or transposons that may confer resistance to multiple drugs and facilitate spread to other organisms. Bacteria in which clinically significant resistance has now become a potential problem include methicillin-resistant staphylococci, enterococci, a wide variety of Enterobacteriaceae, Pseudomonas aeruginosa, Pseudomonas cepacia, and Xanthomonas (Pseudomonas) maltophilia. Judicious limitation in the use of antimicrobials, especially in prophylactic regimens; use of antibiotics in appropriate doses; and, where possible, avoidance of drugs to which resistance has been shown to emerge rapidly in a specific clinical setting will help to minimize the evolution and spread of resistant bacterial isolates.

Cross Infection↗

PubMed2005

Biochemical and mutational analyses of a unique clamp loader complex in the archaeon Methanosarcina acetivorans.

Clamp loaders orchestrate the switch from distributive to processive DNA synthesis. Their importance in cellular processes is underscored by their conservation across all forms of life. Here, we describe a new form of clamp loader from the archaeon Methanosarcina acetivorans. Unlike previously described archaeal clamp loaders, which are composed of one small subunit and one large subunit, the M. acetivorans clamp loader comprises two similar small subunits (M. acetivorans replication factor C small subunit (MacRFCS)) and one large subunit (MacRFCL). The relatedness of the archaeal and eukaryotic clamp loaders (which are made up of four similar small subunits and one large subunit) suggests that the M. acetivorans clamp loader may be an intermediate form in the archaeal/eukaryotic sister lineages. The clamp loader complex reconstituted from the three subunits MacRFCS1, MacRFCS2, and MacRFCL stimulated DNA synthesis by a cognate DNA polymerase in the presence of its sliding clamp. We used site-directed mutagenesis in the Walker A and SRC motifs to examine the contribution of each subunit to the function of the M. acetivorans clamp loader. Although mutations in MacRFCL and MacRFCS2 did not impair clamp loading activity, any mutant clamp loader harboring a mutation in MacRFCS1 was devoid of the clamp loading property. Mac-RFCS1 is therefore critical to the clamp loading activity of the M. acetivorans clamp loader. It is our anticipation that the discovery of this unique replication factor C homolog will lead to critical insights into the evolution of more complex clamp loaders from simpler ones as more complex organisms evolved in the archaeal/eukaryotic sister lineages.

Amino Acid Sequence↗

PubMed1983

Complete nucleotide sequence of the influenza B/Singapore/222/79 virus hemagglutinin gene and comparison with the B/Lee/40 hemagglutinin.

The complete nucleotide sequence of the hemagglutinin (HA) gene of the human type B influenza virus B/Singapore/222/79 is presented. Comparison with the only other known sequence of a B hemagglutinin (B/Lee/40) shows that antigenic drift in type B HA genes is essentially the same as already observed within the influenza A H3 subtype, i.e., an accumulation of point mutations. The main difference is that the apparent evolution is significantly slower, most likely due to the cumulative effect of a lower occurrence in the population (slower evolution) and/or less immunological pressure. There is a striking cluster of changes at positions 127 until 137 of the HA1 subunit which may represent one of the antigenic sites of the molecule.

Amino Acid Sequence↗

PubMed2006

Natural transformation of Neisseria gonorrhoeae: from DNA donation to homologous recombination.

Gonococci undergo frequent and efficient natural transformation. Transformation occurs so often that the population structure is panmictic, with only one long-lived clone having been identified. This high degree of genetic exchange is likely necessary to generate antigenic diversity and allow the persistence of gonococcal infection within the human population. In addition to spreading different alleles of genes for surface markers and allowing avoidance of the immune response, transformation facilitates the spread of antibiotic resistance markers, a continuing problem for treatment of gonococcal infections. Transforming DNA is donated by neighbouring gonococci by two different mechanisms: autolysis or type IV secretion. All types of DNA are bound non-specifically to the cell surface. However, for DNA uptake, Neisseria gonorrhoeae recognizes only DNA containing a 10-base sequence (GCCGTCTGAA) present frequently in the chromosome of neisserial species. Type IV pilus components and several pilus-associated proteins are necessary for gonococcal DNA uptake. Incoming DNA is subject to restriction, making establishment of replicating plasmids difficult but not greatly affecting chromosomal transformation. Processing and integration of transforming DNA into the chromosome involves enzymes required for homologous recombination. Recent research on DNA donation mechanisms and extensive work on type IV pilus biogenesis and recombination proteins have greatly improved our understanding of natural transformation in N. gonorrhoeae. The completion of the gonococcal genome sequence has facilitated the identification of additional transformation genes and provides insight into previous investigations of gonococcal transformation. Here we review these recent developments and address the implications of natural transformation in the evolution and pathogenesis N. gonorrhoeae.

