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Yfr2
Yfr2 (cYanobacterial functional RNA-2 later published as Cyano-1 RNA motif) is a family of non-coding RNAs. Members of the Yrf2 family have been identified in almost all studied species of cyanobacteria. The family was identified through a bioinformatics screen of published cyanobacterial genomes, having previously been grouped in a family of Yfr2–5. The cyano-1 RNA motif family is essentially a synonym for Yfr2, although Cyano-1 does not include the terminator sequence and Yfr2 does. The function of this ncRNA is unknown, though it has been hypothesised that family members interact with RNA targets through kissing complexes using their highly conserved exposed central consensus element (CSE: IUPAC 5′-RKT SGA AAC WHG GHM ASA M-3′). Earlier studies noted a similarity to quorum sensing ncRNAs in ''Vibrio'' bacteria. The family can be divided into two subgroups, one found in marine cyanobacteria (e.g. the ''Prochlorococcus'' and ''Synechococcus'' genera) and the other from ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cyano-2 RNA Motif
The Cyano-2 RNA motif is a conserved RNA structure identified by bioinformatics. Cyano-2 RNAs are found in Cyanobacterial species classified within the genus ''Synechococcus''. Many terminal loops in the two conserved stem-loops contain the nucleotide sequence GCGA, and these sequences might in some cases form stable GNRA tetraloops. Since the two stem-loops are somewhat distant from one another it is possible that they represent two independent non-coding RNAs that are often or always co- transcribed. The region one thousand base pairs upstream of predicted Cyano-2 RNAs is usually devoid of annotated features such as RNA or protein-coding genes. This absence of annotated genes within one thousand base pairs is relatively unusual within bacteria. See also * Yfr1 *Yfr2 Yfr2 (cYanobacterial functional RNA-2 later published as Cyano-1 RNA motif) is a family of non-coding RNAs. Members of the Yrf2 family have been identified in almost all studied species of cyanobacteria. The ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Yfr1
Yfr1 is a Cyanobacterial functional RNA that was identified by a comparative genome based screen for RNAs in cyanobacteria. Further analysis has shown that the RNA is well conserved and highly expressed in cyanobacteria. and is required for growth under several stress condition Bioinformatics research combined with follow-up experiments have shown that Yfr1 inhibits the translation of the proteins PMM1119 and PMM1121 by an antisense interaction by base pairing at the ribosomal binding site. See also * Yfr2 RNA * Cyano-S1 RNA motif * Cyano-2 RNA motif The Cyano-2 RNA motif is a conserved RNA structure identified by bioinformatics. Cyano-2 RNAs are found in Cyanobacterial species classified within the genus ''Synechococcus''. Many terminal loops in the two conserved stem-loops contain the nuc ... References External links * Non-coding RNA Antisense RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Yfr1
Yfr1 is a Cyanobacterial functional RNA that was identified by a comparative genome based screen for RNAs in cyanobacteria. Further analysis has shown that the RNA is well conserved and highly expressed in cyanobacteria. and is required for growth under several stress condition Bioinformatics research combined with follow-up experiments have shown that Yfr1 inhibits the translation of the proteins PMM1119 and PMM1121 by an antisense interaction by base pairing at the ribosomal binding site. See also * Yfr2 RNA * Cyano-S1 RNA motif * Cyano-2 RNA motif The Cyano-2 RNA motif is a conserved RNA structure identified by bioinformatics. Cyano-2 RNAs are found in Cyanobacterial species classified within the genus ''Synechococcus''. Many terminal loops in the two conserved stem-loops contain the nuc ... References External links * Non-coding RNA Antisense RNA {{molecular-cell-biology-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleotides
Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules within all life-forms on Earth. Nucleotides are obtained in the diet and are also synthesized from common nutrients by the liver. Nucleotides are composed of three subunit molecules: a nucleobase, a five-carbon sugar (ribose or deoxyribose), and a phosphate group consisting of one to three phosphates. The four nucleobases in DNA are guanine, adenine, cytosine and thymine; in RNA, uracil is used in place of thymine. Nucleotides also play a central role in metabolism at a fundamental, cellular level. They provide chemical energy—in the form of the nucleoside triphosphates, adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) and uridine triphosphate (UTP)—throughout the cell for the many cellular fun ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Non-coding RNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR. The number of non-coding RNAs within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest that there are thousands of non-coding transcripts. Many of the newly identified ncRNAs have not been validated for their function. There is no consensus in the literature on how much of non-coding transcription is functional. Some researchers have argued that many ncRNAs are non-functional (sometimes referred to as "junk RNA"), spurious transcriptions. Others, however, disagree, arguing instead that many ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stress (biology)
Stress, either physiological, biological or psychological, is an organism's response to a stressor such as an environmental condition. Stress is the body's method of reacting to a condition such as a threat, challenge or physical and psychological barrier. There are two hormones that an individual produces during a stressful situation, these are well known as adrenaline and cortisol. There are two kinds of stress hormone levels. Resting (basal) cortisol levels are normal everyday quantities that are essential for standard functioning. Reactive cortisol levels are increases in cortisol in response to stressors. Stimuli that alter an organism's environment are responded to by multiple systems in the body. In humans and most mammals, the autonomic nervous system and hypothalamic-pituitary-adrenal (HPA) axis are the two major systems that respond to stress. The sympathoadrenal medullary (SAM) axis may activate the fight-or-flight response through the sympathetic nervous system ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Upregulated
