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At least 631 records · Page 35Linked to original sources
PubMed2005

Fatty acid and DNA analyses of Permian bacteria isolated from ancient salt crystals reveal differences with their modern relatives.

The isolation of living microorganisms from primary 250-million-year-old (MYA) salt crystals has been questioned by several researchers. The most intense discussion has arisen from questions about the texture and age of the crystals used, the ability of organisms to survive 250 million years when exposed to environmental factors such as radiation and the close similarity between 16S rRNA sequences in the Permian and modern microbes. The data in this manuscript are not meant to provide support for the antiquity of the isolated bacterial strains. Rather, the data presents several comparisons between the Permian microbes and other isolates to which they appear related. The analyses include whole cell fatty acid profiling, DNA-DNA hybridizations, ribotyping, and random amplified polymorphic DNA amplification (RAPD). These data show that the Permian strains, studied here, differ significantly from their more modern relatives. These differences are accumulating in both phenotypic and molecular areas of the cells. At the fatty acid level the differences are approaching but have not reached separate species status. At the molecular level the variation appears to be distributed across the genome and within the gene regions flanking the highly conserved 16S rRNA itself. The data show that these bacteria are not identical and help to rule out questions of contamination by putatively modern strains.

Bacteria↗
PubMed2006

Composition of archaeal, bacterial, and eukaryal RuBisCO genotypes in three Western Pacific arc hydrothermal vent systems.

We studied the diversity of all forms of the RuBisCO large subunit-encoding gene cbbL in three RuBisCO uncharacterized hydrothermal vent communities. This diversity included the archaeal cbbL and the forms IC and ID, which have not previously been studied in the deep-sea environment, in addition to the forms IA, IB and II. Vent plume sites were Fryer and Pika in the Mariana arc and the Suiyo Seamount, Izu-Bonin, Japan. The cbbL forms were PCR amplified from plume bulk microbial DNA and then cloned and sequenced. Archaeal cbbL was detected in the Mariana samples only. Both forms IA and II were amplified from all samples, while the form IC was amplified only from the Pika and Suiyo samples. Only the Suiyo sample showed amplification of the form ID. The form IB was not recorded in any sample. Based on rarefaction analysis, nucleotide diversity and average pairwise difference, the archaeal cbbL was the most diverse form in Mariana samples, while the bacterial form IA was the most diverse form in the Suiyo sample. Also, the Pika sample harbored the highest diversity of cbbL phylogenetic lineages. Based on pairwise reciprocal library comparisons, the Fryer and Pika archaeal cbbL libraries showed the most significant difference, while Pika and Suiyo showed the highest similarity for forms IA and II libraries. This suggested that the Fryer supported the most divergent sequences. All archaeal cbbL sequences formed unique phylogenetic lineages within the branches of anaerobic thermophilic archaea of the genera Pyrococcus, Archaeoglobus, and Methanococcus. The other cbbL forms formed novel phylogenetic clusters distinct from any recorded previously in other deep-sea habitats. This is the first evidence for the diversity of archaeal cbbL in environmental samples.

Archaea↗
PubMed2006

Novel organization of catechol meta pathway genes in the nitrobenzene degrader Comamonas sp. JS765 and its evolutionary implication.

The catechol meta cleavage pathway is one of the central metabolic pathways for the degradation of aromatic compounds. A novel organization of the pathway genes, different from that of classical soil microorganisms, has been observed in Sphingomonas sp HV3 and Pseudomonas sp. DJ77. In a Comamonas sp. JS765, cdoE encoding catechol 2,3-dioxygenase shares a common ancestry only with tdnC of a Pseudomonas putida strain, while codG encoding 2-hydroxymuconic semialdehyde dehydrogenase shows a higher degree of similarity to those genes in classical bacteria. Located between cdoE and cdoG are several putative genes, whose functions are unknown. These genes are not found in meta pathway operons of other microorganisms with the exception of cdoX2, which is similar to cmpX in strain HV3. Therefore, the gene cluster in JS765 reveals a third type of gene organization of the meta pathway.

Amino Acid Sequence↗
PubMed2005

Chromosomal polymorphism and comparative painting analysis in the zebra finch.

The zebra finch (Taeniopygia guttata) is often studied because of its interesting behaviour and neurobiology. Genetic information on this species has been lacking, making analysis of informative mutants difficult. Here we report on an improved cytological method for preparation of metaphase chromosomes suitable for fluorescent in situ hybridization of adult birds. We found that individual chicken chromosome paints usually hybridized to single zebra finch chromosomes, indicating only minor chromosomal rearrangements since the evolutionary divergence of these two species, and suggesting that the genomic location of chicken genes will predict the location of zebra finch orthologues. Chicken chromosome 1 appears to have split into two macrochromosomes in zebra finches, and chicken chromosome 4 paint hybridizes to a zebra finch macrochromosome and a microchromosome. This pattern was confirmed by mapping the androgen receptor (AR), which is located on chicken chromosome 4 but on a zebra finch microchromosome. We detected a telocentric/submetacentric polymorphism of chromosome 6 in our colony of zebra finches, and found that the polymorphism was inherited in a Mendelian pattern.

