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FlmB RNA
The FlmA-FlmB toxin-antitoxin system consists of FlmB RNA (F leading-region maintenance B), a family of non-coding RNAs and the protein toxin FlmA. The FlmB RNA transcript is 100 nucleotides in length and is homologous to sok RNA from the hok/sok system and fulfills the identical function as a post-segregational killing (PSK) mechanism. flmB is found on the F-plasmid of ''Escherichia coli'' and ''Salmonella enterica''. It is responsible for stabilising the plasmid. If the plasmid is not inherited, long-lived FlmA mRNA and protein will be highly toxic to the cell, possibly to the point of causing cell death. Daughter cells which inherit the plasmid inherit the ''FlmB'' gene, coding for FlmB RNA which binds the leader sequence of FlmA mRNA and represses its translation. See also *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 wi ... [...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] |
Plasmid
A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria; however, plasmids are sometimes present in archaea and eukaryotic organisms. In nature, plasmids often carry genes that benefit the survival of the organism and confer selective advantage such as antibiotic resistance. While chromosomes are large and contain all the essential genetic information for living under normal conditions, plasmids are usually very small and contain only additional genes that may be useful in certain situations or conditions. Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation. Synthetic plasmids are available for procurement over the inter ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PtaRNA1
PtaRNA1 (plasmid transferred antisense RNA) is a family of non-coding RNAs. Homologs of PtaRNA1 can be found in the bacterial families, Betaproteobacteria and Gammaproteobacteria. In all cases the PtaRNA1 is located anti-sense to a short protein-coding gene. In ''Xanthomonas campestris'' pv. ''vesicatoria'', this gene is annotated aXCV2162and is included in the plasmid toxin family of proteins. Distribution and function Both PtaRNA1 and the adjacent coding gene, which only appear only in combination, have an erratic phylogenetic distribution. The distribution of ''ptaRNA1'' is not congruent with the phylogeny of the host species as it is with other sRNA families such as Yfr1 and Yfr2. This indicates that ptaRNA1 has undergone frequent horizontal gene transfer. These observations are in accordance with those made of Type I toxin-antitoxin systems. In type I toxin-antitoxin systems, the gene expression of a toxic protein is regulated by a small non-coding RNA. Type I toxin-an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SymR RNA
__NOTOC__ The SymE-SymR toxin-antitoxin system consists of a small symbiotic endonuclease toxin, SymE, and a non-coding RNA symbiotic RNA antitoxin, SymR, which inhibits SymE translation. SymE-SymR is a type I toxin-antitoxin system, and is under regulation by the antitoxin, SymR. The SymE-SymR complex is believed to play an important role in recycling damaged RNA and DNA. The relationship and corresponding structures of SymE and SymR provide insight into the mechanism of toxicity and overall role in prokaryotic systems. Discovery SymR was originally labelled RyjC and is a 77 nucleotide (nt) RNA with a σ70 promoter. RyjC was found to overlap the ''yjiW'' open reading frame on the opposite strand by 6 nt, and was characterized as an antisense RNA which bound the 5' untranslated region of ''yjiW''. Further study led to the renaming of both ''yjiW'' and RyjC to SymE (SOS-induced yjiW gene with similarity tMazE and SymR, respectively. Despite similarities to the AbrB superfamily ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sib RNA
Sib RNA refers to a group of related non-coding RNA. They were originally named QUAD RNA after they were discovered as four repeat elements in ''Escherichia coli'' intergenic regions. The family was later renamed Sib (for short intergenic abundant sequences) when it was discovered that the number of repeats is variable in other species and in other ''E. coli'' strains. Identification These small RNA were identified computationally by searching the genome of ''E. coli'' for intergenic regions of high sequence identity (sequence conservation) with the genomes of closely related bacteria (several salmonella species and ''Klebsiella pneumoniae''). This data was combined with microarray expression analysis and potential novel ncRNAs identified. The expression of novel ncRNA of interest was confirmed by northern blotting. In this large scale screen these ncRNAs were simply referred to as candidates 43, 55 and 61. These 3 ncRNA appear to be highly homologous and are derived from a rep ... [...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] |
IstR RNA
The TisB-IstR toxin-antitoxin system is the first known toxin-antitoxin system which is induced by the SOS response in response to DNA damage. IstR-1 and IstR-2 IstR sRNA (inhibitor of SOS-induced toxicity by RNA) is a family of non-coding RNA first identified in ''Escherichia coli''. There are two small RNAs encoded by the IstR locus: IstR-1 and IstR-2, of which IstR-1 works as antitoxins against the toxic proteinbr>TisB(toxicity-induced by SOS B) which is encoded by the neighbouring ''tisAB'' gene. IstR-1 is a 75 nucleotide transcript expressed constitutively throughout growth, whereas IstR-2 is a 140 nucleotide transcript induced by Mitomycin C (MMC). Both IstR-2 and ''tisAB'' are thought to be regulated by LexA while IstR-1 is constitutively transcribed. Deletion analysis confirmed the function of IstR, ''E. coli'' strain K-12 could not grow in the absence of IstR when ''tisAB'' was present. Inserting IstR genes on a plasmid allowed the bacteria to grow normally. Further studi ... [...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] |
Translation (genetics)
In molecular biology and genetics, translation is the process in which ribosomes in the cytoplasm or endoplasmic reticulum synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus. The entire process is called gene expression. In translation, messenger RNA (mRNA) is decoded in a ribosome, outside the nucleus, to produce a specific amino acid chain, or polypeptide. The polypeptide later folds into an active protein and performs its functions in the cell. The ribosome facilitates decoding by inducing the binding of complementary tRNA anticodon sequences to mRNA codons. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is "read" by the ribosome. Translation proceeds in three phases: # Initiation: The ribosome assembles around the target mRNA. The first tRNA is attached at the start codon. # Elongation: The last tRNA validated by the small ribosomal subunit (''accommodation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Five Prime Untranslated Region
The 5′ untranslated region (also known as 5′ UTR, leader sequence, transcript leader, or leader RNA) is the region of a messenger RNA (mRNA) that is directly upstream from the initiation codon. This region is important for the regulation of translation of a transcript by differing mechanisms in viruses, prokaryotes and eukaryotes. While called untranslated, the 5′ UTR or a portion of it is sometimes translated into a protein product. This product can then regulate the translation of the main coding sequence of the mRNA. In many organisms, however, the 5′ UTR is completely untranslated, instead forming a complex secondary structure to regulate translation. The 5′ UTR has been found to interact with proteins relating to metabolism, and within the 5′ UTR. In addition, this region has been involved in transcription regulation, such as the sex-lethal gene in ''Drosophila''. Regulatory elements within 5′ UTRs have also been linked to mRNA export. General structure Le ... [...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 gen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Programmed Cell Death
Programmed cell death (PCD; sometimes referred to as cellular suicide) is the death of a cell as a result of events inside of a cell, such as apoptosis or autophagy. PCD is carried out in a biological process, which usually confers advantage during an organism's lifecycle. For example, the differentiation of fingers and toes in a developing human embryo occurs because cells between the fingers apoptose; the result is that the digits are separate. PCD serves fundamental functions during both plant and animal tissue development. Apoptosis and autophagy are both forms of programmed cell death. Necrosis is the death of a cell caused by external factors such as trauma or infection and occurs in several different forms. Necrosis was long seen as a non-physiological process that occurs as a result of infection or injury, but in the 2000s, a form of programmed necrosis, called necroptosis, was recognized as an alternative form of programmed cell death. It is hypothesized that necroptosis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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