| genome-based taxonomic classification of bacteroidetes. | the bacterial phylum bacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16s rrna gene sequence. here we use a large collection of type-strain genomes from bacteroidetes and closely related ... | 2016 | 28066339 |
| draft genome sequence of cellulose-digesting bacterium sporocytophaga myxococcoides pg-01. | sporocytophaga myxococcoides, a gram-negative bacterium isolated from soil, is an efficient hydrolyzer of crystalline cellulose. here, we report its draft genome sequence, which may provide important genetic information regarding the cellulolytic and hemicellulolytic enzymes that contribute to the cellulose-degrading abilities of this bacterium. | 2014 | 25414493 |
| structure/function analysis of a type iii polyketide synthase in the brown alga ectocarpus siliculosus reveals a biochemical pathway in phlorotannin monomer biosynthesis. | brown algal phlorotannins are structural analogs of condensed tannins in terrestrial plants and, like plant phenols, they have numerous biological functions. despite their importance in brown algae, phlorotannin biosynthetic pathways have been poorly characterized at the molecular level. we found that a predicted type iii polyketide synthase in the genome of the brown alga ectocarpus siliculosus, pks1, catalyzes a major step in the biosynthetic pathway of phlorotannins (i.e., the synthesis of ph ... | 2013 | 23983220 |
| plasmid diversity in arctic strains of psychrobacter spp. | six strains of psychrobacter spp. isolated from guano of little auks collected on spitsbergen island (arctic) carried nine plasmids that were fully sequenced. these replicons (ranging in size from 2917 to 14924 bp) contained either repa (cole2-type) or repb (iteron-type) replication systems of a relatively narrow host range, limited to psychrobacter spp. all but one of the plasmids carried predicted mobilization for conjugal transfer systems, encoding relaxases of the mobq, mobv or mobp families ... | 2013 | 23479249 |
| crispr regulation of intraspecies diversification by limiting is transposition and intercellular recombination. | mobile genetic elements (mges) and genetic rearrangement are considered as major driving forces of bacterial diversification. previous comparative genome analysis of porphyromonas gingivalis, a pathogen related to periodontitis, implied such an important relationship. as a counterpart system to mges, clustered regularly interspaced short palindromic repeats (crisprs) in bacteria may be useful for genetic typing. we found that crispr typing could be a reasonable alternative to conventional method ... | 2013 | 23661565 |
| complete genome sequence of the aquatic bacterium runella slithyformis type strain (lsu 4(t)). | runella slithyformis larkin and williams 1978 is the type species of the genus runella, which belongs to the cytophagaceae, a family that was only recently classified to the order cytophagales in the class cytophagia. the species is of interest because it is able to grow at temperatures as low as 4°c. this is the first completed genome sequence of a member of the genus runella and the sixth sequence from the family cytophagaceae. the 6,919,729 bp long genome consists of a 6.6 mbp circular genome ... | 2012 | 22768358 |
| the genome of cardinium cbtq1 provides insights into genome reduction, symbiont motility, and its settlement in bemisia tabaci. | many insects harbor inherited bacterial endosymbionts. although some of them are not strictly essential and are considered facultative, they can be a key to host survival under specific environmental conditions, such as parasitoid attacks, climate changes, or insecticide pressures. the whitefly bemisia tabaci is at the top of the list of organisms inflicting agricultural damage and outbreaks, and changes in its distribution may be associated to global warming. in this work, we have sequenced and ... | 2014 | 24723729 |
| bacterial gras domain proteins throw new light on gibberellic acid response mechanisms. | gibberellic acids (gas) are key plant hormones, regulating various aspects of growth and development, which have been at the center of the 'green revolution'. gras family proteins, the primary players in ga signaling pathways, remain poorly understood. using sequence-profile searches, structural comparisons and phylogenetic analysis, we establish that the gras family first emerged in bacteria and belongs to the rossmann fold methyltransferase superfamily. all bacterial and a subset of plant gras ... | 2012 | 22829623 |
| a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes. | for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ... | 2016 | 26511485 |
| a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes. | for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ... | 2016 | 26511485 |
| autoantigen cross-reactive environmental antigen can trigger multiple sclerosis-like disease. | multiple sclerosis is generally considered an autoimmune disease resulting from interaction between predisposing genes and environmental factors, together allowing immunological self-tolerance to be compromised. the precise nature of the environmental inputs has been elusive, infectious agents having received considerable attention. a recent study generated an algorithm predicting naturally occurring t cell receptor (tcr) ligands from the proteome database. taking the example of a multiple scler ... | 2015 | 25962509 |
| multiple conversion between the genes encoding bacterial class-i release factors. | bacteria require two class-i release factors, rf1 and rf2, that recognize stop codons and promote peptide release from the ribosome. rf1 and rf2 were most likely established through gene duplication followed by altering their stop codon specificities in the common ancestor of extant bacteria. this scenario expects that the two rf gene families have taken independent evolutionary trajectories after the ancestral gene duplication event. however, we here report two independent cases of conversion b ... | 2015 | 26257102 |
| perspective for aquaponic systems: "omic" technologies for microbial community analysis. | aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. in this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. the nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. in this particular field, the microbial research, the "omic" technologies will allow a broader scope of studies about a cu ... | 2015 | 26509157 |
| plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. | extremely cold environments are a challenge for all organisms. they are mostly inhabited by psychrophilic and psychrotolerant bacteria, which employ various strategies to cope with the cold. such harsh environments are often highly vulnerable to the influence of external factors and may undergo frequent dynamic changes. the rapid adjustment of bacteria to changing environmental conditions is crucial for their survival. such "short-term" evolution is often enabled by plasmids-extrachromosomal rep ... | 2014 | 25426110 |
| high phylogenetic diversity of glycosyl hydrolase family 10 and 11 xylanases in the sediment of lake dabusu in china. | soda lakes are one of the most stable naturally occurring alkaline and saline environments, which harbor abundant microorganisms with diverse functions. in this study, culture-independent molecular methods were used to explore the genetic diversity of glycoside hydrolase (gh) family 10 and gh11 xylanases in lake dabusu, a soda lake with a ph value of 10.2 and salinity of 10.1%. a total of 671 xylanase gene fragments were obtained, representing 78 distinct gh10 and 28 gh11 gene fragments respecti ... | 2014 | 25392912 |