DNA, Bacterial↗

PubMed1994

Changing the substrate specificity of penicillin G acylase from Kluyvera citrophila through selective pressure.

Escherichia coli (muT, mutD, Leu-) cells transformed with plasmid pYKD59 harbouring the pac gene encoding penicillin acylase (PA) from Kluyvera citrophila ATCC 21285 were exposed to environmental conditions that made expression of this enzyme essential for growth. Under these conditions, spontaneous mutants were isolated that used adipyl-L-leucine as the sole source of L-leucine. DNA sequencing of the mutant pac genes identified a transversion mutation of thymine to guanine at position 1163. This mutation was located in the beta-subunit of the enzyme and resulted in conversion of Phe-360 to valine. The assignment of this mutation to the shift in substrate specificity was further confirmed by site-directed mutagenesis. Secondary-structure prediction of the region surrounding Phe-360 suggests that this mutation should not produce any significant structural change. The purified mutant acylase was able to hydrolyse adipyl-, glutaryl-, valeryl-, caproyl-, heptanoyl- and phenoxyacetyl-L-leucine at pH 5 with greater efficiency than the wild-type enzyme. However, the mutant enzyme was not able to hydrolyse glutaryl-7-aminocephalosporanic acid and had lost 90% and 50% of activity on penicillin G and phenylacetyl-L-leucine respectively. Nevertheless, mutant PA retained its original activity on 6-nitro-3-phenylacetamidobenzoate and p-nitrophenylphenylacetate, suggesting that the binding specificity of PA by the acyl and amine moieties of the substrate are not independent phenomena. The small differences observed between the c.d. spectra of the mutant enzyme recorded at pH 5 and 8 suggest the existence of different conformational states at the two pH values, but these differences were indistinguishable from those observed in the native enzyme and cannot be correlated with the shift in substrate specificity. Our results demonstrate that it is possible to change the specificity of PA by laboratory evolution and use it to identify the amino acids involved in substrate recognition. However, the synchronous participation of the alpha- and beta-subunits in the complex induced-fit-like mechanism of acylases suggests that, to obtain new enzymes for industrial application, the selection pressure should be specifically designed for the compound of interest.

Amino Acid Sequence↗

PubMed2006

Interstrain transfer of the large pathogenicity island (PAPI-1) of Pseudomonas aeruginosa.

The large Pseudomonas aeruginosa pathogenicity island PAPI-1 of strain PA14 is a cluster of 108 genes that encode a number of virulence features. We demonstrate that, in a subpopulation of cells, PAPI-1 can exist in an extrachromosomal circular form after precise excision from its integration site within the 3' terminus of the tRNA(Lys) gene. Circular PAPI-1 can reintegrate into either of the two tRNA(Lys) genes, including the one that was used for integration of small pathogenicity island PAPI-2 in strain PA14. The excision requires PAPI-1-encoded integrase, a member of the tyrosine recombinase family. PAPI-1 Soj contains the conserved domains of proteins that are related to chromosome and plasmid partition. soj plays a role in maintaining PAPI-1 and mutations in soj result in the loss of PAPI-1 from P. aeruginosa. We further demonstrate that, during coculture, the PAPI-1-containing strains are able to transfer it into P. aeruginosa recipient strains that do not harbor this island naturally. After transfer, PAPI-1 integrates into either of the two tRNA(Lys) genes. PAPI-1 encompasses many features of mobile elements, including mobilization and maintenance modules. Together with the virulence determinants, PAPI-1 plays an important role in the evolution of P. aeruginosa, by expanding its natural habitat from soil and water to animal and human infections.

