Infobox rfam Name SAMriboswitch S boxleader image RF00162.jpg width caption Predicted secondary structure and sequence conservation of SAM Symbol SAM AltSymbols S box Rfam RF00162 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO SO SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The SAMriboswitch also known as the S boxleader and now also called the SAM I riboswitch is found Upstream molecular biology ... the SAM I like pseudoknot. See also SAM II riboswitch SMK boxriboswitchSAM III riboswitchSAM IV riboswitchSAM V riboswitch References reflist External links Rfam id RF00162 name SAMriboswitch S boxleader http www.rcsb.org pdb explore explore.do?structureId 2GIS PDB entry for the SAMriboswitch tertiary structure DEFAULTSORT SamRiboswitch S BoxLeader Category Cis regulatory RNA elements ... SAMriboswitch pdb 2gis.png thumb 200px left A 3D representation of the SAMriboswitch The structure of the SAMriboswitch has been determined with X ray crystallography . ref cite journal last Montange ... issue 7097 ref The SAMriboswitch is organized about a four way junction, with two sets of coaxially ... of SAM binding riboswitches have been found that are entirely different from that of the SAM I riboswitch. These unrelated SAM binding riboswitches are SAM II riboswitch es, SMK boxriboswitchSAM III riboswitches and SAM SAH riboswitch es. The details of these riboswitches are covered in their articles .... SAM IV riboswitch es, appears to share a similar ligand binding site with that of SAM I ... in Gram positive bacteria. Two SAM riboswitches in Bacillus subtilis that were experimentally ... cite journal author Grundy FJ, Henkin TM title The S box regulon a new global transcription ... title The riboswitch mediated control of sulfur metabolism in bacteria journal Proc Natl Acad Sci ... 10 issue 9 pages 701 7 year 2003 pmid 12910260 doi 10.1038 nsb967 ref However, many SAM riboswitches ... more details
Infobox rfam Name S adenosyl methionine SAMriboswitch, image SAM IV secondary structure.jpg width caption Predicted secondary structure and sequence conservation of SAM IV Symbol SAM IV AltSymbols Rfam RF00634 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO SO SO 0005836 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData SAM IV riboswitches are a kind of riboswitch that specifically binds S adenosylmethionine SAM ref cite journal author Weinberg Z, Regulski EE, Hammond MC, et al. title The aptamer core of SAM IV riboswitches mimics the ligand binding site of SAM I riboswitches journal RNA volume 14 issue 5 pages 822 year 2008 pmid 18369181 doi 10.1261 rna.988608 pmc 2327355 ref , a cofactor used in many methylation reactions. Originally identified by bioinformatics ref cite journal author Weinberg Z, Barrick JE, Yao Z, et al. title Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline journal Nucleic Acids Res. volume 35 issue 14 pages 4809 19 year 2007 pmid 17621584 doi 10.1093 nar gkm487 pmc 1950547 ref , SAM IV riboswitches are largely confined to the Actinomycetales , an order of Bacteria . Conserved features of SAM IV riboswitch and experiments imply that they probably share a similar SAM binding site to another class of SAM binding riboswitches called SAMriboswitchSAM I riboswitches . However, the scaffolds of these two types of riboswitch appear to be quite distinct. See also SAMriboswitch S boxleaderSAM I riboswitchSAM II riboswitch SMK boxriboswitchSAM III riboswitchSAM V riboswitch References references External links Rfam id RF00634 name SAM IV riboswitch DEFAULTSORT Sam Iv Riboswitch Category Cis regulatory RNA elements Category Riboswitch molecular cell biology stub ... more details
appear to be unrelated to the SAMriboswitch S boxleaderSAMriboswitch found in Gram positive bacteria . This SAMriboswitch is located upstream of the metA and metC genes in Agrobacterium tumefaciens , and other methionine and SAM biosynthesis genes in other alpha proteobacteria. Like the other SAMriboswitch, it probably functions to turn off expression of these genes in response to elevated SAM levels. A significant variant of SAM II riboswitches was found in Pelagibacter ubique and related marine ocean marine bacteria and called SAM V riboswitchSAM V . ref cite journal author Poiata E, Meyer MM, Ames TD, Breaker RR title A variant riboswitch aptamer class for S adenosylmethionine common ... stem loop hairpin and a pseudoknot . See also SAMriboswitch S boxleader SMK boxriboswitchSAM IV riboswitchSAM V riboswitch References reflist 1 External links Rfam id RF00521 name SAMriboswitch alpha proteobacteria Category Cis regulatory RNA elements Category Riboswitch molecular cell ...Infobox rfam Name SAMriboswitch alpha proteobacteria image RF00521.jpg width caption Predicted secondary structure and sequence conservation of SAM alpha Symbol SAM alpha AltSymbols Rfam RF00521 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO GO 0045814 SO SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The SAM II riboswitch is a Cis regulatory element RNA element found predominantly in alpha proteobacteria that binds S adenosyl methionine SAM ref name pmid16086852 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 ... March pmid 20230605 doi 10.1186 gb 2010 11 3 r31 url pmc 2864571 ref Structure The SAM II riboswitch ... pmc 2764483 doi 10.1261 rna.1824209 url ref Also, like many structured RNAs, SAM II riboswitches ... more details
