operons nifRLA, nifJ, nifHDK,nifEN, nifUSVM, nifWF, nifBQ . nifRLA operon The tight expression regulation of the nitrogen fixation nif genes is mediated by the products of the nifRLA operon. NifA activates ... binding site, between the promoter of the nifRLA operon and the nifL gene. No protein coded by nifR gene has been found. nifHDK operon It comprises three structural genes viz nifK nif D and nifH ... protein. Mo Fe co catalytic site for nitrogenase. nifQ is not absolutely essential. nifJ operon The nifJ ... transfer to nitrogenase. nifUSVM operon The nifS, nifV and nifM genes encode for a protein that is required to process component II. Function of the nifU gene is undetermined. nifWF operon The function ... enzyme binds to the nifR region of the nifRLA operon and prevents the transcription of the genes, nifL ... more details
allows the transcription of the lac operon to proceed. A non hydrolyzable analog of allolactose ... operon. See also Lac operon Regulation by allolactose Lac repressor Inducer External links MeshName ... more details
Orphan date December 2010 Infobox rfam Name hopC RNA image HopC RNA.svg width 290 caption Consensus secondary structure of hopC RNAs Symbol hopC RNA AltSymbols Rfam RF01741 miRBase miRBase family RNA type Cis regulatory element Tax domain Helicobacter GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The hopC RNA motif is a predicted cis regulatory element identified by a bioinformatics bioinformatic screen for conserved RNA secondary structure s. ref name Weinberg2010 cite journal author Weinberg Z, Wang JX, Bogue J, et al. title Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes journal Genome Biol volume 11 issue 3 pages R31 year 2010 month March pmid 20230605 doi 10.1186 gb 2010 11 3 r31 url pmc 2864571 ref hopC RNAs are exclusively found within bacteria classified within the genus Helicobacter , some of which are human pathogen s that infect the stomach and can cause peptic ulcer ulcers . hopC RNAs are found upstream of an operon of two genes called hopC and hopB also called alpa and alpB . Experiments on the start of transcription genetics transcription for the hopCB operon ref name McGowan indicate that hopC RNAs lie within the 5 untranslated region of this operon. The hopCB operon is induced to higher levels of expression in response to low pH . ref name McGowan This fits in with data that HopCB is involved in binding to human epithelial cells, ref cite journal author Odenbreit S, Faller G, Haas R title Role of the alpAB proteins and lipopolysaccharide in adhesion of Helicobacter pylori to human gastric tissue journal Int. J. Med. Microbiol. volume 292 issue 3 4 pages 247 56 year 2002 month September pmid 12398215 doi url ref which is presumably something that the bacteria do during infection of the low pH environment of the stomach. Previous work suggested that a repeat of 13 thymidine nucleotide s might be involved in regulating the abundance of the hopCB opero ... more details
Orphan date February 2009 Infobox rfam Name RtT RNA image RF00391.jpg width caption Predicted secondary structure and sequence conservation of RtT Symbol RtT AltSymbols Rfam RF00391 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Bacteria GO SO SO 0000655 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The RtT RNA repeat structure of the tyrT operon ref name Bos91 cite journal last Bosl first M coauthors Kersten H year 1991 title A novel RNA product of the tyrT operon of Escherichia coli journal Nucleic Acids Res volume 19 pages 5863&ndash 5870 pmid 1840671 doi 10.1093 nar 19.21.5863 issue 21 pmc 329039 ref is a cis regulatory element RNA element that is released from the tyrT operon of Escherichia coli . The exact function of RtT is unknown although it is thought that it may be involved in changing the cellular response in relation to amino acid starvation. ref name Bos91 The functional prediction is strengthened when the tyrT locus of E. coli K 12 K 12 E. coli K12 is compared with the E. coli K 12 B strain B strain , which lacks RtT RNA and has an alternate starvation response. ref cite journal last Timms first AR coauthors Bridges, BA title The tyrT locus of Escherichia coli B. journal Journal of bacteriology date 1996 Apr volume 178 issue 8 pages 2469 70 pmid 8636060 accessdate 21 July 2011 ref References reflist 1 External links Rfam id RF00391 name RtT RNA Category Cis regulatory RNA elements molecular cell biology stub ... more details
