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At least 1,369 records · Page 76Linked to original sources
PubMed1994

Genetics and biochemistry of dehalogenating enzymes.

Microorganisms that can utilize halogenated compounds as a growth substrate generally produce-enzymes whose function is carbon-halogen bond cleavage. Based on substrate range, reaction type and gene sequences, the dehalogenating enzymes can be classified in different groups, including hydrolytic dehalogenases, glutathione transferases, monooxygenases and hydratases. X-ray crystallographic and biochemical studies have provided detailed mechanistic insight into the action of haloalkane dehalogenase. The essential features are nucleophilic substitution of the halogen by a carboxylate group and the presence of a distinct halogen binding site, formed by tryptophan residues. This review summaries current knowledge on a variety of other dehalogenating enzymes and indicates the existence of a widespread and diverse microbial potential for dechlorination of natural and xenobiotic halogenated compounds.

Amino Acid Sequence↗
PubMed2005

Type III secretion: more systems than you think.

The type III secretion (T3S) pathway allows bacteria to inject effector proteins into the cytosol of target animal or plant cells. T3S systems evolved into seven families that were distributed among Gram-negative bacteria by horizontal gene transfer. There are probably a few hundred effectors interfering with control and signaling in eukaryotic cells and offering a wealth of new tools to cell biologists.

Animals↗
PubMed2003

Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes.

BACKGROUND: Peptidoglycan is hydrolyzed by a diverse set of enzymes during bacterial growth, development and cell division. The N1pC/P60 proteins define a family of cell-wall peptidases that are widely represented in various bacterial lineages. Currently characterized members are known to hydrolyze D-gamma-glutamyl-meso-diaminopimelate or N-acetylmuramate-L-alanine linkages. RESULTS: Detailed analysis of the N1pC/P60 peptidases showed that these proteins define a large superfamily encompassing several diverse groups of proteins. In addition to the well characterized P60-like proteins, this superfamily includes the AcmB/LytN and YaeF/YiiX families of bacterial proteins, the amidase domain of bacterial and kinetoplastid glutathionylspermidine synthases (GSPSs), and several proteins from eukaryotes, phages, poxviruses, positive-strand RNA viruses, and certain archaea. The eukaryotic members include lecithin retinol acyltransferase (LRAT), nematode developmental regulator Egl-26, and candidate tumor suppressor H-rev107. These eukaryotic proteins, along with the bacterial YaeF/poxviral G6R family, show a circular permutation of the catalytic domain. We identified three conserved residues, namely a cysteine, a histidine and a polar residue, that are involved in the catalytic activities of this superfamily. Evolutionary analysis of this superfamily shows that it comprises four major families, with diverse domain architectures in each of them. CONCLUSIONS: Several related, but distinct, catalytic activities, such as murein degradation, acyl transfer and amide hydrolysis, have emerged in the N1pC/P60 superfamily. The three conserved catalytic residues of this superfamily are shown to be equivalent to the catalytic triad of the papain-like thiol peptidases. The predicted structural features indicate that the N1pC/P60 enzymes contain a fold similar to the papain-like peptidases, transglutaminases and arylamine acetyltransferases.

Amino Acid Sequence↗
PubMed2000

[Thermophiles and life science in space].

Thermophiles are microorganisms that can grow at temperatures higher than 50 or 60 degrees C. There are thermophilic eubacteria and thermophilic archaebacteria. Thermophilic microorganisms can be found geothermally and hydrothermally active area. The water penetrates into deep subsurface around thermal area and reacts with hot basalt. Some of the compounds in the water are reduced by the reaction. The water returned to the surface and reacts with seawater or air, depending on the location of the thermal area. Many types of autotrophes and heterotrophes were found near thermally active area. The microorganisms form the ecosystem based on the redox chemical reactions. All of the structural elements in thermophilic microorganisms are thermophilic or thermostable. Proteins found in microorganisms are thermostable. Though several common characteristics can be found in thermostable proteins, it is not easy to attribute the stability to specific amino acid residues. DNA in thermophiles is stabilized by increasing the G+C content or by histone-like DNA binding proteins. There are several molecular biological and geological evidences to support the relation between ancient life forms and thermal activity on the Earth. Thermophiles of different life forms may be found in thermally active area, in such as those that may be present in satellites of Jupiter.