by which SAM SAH riboswitches regulate expression of the downstream genes. See also SAMriboswitch S boxleaderSAM II riboswitchSAM IV riboswitch References references External links Rfam id RF01727 name SAM SAH riboswitch Category Cis regulatory RNA elements Category Riboswitch molecular ...Infobox rfam Name SAM SAH riboswitch image SAM SAH riboswitch.svg width caption Consensus secondary structure of SAM SAH riboswitches Symbol SAM SAH riboswitch AltSymbols Rfam RF01727 miRBase miRBase family RNA type Riboswitch Tax domain Rhodobacterales GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The SAM SAH riboswitch is a conserved RNA structure in certain bacteria that binds S Adenosyl methionine S adenosylmethionine SAM and S Adenosyl L homocysteine S adenosylhomocysteine SAH and is therefore presumed to be a riboswitch . 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 SAM SAH riboswitches do not share any apparent structural resemblance to known riboswitches that bind SAM or SAH. The binding affinities for both compounds are similar, but binding for SAH is at least somewhat stronger. SAM SAH riboswitches are exclusively found in Rhodobacterales , an order biology ... genes, which encode the enzyme Methionine adenosyltransferase that synthesizes SAM. Given this gene association, it was proposed that SAM SAH riboswitches more likely function as SAM sensing RNAs. SAM SAH riboswitches are relatively small among known riboswitches, which might relate to their inability ... under physiological conditions, because the cellular concentration of SAM is higher. ref cite ... month September pmid 6760211 doi url ref A region of the conserved structure of SAM SAH riboswitches ... more details
parts of the sulfur metabolism of marine bacteria. ref name Poi09 See also SAMriboswitch S boxleaderSAM I riboswitchSAM II riboswitch SMK boxriboswitchSAM III riboswitchSAM IV riboswitch ... 1471 2164 10 268 accessdate 2010 08 20 ref SAM V features a similar consensus sequence and secondary structure as the binding site of SAM II riboswitch , but bioinformatics scans cluster the two aptamer ... 08 20 ref SAM binding was confirmed using equilibrium dialysis . The riboswitch has been characterised as a tandem riboswitch it is able to regulate both translation genetics translation and transcription genetics transcription . When SAM is present in high concentration, SAM II will bind its ligand and form a terminator genetics terminator stem to halt transcription. If SAM exists in lower concentrations, SAM V will be transcribed and, if SAM concentration should then increase, it can bind SAM ... journal.pbio.0050016 accessdate 2010 08 26 refend External links Rfam id RF01826 name SAM V riboswitch Category Riboswitch Category Cis regulatory RNA elements ...Infobox rfam Name SAM V image SAM V SScon.png width caption Conserved secondary structure of the SAM V riboswitch. Symbol SAM V AltSymbols Rfam RF01826 RNA type Cis regulatory element Cis reg Riboswitch Tax domain Metagenomics Marine metagenome SAM V riboswitch is the fifth known riboswitch to bind S adenosyl methionine SAM . It was first discovered in the marine organism Pelagibacter ubique Candidatus Pelagibacter ubique and can also be found in marine metagenomics metagenomes . ref name Mey09 cite journal author Meyer MM, Ames TD, Smith DP, et al. title Identification of candidate structured RNAs in the marine organism Candidatus Pelagibacter ubique journal BMC Genomics volume 10 issue pages ... RR title A variant riboswitch aptamer class for S adenosylmethionine common in marine bacteria journal ... A glycine dependent riboswitch that uses cooperative binding to control gene expression journal Science ... more details
known SAM binding riboswitches such as SAMriboswitch S boxleaderSAM I and SAM II riboswitchSAM II , but these appear to share no similarity in sequence or structure to SAM III. Structure The crystal structure of the riboswitch from E. faecalis was solved by X ray crystallography . The structure showed that the most conserved nucleotides involved in S adenosyl methionine SAM binding were ... insertions of up to 210 nucleotides within this structure. See also SAH riboswitchSAMriboswitch S boxleaderSAM I riboswitchSAM II riboswitchSAM IV riboswitchSAM V riboswitchSAM Chlorobi RNA motif SAM SAH riboswitch References reflist External links Rfam id RF01767 name SMK box translational .... Symbol SMK boxriboswitch AltSymbols SAM III, SMK Rfam RF01767 RNA type Riboswitch Tax domain ...Infobox rfam Name S sub MK sub box translational riboswitch image SMK riboswitch structure.jpg width 200px caption A representation of the S sub MK sub box translational riboswitch