Infobox rfam Name Long range pseudoknot image RF01086.png width 200 caption Secondary structure of the long range pseudoknot Symbol AltSymbols Rfam RF01086 miRBase miRBase family RNA type Cis reg Tax domain Eukaryote Prokaryote CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData A long range pseudoknot is a pseudoknot containing a long loop region, and may be a mechanism of translational control. A long range pseudoknot is thought to negatively regulate the translation of the IF3 L35 L20 operon in E. coli . This operon encodes the translation factor 3 IF3 and ribosomal proteins L35 and L20. In this example, the RNA RNA interaction occurs between nucleotides separated by a 300 nucleotide loop region. ref cite journal title A long range RNA RNA interaction forms a pseudoknot required for translational control of the IF3 L35 L20 ribosomal protein operon in Escherichia coli journal EMBO J year 1996 first C last Chiaruttini coauthors M Milet, M Springer volume 15 16 issue 16 pages 4402 13 pmid 8861967 pmc 452164 ref A long range pseudoknot is also believed to be required for the activity of the Neurospora VS ribozyme . ref cite journal title A long range pseudoknot is required for activity of the Neurospora VS ribozyme journal EMBO J year 1996 first T last Rastogi coauthors T L Beattie, J E Olive, and R A Collins volume 15 11 issue 11 pages 2820 25 pmid 8654379 pmc 450219 ref References Reflist External links http rfam.sanger.ac.uk family RF01086 Rfam entry for Long range pseudoknots Category Non coding RNA ... more details
Unreferenced date December 2009 A structural gene is a gene that codes for any RNA or protein product other than a regulatory factor i.e. regulatory protein . It may code for a Protein Structural proteins structural protein , an enzyme , or an RNA molecule not involved in regulation. Structural genes represent an enormous variety of protein structures and functions, including structural proteins, enzymes with catalytic activities and so on. These genes are needed for the morphological or functional traits of the cell. In Eukaryotes, these occur in spilt form, segmented into introns and exons. But Prokaryotes, these are continuous. The structural genes are concerned with the synthesis of polypeptide chain or a number of polypeptide chains and are also concerned with the synthesis of different types of RNA required during protein synthesis. In the Lac Operon concept , these genes are associated with the synthesis of those enzymes that are needed for the catabolism of Lactose. In lac operon, there are three structural genes a, Lac Z gene for beta galactosodase enzyme. b, Lac Y gene for galactose permease enzyme. c, Lac A gene for thio galactoside trans acetylase enzyme. DEFAULTSORT Structural Gene Category Genes Category Gene expression Genetics stub ja ur ... more details
Infobox rfam Name Pseudomonas rpsL leader image Pseudomonas rpsL leader.png width caption Conserved secondary structure of rpsL leader showing the fraction of canonical base pairs Symbol rpsL psuedo AltSymbols Rfam RF01773 RNA type Gene cis reg Tax domain Pseudomonadaceae DISPLAYTITLE Pseudomonas rpsL leader The Pseudomonas rpsL leader is a putative attenuator RNA element identified by bioinformatics searches within bacteria of the Pseudomonadaceae phylum. ref name Nav10 cite journal last Naville first M coauthors Gautheret, D title Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation. journal Genome Biology date 2010 volume 11 issue 9 pages R97 pmid 20920266 accessdate 21 July 2011 doi 10.1186 gb 2010 11 9 r97 pmc 2965389 ref It is located upstream of the operon encoding ribosomal protein s S12 and S7 rpsL and rpsG genes respectively , and presents a Intrinsic termination Rho independent terminator at the 3 end. This RNA is presumed to operate as a non coding ribosomal protein leader potentially interacting with the S12 or S7 proteins, which are encoded by the operon . The motif might be related to other rpsL leaders, such as the Rickettsia rpsL leader . ref name Nav10 References reflist 1 External links Rfam id RF01773 name Psuedomonas rpsL leader Category Cis regulatory RNA elements ... more details
