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Sigma Factor
A sigma factor (σ factor or specificity factor) is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it. They are also found in plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP). The sigma factor, together with RNA polymerase, is known as the RNA polymerase holoenzyme. Every molecule of RNA polymerase holoenzyme contains exactly one sigma factor subunit, which in the model bacterium ''Escherichia coli'' is one of those listed below. The number of sigma f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transcription (biology)
Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA (mRNA). Other segments of DNA are copied into RNA molecules called non-coding RNAs (ncRNAs). mRNA comprises only 1–3% of total RNA samples. Less than 2% of the human genome can be transcribed into mRNA ( Human genome#Coding vs. noncoding DNA), while at least 80% of mammalian genomic DNA can be actively transcribed (in one or more types of cells), with the majority of this 80% considered to be ncRNA. Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. Transcription proceeds in the following general steps: # RNA polymerase, together with one or more general transcription factors, binds to promoter ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RpoE
The gene ''rpoE'' (RNA polymerase, extracytoplasmic E) encodes the sigma factor ''sigma-24'' (σ24, sigma E, or RpoE), a protein in ''Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...'' and other species of bacteria. Depending on the bacterial species, this gene may be referred to as ''sigE''. RpoE appears to be necessary for the exocytoplasmic stress response. ''E. coli'' mutants without ''rpoE'' cannot grow at high temperatures (that is, above 42 degrees C) and show growth defects at lower temperatures, though this may be due to compensatory mutations. In some bacterial species, such as '' Clostridium botulinum'', this sigma factor may be necessary for sporulation. The stress response regulation activities of RpoE are modulated by the Hfq protein in ''E. coli'' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fluorescence Resonance Energy Transfer
Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence. In most cases, the emitted light has a longer wavelength, and therefore a lower photon energy, than the absorbed radiation. A perceptible example of fluorescence occurs when the absorbed radiation is in the ultraviolet region of the electromagnetic spectrum (invisible to the human eye), while the emitted light is in the visible region; this gives the fluorescent substance a distinct color that can only be seen when the substance has been exposed to UV light. Fluorescent materials cease to glow nearly immediately when the radiation source stops, unlike phosphorescent materials, which continue to emit light for some time after. Fluorescence has many practical applications, including mineralogy, gemology, medicine, chemical sensors (fluorescence spectroscopy), fluorescent labelling, dyes, biological detectors, cosmic-ray detection, vacuum ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Holoenzyme
Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as product (chemistry), products. Almost all metabolism, metabolic processes in the cell (biology), cell need enzyme catalysis in order to occur at rates fast enough to sustain life. Metabolic pathways depend upon enzymes to catalyze individual steps. The study of enzymes is called ''enzymology'' and the field of pseudoenzyme, pseudoenzyme analysis recognizes that during evolution, some enzymes have lost the ability to carry out biological catalysis, which is often reflected in their amino acid sequences and unusual 'pseudocatalytic' properties. Enzymes are known to catalyze more than 5,000 biochemical reaction types. Other biocatalysts are Ribozyme, catalytic RNA molecules, called ribozymes. Enzymes' Chemical specificity, specificity comes from their u ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pribnow Box
The Pribnow box (also known as the Pribnow-Schaller box) is a sequence of ''TATAAT'' of six nucleotides (thymine, adenine, thymine, etc.) that is an essential part of a promoter site on DNA for transcription to occur in bacteria. It is an idealized or consensus sequence—that is, it shows the most frequently occurring base at each position in many promoters analyzed; individual promoters often vary from the consensus at one or more positions. It is also commonly called the -10 sequence, because it is centered roughly ten base pairs upstream from the site of initiation of transcription. The Pribnow box has a function similar to the TATA box that occurs in promoters in eukaryotes and archaea: it is recognized and bound by a subunit of RNA polymerase during initiation of transcription. This region of the DNA is also the first place where base pairs separate during prokaryotic transcription to allow access to the template strand. The AT-richness is important to allow this separ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sigma 70 Domains
Sigma (; uppercase Σ, lowercase σ, lowercase in word-final position ς; grc-gre, σίγμα) is the eighteenth letter of the Greek alphabet. In the system of Greek numerals, it has a value of 200. In general mathematics, uppercase Σ is used as an operator for summation. When used at the end of a letter-case word (one that does not use all caps), the final form (ς) is used. In ' (Odysseus), for example, the two lowercase sigmas (σ) in the center of the name are distinct from the word-final sigma (ς) at the end. The Latin letter S derives from sigma while the Cyrillic letter Es derives from a lunate form of this letter. History The shape (Σς) and alphabetic position of sigma is derived from the Phoenician letter ( ''shin''). Sigma's original name may have been ''san'', but due to the complicated early history of the Greek epichoric alphabets, ''san'' came to be identified as a separate letter in the Greek alphabet, represented as Ϻ. Herodotus reports that "san" ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Anti-sigma Factors