Nucleic acid secondary ... MK sub boxriboswitch structure. ref name pmid18806797 cite journal doi 10.1038 nsmb.1494 author Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ke A title Crystal structures of the SAM III S MK riboswitch reveal the SAM dependent translation inhibition mechanism. journal Nat Struct Mol Biol volume 15 issue 10 pages 1076 83 year 2008 pmid 18806797 ref The S sub MK sub boxriboswitch also known as SAM III is a cis regulatory element RNA element that regulates gene expression in bacteria. ref name pmid16491091 cite journal author Fuchs RT, Grundy FJ, Henkin TM title The S MK box is a new SAM binding RNA for translational regulation of SAM synthetase journal Nat. Struct. Mol ... binding of 30S ribosomal subunits to the SMK box translational riboswitch RNA journal Proc. Natl ... pmc 1829232 ref The S sub MK sub boxriboswitch is found in the 5 UTR of the MetK gene in lactic acid bacteria . The structure of this element changes upon binding to S adenosyl methionine SAM ... more details
riboswitches are known SAMriboswitch S boxleaderSAM I originally called S box , SAM II riboswitchSAM II and the SMK boxriboswitch S sub MK sub boxriboswitch . SAM I is widespread in bacteria, but SAM II is found only in alpha , beta and a few gamma proteobacteria . The S sub MK sub boxriboswitch ... 737 49 doi 10.1046 j.1365 2958.1998.01105.x ref now the SAM I riboswitch , the THI box ref name pmid11470904 ... riboswitch and the B sub 12 sub box ref cite journal author Franklund CV, Kadner RJ title Multiple ... SAM PDB 2gis.png thumb 200px A 3D representation of the SAMriboswitch Image RF00167.jpg thumb 200px ... by two adjacent aptamer domains in the same mRNA. Lysine riboswitch also L box binds lysine to regulate ... riboswitch bind guanine a form originally known as the G box or adenine . The specificity for either ... similarities in terms of sequence or structure. A fourth variety, SAM IV riboswitch es, appears to have .... SAM SAH riboswitch es bind both SAM and SAH with similar affinities. Since they are always ... their binding to SAM is physiologically relevant. Tetrahydrofolate riboswitch es bind tetrahydrofolate to regulate synthesis and transport genes. TPP riboswitch es also THI box binds thiamin pyrophosphate ... RF00167 . Image RF00162.jpg SAMriboswitch Secondary structure for the riboswitch marked up by sequence ... rfam.sanger.ac.uk family RF00521 RF00521 . Image SMK riboswitch structure.jpg SAM III riboswitch S sub MK sub Secondary structure for the riboswitch marked up by sequence conservation. Image SAM IV secondary structure.jpg SAM IV riboswitch Secondary structure for the riboswitch marked up by sequence ... riboswitch Secondary structure for the riboswitch marked up by sequence conservation. Image SAM SAH riboswitch.svg SAM SAH riboswitch Secondary structure for the riboswitch marked up by sequence conservation ... structure for the riboswitch marked up by sequence conservation. Image RF00380.jpg YkoK leader ...Image Lys ribosw 1.jpg thumb 200px right A 3D representation of the lysine riboswitch In molecular biology ... more details
about Sam Pollock, an American labor leaderSam Pollock, a hockey manager Sam Pollock Samuel Sam Pollock June 21, 1909 &ndash March 4, 1983 ref name Encyclopedia Encyclopedia of Cleveland History, 1996. ref was an United States American trade union labor union activist and leader. He helped lead two important strikes in 1934, the Auto Lite Strike and the Hardin County onion pickers strike , before becoming district president of the Amalgamated Meat Cutters Amalgamated Meat Cutters and Butcher Workmen of North America . Personal life Pollock was born in Cleveland, Ohio , in 1909 to Isadore and Sonia Gordon Pollock. In 1914, the Pollocks moved to Toledo, Ohio Toledo . Pollock attended public school in Toledo, and graduated in 1926. He attended both the University of Toledo and Bowling Green State University , but did not graduate from either institution. ref name Encyclopedia Pollock s daughter, Frances Pollock Packard, died in 1968. ref name Encyclopedia ref name McLaird He married Sally DeVera Kooperman in April 1934. The couple had a daughter, Frances. ref name Encyclopedia During his lifetime, Sam Pollock developed an extensive collection of labor literature. It became one of the largest ... Unemployed League, ref name McLaird McLaird, Sam Pollock Labor Collection, Archival Chronicle ... A History of the American Worker, 1933 1941, 1970. ref In April 1934, Pollock became a leader in the bitter ... leader Louis Budenz . They helped plan mass marches which forced the plant to close. When a local ... Hall, Roger H. Sam Pollock, Labor Activist From Radical to Reformer, 1932 1972. Ph.D. Dissertation .... Frozen Tears 2. John Russell, ed. 2004. McLaird, Lee N. Sam Pollock Labor Collection. Archival ... links Portal Organized labour http www.bgsu.edu colleges library cac ac8803.html Sam Pollock Papers .... Persondata Metadata see Wikipedia Persondata . NAME Pollock, Sam ALTERNATIVE NAMES SHORT DESCRIPTION ... Pollock, Sam Category 1983 deaths Category People from Cleveland, Ohio Category People from Toledo ... more details