Infobox rfam Name Rickettsia rpsL leader image Rickettsia rpsL leader.png width caption Conserved secondary structure of Rickettsia rpsL leader showing the fraction of canonical base pairs Symbol rpsL ricks Rfam RF01774 RNA type Gene cis reg Tax domain Rickettsia DISPLAYTITLE Rickettsia rpsL leader The Rickettsia rpsL leader is a putative attenuator element identified by bioinformatics within bacteria of the proteobacterial Rickettsia genus. ref name Nav10 cite journal last Naville first M coauthors Gautheret, D title Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation. journal Genome Biology year 2010 volume 11 issue 9 pages R97 pmid 20920266 accessdate 21 July 2011 doi 10.1186 gb 2010 11 9 r97 pmc 2965389 ref It is located upstream of the operon encoding ribosomal protein s S12 and S7 rpsL and rpsG genes respectively , and presents a intrinsic termination Rho independent terminator at the 3 end. This RNA is presumed to operate as a non coding ribosomal protein leader potentially interacting with the S12 or S7 proteins, encoded by the operon. The motif might be related to other rpsL leaders, such as that from Pseudomonas rpsL leader Pseudomonas . ref name Nav10 References reflist 1 External links Rfam id RF01774 name Rickettsia rpsL leader Category Cis regulatory RNA elements ... more details
A ribosomal binding site RBS is a sequence on mRNA that is bound by the ribosome when initiating translation biology protein translation . It can be either the 5 cap of a messenger RNA in eukaryotes , a region 6 7 nucleotides upstream of the start codon AUG in prokaryotes called the Shine Dalgarno sequence , or an internal ribosome entry site IRES in viruses. The sequence is complementary to the 3 end of the rRNA. The ribosome searches for this site and binds to it through base pairing of nucleotides. Then, the ribosome begins the translation process and recruits initiation factors. After finding the ribosome binding site in eukaryotes, the ribosome recognizes the Kozak consensus sequence and begins translation at the 1 AUG codon. See also Alpha operon ribosome binding site GeneticTranslation Category Protein biosynthesis Category Molecular biology Category Drug interaction Category Cell biology genetics stub ... more details
Orphan date April 2012 Expert subject Microbiology date March 2010 E coli also has an alternative Cyclic adenosine monophosphate cAMP independent catabolite repression mechanism that utilizes a protein called catabolite repressor activator Cra . This same mechanism is also present in Gram positive bacteria such as Bacilus subtilis , however it is called catabolite control protein A CcpA . In this alternative pathway CcpA negatively represses other sugar operon s so they are off in the presence of glucose. It works by the fact that Hpr is Phosphorylation phosphorylated by a specific mechanism, when glucose enters through the cell membrane protein EIIC, and when Hpr is phosphoralated it can then allow CcpA to block transcription of the alternative sugar pathway operons at their respective cre sequence binding sites. DEFAULTSORT Ccpa Category Proteins ... more details
by RNA polymerase thereby inhibiting expression of the operon citation needed date October 2011 . Additionally ... the lac operon, and released the DNA when IPTG was added. IPTG is an allolactose analog chemistry ... confirmed the mechanism of the lac operon, earlier proposed by Jacques Monod and Francois Jacob . See also Lac operon References reflist 2 External links MeshName Lac Repressors More information ... more details
bound to the Operon Operator operator region of the promoter which interferes with the ability of RNA polymerase RNAP begin transcription of the lacZYA operon. ref name foster In the presence of the inducer .... Print. ref met operon An example of a repressor protein is the methionine repressor MetJ . MetJ interacts ... site allowing more methionine to be produced. See also Promoter biology Activator genetics Operon ... more details
structure of activated HutP an RNA binding protein that regulates transcription of the hut operon ..., Allosteric activation of HutP protein, that regulates transcription of hut operon in Bacillus subtilis ... subtilis hut operon and histidine dependent binding of HutP to the transcript containing the regulatory ... chemical groups of the hut mRNA for HutP interactions that regulate the hut operon in Bacillus subtilis ... more details
operon of E. coli , Joshua Lederberg isolated galactosidase and found it in greater quantities in colonies ... replaced with the concept of enzyme induction , in which a molecule induces expression of a gene or operon ... operon, which includes genes necessary for lactose metabolism. The presence of lactose is sensed through the activity of the lac repressor , which inhibits transcription of the lac operon until lactose ... of the lac operon, regardless of the presence or absence of lactose. Upon the exhaustion ... more details
