Riboswitch 507342 222849574 2008-07-01T12:23:35Z DOI bot 6652755 Citation maintenance. Removed redundant parameters. You can [[WP:DOI|use this bot]] yourself! Please [[User:DOI_bot/bugs|report any bugs]]. In [[molecular biology]], a '''riboswitch''' is a part of an [[mRNA]] molecule that can directly bind a [[small molecule|small target molecule]], and whose binding of the target affects the [[gene]]'s activity.<ref name="pmid15919195 ">{{cite journal | author = Tucker BJ, Breaker RR | title = Riboswitches as versatile gene control elements | journal = Curr Opin Struct Biol | volume = 15| issue = 3 | pages = 342–8 | year = 2005 | pmid = 15919195| doi = 10.1016/j.sbi.2005.05.003 }}</ref><ref name="pmid14698618">{{cite journal | author = Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS | title = Riboswitches: the oldest mechanism for the regulation of gene expression? | journal = Trends Genet | volume = 20 | issue = 1 | pages = 44–50 | year = 2004 | pmid = 14698618 | doi = 10.1016/j.tig.2003.11.008 }}</ref><ref name="pmid16707260">{{cite journal | author = Batey RT | title = Structures of regulatory elements in mRNAs | journal = Curr Opin Struct Biol | volume = 16 | issue = 3 | pages = 299–306 | year = 2006 | pmid = 16707260 | doi = 10.1016/j.sbi.2006.05.001}}</ref> Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, depending on the presence or absence of its target molecule. Although the metabolic pathways in which some riboswitches are involved have been studied for decades, the existence of riboswitches has only been relatively recently discovered, with the first experimental validations of riboswitches being published in 2002.<ref name="pmid12323379">{{cite journal | pmid=12323379 | 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|year=2002|pages=1043|doi=10.1016/S1074-5521(02)00224-7}}</ref><ref name="pmid12464185">{{cite journal | pmid=12464185 | author=Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E | title = Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria | journal = Cell | year=2002|volume = 111 | issue = 5 | pages = 747–56 | doi=10.1016/S0092-8674(02)01134-0}}</ref><ref name="pmid12410317">{{cite journal|pmid=12410317 |author=Winkler W, Nahvi A, Breaker RR|title=Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression|journal=Nature|volume=419|issue=6910|year=2002|pages=890–1|doi=10.1038/nature01145}}</ref><ref name="pmid12456892">{{cite journal|pmid=12456892 |author=Winkler WC, Cohen-Chalamish S, Breaker RR|title=An mRNA structure that controls gene expression by binding FMN|journal=Proc Natl Acad Sci U S A|volume=99|issue=25|year=2002|pages=15908–13|doi=10.1073/pnas.212628899}}</ref> This oversight may relate to an earlier assumption that genes are regulated by proteins, not by the mRNA transcript itself. Now that riboswitches are a known mechanism of genetic control, it is reasonable to speculate that more riboswitches will be found. Most known riboswitches occur in [[eubacteria]], but functional riboswitches of one type (the TPP riboswitch) have been discovered in [[plant]]s and certain [[fungus|fungi]]. TPP riboswitches have also been predicted in [[archaea]],<ref name="pmid12756322">{{cite journal | author = Sudarsan N, Barrick JE, Breaker RR | title = Metabolite-binding RNA domains are present in the genes of eukaryotes | journal = RNA | volume = 9 | issue =6 | pages = 644–7 | pmid = 12756322 | doi = 10.1261/rna.5090103 | year = 2003 }}</ref> but have not been experimentally tested. ==Mechanics of riboswitches== Riboswitches are conceptually divided into two parts: an [[aptamer]] and an expression platform. The aptamer directly binds the small molecule, and the expression platform undergoes structural changes in response to the changes in the aptamer. The expression platform is what regulates gene expression. Expression platforms typically turn off gene expression in response to the small molecule, but some turn it on. Expression platforms