Infobox rfam Name T boxleader image RF00230.jpg width caption Predicted secondary structure and sequence conservation of T box Symbol T box AltSymbols Rfam RF00230 miRBase miRBase family RNA type Cis regulatory element Cis reg Tax domain Bacteria GO GO 0000049 SO SO 0000140 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The T boxleader element is involved in the regulation of Translation genetics translation associated genes , usually in gram positive bacteria. Typically T box leaders are found upstream of Transfer RNA aminoacyl tRNA synthetase genes and some amino acid biosynthetic genes. Uncharged tRNA acts as the Effector biology effector for Transcription genetics transcription antitermination of genes in the T boxleader family. ref cite journal last Grundy first FJ coauthors Rollins SM, Henkin TM year 1994 title Interaction between the acceptor end of tRNA and the T box stimulates antitermination in the Bacillus subtilis tyrS gene a new role for the discriminator base journal J Bacteriol volume 176 pages 4518&ndash 4526 pmid 8045882 issue 15 pmc 196270 ref ref cite journal last Grundy first FJ coauthors Collins JA, Rollins SM, Henkin TM year 2000 title tRNA determinants for transcription antitermination of the Bacillus subtilis tyrS gene journal RNA volume 6 pages 1131&ndash 1141 pmid 10943892 doi 10.1017 S1355838200992100 issue 8 pmc 1369987 ref ref cite journal last Winkler first WC coauthors Grundy FJ, Murphy BA, Henkin TM year 2001 title The GA motif an RNA element common to bacterial antitermination systems, rRNA, and eukaryotic ... name T boxleader Category Cis regulatory RNA elements molecular cell biology stub ... issue 8 pmc 1370163 ref The anticodon of a specific tRNA base pairs to a specifier sequence within the T box motif, and the NCCA acceptor tail of the tRNA base pairs to a conserved bulge in the T box ... title Solution structure of the Bacillus subtilis T box antiterminator RNA seven nucleotide bulge ... more details
Infobox rfam Name PreQ1 riboswitch image RF00522.jpg width caption Predicted secondary structure and sequence conservation of PreQ1 Symbol PreQ1 AltSymbols Rfam RF00522 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO SO SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The PreQ1 I riboswitch is a cis acting element identified in bacteria which regulates expression of genes involved in biosynthesis of the nucleoside queuosine from Guanosine triphosphate GTP ref name pmid17384645 cite journal author Roth A, Winkler WC, Regulski EE, Lee BW, Lim J, Jona I, Barrick JE, Ritwik A, Kim JN, Welz R, Iwata Reuyl D, Breaker RR title A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain journal Nat Struct Mol Biol volume 14 issue 4 pages 308 317 year 2007 pmid 17384645 doi 10.1038 nsmb1224 ref . This RNA element known as a riboswitch binds preQ sub 1 sub pre queuosine sub 1 sub , an intemediate in the queuosine pathway. Riboswitch function has been characterised in the bacterium Bacillus subtilis , where the riboswitch is located in the leader of the ykvJKLM queCDEF operon which encodes four genes necessary for queuosine production ref name pmid14660578 ..., PreQ sub 1 sub binding to the riboswitch aptamer is thought to induce premature Transcription genetics transcription termination within the leader to down regulate expression of these genes. The preQ sub 1 sub riboswitch is distinguished by its unusually small aptamer, compared to other riboswitches ... DJ, Edwards TE, Ferr D Amar AR title Cocrystal structure of a class I preQ1 riboswitch reveals ... ref PreQ1 II riboswitch es also bind preQ sub 1 sub , but have an unrelated, distinct structure. References references External links Rfam id RF00522 name PreQ1 riboswitch Category Cis regulatory RNA elements Category Riboswitch molecular cell biology stub ... more details
290268 ref The lysine riboswitch has also been identified independently and called the L box. ref cite journal last Grundy first FJ coauthors Lehman SC, Henkin TM year 2003 title The L box regulon Lysine sensing by leader RNAs of bacterial lysine biosynthesis genes journal Proc Natl Acad Sci USA volume ...Image Lys ribosw 1.jpg thumb 200px left A 3D representation of the lysine riboswitch with a bound lysine molecule shown in space filling spheres. ref name pmid18784651 cite journal author Serganov A, Huang L, Patel DJ title Structural insights into amino acid binding and gene control by a lysine riboswitch. journal Nature volume 455 issue 7217 pages 1263 7 year 2008 pmid 18784651 doi 10.1038 nature07326 ref Infobox rfam Name Lysine riboswitch image RF00168.jpg width caption Predicted secondary structure and sequence conservation of Lysine riboswitch Symbol Lysine AltSymbols Rfam RF00168 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO SO SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The Lysine riboswitch is a metabolite binding cis regulatory element RNA element found within