Attachment Sites, Microbiological↗

PubMed1998

Three phylogenetic groups of nodA and nifH genes in Sinorhizobium and Mesorhizobium isolates from leguminous trees growing in Africa and Latin America.

The diversity and phylogeny of nodA and nifH genes were studied by using 52 rhizobial isolates from Acacia senegal, Prosopis chilensis, and related leguminous trees growing in Africa and Latin America. All of the strains had similar host ranges and belonged to the genera Sinorhizobium and Mesorhizobium, as previously determined by 16S rRNA gene sequence analysis. The restriction patterns and a sequence analysis of the nodA and nifH genes divided the strains into the following three distinct groups: sinorhizobia from Africa, sinorhizobia from Latin America, and mesorhizobia from both regions. In a phylogenetic tree also containing previously published sequences, the nodA genes of our rhizobia formed a branch of their own, but within the branch no correlation between symbiotic genes and host trees was apparent. Within the large group of African sinorhizobia, similar symbiotic gene types were found in different chromosomal backgrounds, suggesting that transfer of symbiotic genes has occurred across species boundaries. Most strains had plasmids, and the presence of plasmid-borne nifH was demonstrated by hybridization for some examples. The nodA and nifH genes of Sinorhizobium teranga ORS1009T grouped with the nodA and nifH genes of the other African sinorhizobia, but Sinorhizobium saheli ORS609T had a totally different nodA sequence, although it was closely related based on the 16S rRNA gene and nifH data. This might be because this S. saheli strain was originally isolated from Sesbania sp., which belongs to a different cross-nodulation group than Acacia and Prosopis spp. The factors that appear to have influenced the evolution of rhizobial symbiotic genes vary in importance at different taxonomic levels.

Acyltransferases↗

PubMed2004

Comparative genomics of streptococcal species.

Microbial genome sequencing has produced an unprecedented amount of new information and insights into an organism's metabolic activities, virulence properties, and evolution. The complete genome sequence has been reported for four different species of streptococci, including Streptococcus pyogenes, S. agalactiae, S. pneumoniae and S. mutans. Comparative genome analysis among organisms of the same species not only shows a high degree of similarity in gene content and organization, but also a high degree of sequence heterogeneity as evidenced by the large number of single nucleotide polymorphisms present. Considerable differences were also observed in the number of mobile genetic elements found in each organism, including complete and partial bacteriophage genomes, IS elements, transposons, and plasmids. S. pyogenes was the only species to contain complete bacteriophage genomes in its genome, while only S. pneumoniae and S. mutans contained the full complement of competence genes essential for natural transformation. Comparative genome analysis between the species showed that S. pyogenes was more closely related to S. agalactiae than with S. pneumoniae or S. mutans.

Genome, Bacterial↗

PubMed1997

Structural characterization of the gene and corresponding cDNA for the cytochrome P450rm from Rhodotorula minuta which catalyzes formation of isobutene and 4-hydroxylation of benzoate.

Cytochrome P450rm was previously isolated from the basidiomycete yeast Rhodotorula minuta as a bifunctional enzyme with isobutene-forming and benzoate 4-hydroxylase activities. We cloned the gene and corresponding cDNA for P450rm in order to characterize the enzyme in the context of fungal phylogeny and physiology. From the cDNA sequence, P450rm was deduced to have 527 amino acids with a calculated molecular weight of 59136. P450rm shared 48% amino acid sequence identity with CYP53A1 from Aspergillus niger, indicating that the gene belongs to a novel subfamily of CYP53, CYP53B. However, the organization of the P450rm gene, which has eight exons and seven introns, differed completely to that of CYP53A1. Northern analysis demonstrated that the level of P450rm mRNA expression increased when L-phenylalanine was used as sole carbon source. These results suggest that P450rm has been well conserved during the evolution of fungi as a benzoate 4-hydroxylase in the dissimilation pathway starting from L-phenylalanine

Amino Acid Sequence↗

PubMed2004

Cyclic AMP-dependent protein kinase catalytic subunits have divergent roles in virulence factor production in two varieties of the fungal pathogen Cryptococcus neoformans.