include: * The formation of [[rho-independent transcription termination]] hairpins * Folding in such a way as to sequester the [[ribosome]]-binding site, thereby blocking [[translation]] * Self-cleavage (i.e. the riboswitch contains a [[ribozyme]] that cleaves itself in the presence of sufficient concentrations of its metabolite) * Folding in such a way as to affect the [[Splicing (genetics)|splicing]] of the pre-mRNA. ** A TPP riboswitch in ''[[Neurospora crassa]]'' (a fungus) controls alternative splicing to conditional produce a [[uORF]], thereby affecting expressing of downstream genes<ref name="pmid17468745">{{cite journal | author = Cheah MT, Wachter A, Sudarsan N, Breaker RR | title = Control of alternative RNA splicing and gene expression by eukaryotic riboswitches | journal = Nature | volume = 447 | issue = 7143 | pages = 497–500 | year = 2007 | pmid = 17468745 | doi = 10.1038/nature05769 }}</ref> ** A TPP riboswitch in plants modifies splicing and alternative 3'-end processing <ref>{{cite journal |author=Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR |title=Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs |journal=Plant Cell |volume=19 |issue=11 |pages=3437–50 |year=2007 |pmid=17993623 |doi=10.1105/tpc.107.053645}}</ref><ref>{{cite journal |author=Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A |title=Riboswitch-dependent gene regulation and its evolution in the plant kingdom |journal=Genes Dev. |volume=21 |issue=22 |pages=2874–9 |year=2007 |pmid=18006684 |doi=10.1101/gad.443907}}</ref> ==Types of riboswitches== The following riboswitch classes are known: * ''[[TPP riboswitch (THI element)|TPP riboswitch]]'' (also THI-box) binds [[thiamin pyrophosphate]] (TPP) to regulate [[thiamin]] biosynthesis and transport, as well as transport of similar metabolites * ''[[FMN riboswitch (RFN element)|FMN riboswitch]]'' (also ''RFN-element'') binds [[flavin mononucleotide]] (FMN) to regulate [[riboflavin]] [[biosynthesis]] and transport. * ''[[Cobalamin riboswitch]]'' (also ''B12-element''), which binds [[adenosylcobalamin]] (the coenzyme form of [[vitamin B12]]) to regulate [[cobalamin]] biosynthesis and transport of cobalamin and similar metabolites, and other genes. * ''SAM riboswitches'' bind [[S-adenosyl methionine]] (SAM) to regulate [[methionine]] and SAM biosynthesis and transport. Three distinct SAM riboswitches are known: ''[[SAM riboswitch (S box leader)|SAM-I]]'' (originally called ''S-box''), ''[[SAM riboswitch (alpha-proteobacteria)|SAM-II]]'' and the ''[[SMK box riboswitch|S<sub>MK</sub> box riboswitch]]''. 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> box riboswitch is found only in the order [[Lactobacillales]]. These three varieties of riboswitch have no obvious similarities in terms of sequence or structure. A fourth variety, [[SAM-IV riboswitch]]es, appears to have a similar ligand-binding core to that of SAM-I riboswitches, but in the context of a distinct scaffold. * ''PreQ1 riboswitches'' bind pre-queuosine<sub>1</sub>, to regulate genes involved in the synthesis or transport of this precursor to [[queuosine]]. Two entirely distinct classes of PreQ1 riboswitches are known: [[PreQ1 riboswitch|PreQ1-I riboswitches]] and [[PreQ1-II riboswitch]]es. The binding domain of PreQ1-I riboswitches are unusually small among naturally occurring riboswitches. PreQ1-II riboswitches, which are only found in certain species in the genera ''Streptococcus'' and ''Lactococcus'', have a completely different structure, and are larger. * ''[[SAH riboswitch]]es'' bind [[S-adenosylhomocysteine]] to regulate genes involved in recycling this metabolite that is produced when [[S-adenosylmethionine]] is used in methylation reactions. * ''[[Purine riboswitch]]es'' binds [[purine]]s to regulate purine metabolism and transport. Different forms of the purine riboswitch bind [[guanine]] (a form originally known as the ''G-box'') or [[adenine]]. The specificity for either