Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes.
Dispersed repetitive DNA sequences have been described recently in eubacteria. To assess the distribution and evolutionary conservation of two distinct prokaryotic repetitive elements, consensus oligonucleotides were used in polymerase chain reaction [PCR] amplification and slot blot hybridization experiments with genomic DNA from diverse eubacterial species. Oligonucleotides matching Repetitive Extragenic Palindromic [REP] elements and Enterobacterial Repetitive Intergenic Consensus [ERIC] sequences were synthesized and tested as opposing PCR primers in the amplification of eubacterial genomic DNA. REP and ERIC consensus oligonucleotides produced clearly resolvable bands by agarose gel electrophoresis following PCR amplification. These band patterns provided unambiguous DNA fingerprints of different eubacterial species and strains. Both REP and ERIC probes hybridized preferentially to genomic DNA from Gram-negative enteric bacteria and related species. Widespread distribution of these repetitive DNA elements in the genomes of various microorganisms should enable rapid identification of bacterial species and strains, and be useful for the analysis of prokaryotic genomes.
Genomic islands: tools of bacterial horizontal gene transfer and evolution
Bacterial genomes evolve through mutations, rearrangements or horizontal gene transfer. Besides the core genes encoding essential metabolic functions, bacterial genomes also harbour a number of accessory genes acquired by horizontal gene transfer that might be beneficial under certain environmental conditions. The horizontal gene transfer contributes to the diversification and adaptation of microorganisms, thus having an impact on the genome plasticity. A significant part of the horizontal gene transfer is or has been facilitated by genomic islands (GEIs). GEIs are discrete DNA segments, some of which are mobile and others which are not, or are no longer mobile, which differ among closely related strains. A number of GEIs are capable of integration into the chromosome of the host, excision, and transfer to a new host by transformation, conjugation or transduction. GEIs play a crucial role in the evolution of a broad spectrum of bacteria as they are involved in the dissemination of variable genes, including antibiotic resistance and virulence genes leading to generation of hospital ‘superbugs’, as well as catabolic genes leading to formation of new metabolic pathways. Depending on the composition of gene modules, the same type of GEIs can promote survival of pathogenic as well as environmental bacteria.
C‐di‐GMP: the dawning of a novel bacterial signalling system
Bis‐(3′‐5′)‐cyclic dimeric guanosine monophosphate (c‐di‐GMP) has come to the limelight as a result of the recent advances in microbial genomics and increased interest in multicellular microbial behaviour. Known for more than 15 years as an activator of cellulose synthase in Gluconacetobacter xylinus, c‐di‐GMP is emerging as a novel global second messenger in bacteria. The GGDEF and EAL domain proteins involved in c‐di‐GMP synthesis and degradation, respectively, are (almost) ubiquitous in bacterial genomes. These proteins affect cell differentiation and multicellular behaviour as well as interactions between the microorganisms and their eukaryotic hosts and other phenotypes. While the role of GGDEF and EAL domain proteins in bacterial physiology and behaviour has gained appreciation, and significant progress has been achieved in understanding the enzymology of c‐di‐GMP turnover, many questions regarding c‐di‐GMP‐dependent signalling remain unanswered. Among these, the key questions are the identity of targets of c‐di‐GMP action and mechanisms of c‐di‐GMP‐dependent regulation. This review discusses phylogenetic distribution of the c‐di‐GMP signalling pathway in bacteria, recent developments in biochemical and structural characterization of proteins involved in its metabolism, and biological processes affected by c‐di‐GMP. The accumulated data clearly indicate that a novel ubiquitous signalling system in bacteria has been discovered.
cloud computing social network regression model gene expression sample size confidence interval logistic regression social science systematic review linear regression model cloud datum xml document immune system carbon dioxide amino acid logistic regression model keyword search mental model process analysi background and objective encrypted datum quantitative assessment plant growth escherichia coli sequence analysi discourse analysi scientific publication channel condition immune response choice behavior programming paradigm natural selection organic matter odds ratio social structure microbial community signal transduction membrane protein encrypted cloud datum encrypted cloud lactic acid plant root oral cavity quorum sensing gene transfer antibiotic resistance cardiac surgery critical discourse analysi dental cary cell count marine ecosystem recombinant dna oxidative stres critical discourse aquatic ecosystem horizontal gene transfer bibliographic reference ribosomal rna horizontal gene lactic acid bacterium plasma membrane acute kidney acute kidney injury resistance gene cell survival genetic selection acid bacterium physiological aspect gram-negative bacterium social characteristic social inequality ranked keyword search ranked keyword abbott laboratory dental plaque oligonucleotide probe base pairing resistant bacterium antibiotic resistance gene lactobacillus acidophilu gram-positive bacterium genetic heterogeneity biofilm development nitrogen cycle microbial biofilm transcription, genetic interface device component metabolic process, cellular national origin biological adaptation to stress clone cell ethanol 0.62 ml/ml topical gel clinical act of insertion genetic translation proces hereditary disease greater than cognition disorder phobia, social nucleic acid hybridization gel electrophoresis (lab technique) stimulation (motivation) meta analysis (statistical procedure) the superficial genome, bacterial amino acid metabolism, inborn error denial (psychology) immunoglobulin lambda-chain fifty nine reservoir device component document completion status - documented gastrointestinal tract structure genus (mathematics) domain of discourse phylum (taxon) intestinal microbiome microbiota (plant) genus mycobacterium antibiotic resistance, microbial ammonia measurement ammonia oxidation models, mental anabolic steroid actinobacteria clas fecal microbiota transplantation kidney failure, acute gene transfer, horizontal ferrosoferric oxide dennis fairclough ruth teitelbaum shoshana wodak excretory function entity name part qualifier - adopted cessation of life anatomical layer biopolymer sequencing ephrin type-b receptor 1, human one thousand copy (object) review [publication type] promotion (action) pathogenic organism