A cistron is a gene . ref cite book last Lewin first Benjamin authorlink Benjamin Lewin title Genes VII year 2000 publisher Oxford University Press and Cell Press location New York isbn 0 19 879276 X page 955 ref The term cistron is used to emphasize that genes exhibit a specific behavior in a complementation test cis trans test distinct positions or locus genetics loci within a genome are cistronic i.e. , within the same gene when mutations at the loci exhibit the same simple Mendelian inheritance as would mutations at a single locus. For example, suppose a mutation at a chromosome position math x math is responsible for a recessive trait in a diploid organism where chromosomes come in pairs . We say that the mutation is recessive because the organism will exhibit the wild type phenotype ordinary trait unless both chromosomes of a pair have the mutation homozygous mutation . Similarly, suppose a mutation at another position, math y math , is responsible for the same recessive trait. The positions math x math and math y math are said to be within the same cistron when an organism that has the mutation at math x math on one chromosome and has the mutation at position math y math on the paired chromosome exhibits the recessive trait even though the organism is not homozygous for either mutation. When instead the wild type trait is expressed, the positions are said to belong to distinct cistrons genes. For example, an operon is a stretch of DNA that is Transcription genetics transcribed , to create a contiguous segment of RNA , but contains more than one cistron gene. The operon is said to be polycistronic , whereas ordinary genes are said to be monocistronic . References Reflist Category Genetics molecular cell biology stub genetics stub de Cistron fr Cistron pl Cistron pt C stron ru zh ... more details
Luminescent bacteria emit light as the result of a chemical reaction during which chemical energy is converted to light energy. Luminescent bacteria exist as symbiotic organisms carried within a larger organism, such as many deep sea organisms, including the Lantern Fish , the Angler fish , certain jellyfish , certain clam s and the Gulper eel . The light is generated by an enzyme catalyzed chemoluminescence reaction, wherein the pigment luciferin is oxidisation oxidised by the enzyme luciferase . The expression of gene s related to bioluminescence is controlled by an operon called the lux operon . Some species of luminescent bacteria possess quorum sensing, the ability to determine local population by the concentration of chemical messengers. Species which have quorum sensing can turn on and off certain chemical pathways, commonly luminescence in this way, once population levels reach a certain point the bacteria switch off light production ref http www.ncbi.nlm.nih.gov pubmed 10398554 Autoinduction of light emission in different species of bioluminescent bacteria . Luminescence 1999, 14 1 3 9. ref Characteristics of the phenomenon Bioluminescence is a form of luminescence , or cold light light emission emission less than 20 of the light generates thermal radiation . It should not be confused with fluorescence , phosphorescence or refraction of light. Most forms of bioluminescence are lighter or only exist at night, following a circadian rhythm . See also Dinoflagellate s Vibrionaceae e.g. Vibrio fischeri , Vibrio harveyi , Photobacterium phosphoreum Vibrio phosphoreum References reflist 2 External links http www.rhizobium.net environmental microbiology sites.htm h8 Bioluminescence Lecture Notes http lifesci.ucsb.edu biolum Bioluminescence Webpage http www.disknet.com indiana biolab b203.htm Isolation of Vibrio phosphoreum http www.biology.pl bakterie sw index en.html Luminescent Bacteria http siobiolum.ucsd.edu Biolum intro.html Scripps Institution of Oceanography ... more details
dablink This article is about enzyme regulation at the gene expression level. For the inhibition of enzymes at the enzyme level, see enzyme inhibitor . Enzyme induction is a process in which a molecule e.g. a drug Induction biology induces i.e. initiates or enhances the gene expression expression of an enzyme . Enzyme inhibition can refer to the inhibition of the expression of the enzyme by another molecule Enzyme inhibitor interference at the enzyme level , basically with how the enzyme works. This can be competitive inhibition , uncompetitive inhibition , non competitive inhibition or partially competitive inhibition. If the molecule induces enzymes that are responsible for its own metabolism , this is called auto induction or auto inhibition if there is inhibition . These processes are particular forms of Regulation of gene expression