guanine or adenine depends completely upon Watson-Crick interactions with a single [[pyrimidine]] in the riboswitch at position Y74. In the guanine riboswitch this residue is always a [[cytosine]] (i.e. C74), in the adenine residue it is always a [[uracil]] (i.e. U74). Homologous types of purine riboswitches bind [[deoxyguanosine]], but have more significant differences than a single nucleotide mutation. * ''[[Lysine riboswitch]]'' (also ''L-box'') binds [[lysine]] to regulate lysine biosynthesis, [[catabolism]] and transport. * ''[[GlmS glucosamine-6-phosphate activated ribozyme|glmS riboswitch]]'', which is a ribozyme that cleaves itself when there is a sufficient concentration of [[Glucosamine#Biochemistry|glucosamine-6-phosphate]]. * ''[[Glycine riboswitch]]'' binds glycine to regulate glycine metabolism genes, including the use of glycine as an energy source. As of 2007, this riboswitch is the only known natural RNA that exhibits [[cooperative binding]], which is accomplished by two adjacent aptamer domains in the same mRNA. Presumed riboswitches: * ''[[Moco RNA motif]]'' is presumed to bind [[molybdenum cofactor]], to regulate genes involved in biosynthesis and transport of this coenzyme, as well as enzymes that use it or its derivatives as a cofactor. ==Riboswitches and the RNA World hypothesis== Riboswitches demonstrate that naturally occurring [[RNA]] can bind small molecules specifically, a capability that many previously believed was the domain of [[protein]]s or artificially constructed RNAs called [[aptamer]]s. The existence of riboswitches in all domains of life therefore adds some support to the [[RNA world hypothesis]], which holds that life originally existed using only RNA, and proteins came later; this hypothesis requires that all critical functions performed by proteins could be performed by RNA. It has been suggested that some riboswitches might represent ancient regulatory systems, or even remnants of RNA-world [[ribozyme]]s whose bindings domains are conserved.<ref>{{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 |url=}}</ref><ref name="pmid12410317"/><ref>{{cite journal |author=Cochrane JC, Strobel SA |title=Riboswitch effectors as protein enzyme cofactors |journal=RNA |volume= 14|issue= |pages= 993|year=2008 |month=April |pmid=18430893 |doi=10.1261/rna.908408 |url=}}</ref> ==Identification of riboswitches== Before riboswitches were experimentally demonstrated, several groups had identified conserved sequence "motifs" (patterns) in [[Five prime untranslated region|5' UTRs]] that appeared to correspond to a structured RNA. For example, comparative analysis of upstream regions of several genes expected to be co-regulated led to the description of the S-box<ref name="pmid10094622">{{cite journal|pmid=10094622|author=Grundy FJ, Henkin TM|title=The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria|journal=Mol Microbiol|year=1998|volume=30|issue=4|pages=737–49|doi=10.1046/j.1365-2958.1998.01105.x}}</ref> (now the SAM-I riboswitch), the THI-box <ref name="pmid11470904">{{cite journal|pmid=11470904 |author=Miranda-Ríos J, Navarro M, Soberón M|title=A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria|journal=Proc Natl Acad Sci U S A|year=2001|volume=98|issue=17|pages=9736–41|doi=10.1073/pnas.161168098}}</ref> (now the TPP riboswitch) and the RFN element<ref name="pmid10529804">{{cite journal|pmid=10529804|author=Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA|title=A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes|journal=Trends Genet|year=1999|volume=15|issue=11|pages=439–42|doi=10.1016/S0168-9525(99)01856-9}}</ref> (now the FMN riboswitch), and in some cases experimental demonstrations that they were involved in gene regulation via an unknown mechanism. Some researchers, hypothesizing that riboswitches would exist, identified them in part by inspecting the scientific literature for pathways, such as cobalamin biosynthesis, whose regulation