Animals↗
PubMed1984

Nucleotide base sequence of vibrionaceae 5 S rRNA.

Nucleotide base sequences of 5 S rRNAs isolated from Vibrio vulnificus, Vibrio anguillarum, and Aeromonas hydrophila were determined. Comparisons among these and sequences of 5 S rRNAs from other species of Vibrionaceae provide information useful in the evaluation of the evolution of bacterial species.

Aeromonas↗
PubMed1996

Adaptation of a conjugal transfer system for the export of pathogenic macromolecules.

Conjugal transfer of bacterial plasmids requires a pore through which DNA can traverse the envelopes of the donor and recipient cells. Recent studies indicate that these pores, which are composed of approximately ten proteins, are evolutionarily related to the transport systems required for the transfer of oncogenic T-DNA from Agrobacterium tumefaciens to plant cells and for toxin secretion from Bordetella pertussis.

Bacterial Proteins↗
PubMed2005

Alternative oxidase and plastoquinol terminal oxidase in marine prokaryotes of the Sargasso Sea.

Alternative oxidase (AOX) represents a non-energy conserving branch in mitochondrial electron transport while plastoquinol terminal oxidase (PTOX) represents a potential branch in photosynthetic electron transport. Using a metagenomics dataset, we have uncovered numerous and diverse AOX and PTOX genes from the Sargasso Sea. Sequence similarity, synteny and phylogenetic analyses indicate that the large majority of these genes are from prokaryotes. AOX appears to be widely distributed among marine Eubacteria while PTOX is widespread among strains of cyanobacteria closely related to the high-light adapted Prochlorococcus marinus MED4, as well as Synechococcus. The wide distribution of AOX and PTOX in marine prokaryotes may have important implications for productivity in the world's oceans.

Amino Acid Motifs↗
PubMed2004

Comparative sequence analysis of the icm/dot genes in Legionella.

The icm/dot genes in Legionella pneumophila are essential for the ability of the bacteria to survive within macrophages in lung infections such as Legionnaires' disease, or amoebae in nature. The 22 genes of the complex, thought to encode a transport apparatus for transfer of effector molecules into the host cell cytoplasm, are located in two chromosomal loci. We demonstrate that these genes are present in all the L. pneumophila strains examined herein, but display a wide range of sequence variation among the different strains, none of which are clearly associated with virulence potential. The strains fall within seven phylogenetic groups, but discrepancies among the gene trees indicate a complicated evolutionary history for the icm/dot loci, with perhaps two independent gene acquisition events and subsequent genomic rearrangements. Significant findings include a probable t-SNARE domain in IcmG that may indicate a direct role for this putative inner membrane protein in altering the host's membrane fusion machinery, a potential functional domain in the central hydrophobic portion of IcmK that may allow it to participate in forming the pore of the secretion complex, and strict conservation of the amino acid physicochemical characteristics in the IcmP region corresponding to the trbA domain that could play a role in molecular transfer.

Amino Acid Sequence↗
PubMed2005

Distribution of F- and A/V-type ATPases in Thermus scotoductus and other closely related species.

The presence of an A/V-type ATPase in different Thermus species and in the deeper branching species Meiothermus ruber and Deinococcus radiodurans suggests that the presence of the archaeal-type ATPase is a primitive character of the Deinococci that was acquired through horizontal gene transfer (HGT). However, the presence of a bacterial type F-ATPases was reported in two newly identified Thermus species (Thermus scotoductus DSM 8553 and Thermus filiformis DSM 4687). Two different scenarios can explain this finding, either the recent replacement of the ancestral A/V-type ATPase in Thermus scotoductus and Thermus filiformis with a newly acquired F-type ATPase or a long-term persistence of both F and A type ATPase in the Deinococci, which would imply several independent losses of the F-type ATPase in the Deinococci. Using PCR with redundant primers, sequencing and Southern blot analyses, we tried to confirm the presence of an F-type ATPase in the genome of Thermus scotoductus and Thermus filiformis, and determine its phylogenetic affinities. Initial experiments appeared to confirm the presence of an F-type ATPase in Thermus scotoductus that was similar to the F-ATPases found in Bacillus. However, further experiments revealed that the detection of an F-ATPase was due to a culture contamination. For all the Thermus and Deinococcus species surveyed, including Thermus scotoductus, cultures that were free of contamination only contained an A/V-type ATP synthases.