gene expression regulation . These terms are of particular interest to pharmacology , and more specifically to drug metabolism and drug interaction s. They also apply to molecular biology . History In the late 1950s and early 1960s, the French molecular biologists Fran ois Jacob and Jacques Monod became the first to explain enzyme induction, in the context of the lac operon of Escherichia coli . In the absence of lactose, the constitutively expressed lac repressor protein binds to the operator region of the DNA and prevents the transcription of the operon genes. When present, lactose binds to the lac repressor, causing it to separate from the DNA and thereby enabling transcription to occur. Monod and Jacob generated this theory following 15 years of work by them and others including Joshua Lederberg , partially as an explanation for Monod s observation of diauxie . Previously, Monod had hypothesized that enzymes could physically adapt themselves to new substrates a series of experiments by him, Jacob, and Arthur Pardee eventually demonstrated this to be incorrect and led them to the modern theory, for which he and Jacob shared the 1 ... more details
Infobox rfam Name speF leader image RF00518.jpg width caption Predicted secondary structure and sequence conservation of speF Symbol speF AltSymbols Rfam RF00518 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Bacteria GO SO SO 0005836 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData SpeF is a putative cis acting element identified in several gram negative alpha proteobacteria. Its is proposed to be involved in regulating expression of genes involved in polyamide biosynthesis . SpeF is one of five putative regulatory elements identified by a computational screen of Agrobacterium tumefaciens and other alpha proteobacterial genomes for conserved sequence motifs in operon leaders ref name Cor05 cite journal author Corbino KA, Barrick JE, Lim J, et al. title Evidence for a second class of S adenosylmethionine riboswitches and other regulatory RNA motifs in alpha proteobacteria journal Genome Biol. volume 6 issue 8 pages R70 year 2005 pmid 16086852 doi 10.1186 gb 2005 6 8 r70 pmc 1273637 ref . In the majority of species analysed it is located in the leader of an operon containing the speF gene an ornithine decarboxylase enzyme that catalyse s one of the first steps in polyamine biosynthesis. However, the authors did not detect binding of metabolites related to this pathway ornithine L ornithine , lysine L lysine , meso diaminopimelate , putrescine , cadaverine , or spermidine to the SpeF leader. ref name Cor05 Other non coding RNAs uncovered in the same analysis include suhB , YbhL leader ybhL , metA and serC. ref name Cor05 References references External links Rfam id RF00518 name speF leader Category Cis regulatory RNA elements molecular cell biology stub ... more details
Orphan date April 2012 Infobox rfam Name iscR stability element image IscRS SS.png width caption Secondary structure of iscR stability element RNA Symbol iscRS AltSymbols Rfam RF01517 miRBase miRBase family RNA type Cis regulatory element Tax domain Enterobacteriales GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The IscR stability element is a conservation genetics conserved secondary structure found in the intergenic regions of iscRSUA polycistronic mRNA. This secondary structure prevents the degradation of the iscR mRNA . The iscRSUA operon encodes for the protein s required in iron sulfur cluster biosynthesis where the gene expression expression of this operon is regulated by RyhB RNA RhyB and iscR, a transcription repressor. ref name pmid12975324 Cite pmid 12975324 ref ref name pmid16199566 Cite pmid 16199566 ref ref name pmid12446632 Cite pmid 12446632 ref Under sufficient iron conditions RhyB binds to iscRSUA mRNA and promotes the degradation of the mRNA located downstream of iscR. Scanning the intergenic regions of this polycistronic mRNA and using Mfold software a secondary structure was predicted within the intergenic region between iscR and iscS and later confirmed by lead acetate probing. ref name pmid19407815 Cite pmid 19407815 ref Mutant Mutations that disrupt this secondary structure resulted in the degradation of iscR mRNA after RhyB binding. 3 Rapid Amplification of cDNA Ends RACE analysis of the iscR mRNA fragment identified the intergenic RNA at the 3 end. These results suggest that this intergenic RNA element acts as a iscR mRNA stability element by protecting iscR from exonuclease degradation. References reflist External links Rfam id RF01517 name iscR stability element Category RNA Category Gene expression Category Non coding RNA ... more details
