|
TxpA-RatA Toxin-antitoxin System
__NOTOC__ The TxpA/RatA toxin-antitoxin system was first identified in '' Bacillus subtilis''. It consists of a non-coding 222nt sRNA called RatA (RNA anti-toxin A) and a protein toxin named TxpA (Toxic protein A). RatA was discovered in intergenic regions of the ''B. subtilis'' genome, in a 728-nucleotide region between genes ''yqdB'' (later renamed ''TxpA'') and ''yqbM''. Initially, Affymetrix microarrays were used to detect transcription in this region, Northern blot experiments and mutation analysis were then employed to characterise the RNA transcript. ''ratA'' and ''txpA'' are transcribed convergently, and have an overlap of 75 base pairs at their 3' ends, providing an area of complementarity. The RatA transcript binds with the TxpA mRNA across the complementary region and the dsRNA is then degraded by an uncharacterised RNase E equivalent, preventing translation of the toxic TxpA protein. Genes ''ratA'' and ''txpA'' are found within a 48 kb phage-like element called ''sk ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Antisense RNA
Antisense RNA (asRNA), also referred to as antisense transcript, natural antisense transcript (NAT) or antisense oligonucleotide, is a single stranded RNA that is complementary to a protein coding messenger RNA (mRNA) with which it hybridizes, and thereby blocks its translation into protein. asRNAs (which occur naturally) have been found in both prokaryotes and eukaryotes, and can be classified into short (200 nucleotides) non-coding RNAs (ncRNAs). The primary function of asRNA is regulating gene expression. asRNAs may also be produced synthetically and have found wide spread use as research tools for gene knockdown. They may also have therapeutic applications. Discovery and history in drug development Some of the earliest asRNAs were discovered while investigating functional proteins. An example was micF asRNA. While characterizing the outer membrane porin in ''E.coli'', some of the promoter clones observed were capable of repressing the expression of other membrane porin s ... [...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] |
Bacillus Subtilis BSR SRNAs
In a screen of the ''Bacillus subtilis'' genome for genes encoding ncRNAs, Saito et al. focused on 123 intergenic regions (IGRs) over 500 base pairs in length, the authors analyzed expression from these regions. Seven IGRs termed bsrC, bsrD, bsrE, bsrF, bsrG, bsrH and bsrI expressed RNAs smaller than 380 nt. All the small RNAs except BsrD RNA were expressed in transformed ''Escherichia coli'' cells harboring a plasmid with PCR-amplified IGRs of ''B. subtilis'', indicating that their own promoters independently express small RNAs. Under non-stressed condition, depletion of the genes for the small RNAs did not affect growth. Although their functions are unknown, gene expression profiles at several time points showed that most of the genes except for bsrD were expressed during the vegetative phase (4–6 h), but undetectable during the stationary phase (8 h). Mapping the 5' ends of the 6 small RNAs revealed that the genes for BsrE, BsrF, BsrG, BsrH, and BsrI RNAs are preceded by a rec ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
RdlD RNA
RdlD RNA (regulator detected in LDR-D) is a family of small non-coding RNAs which repress the protein LdrD in a type I toxin-antitoxin system. It was discovered in ''Escherichia coli'' strain K-12 in a long direct repeat (LDR) named LDR-D. This locus encodes two products: a 35 amino acid peptide toxin (ldrD) and a 60 nucleotide RNA antitoxin. The 374nt toxin mRNA has a half-life of around 30 minutes while rdlD RNA has a half-life of only 2 minutes. This is in keeping with other type I toxin-antitoxin systems. Northern blots showed that ''ldrD'' and ''rdlD'' are both transcribed and primer extension analysis showed the rdlD transcript is not translated. Homologues exist in related Enterobacteriaceae such as ''Salmonella enterica'' and ''Shigella boydii''. The Ldr peptide genes that have been discovered are thought to have evolved from a common ancestor. LDR sequences Four long direct repeat (LDR) sequences were identified during genetic sequencing of a 718 kb segment of the ''E ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hok/sok System
The hok/sok system is a postsegregational killing mechanism employed by the R1 plasmid in ''Escherichia coli''. It was the first type I toxin-antitoxin pair to be identified through characterisation of a plasmid-stabilising locus. It is a type I system because the toxin is neutralised by a complementary RNA, rather than a partnered protein (type II toxin-antitoxin). Genes involved The hok/sok system involves three genes: * ''hok'', host killing - a long lived (half-life 20 minutes) toxin * ''sok'', suppression of killing - a short lived (half-life 30 seconds) RNA antitoxin * ''mok'', modulation of killing - required for ''hok'' translation Killing mechanism When ''E. coli'' undergoes cell division, the two daughter cells inherit the long-lived hok toxin from the parent cell. Due to the short half-life of the sok antitoxin, daughter cells inherit only small amounts and it quickly degrades. If a daughter cell has inherited the R1 plasmid, it has inherited the ''sok'' gene and a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Toxin-antitoxin System