Adenosine Triphosphatases↗
PubMed2006

Chlamydiae-specific proteins and indels: novel tools for studies.

Chlamydiae species are important human and animal pathogens. Their obligate intracellular mode of replication has precluded the use of genetic and molecular biological approaches for understanding their biology. Comparative genomics have identified many rare genetic changes consisting of whole proteins and conserved indels (i.e. inserts or deletions) in widely distributed proteins that are distinctive characteristics of either all, or various subgroups within, chlamydiae. Additionally, several interesting cases of the lateral transfer of genes from free-living bacteria to a common ancestor of chlamydiae, and from chlamydiae to Trypanosoma/Leishmania, have been identified. These novel signatures have possible applications for advancing our understanding of the chlamydiae.

Bacterial Proteins↗
PubMed2004

Assessing the phylogeny of Frankia-actinorhizal plant nitrogen-fixing root nodule symbioses with Frankia 16S rRNA and glutamine synthetase gene sequences.

Actinomycetes from the genus Frankia induce nitrogen-fixing root nodules on actinorhizal plants in the "core rosid" clade of eudicots. Reported here are nine partial Frankia 16S rRNA gene sequences including the first from host plants of the rosaceous genera Cercocarpus and Chamaebatia, 24 partial glutamine synthetase (GSI; glnA) sequences from Frankia in nodules of 17 of the 23 actinorhizal genera, and the partial glnA sequence of Acidothermus cellulolyticus. Phylogenetic analyses of combined Frankia 16S rDNA and glnA sequences indicate that infective strains belong to three major clades (I-III) and that Clade I strains consisting of unisolated symbionts from the Coriariaceae, Datiscaceae, Rosaceae, and Ceanothus of the Rhamnaceae are basal to the other clades. Clock-like mutation rates in glnA sequence alignments indicate that all three major Frankia clades diverged early during the emergence of eudicots in the Cretaceous period, and suggest that present-day symbioses are the result of an ancestral symbiosis that emerged before the divergence of extant actinorhizal plants.

DNA, Bacterial↗
PubMed1997

Cyanobacterial tRNA(Leu)(UAA) group I introns have polyphyletic origin.

Self-splicing group I introns in tRNA anticodon loops have been found in diverse groups of bacteria (alpha, beta purple bacteria and cyanobacteria). In particular, the cyanobacterial tRNA(Leu)(UAA) group I introns have attracted considerable attention because of their presumed ancient origin and immobility. In this work, however, we identified tRNA(Leu)(UAA) group I introns in six out of 16 closely related isolated belonging to the cyanobacterial genus Microcystis. Interestingly, these introns are more closely related to the group I introns identified in the alpha and beta purple bacteria (located in tRNA(Arg)(CCU) and tRNA(Ile)(CAU), respectively) than to other cyanobacterial introns. Our sequence comparison and phyletic reconstruction suggest lateral transfer of the intron (possibly trough mobility), and a polyphyletic origin of cyanobacterial tRNA(Leu)(UAA) group I introns.

Base Sequence↗
PubMed2000

Cloning, sequencing, and characterization of the bifunctional xylosidase-arabinosidase from the anaerobic thermophile thermoanaerobacter ethanolicus.

The gene for the bifunctional xylosidase-arabinosidase (xarB) from the thermophilic anaerobe Thermoanaerobacter ethanolicus JW200 was cloned, sequenced, and expressed in Escherichia coli (Genebank Accession No. AF135015). Analysis of the recombinant enzyme revealed activity against multiple substrates with the highest affinity towards p-nitrophenyl beta-D-xylopyranoside (pNPX) and highest activity against p-nitrophenyl alpha-L-arabinopyranoside (pNPAP), respectively. Thus, we classify this enzyme as a bifunctional xylosidase-arabinosidase. Even though both sequences are 96% identical on the amino acid level, excluding the amino-terminal end, a frame-shift mutation in the 5' region of the gene in T. brockii ATCC 33075 and a deletion in a downstream open reading frame in T. ethanolicus seem to have occurred through evolutionary divergence of these two species. This represents an interesting phenomenon of molecular evolution of bacterial species, as PCR analysis of the region around the deletion indicates that the deletion is not present in T. brockii ssp. finnii and T. brockii ssp. brockii type strain HTD4.

Amino Acid Sequence↗
PubMed1997

Glycolytic enzyme operon of Borrelia burgdorferi: characterization and evolutionary implications.