Orphan date April 2012 RRNA Ribosomal RNA rRNA intergenic spacer analysis RISA is a method of microbial community analysis that provides a means of comparing differing environments or treatment impacts without the bias imposed by culture dependent approaches. This type of analysis is often referred to as Community Fingerprinting community fingerprinting . RISA involves PCR amplification of a region of the rRNA gene operon between the small 16S and large 23S subunits called the intergenic spacer intergenic spacer region ISR. By using Oligonucleotide oligonucleotide primers targeted to conserved regions in the 16S and 23S genes, RISA fragments can be generated from most of the dominant bacteria in an environmental sample. While the majority of the rRNA operon serves a structural function, portions of the 16S 23S intergenic region can encode Transfer RNA tRNAs depending on the bacterial species. However the taxonomic value of the ISR lies in the significant heterogeneity in both length and nucleotide sequence. In RISA, we attempt to exploit the length heterogeneity of the ISR, which has been shown to range between 150 and 1500 bp with the majority of the ISR lengths being between 150 and 500 bp. The resulting PCR product will be a mixture of fragments contributed by several dominant community members. This product is electrophoresed in a polyacrylamide gel , and the DNA is visualized following staining. The result is a complex banding pattern that provides a community specific profile, with each DNA band corresponding to a bacterial population on the original assemblage. References references Borneman, J. and E.W. Triplett. 1997. Molecular microbial diversity in soils from eastern Amazonia evidence for unusual microorganisms and microbial population shifts associated with deforestation. Appl. Environ. Microbiol. 63 2647 2653. Sigler, W.V. and J. Zeyer. 2002. Microbial diversity and activity along the forefields of two receding glaciers Microb. Ecol. 43 397 407. Sigler, ... more details
Infobox rfam Name Pseudomon groES image Pseudomon groES RNA.svg width 330 caption Consensus secondary structure of Pseudomon groES RNAs Symbol Pseudomonas groES AltSymbols Rfam RF01721 miRBase miRBase family RNA type Cis regulatory element Tax domain GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The Pseudomon groES RNA motif is a conserved RNA structure identified in certain bacteria using bioinformatics . ref name Weinberg2010 cite journal author Weinberg Z, Wang JX, Bogue J, et al. title Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes journal Genome Biol volume 11 issue 3 pages R31 year 2010 month March pmid 20230605 doi 10.1186 gb 2010 11 3 r31 url pmc 2864571 ref It is found in most species within the family biology family Pseudomonadaceae , and is consistently located in the 5 untranslated region s 5 UTRs of operon s that contain groES gene s. Transcription biology RNA transcripts of the groES genes in Pseudomonas aeruginosa where shown experimentally to be initiated at one of two start sites, from promoter biology promoter s called P1 and P2 ref cite journal author Fujita M, Amemura A, Aramaki H title Transcription of the groESL operon in Pseudomonas aeruginosa PAO1 journal FEMS Microbiol. Lett. volume 163 issue 2 pages 237 42 year 1998 month June pmid 9673028 doi url ref see diagram . The Pseudomon groES RNA is in the 5 UTR of transcripts initiated from the P1 site, but is truncated in P2 transcripts. groES genes are involved in the cellular response to heat shock , but it is not thought that the Pseudomonas groES RNA motif is involved in heat shock regulation. However, it is thought that the motif might regulate groES genes in response to other stimuli. References references External links Rfam id RF01721 name Pseudomon groES RNA Category Cis regulatory RNA elements molecular cell biology stub ... more details