A toxin-antitoxin system is a set of two or more closely linked genes that together encode both a "toxin" protein and a corresponding "antitoxin". Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK). Toxin-antitoxin systems are typically classified according to how the antitoxin neutralises the toxin. In a type I toxin-antitoxin system, the translation of messenger RNA (mRNA) that encodes the toxin is inhibited by the binding of a small non-coding RNA antitoxin that binds the toxin mRNA. The toxic protein in a type II system is inhibited post-translationally ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gene-centered View Of Evolution
With gene defined as "not just one single physical bit of DNA utall replicas of a particular bit of DNA distributed throughout the world", the gene-centered view of evolution, gene's eye view, gene selection theory, or selfish gene theory holds that adaptive evolution occurs through the differential survival of competing genes, increasing the allele frequency of those alleles whose phenotypic trait effects successfully promote their own propagation. The proponents of this viewpoint argue that, since heritable information is passed from generation to generation almost exclusively by DNA, natural selection and evolution are best considered from the perspective of genes. Proponents of the gene-centered viewpoint argue that it permits understanding of diverse phenomena such as altruism and intragenomic conflict that are otherwise difficult to explain from an organism-centered viewpoint. The gene-centered view of evolution is a synthesis of the theory of evolution by natural sele ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sporulation
In biology, a spore is a unit of sexual or asexual reproduction that may be adapted for dispersal and for survival, often for extended periods of time, in unfavourable conditions. Spores form part of the life cycles of many plants, algae, fungi and protozoa. Bacterial spores are not part of a sexual cycle, but are resistant structures used for survival under unfavourable conditions. Myxozoan spores release amoeboid infectious germs ("amoebulae") into their hosts for parasitic infection, but also reproduce within the hosts through the pairing of two nuclei within the plasmodium, which develops from the amoebula. In plants, spores are usually haploid and unicellular and are produced by meiosis in the sporangium of a diploid sporophyte. Under favourable conditions the spore can develop into a new organism using mitotic division, producing a multicellular gametophyte, which eventually goes on to produce gametes. Two gametes fuse to form a zygote which develops into a new sporo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
Skin Element
Skin is the layer of usually soft, flexible outer tissue covering the body of a vertebrate animal, with three main functions: protection, regulation, and sensation. Other animal coverings, such as the arthropod exoskeleton, have different developmental origin, structure and chemical composition. The adjective cutaneous means "of the skin" (from Latin ''cutis'' 'skin'). In mammals, the skin is an organ of the integumentary system made up of multiple layers of ectodermal tissue and guards the underlying muscles, bones, ligaments, and internal organs. Skin of a different nature exists in amphibians, reptiles, and birds. Skin (including cutaneous and subcutaneous tissues) plays crucial roles in formation, structure, and function of extraskeletal apparatus such as horns of bovids (e.g., cattle) and rhinos, cervids' antlers, giraffids' ossicones, armadillos' osteoderm, and os penis/os clitoris. All mammals have some hair on their skin, even marine mammals like whales, dolphins, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bacteriophage
A bacteriophage (), also known informally as a ''phage'' (), is a duplodnaviria virus that infects and replicates within bacteria and archaea. The term was derived from "bacteria" and the Greek φαγεῖν ('), meaning "to devour". Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are either simple or elaborate. Their genomes may encode as few as four genes (e.g. MS2) and as many as hundreds of genes. Phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere. Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It is estimated there are more than 1031 bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined. Viruses are the most abundant biological entity in the water column of the world's oceans, and the second largest component of biom ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Kilobase
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" (or "Watson–Crick–Franklin") base pairs (guanine–cytosine and adenine–thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The complementary nature of this based-paired structure provides a redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins ca ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
_.png "Click for more on -> Antisense RNA")