certain messenger ... This riboswitch is found in a number of genes involved in lysine metabolism, including lysC. ref cite ... Regulation of lysine biosynthesis and transport genes in bacteria yet another RNA riboswitch? journal ... Structure The structure of the lysine riboswitch has recently been determined. ref name pmid18593706 cite journal author Garst AD, H roux A, Rambo RP, Batey RT title Crystal structure of the lysine riboswitch ... acid binding and gene control by a lysine riboswitch journal Nature volume 455 issue 7217 pages ... fashion as are helices 4 and 5. References reflist 1 External links Rfam id RF00168 name Lysine riboswitch http www.rcsb.org pdb explore explore.do?structureId 3DIL PDB entry for the lysine riboswitch tertiary structure Category Cis regulatory RNA elements Category Riboswitch molecular cell biology ... more details
of an SAH riboswitch has been solved using X ray crystallography. ref name Edwards2010 cite journal ... id RF01057 name SAH riboswitch DEFAULTSORT Sah Riboswitch Category Cis regulatory RNA elements Category Riboswitch molecular cell biology stub ... more details
of riboswitch function, a conservation genetics conserved sequence motif called the B sub 12 sub box ...mergefrom AdoCbl riboswitch discuss Talk Cobalamin riboswitch Merger proposal date February 2011 Infobox rfam Name Cobalamin riboswitch image RF00174.jpg width caption Predicted secondary structure and sequence conservation of Cobalamin Symbol Cobalamin AltSymbols Rfam RF00174 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO SO SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData Cobalamin riboswitch is a cis regulatory element which is widely distributed in 5 UTR 5 untranslated regions of vitamin B12 vitamin B sub 12 sub Colbalamin related genes in bacteria . ref name Nahvi2002 cite journal author Nahvi A, Sudarsan N, Ebert MS, Zou X, Brown KL, Breaker RR title Genetic control by a metabolite binding mRNA journal Chem. Biol. volume 9 issue 9 pages 1043 year 2002 month September pmid 12323379 doi 10.1016 S1074 5521 02 00224 7 url ref Riboswitch es are metabolite binding domains within certain mRNA messenger RNAs mRNAs that serve as precision sensors for their corresponding targets. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results in modulation of gene expression or translation genetics translation of mRNA to yield a protein. Cobalamin in the form of adenosylcobalamin Ado CBL is known to repress expression of protein s for vitamin B sub 12 sub biosynthesis via a post transcriptional regulatory mechanism that involves direct binding of Ado CBL to 5 ... riboswitch, ref name Nahvi2002 and a more complete conserved secondary structure structure ... of the riboswitch consensus have been identified. ref name Weinberg2010 cite journal author Weinberg ... External links Rfam id RF00174 name Cobalamin riboswitch Category Cis regulatory RNA elements Category Riboswitch molecular cell biology stub ... more details
Infobox rfam Name TPP riboswitch THI element image RF00059.jpg width caption Predicted secondary structure and sequence conservation of TPP Symbol TPP AltSymbols THI Rfam RF00059 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Eukaryota Bacteria Archaea GO GO 0030976 SO SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData Image TPP riboswitch pdb 2hoj.png thumb 200px left A 3D representation of the TPP riboswitch. ref name pmid16962976 cite journal doi 10.1016 j.str.2006.07.008 author Edwards TE, Ferr D Amar AR title Crystal structures of the thi boxriboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA small molecule recognition. journal Structure volume 14 issue 9 pages 1459 68 year 2006 pmid 16962976 ref The TPP riboswitch , also known as the THI element and Thi boxriboswitch , is a highly conserved RNA secondary structure . It serves as a riboswitch ref cite journal last Winkler first W coauthors Nahvi A, Breaker RR year 2002 title Thiamine derivatives bind messenger RNAs directly ... A year 2007 title Riboswitch dependent gene regulation and its evolution in the plant kingdom journal ... splicing of the intron containing a riboswitch like domain in the 5 UTR journal FEBS Lett volume 555 ... element, the thi box, there is considerable variability in the predicted length and structures ... Miranda Rios first J coauthors Navarro M, Soberon M year 2001 title A conserved RNA structure thi box ... ref The X ray crystallography x ray crystal structure of the TPP riboswitch aptamer has been solved ... 2006 title Structural basis for gene regulation by a thiamine pyrophosphate sensing riboswitch journal ... reflist 1 External links Rfam id RF00059 name TPP riboswitch THI element http www.rcsb.org pdb cgi explore.cgi?pdbId 2HOJ PDB entry for the TPP riboswitch tertiary structure Category Cis regulatory RNA elements Category Riboswitch molecular cell biology stub ... more details