Our earlier findings established that cyclic AMP-dependent protein kinase functions in a signaling cascade that regulates mating and virulence of Cryptococcus neoformans var. grubii (serotype A). Mutants lacking the serotype A protein kinase A (PKA) catalytic subunit Pka1 are unable to mate, fail to produce melanin or capsule, and are avirulent in animal models, whereas mutants lacking the PKA regulatory subunit Pkr1 overproduce capsule and are hypervirulent. Because other mutations have been observed to confer different phenotypes in two diverged varieties of C. neoformans (grubii variety [serotype A] and neoformans variety [serotype D]), we analyzed the functions of the PKA genes in the serotype D neoformans variety. Surprisingly, the Pka1 catalytic subunit was not required for mating, haploid fruiting, or melanin or capsule production of serotype D strains. Here we identify a second PKA catalytic subunit gene, PKA2, that is present in both serotype A and D strains of C. neoformans. The divergent Pka2 catalytic subunit was found to regulate mating, haploid fruiting, and virulence factor production in serotype D strains. In contrast, Pka2 has no role in mating, melanin production, or capsule formation in serotype A strains. Our studies illustrate how different components of signaling pathways can be co-opted and functionally specialized during the evolution of related but distinct varieties or subspecies of a human fungal pathogen.

Alleles↗

PubMed1990

The 5'-flanking region of the mouse vascular smooth muscle alpha-actin gene contains evolutionarily conserved sequence motifs within a functional promoter.

The 5'-flanking, 5'-untranslated, and amino-terminal protein coding regions of the single-copy 13-kilobase mouse vascular smooth muscle (VSM) alpha-actin gene have been cloned and sequenced. Respectively, there is 73 and 89% homology from the start of transcription (+1) to a point 206 base pairs upstream when comparing mouse to chicken and mouse to human VSM alpha-actin 5'-flanking region sequences. Two proximal 16-base pair motifs containing putative cis-acting regulatory elements having the configuration CC(A/T)6GG were found to be 100% conserved and present in the same position upstream from the transcription start site in all three species. A third more distal CC(A/T)6GG-like motif was 100% conserved between only the mouse and human genes whereas a fourth motif was unique to the mouse gene. The two upstream motifs may be important in controlling VSM alpha-actin gene transcription in mammals. Cell transfection assays using hGH reporter gene fusion plasmids showed that all four CC(A/T)6GG elements were required for tissue-specific, core promoter activity and were able to direct hGH expression in both mouse BC3H1 myogenic cells and early-passage rabbit aortic smooth muscle cells. The core promoter was not active in mouse fibroblasts suggesting that the region between -372 and -143 may mediate tissue-restrictive expression of the VSM alpha-actin gene. A putative "cell density responsive element" may be located between -1074 and -372 since fusion plasmids containing this portion of the VSM alpha-actin 5'-flanking region were significantly more active in promoting hGH expression in inducible, density-activated BC3H1 myoblasts compared to aortic smooth muscle cells which are largely constitutive for VSM alpha-actin expression.

Actins↗

PubMed1997

[Meropenem against bacteria carriers of wide spectrum TEM beta-lactamases: evolutive aspects].

The so-called wide spectrum beta-lactamases (WSBLs) are able to hydrolyze wide spectrum cephalosporins or monobactamics such as cefotaxime, ceftriaxone, ceftazidime, cefepime, cefpiroma or aztreonam. The natural wide spectrum beta-lactamases are mutational variants of TEM-1 consisting in the substitution of one of more amino acids within seven well defined positions in the molecule. Given the expected extremely low frequency for the simultaneous production of double or triple mutations, it is plausible that one of the mutational changes has been independently selected. A plurimutational remodelling of the TEM-beta-lactamase molecule is successively produced with the consequent appearance of highly effective ESBLs. Mutagenesis techniques allow clean molecular variants to be produced and allow the mutational effects under homogeneous conditions of bacterial strain, the plasmid implicated or the genic promotor to be studied. Meropenem remains active versus all the wide spectrum beta-lactamases referred in the 2be group of Bush, Jacoby and Medeiros as well as the new beta-lactamases produced in vitro by directed mutagenesis.

