|
OmrA-B RNA
The OmrA-B RNA gene family (also known as SraE RNA, RygA and RygB and OmrA and OmrB) is a pair of homologous OmpR-regulated small non-coding RNA that was discovered in ''E. coli'' during two large-scale screens. OmrA-B is highly abundant in stationary phase, but low levels could be detected in exponentially growing cells as well. RygB is adjacent to RygA a closely related RNA. These RNAs bind to the Hfq protein and regulate gene expression by antisense binding. They negatively regulate the expression of several genes encoding outer membrane proteins, including cirA, CsgD, fecA, fepA and ompT by binding in the vicinity of the Shine-Dalgarno sequence, suggesting the control of these targets is dependent on Hfq protein and RNase E. Taken together, these data suggest that OmrA-B participates in the regulation of outer membrane composition, responding to environmental conditions. Together with the RNA chaperone Hfq, OmrA-B positively controls bacterial motility and negatively cont ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid Secondary Structure
Nucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNAs and RNAs tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar. In a non-biological context, secondary structure is a vital consideration in the nucleic acid design of nucleic acid structures for DNA nanotechnology and DNA computing, since the pattern of basepairing ultimately determines the overall structure of the molecules. Fundamental concepts Base pairing In molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RNase E
Ribonuclease E is a bacterial ribonuclease that participates in the processing of ribosomal RNA (9S to 5S rRNA) and the chemical degradation of bulk cellular RNA. Cellular localization RNase E was suggested to be a part of the cell membrane protein complex, as it sediments with ribosomes and crude membranes. Microscopy has localized tagged RNase E to the inner cytoplasmic membrane or a helical cytoskeletal structure closely associated with the inner layer. Protein structure This enzyme contains 1,061 residues and separates into two distinct functional regions, which are a large domain located at the 5’N-terminus and a small domain located at the 3’ C-terminus. While N-terminal half forms a catalytic domain, C-terminal half forms a degradosome scaffolding domain. A metal-binding pocket separates them in the middle of the RNase E protein structure. Although degradosome formation does not play a key role for E. coli growth, the deletion of the C-terminal half has bee ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OmpT
OmpT is an aspartyl protease found on the outer membrane of ''Escherichia coli''. OmpT is a subtype of the family of omptin proteases, which are found on some gram-negative species of bacteria. Structure OmpT is a 33.5 kDa outer membrane protein consisting of 10 antiparallel strands that are connected by 5 extracellular loops. The antiparallel strands form a beta barrel structure that spans the width of the membrane, creating a pore. ''E. coli'' omptins can be coded either from the ''OmpT'' gene on a chromosome (part of a DLP12 prophage) or from ''OmpP'' on a plasmid (OmpP). The sequences resulting from these two sources differ by 24-25% in the mature protease. Genetic differences between OmpT and other members of the omptin family are found in the extracellular loops, and therefore, this area is thought to be associated with substrate specificity. Also, the barrel is relatively rigid, while the loops have more flexibility to bind to substrates of varying sizes. Mechanism W ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FepA
Many bacteria secrete small iron-binding molecules called siderophores, which bind strongly to ferric ions. FepA is an integral bacterial outer membrane porin protein that belongs to outer membrane receptor family and provides the active transport of iron bound by the siderophore enterobactin from the extracellular space, into the periplasm of Gram-negative bacteria. FepA has also been shown to transport vitamin B12, and colicins B and D as well. This protein belongs to family of ligand-gated protein channels. Because no energy is directly available to the outer membrane, the energy to drive the transport of ferric-enterobactin by FepA originates from the proton motive force ( electrochemical gradient) generated by the inner membrane complex TonB–ExbB–ExbD. This force is relayed physically to FepA through direct interaction between FepA and TonB. Structure Using X-ray crystallography the structure of FepA was found to be a 724-residue 22-stranded β-barrel. T ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CsgD
CsgD is a transcription and response regulator protein referenced to as the master modulator of bacterial biofilm development. In ''E. coli'' cells, CsgD is tasked with aiding the transition from planktonic cell motility to the stationary phase of biofilm formation, in response to environmental growth factors. A transcription analysis assay (happening ''in vitro'') illustrated a heightened decrease in CsgD's DNA-binding capacity when phosphorylated at A.A. D59 of the protein's primary sequence. Therefore, in the protein's active form (unphosphorylated), CsgD is capable of carrying out its normal functions of regulating curli proteins ( fimbria) and producing ECM polysaccharides (cellulose Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units. Cellulose is an important structural component of the primary cell wall ...). Following a promoter-''lacZ'' fusion ass ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacterial Outer Membrane
The bacterial outer membrane is found in gram-negative bacteria. Its composition is distinct from that of the inner cytoplasmic cell membrane - among other things, the outer leaflet of the outer membrane of many gram-negative bacteria includes a complex lipopolysaccharide whose lipid portion acts as an endotoxin - and in some bacteria such as ''E. coli'' it is linked to the cell's peptidoglycan by Braun's lipoprotein. Porins can be found in this layer. Clinical significance If lipid A, part of the lipopolysaccharide, enters the circulatory system it causes a toxic reaction by activating toll like receptor TLR 4. Lipid A is very pathogenic and not immunogenic. However, the polysaccharide component is very immunogenic, but not pathogenic, causing an aggressive response by the immune system. The sufferer will have a high temperature and respiration rate and a low blood pressure. This may lead to endotoxic shock, which may be fatal. The bacterial outer membrane is physiologicall ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene
In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes (many different genes) as well as g ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene Expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product that enables it to produce end products, protein or non-coding RNA, and ultimately affect a phenotype, as the final effect. These products are often proteins, but in non-protein-coding genes such as transfer RNA (tRNA) and small nuclear RNA (snRNA), the product is a functional non-coding RNA. Gene expression is summarized in the central dogma of molecular biology first formulated by Francis Crick in 1958, further developed in his 1970 article, and expanded by the subsequent discoveries of reverse transcription and RNA replication. The process of gene expression is used by all known life— eukaryotes (including multicellular organisms), prokaryotes (bacteria and archaea), and utilized by viruses—to generate the macromolecular machinery for life. In genetics, gene expression is the most fundamental level at which the genotype gives rise to the phen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hfq Protein
The Hfq protein (also known as HF-I protein) encoded by the ''hfq'' gene was discovered in 1968 as an ''Escherichia coli'' host factor that was essential for replication of the bacteriophage Qβ. It is now clear that Hfq is an abundant bacterial RNA binding protein which has many important physiological roles that are usually mediated by interacting with Hfq binding sRNA. In ''E. coli'', Hfq mutants show multiple stress response related phenotypes. The Hfq protein is now known to regulate the translation of two major stress transcription factors ( σS (RpoS) and σE (RpoE) ) in Enterobacteria. It also regulates sRNA in ''Vibrio cholerae'', a specific example being MicX sRNA. In ''Salmonella typhimurium'', Hfq has been shown to be an essential virulence factor as its deletion attenuates the ability of ''S.typhimurium'' to invade epithelial cells, secrete virulence factors or survive in cultured macrophages. In ''Salmonella'', Hfq deletion mutants are also non motile and exhibit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