The genes encoding three enzymes of the glycolytic pathway have been identified and sequenced completely in Borrelia burgdorferi sensu stricto and partially in B. hermsii. They are clustered on the chromosome into an operon with a single putative promoter and are arranged downstream of this promoter in the following order: gapdh (glyceraldehyde-3-phosphate dehydrogenase), pgk (phosphoglycerate kinase), and tpi (triosephosphate isomerase). gapdh and pgk are separated by 19 bp of intergenic sequence and pgk and tpi are separated by only 1 bp. Each of the three genes contains a putative RBS 6-7 bp upstream of each respective translational (ATG) start codon. The deduced protein encoded by gapdh consists of 335 amino acids (aa) with a predicted MW of 36,400, that of pgk is 393 aa (MW of 42,156) and that of tpi is 290 aa (MW of 27,683). The aa sequences of each of the three enzymes share 58.4% (GAPDH), 52.8% (PGK) and 46.1% (TPI) identity with respective enzymes from other prokaryotic organisms. Phylogenetic analyses based on these universal and conserved proteins support the hypothesis that spirochetes are an ancient and distinct eubacterial phylum.

Amino Acid Sequence↗
PubMed2002

Intraspecific variation in the 16S rRNA gene sequences of Mycoplasma agalactiae and Mycoplasma bovis strains.

Intraspecific variation in the 16S rRNA genes of 17 Mycoplasma agalactiae and eight Mycoplasma bovis isolates was investigated to determine the degree of sequence variation in these two species and to determine whether the polymorphisms in the 16S rRNA genes could be used for the construction of an evolutionary tree and as epidemiological markers. A high degree of variation was found within isolates (between operons) and between isolates of both species. In contrast to M. capripneumoniae no distinct evolutionary pattern could be seen, probably because there are functional systems for gene conversion in M. agalactiae and M. bovis. However, the non-European isolates of M. agalactiae shared three characteristic nucleotides and European isolates from the same or neighbouring countries were very similar. Differences within isolates included both polymorphic positions and sequence length differences between operons. The amount of variation within isolates of the respective species ranged from zero to seven polymorphisms for M. agalactiae and from zero to four polymorphisms for M. bovis. The high degree of variation suggests the potential for misdiagnosis of species in diagnostic PCR assays based on the 16S rRNA gene sequences. All isolates of both species had a thymidine in position 912 (E. coli numbering) that causes streptomycin resistance in several bacterial species and which is characteristic for the members of the hominis group. As expected, when five M. agalactiae and three M. bovis isolates were tested for streptomycin susceptibility, they all demonstrated streptomycin resistance. M. agalactiae and M. bovis were found to have high intraspecific variation in their 16S rRNA gene and the polymorphisms patterns indicate that gene conversion takes place.

Animals↗
PubMed2001

Antibiotic resistance with particular reference to soil microorganisms.

Evidence of increasing resistance to antibiotics in soil and other natural isolates highlights the importance of horizontal transfer of resistance genes in facilitating gene flux in bacteria. Horizontal gene transfer in bacteria is favored by the presence of mobile genetic elements and by the organization of bacterial genomes into operons allowing for the cooperative transfer of genes with related functions. The selective pressure for the spread of resistance genes correlates strongly with the clinical and agricultural overuse of antibiotics. The future of antimicrobial chemotherapy may lie in developing new antimicrobials using information from comparative functional microbial genomics to find genetic targets for antimicrobials and also to understand gene expression enabling selective targeting of genes with expression that correlates with the infectious process.

Anti-Bacterial Agents↗
PubMed1998

Combined numerical analysis based on the molecular description of Mycobacterium tuberculosis by four repetitive sequence-based DNA typing systems.

Mycobacterium tuberculosis clinical isolates (113 isolates from 78 patients) were typed using IS6110-RFLP, DR-RFLP, DR-based spoligotyping and direct repetitive element PCR (DRE-PCR). The similarities among isolates were compared for each individual method. The individual matrix distance files for each method were summed and averaged, and the resulting unique distance file was analysed by the UPGMA (unweighted pair group method with arithmetic averages). Combined numerical analysis with 3 genetic markers (IS6110-RFLP, DR-RFLP and spoligotyping) was performed for all 78 clinical isolates, whereas analysis with 4 genetic markers (with the addition of DRE-PCR) was performed on the 10 main clusters described. When compared to molecular analysis based on individual markers, the molecular description based on multiple genetic markers enabled comparison of the results obtained by individual methods and the obtaining of a more accurate view of strain identity and clusters comparison. The resulting cumulative dendrogram was more accurate for studying the population structure of M. tuberculosis and may be a good tool for elucidating intraspecies genetic microevolution.

Bacterial Typing Techniques↗
PubMed1996

Cholera: nice bacteria and bad viruses.

The genes coding for cholera toxin are borne on, and can be infectiously transmitted by, a filamentous bacteriophage, raising intriguing questions about the mechanisms and evolution of bacterial pathogenesis, and the taxonomy, epidemiology and control of cholera and other bacterial diseases.

Animals↗