mergeto Cobalamin riboswitch discuss Talk Cobalamin riboswitch Merger proposal date February 2011 Infobox rfam Name AdoCbl riboswitch image AdoCbl riboswitch secondary structure.jpg width caption Predicted secondary structure and sequence conservation of AdoCbl riboswitch Symbol AdoCbl riboswitch AltSymbols rli55 Rfam RF01482 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO GO 0061020 GO 0046336 SO SO 0005836 SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData AdoCbl riboswitch is a cis regulatory riboswitch element present in untranslated region untranslated regions of mRNA where binding adenosylcobalamin AdoCbl causes a change in gene expression . This riboswitch has been shown to be conservation genetics conserved across several strains of bacteria and has an influence over the expression of the ethanolamine utilization genes. Its is proposed to be a subclass of the previously described classical Cobalamin AdoCbl sensing riboswitch . ref name pmid19246383 Cite pmid 19246383 ref Ethanolamine is abundant in the human intestinal tract as it is the product of the breakdown of the phosphatidylethanolamine from cell membranes and is also present in processed food. Most bacteria that inhabit the intestinal tract can utilize ethanolamine as a carbon and nitrogen source by upregulating the expression ... system that senses the presence of ethanolamine and the second mechanism is a AdoCbl riboswitch .... ref name pmid19246383 . RNA structure probing In line probing analysis of this new riboswitch ... in the riboswitch. ref name pmid19246383 This riboswitch unlike previously characterized AdoCbl ... terminator helices have been identified downstream of the riboswitch. ref name pmid14704351 Cite ... biosythesis by promoting transcription termination this newly identified AdoCbl riboswitch ... AdoCbl riboswitch Category Cis regulatory RNA elements Category Riboswitch ... more details
Infobox rfam Name Glycine riboswitch image RF00504.jpg width caption Predicted secondary structure and sequence conservation of Glycine Symbol Glycine AltSymbols gcvT Rfam RF00504 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO SO SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData The bacterial glycine riboswitch is an Cis regulatory element RNA element that can bind the amino acid glycine . Glycine riboswitch es usually consist of two metabolite binding aptamers domains with similar structures in tandem. The aptamers cooperatively bind glycine to regulate the expression of downstream genes. In Bacillus subtilis , this riboswitch is found upstream of the gcvT operon which controls glycine degradation. It is thought that when glycine is in excess it will bind to both aptamers to activate these genes and facilitate glycine degradation. ref name breaker cite journal last Mandal first M coauthors Lee M, Barrick JE, Weinberg Z, Emilsson GM, Ruzzo WL, Breaker RR year 2004 title A glycine dependent riboswitch that uses cooperative binding to control gene expression journal Science volume 306 pages 275&ndash 279 pmid 15472076 doi 10.1126 science.1100829 issue 5694 ref Examples of the glycine riboswitch exhibit sigmoidal binding curves with Hill coefficient s greater than one, indicating cooperativity positive cooperativity between the two aptamer domains. ref name breaker ref cite journal last Kwon first M coauthors Strobel SA year 2008 title Chemical basis of glycine riboswitch cooperativity journal RNA volume 14 pages 25&ndash 34 pmid 18042658 doi 10.1261 rna.771608 issue 1 pmc 2151043 ref This type of binding is unusual for a riboswitch and is thought to have important physiological ... name Glycine riboswitch DEFAULTSORT Glycine Riboswitch Category Cis regulatory RNA elements Category Riboswitch molecular cell biology stub ... more details
Infobox rfam Name Tetrahydrofolate riboswitche image THF riboswitch.svg width 260 caption Consensus secondary structure of tetrahydrofolate THF riboswitches Symbol THF riboswitch AltSymbols Rfam RF01831 miRBase miRBase family RNA type Riboswitch Tax domain Clostridiales , Lactobacillales GO SO CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData Tetrahydrofolate riboswitches are a class of homology biology homologous RNA s in certain bacteria that bind tetrahydrofolate THF . ref name Ames2010 cite journal author Ames TD, Rodionov DA, Weinberg Z, Breaker RR title A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate journal Chem. Biol. volume 17 issue 7 pages 681 5 year 2010 month July pmid 20659680 doi 10.1016 j.chembiol.2010.05.020 url ref It is almost exclusively located in the probable 5 untranslated region s of protein coding gene s, and most of these genes are known to encode either folate membrane transport protein transporters or enzyme s involved in folate metabolism . For these reasons it was inferred that the RNAs function as riboswitch es. THF riboswitches are found in a variety of Firmicute s, specifically the order biology orders Clostridiales and Lactobacillales , and more rarely in other lineages of bacteria. The THF riboswitch was one of many conserved RNA structures found in a project based on comparative genomics. 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 References references External links Rfam id RF01831 name THF riboswitch Category Cis regulatory RNA elements Category Riboswitch molecular cell biology stub ... more details