In the regulation of gene expression in prokaryotes, anti-sigma factors bind to sigma factors and inhibit transcriptional activity. Anti-sigma factors have been found in a number of bacteria, including ''Escherichia coli'' and ''Salmonella'', and in the T4 bacteriophage. Anti-sigma factors are antagonists to the sigma factors, which regulate numerous cell processes including flagellar production, stress response, transport and cellular growth. For example, anti-sigma factor 70 Rsd in ''E. coli'' is present in the stationary phase and blocks the activity of sigma factor 70 which in essence initiates gene transcription. This allows the sigma S factor to associate with RNA polymerase and direct the expression of the stationary genes. Although binding of Rsd to σ70 has been shown and numerous structural studies on Rsd have been performed, the detailed mechanism of action is still unknown. General information Sigma factor is an important protein which starts the transcription by bi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RpoN
The gene ''rpoN'' (RNA polymerase, nitrogen-limitation N) encodes the sigma factor ''sigma-54'' (σ54, sigma N, or RpoN), a protein in ''Escherichia coli ''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus ''Escher ...'' and other species of bacteria. RpoN antagonizes RpoS sigma factors. Biological role Originally identified as a regulator of genes involved in nitrogen metabolism and assimilation under nitrogen limiting conditions, ''E. coli'' σ54 has since been shown to play important regulatory roles in a variety of other cellular processes. Similarly, σ54 homologues in other species regulate a wide range of processes, including flagellar synthesis and virulence. Sequence specificity and mechanism of action σ54 promoter elements consist of conserved nucleotides located at −12 and −2 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RpoS
The gene ''rpoS'' (RNA polymerase, sigma S, also called katF) encodes the sigma factor ''sigma-38'' (σ38, or RpoS), a 37.8 kD protein in ''Escherichia coli''. Sigma factors are proteins that regulate transcription in bacteria. Sigma factors can be activated in response to different environmental conditions. ''rpoS'' is transcribed in late exponential phase, and RpoS is the primary regulator of stationary phase genes. RpoS is a central regulator of the general stress response and operates in both a retroactive and a proactive manner: it not only allows the cell to survive environmental challenges, but it also prepares the cell for subsequent stresses (cross-protection). The transcriptional regulator CsgD is central to biofilm formation, controlling the expression of the curli structural and export proteins, and the diguanylate cyclase, adrA, which indirectly activates cellulose production. The ''rpoS'' gene most likely originated in the gammaproteobacteria. Environmental signal ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteases
A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalyzes (increases reaction rate or "speeds up") proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products. They do this by cleaving the peptide bonds within proteins by hydrolysis, a reaction where water breaks bonds. Proteases are involved in many biological functions, including digestion of ingested proteins, protein catabolism (breakdown of old proteins), and cell signaling. In the absence of functional accelerants, proteolysis would be very slow, taking hundreds of years. Proteases can be found in all forms of life and viruses. They have independently evolved multiple times, and different classes of protease can perform the same reaction by completely different catalytic mechanisms. Hierarchy of proteases Based on catalytic residue Proteases can be classified into seven broad groups: * Serine proteases - ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chaperone (protein)
In molecular biology, molecular chaperones are proteins that assist the conformational folding or unfolding of large proteins or macromolecular protein complexes. There are a number of classes of molecular chaperones, all of which function to assist large proteins in proper protein folding during or after synthesis, and after partial denaturation. Chaperones are also involved in the translocation of proteins for proteolysis. The first molecular chaperones discovered were a type of assembly chaperones which assist in the assembly of nucleosomes from folded histones and DNA. One major function of molecular chaperones is to prevent the aggregation of misfolded proteins, thus many chaperone proteins are classified as heat shock proteins, as the tendency for protein aggregation is increased by heat stress. The majority of molecular chaperones do not convey any steric information for protein folding, and instead assist in protein folding by binding to and stabilizing folding interme ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Heat Shock Response
The heat shock response (HSR) is a cell stress response that increases the number of molecular chaperones to combat the negative effects on proteins caused by stressors such as increased temperatures, oxidative stress, and heavy metals. In a normal cell, proteostasis (protein homeostasis) must be maintained because proteins are the main functional units of the cell. Many proteins take on a defined configuration in a process known as protein folding in order to perform their biological functions. If these structures are altered, critical processes could be affected, leading to cell damage or death. The heat shock response can be employed under stress to induce the expression of heat shock proteins (HSP), many of which are molecular chaperones, that help prevent or reverse protein misfolding and provide an environment for proper folding. Protein folding is already challenging due to the crowded intracellular space where aberrant interactions can arise; it becomes more diff ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