Infobox rfam Name SAM Chlorobi RNA image SAM Chlorobi RNA.svg width 450 caption Consensus secondary structure of SAM Chlorobi RNAs Symbol SAM Chlorobi RNA AltSymbols Rfam RF01724 miRBase miRBase family RNA type Cis regulatory element Tax domain Chlorobi GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The SAM Chlorobi RNA motif is a conserved RNA structure that was identified by bioinformatics . ref name Weinberg2010 cite journal author Weinberg Z, Wang JX, Bogue J, et al. title Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes journal Genome Biol volume 11 issue 3 pages R31 year 2010 month March pmid 20230605 doi 10.1186 gb 2010 11 3 r31 url pmc 2864571 ref The RNAs are found only in bacteria classified as within the phylum Chlorobi . These RNAs are always in the 5 untranslated region s of operon s that contain metK and ahcY genes. metK genes encode methionine adenosyltransferase , which synthesizes S adenosyl methionine SAM , and ahcY genes encode S adenosylhomocysteine hydrolase , which degrade the related metabolite S Adenosyl L homocysteine SAH . In fact all predicted metK and ahcY genes within Chlorobi bacteria as of 2010 are preceded by predicted SAM Chlorobi RNAs. ref name Weinberg2010 Predicted promoter biology promoter sequences are consistently found upstream of SAM Chlorobi RNAs, ref name Weinberg2010 and these promoter sequences imply that SAM Chlorobi RNAs are indeed transcription biology transcribed as RNAs. The promoter sequences are commonly associated with strong transcription in the phyla Chlorobi and Bacteroidetes , but are not used by most lineages of bacteria. The placement of SAM Chlorobi RNAs suggests that they are involved in the regulation of the metK ahcY operon through an unknown mechanism. References references External links Rfam id RF01724 name SAM Chlorobi RNA Category Cis regulatory RNA elements molecular cell biology stub ... more details
Infobox protein family Symbol CodY Name CodY image PDB 2b0l EBI.jpg width caption c terminal dna binding domain of transcriptional pleiotropic repressor cody. Pfam PF06018 Pfam clan CL0161 InterPro IPR010312 SMART PROSITE MEROPS SCOP TCDB OPM family OPM protein CAZy CDD In molecular biology, the CodY protein family consists of several bacteria bacterial GTP sensing Transcription genetics transcriptional pleiotropic repressor CodY protein s. CodY has been found to repress the dipeptide transport operon dpp of Bacillus subtilis in nutrient rich conditions. ref name pmid7783641 cite journal author Slack FJ, Serror P, Joyce E, Sonenshein AL title A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon journal Mol. Microbiol. volume 15 issue 4 pages 689 702 year 1995 month February pmid 7783641 doi url ref The CodY protein also has a repressor effect on many genes in Lactococcus lactis during cell growth growth in milk . ref name pmid11401725 cite journal author Guedon E, Serror P, Ehrlich SD, Renault P, Delorme C title Pleiotropic transcriptional repressor CodY senses the intracellular pool of branched chain amino acids in Lactococcus lactis journal Mol. Microbiol. volume 40 issue 5 pages 1227 39 year 2001 month June pmid 11401725 doi 10.1046 j.1365 2958.2001.02470.x url ref References reflist InterPro content IPR010312 Category Protein domains ... more details
Orphan date September 2011 Infobox protein family Symbol DHBP synthase Name DHBP synthase image PDB 1g58 EBI.jpg width caption crystal structure of 3,4 dihydroxy 2 butanone 4 phosphate synthase gold derivative Pfam PF00926 Pfam clan InterPro IPR000422 SMART PROSITE MEROPS SCOP 1iez TCDB OPM family OPM protein CAZy CDD In molecular biology, 3,4 dihydroxy 2 butanone 4 phosphate synthase DHBP synthase RibB EC number 4.1.99.12 is an enzyme which catalysis catalyses the conversion of ribulose 5 phosphate D ribulose 5 phosphate to formate and 3,4 dihydroxy 2 butanone 4 phosphate , the latter serving as the biosynthetic precursor for the xylene ring of riboflavin . ref name pmid9211332 cite journal author Richter G, Krieger C, Volk R, Kis K, Ritz H, Gotze E, Bacher A title Biosynthesis of riboflavin 3,4 dihydroxy 2 butanone 4 phosphate synthase journal Meth. Enzymol. volume 280 issue pages 374 82 year 1997 pmid 9211332 doi 10.1016 S0076 6879 97 80128 0 url ref In Photobacterium leiognathi , the riboflavin synthesis genes ribB DHBP synthase , ribE riboflavin synthase , ribH lumazone synthase and ribA GTP cyclohydrolase II all reside in the lux operon . ref name pmid11396941 cite journal author Lin JW, Chao YF, Weng SF title Riboflavin synthesis genes ribE, ribB, ribH, ribA reside in the lux operon of Photobacterium leiognathi journal Biochem. Biophys. Res. Commun. volume 284 issue 3 pages 587 95 year 2001 month June pmid 11396941 doi 10.1006 bbrc.2001.5013 url ref RibB is sometimes found as a bifunctional enzyme with GTP cyclohydrolase II that catalyses the first committed step in the biosynthesis of riboflavin. No sequence biology sequence s with significant homology to DHBP synthase are found in the metazoa . References reflist InterPro content IPR000422 Category Protein families ... more details
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