Escherichia coli↗

PubMed2002

A dynamin-like protein (ADL2b), rather than FtsZ, is involved in Arabidopsis mitochondrial division.

Recently, the FtsZ protein, which is known as a key component in bacterial cell division, was reported to be involved in mitochondrial division in algae. In yeast and animals, however, mitochondrial fission depends on the dynamin-like proteins Dnm1p and Drp1, respectively, whereas in green plants, no potential mitochondrial division genes have been identified. BLAST searches of the nuclear and mitochondrial genome sequences of Arabidopsis thaliana did not find any obvious homologue of the alpha-proteobacterial-type ftsZ genes. To determine whether mitochondrial division of higher plants depends on a dynamin-like protein, we cloned a cDNA for ADL2b, an Arabidopsis homologue of Dnm1p, and tested its subcellular localization and its dominant-negative effect on mitochondrial division. The fusion protein of green fluorescent protein and ADL2b was observed as punctate structures localized at the tips and at the constriction sites of mitochondria in live plant cells. Cells expressing dominant-negative mutant ADL2b proteins (K56A and T77F) showed a significant fusion, aggregation, and/or tubulation of mitochondria. We propose that mitochondrial division in higher plants is conducted by dynamin-like proteins similar to ADL2b in Arabidopsis. The evolutional points of loss of mitochondrial FtsZ and the functional acquisition of dynamin-like proteins in mitochondrial division are discussed.

Amino Acid Motifs↗

PubMed2003

CCHX zinc finger derivatives retain the ability to bind Zn(II) and mediate protein-DNA interactions.

Classical (CCHH) zinc fingers are among the most common protein domains found in eukaryotes. They function as molecular recognition elements that mediate specific contact with DNA, RNA, or other proteins and are composed of a betabetaalpha fold surrounding a single zinc ion that is ligated by two cysteine and two histidine residues. In a number of variant zinc fingers, the final histidine is not conserved, and in other unrelated zinc binding domains, residues such as aspartate can function as zinc ligands. To test whether the final histidine is required for normal folding and the DNA-binding function of classical zinc fingers, we focused on finger 3 of basic Krüppel-like factor. The structure of this domain was determined using NMR spectroscopy and found to constitute a typical classical zinc finger. We generated a panel of substitution mutants at the final histidine in this finger and found that several of the mutants retained some ability to fold in the presence of zinc. Consistent with this result, we showed that mutation of the final histidine had only a modest effect on DNA binding in the context of the full three-finger DNA-binding domain of basic Krüppel-like factor. Further, the zinc binding ability of one of the point mutants was tested and found to be indistinguishable from the wild-type domain. These results suggest that the final zinc chelating histidine is not an essential feature of classical zinc fingers and have implications for zinc finger evolution, regulation, and the design of experiments testing the functional roles of these domains.

Amino Acid Sequence↗

PubMed1982

[Evolution of the intestinal flora in patients under preventive treatment with cephalosporins].

The evolution of the intestinal flora has been studied in 20 patients undergoing chemoprophylaxis with cephalosporins. The patients, admitted to the Cantonal Hospital of Geneva for heart surgery, all received intravenous treatment initiated on the day of admission. Subsequently, one group continued to receive a cephalosporin orally while prophylaxis was discontinued in a second group. Microbiological analysis of aerobic bacteria in faeces demonstrated in both groups (1) a significant increase in resistance to beta-lactamines (ampicillin); (2) a parallel though lesser increase in resistance to other antibiotics (which shows the probable role of plasmids carrying drug resistance markers); and (3) an increase in bacteria known for their resistance to beta-lactamines (klebsiella, enterobacter, pseudomonas). These results demonstrate that a single intravenous administration of beta-lactamines has a selective effect on the intestinal flora and notably on bacteria which are known to be the cause of infectious diseases acquired in hospitals.

Administration, Oral↗