similarities in sequence or structure to preQ1 riboswitch preQ1 I riboswitches , a previously discovered ... as the second metabolite to be found that is the ligand of more than one riboswitch class. References references External links Rfam id RF01054 name PreQ1 II riboswitch DEFAULTSORT Preq1 Ii Riboswitch Category Cis regulatory RNA elements Category Riboswitch molecular cell biology stub ... more details
Image Adenosine riboswitch pdb 1y26.png thumb 200px left A 3D representation of the adenine riboswitch. ref name pmid15610857 cite journal author Serganov A, Yuan YR, Pikovskaya O, Polonskaia A, Malinina L, Phan AT, Hobartner C, Micura R, Breaker RR, Patel DJ title Structural basis for discriminative regulation of gene expression by adenine and guanine sensing mRNAs journal Chem Biol volume 11 issue 12 pages 1729 41 year 2004 pmid 15610857 doi 10.1016 j.chembiol.2004.11.018 ref Image Guanosine riboswitch pdb 1y27.png thumb 205px right A 3D representation of the guanine riboswitch. ref name pmid15610857 Infobox rfam Name Purine riboswitch image RF00167.jpg width caption Predicted secondary structure and sequence conservation of Purine Symbol Purine AltSymbols Rfam RF00167 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO SO SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData Purine riboswitches ... guanine responsive riboswitch complexed with the metabolite hypoxanthine journal Nature. volume 432 pages 411&ndash 415 pmid 15549109 doi 10.1038 nature03037 issue 7015 ref Purine riboswitch es are a class of riboswitches that selectively recognises guanine and adenine , the riboswitch becomes saturated ... title Guanine riboswitch variants from Mesoplasma florum selectively recognize 2 deoxyguanosine journal ... pnas.0705884104 pmc 1999398 ref , this family are termed purine riboswitches. The purine riboswitch is the only riboswitch so far that has been mutated to respond to non natural ligands, opening ... id RF00167 name Purine riboswitch http www.rcsb.org pdb explore explore.do?structureId 1Y26 PDB entry for the adenosine riboswitch tertiary structure http www.rcsb.org pdb explore explore.do?structureId 1Y27 PDB entry for the guanine riboswitch tertiary structure Category Cis regulatory RNA elements Category Riboswitch molecular cell biology stub ... more details
Infobox rfam Name FMN riboswitch RFN element image RF00050.jpg width caption Predicted secondary structure and sequence conservation of FMN Symbol FMN AltSymbols RFN Rfam RF00050 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO GO 0010181 SO SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData Image PDB 3f4e EBI.png thumb 200px left A representation of the 3D structure of the FMN riboswitch. This derived from a crystal structure of the FMN riboswitch bound to FMN. ref name pmid19169240 cite journal author Serganov A, Huang L, Patel DJ title Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch. journal Nature volume 458 issue 7235 pages 233 7 year 2009 pmid 19169240 doi 10.1038 nature07642 ref The FMN riboswitch also known as RFN element is a highly conserved Cis regulatory element RNA element that is found frequently in the Five prime untranslated region 5 untranslated region s of prokaryotic mRNA s that encode for flavin mononucleotide FMN biosynthesis and transport proteins. ref name pmid12136096 cite journal doi 10.1093 nar gkf433 author Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS title Regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation. journal Nucleic Acids Res volume 30 issue 14 pages 3141 51 year 2002 pmid 12136096 pmc 135753 ref ref name pmid10529804 cite journal author Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA title A conserved RNA structure element involved ... dependent riboswitch that directly binds FMN in the absence of proteins. ref name Mironov 2002 747 ... 10.1016 S0092 8674 02 01134 0 ref In Bacillus subtilis , the riboswitch controls gene expression by causing ... reflist 2 External links Rfam id RF00050 name FMN riboswitch RFN element Category Cis regulatory RNA elements Category Riboswitch molecular cell biology stub ... more details