In the biological context of organisms' production of gene products, downregulation is the process by which a cell decreases the quantity of a cellular component, such as RNA or protein, in response to an external stimulus. The complementary process that involves increases of such components is called upregulation. An example of downregulation is the cellular decrease in the expression of a specific receptor in response to its increased activation by a molecule, such as a hormone or neurotransmitter, which reduces the cell's sensitivity to the molecule. This is an example of a locally acting (negative feedback) mechanism. An example of upregulation is the response of liver cells exposed to such xenobiotic molecules as dioxin. In this situation, the cells increase their production of cytochrome P450 enzymes, which in turn increases degradation of these dioxin molecules. Downregulation or upregulation of an RNA or protein may also arise by an epigenetic alteration. Such an epigene ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NcRNA
A non-coding RNA (ncRNA) is a functional RNA molecule that is not translated into a protein. The DNA sequence from which a functional non-coding RNA is transcribed is often called an RNA gene. Abundant and functionally important types of non-coding RNAs include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs, exRNAs, scaRNAs and the long ncRNAs such as Xist and HOTAIR. The number of non-coding RNAs within the human genome is unknown; however, recent transcriptomic and bioinformatic studies suggest that there are thousands of non-coding transcripts. Many of the newly identified ncRNAs have not been validated for their function. There is no consensus in the literature on how much of non-coding transcription is functional. Some researchers have argued that many ncRNAs are non-functional (sometimes referred to as "junk RNA"), spurious transcriptions. Others, however, disagree, arguing instead that many ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
50S Ribosomal Subunit
50 S is the larger subunit of the 70S ribosome of prokaryotes, i.e. bacteria and archaea. It is the site of inhibition for antibiotics such as macrolides, chloramphenicol, clindamycin, and the pleuromutilins. It includes the 5S ribosomal RNA and 23S ribosomal RNA. Despite having the same sedimentation rate, bacterial and archaeal archaeal ribosomes can be quite different. Structure 50S, roughly equivalent to the 60S ribosomal subunit in eukaryotic cells, is the larger subunit of the 70S ribosome of prokaryotes. The 50S subunit is primarily composed of proteins but also contains single-stranded RNA known as ribosomal RNA (rRNA). rRNA forms secondary and tertiary structures to maintain the structure and carry out the catalytic functions of the ribosome. X-ray crystallography has yielded electron density maps allowing the structure of the 50S in ''Haloarcula marismortui'' (archaeon) to be determined to 2.4 Å resolutionand of the 50S in the ''Deinococcus radiodurans'' (bacte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
3′
Directionality, in molecular biology and biochemistry, is the end-to-end chemical orientation of a single strand of nucleic acid. In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide pentose-sugar-ring means that there will be a 5′ end (usually pronounced "five-prime end"), which frequently contains a phosphate group attached to the 5′ carbon of the ribose ring, and a 3′ end (usually pronounced "three-prime end"), which typically is unmodified from the ribose -OH substituent. In a DNA double helix, the strands run in opposite directions to permit base pairing between them, which is essential for replication or transcription of the encoded information. Nucleic acids can only be synthesized in vivo in the 5′-to-3′ direction, as the polymerases that assemble various types of new strands generally rely on the energy produced by breaking nucleoside triphosphate bonds to attach new nucleoside monophosphates to the 3′- ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ortholog
Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal (or lateral) gene transfer event (xenologs). Homology among DNA, RNA, or proteins is typically inferred from their nucleotide or amino acid sequence similarity. Significant similarity is strong evidence that two sequences are related by evolutionary changes from a common ancestral sequence. Alignments of multiple sequences are used to indicate which regions of each sequence are homologous. Identity, similarity, and conservation The term "percent homology" is often used to mean "sequence similarity”, that is the percentage of identical residues (''percent identity''), or the percentage of residues conserved with similar physicochemical properties ('' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Stem Loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when read in opposite directions, base-pair to form a double helix that ends in an unpaired loop. The resulting structure is a key building block of many RNA secondary structures. As an important secondary structure of RNA, it can direct RNA folding, protect structural stability for messenger RNA (mRNA), provide recognition sites for RNA binding proteins, and serve as a substrate for enzymatic reactions. Formation and stability The formation of a stem-loop structure is dependent on the stability of the resulting helix and loop regions. The first prerequisite is the presence of a sequence that can fold back on itself to form a paired double helix. The stability of this helix is determined by its length, the number of mismatches or bulges it co ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