Archaea↗
PubMed2003

DNA mismatch repair and cancer.

DNA mismatch repair (MMR) is an important genome caretaker system. It ensures genomic stability by correcting mismatches generated during DNA replication and recombination and by triggering apoptosis of cells with large amounts of DNA damage. Protein components responsible for these reactions are highly conserved through evolution, and homologs of bacterial MutS and MutL, which are key players in the initiation steps of both the strand-specific mismatch correction and MMR-dependent apoptotic signaling, have been identified in human cells. Inactivation of genes encoding these activities leads to genome-wide instability, particularly in simple repetitive sequences, and predisposition to certain types of cancer, including hereditary non-polyposis colorectal cancer.

Animals↗
PubMedDate not supplied

[Competence pheromones in bacteria].

This article deals with general concepts concerning bacterial pheromones, including sex pheromones. The data on the structure and mode of action of competence pheromones in streptococci and bacilli are discussed, raising the question of the selective value of the process of genetic transformation of bacterial life activities and evolution.

Bacillus↗
PubMed1992

[Control of homologous recombination by mismatch base repair system in bacteria: implications concerning the chromosome stability and the evolution of species].

The generalized mismatch repair system controls, in bacteria, the homologous recombination between diverged (homologous) DNA. It thus constitute, together with the sequence divergence, a barrier to recombination between bacteria of different species as we have shown for E. coli and S. typhimurium. It is moreover, by preventing the recombination between diverged repeated sequences, a key component of the chromosome stability.

Biological Evolution↗
PubMed1991

Bioreactor and process design for large-scale mammalian cell culture manufacturing.

Good Manufacturing Practice for pharmaceuticals requires that the manufacturing processes be controlled and reproducible. The biological nature of cell culture-based processes lends them an inherently higher variability than is generally found for processes involving production of defined chemical entities. As one regulatory body has pointed out, this places a greater emphasis on in-process controls and adherence to GMPs in the manufacture of cell culture products. Design of bioreactors and associated process control systems is a key element in the successful implementation of a commercial-scale cell culture manufacturing process capable of meeting such high standards. It should be noted that reactor and control system designs for animal cell culture are still very much in a state of evolution from the modified bacterial fermentation systems that currently predominate, and it is difficult to predict how design strategies may change in the coming years. Having said this, however, it should be clear from the information presented here that satisfactory processes can be devised today using proven equipment configurations such as the stirred-tank reactor.

Animals↗
PubMed2005

The Obg subfamily of bacterial GTP-binding proteins: essential proteins of largely unknown functions that are evolutionarily conserved from bacteria to humans.

Members of the Obg subfamily of small GTP-binding proteins (called Obg, CgtA, ObgE or YhbZ in different bacterial species) have been found in various prokaryotic and eukaryotic organisms, ranging from bacteria to humans. Although serious changes in phenotypes are observed in mutant bacteria devoid of Obg or its homologues, specific roles of these GTP-binding proteins remain largely unknown. Recent genetic and biochemical studies, as well as determination of the structures of Obg proteins from Bacillus subtilis and Thermus thermophilus, shed new light on the possible functions of the members of the Obg subfamily and may constitute a starting point for the elucidation of their exact biological role.

Bacterial Proteins↗
PubMed1990

Mapping the active site of yeast RNA polymerase B (II).

Yeast RNA polymerase B (II) was incubated with a collection of 13 different nucleotide derivatives and affinity labeled by allowing DNA-directed phosphodiester bond formation. The 32P-labeled site was localized in the C-terminal part of the B150 subunit by microsequencing a proteolytic fragment, then further mapped by a combination of extensive or single-hit chemical cleavage reactions and analysis of the labeled peptide patterns. The affinity label was mapped to between Asn946 and Met999, within one of the nine regions that are conserved between B150 and the bacterial beta subunit. The results underscore the conservative evolution of the catalytic center of eukaryotic and bacterial RNA polymerases.

Amino Acid Sequence↗
PubMed1988

Genetic analysis of bacterial cell division.

A relatively small number of cell division genes have been identified in Escherichia coli. The available evidence, however, suggests that several of these genes play a crucial role in the process.

Bacteria↗