Orphan date August 2011 Infobox rfam Name Mesoplasma florum riboswitch image MFR secondary structure.jpg width caption Predicted secondary structure and sequence conservation of MFR Symbol MFR AltSymbols Rfam RF01510 miRBase miRBase family RNA type Cis regulatory element Cis reg riboswitch Tax domain Bacteria GO GO 0032546 GO 0031554 SO SO 0000035 CAS number EntrezGene HGNCid OMIM PDB RefSeq Chromosome Arm Band LocusSupplementaryData Riboswitches are cis acting regulatory elements located within the 5 untranslated region UTR of mRNA transcripts. These regulatory elements bind small molecules which results in a conformational change within the 5 UTR of the mRNA. The changes in the mRNA secondary structure subsequently result in changes in the expression of the adjacent open reading frame. Bioinformatic studies have identified several riboswitches present in M. florum . ref name pmid17911257 cite journal author Kim JN, Roth A, Breaker RR title Guanine riboswitch variants from Mesoplasma florum selectively recognize 2 deoxyguanosine journal Proc. Natl. Acad. Sci. U.S.A. volume 104 issue 41 pages 16092 7 year 2007 month October pmid 17911257 pmc 1999398 doi 10.1073 pnas.0705884104 url ref These riboswitches have been mapped to regions located upstream of the guaAB operon and resemble purine riboswitch es. The riboswitches identified in M. florum can be classed as novel riboswitches as they deviate in sequence and structure within the loops regions that are required in aptamer binding compared to conventional purine riboswitches. Mutagenesis confirmed that changing nucleotides within the loop regions of this riboswitch altered the specificity for ligand binding. This study showed that the novel riboswitches have a greater diversity in ligands they bind as they were found to bind alternative ligands such as nucleosides . The novel riboswitches were all shown to lie upstream ... References reflist External links Rfam id RF01510 name M. florum riboswitch Category Riboswitch ... more details
wiktionary SamsamSam , SAM or SAm may refer to tocright Samuel Sam People Samuel name , includes a list of people known as Sam Samantha S m , a Persian folk hero, whose name means very dark Sam Book of Mormon , the third son of Lehi and elder brother to the prophet Nephi Animals Sam ugly dog 1990 2005 , dog voted the world s ugliest dog in 2003, 2004, and 2005 Sam army dog died 2000 , former army dog that was awarded the Dickin Medal Sam koala died 2009 , koala rescued after the 2009 bush fires in Victoria, Australia Sam orangutan , an orangutan that starred in the movie Dunston Checks In Places Sam, Burkina Faso disambiguation , several towns in Burkina Faso Sam, Benin , a town in Benin can be called Sammy In entertainment Sam kabo album Sam kabo album , 2003 Sam Osvaja i album Sam Osvaja i album , 1995 Sam film Sam film , a 1986 documentary film Sam 1967 film Sam 1967 film , a 1976 film directed by Larry Buchanan Sam Meat Puppets song Sam Meat Puppets song , 1991 Sam Olivia Newton John song Sam Olivia Newton John song , 1977 Sam 1973 TV series Sam 1973 TV series , a 1973 British television drama series Sam 1978 TV series , an American crime drama television series Sam Trick r Treat , the main character in the horror movie Trick r Treat Other uses Sam Olympic mascot , the mascot of the 1984 Summer Olympics Sam text editor , a text editor by Rob Pike Microsoft Sam , the default voice for the screen reader program in Windows 2000 and Windows XP SAM or SAm Software Norton AntiVirus Mac edition Symantec Anti Virus for Macintosh SAM card Security Authentication Module card , a small ... management Software Automatic Mouth , a computer program for speech synthesis SAM Broadcaster In science ... that resembles a simple Atwood s machine In mathematics, SAM is an acronym for Sparse anti magic square , another name for Antimagic square In astrophysics, SAm is an acronym for a type of Magellanic spiral galaxy In business SAM Records , an American disco post disco record company SAM vehicles , a Greek ... more details
Sam. can refer to Samvat Books of Samuel disambiguation Short pages monitor This long comment was added to the page to prevent it being listed on Special Shortpages. It and the accompanying monitoring template were generated via Template Longcomment. Please do not remove the monitor template without removing the comment as well. ... more details
Unreferenced stub auto yes date December 2009 Sam A village in the northeastern New Territories of Hong Kong is named after the idyllic bay of Sam A Wan . In its heyday in the 1950s and 1960s, there were more than 200 residents here, but at the end of the 1960s most of the men left the village to seek employment in the United Kingdom and the Netherlands. Today, the Zeng Tsang ancestral hall and the abandoned three village school still stand, but there is little life here on a week day. On week ends, however, some Tsang clan members return to their ancestral village to run a couple of stores that offer food and lodgings for the ever increasing number of visitors. Still, even today, Sam A is still only accessible by boat or hiking. See also List of villages in Hong Kong Coord missing Hong Kong Category North District, Hong Kong Category Populated places in Hong Kong HongKong geo stub ... more details
Non free use rationale video game cover Article Serious Sam Use Infobox ADDITIONAL INFORMATION Name Serious Sam The First Encounter Distributor Publisher Type Website Owner Commentary OVERRIDE FIELDS Description Source Portion Low resolution Purpose Must be specified if Use is not Infobox Header Section Artist Replaceability other information Licensing Non free game cover Windows ... more details
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