had long been studied without successful elucidation of a regulatory mechanism <ref name="pmid12323379">q</ref>. As noted in the introduction, in 2002, several reports demonstrated that identified motifs, or pathways with stubbornly unknown means of regulation, were controlled by riboswitches. Proof that an RNA element is a riboswitch most often includes ''in vitro'' evidence that the RNA can bind the putative small molecule ligand, and ''in vivo'' genetic evidence that the riboswitch controls gene expression in the cell. ''In vitro'' binding assays include [[structural probing]] assays, most often in-line probing, size-exclusion assays (where the radiolabeled metabolite ligand is observed to not travel through a membrane when it binds to a much larger riboswitch RNA) and [[equilibrium dialysis]] (where radiolabeled ligand is observed to be more concentrated in an RNA-containing chamber, than in an RNA-free chamber connect by a membrane). [[Bioinformatics]] has played a role in more recent discoveries, with increasing automation of the basic comparative genomics strategy. Barrick ''et al.'' (2004) <ref name="pmid15096624">{{cite journal|pmid=15096624 |author=Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR|title=New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control|journal=Proc Natl Acad Sci USA|year=2004|volume=101|issue=17|pages=6421–6|doi=10.1073/pnas.0308014101}}</ref> used [[BLAST]] to find UTRs [[homology|homologous]] to all UTRs in ''[[Bacillus subtilis]]''. Some of these homologous sets were inspected for conserved structure, resulting in 10 RNA-like motifs. Three of these were later experimentally confirmed as the glmS, glycine and PreQ1-I riboswitches. Subsequent comparative genomics efforts using additional taxa of bacteria and improved computer algorithms have identified further riboswitches.<ref name="pmid16086852">{{cite journal|pmid=16086852|author=Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR|title=Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria|journal=Genome Biol|year=2005|volume=6|issue=8|pages=R70|doi=10.1186/gb-2005-6-8-r70}}</ref><ref name="pmid17621584">{{cite journal|pmid=17621584 |author=Weinberg Z, Barrick JE, Yao Z, Roth A, Kim JN, Gore J, Wang JX, Lee ER, Block KF, Sudarsan N, Neph S, Tompa M, Ruzzo WL, Breaker RR|title=Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline|journal=Nucleic Acids Res|year=2007|doi=10.1093/nar/gkm487|volume=35|pages=4809}}</ref> ==Riboswitches as antibiotic targets== Riboswitches could be a target for novel [[antibiotic]]s. Indeed, some antibiotics whose mechanism of action was unknown for decades have been shown to operate by targeting riboswitches.<ref name="pmid17160062">{{cite journal|pmid=17160062|author=Blount KF, Breaker RR|title=Riboswitches as antibacterial drug targets|journal=Nat Biotechnol|year=2006|volume=24|issue=12|pages=1558–64|doi=10.1038/nbt1268}}</ref> For example, when the antibiotic [[pyrithiamine]] enters the cell, it is metabolized into pyrithiamine pyrophosphate. Pyrithiamine pyrophosphate has been shown to bind and activate the TPP riboswitch, causing the cell to cease the synthesis and import of TPP. Because pyrithiamine pyrophosphate does not substitute for TPP as a coenzyme, the cell dies. One potential advantage that riboswitches have as an antibiotic target is that many of the riboswitches have multiple instances per genome, where each instance controls an [[operon]] containing many genes, many of which are essential. Therefore, in order for bacteria to evolve resistance to the antibiotic by mutations in the riboswitch, ''all'' riboswitches must be mutated. However, other mechanisms for resistance may exist, and some — such as altering the specificity of an exporter to export the drug — may require fewer mutations. ==References== <references/> [[Category:RNA]] [[Category:Cis-regulatory RNA elements]] [[Category:Riboswitch]] [[de:Riboswitch]] [[pl:Ryboprzełącznik]]