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A 3D representation of the lysine riboswitch

In molecular biology, a riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the gene's activity.[1][2][3] Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its target molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, significantly expanded the known natural repertoire of RNA beyond its ability to code for proteins or to bind other RNA or protein macromolecules.

The original definition of the term "riboswitch" specified that they directly sense small-molecule metabolite concentrations.[4] Although this definition remains in common use, some biologists have used a broader definition that includes other cis-regulatory RNAs. However, this article will discuss only metabolite-binding riboswitches.

Most known riboswitches occur in Bacteria, but functional riboswitches of one type (the TPP riboswitch) have been discovered in plants and certain fungi. TPP riboswitches have also been predicted in Archaea,[5] but have not been experimentally tested.

History and discovery of riboswitches

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Before the discovery of riboswitches, the mechanism by which some genes involved in multiple metabolic pathways were regulated remained mysterious. Based on accumulating evidence, some groups proposed the then-unprecented idea that the mRNAs involved might bind metabolites directly, to effect their own regulation. These proposals were based on suggestive experimental data, conserved RNA secondary structures often found in the UTRs of the relevant genes and the success of procedures to create artificial small molecule-binding RNAs called aptamers.[6][7][8][9][10] In 2002, the first comprehensive proofs of multiple classes of riboswitches were published, including protein-free binding assays, and metabolite-binding riboswitches were established as a new mechanism of gene regulation.[4][11][12][13]

Many of the earliest riboswitches to be discovered corresponded to conserved sequence "motifs" (patterns) in 5' UTRs that appeared to correspond to a structured RNA, although in some cases the motifs did not correspond to the entire riboswitch binding domain. For example, comparative analysis of upstream regions of several genes expected to be co-regulated led to the description of the S-box[14] (now the SAM-I riboswitch), the THI-box [15] (a region within the TPP riboswitch) and the RFN element[16] (now the FMN riboswitch) and the B12-box[17] (a part of the cobalamin riboswitch), and in some cases experimental demonstrations that they were involved in gene regulation via an unknown mechanism. Bioinformatics has played a role in more recent discoveries, with increasing automation of the basic comparative genomics strategy. Barrick et al. (2004) [18] used BLAST to find UTRs 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 (see below). Subsequent comparative genomics efforts using additional taxa of bacteria and improved computer algorithms have identified further riboswitches.[19][20][21]

Mechanisms of riboswitches

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Riboswitches are often 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. The following riboswitch mechanisms have been experimentally demonstrated.

  • Riboswitch-controlled formation of rho-independent transcription termination hairpins leads to premature transcription termination.
  • Riboswitch-mediated folding sequesters the ribosome-binding site, thereby blocking translation.
  • The riboswitch is a ribozyme that cleaves itself in the presence of sufficient concentrations of its metabolite).
  • Riboswitch alternate structures affect the splicing of the pre-mRNA.
    • A TPP riboswitch in Neurospora crassa (a fungus) controls alternative splicing to conditionally produce an Upstream Open Reading Frame (uORF), thereby affecting the expression of downstream genes[22]
    • A TPP riboswitch in plants modifies splicing and alternative 3'-end processing [23][24]
  • A riboswitch in Clostridium acetobutylicum regulates an adjacent gene that is not part of the same mRNA transcript. In this regulation, the riboswitch controls transcription that interferes with the transcription of the gene, perhaps caused by clashes between two RNA polymerase units as they simultaneously transcribe the same DNA.[25]
  • A riboswitch in Listeria monocytogenes regulates the expression of its downstream gene. However, riboswitch transcripts subsequently modulate the expression of a genes located elsewhere in the genome.[26] This trans regulation occurs via base-pairing to the mRNA of the distal gene.

Types of riboswitches

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Secondary structure of a purine riboswitch from Bacillus subtilis

The following is a list of experimentally validated riboswitches, organized by ligand.

  • 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.
  • cyclic di-GMP riboswitches bind the signaling molecule cyclic di-GMP in order to regulate a variety of genes controlled by this second messenger.
  • FMN riboswitch (also RFN-element) binds flavin mononucleotide (FMN) to regulate riboflavin biosynthesis and transport.
  • glmS riboswitch, which is a ribozyme that cleaves itself when there is a sufficient concentration of glucosamine-6-phosphate.
  • Glycine riboswitch binds glycine to regulate glycine metabolism genes, including the use of glycine as an energy source. As of 2008, this riboswitch is the only known natural RNA that exhibits cooperative binding, which is accomplished by two adjacent aptamer domains in the same mRNA.
  • Lysine riboswitch (also L-box) binds lysine to regulate lysine biosynthesis, catabolism and transport.
  • PreQ1 riboswitches bind pre-queuosine1, to regulate genes involved in the synthesis or transport of this precursor to queuosine. Two entirely distinct classes of PreQ1 riboswitches are known: PreQ1-I riboswitches and PreQ1-II riboswitches. 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.
  • Purine riboswitches binds purines 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.
  • SAH riboswitches bind S-adenosylhomocysteine to regulate genes involved in recycling this metabolite that is produced when S-adenosylmethionine is used in methylation reactions.
  • SAM riboswitches bind S-adenosyl methionine (SAM) to regulate methionine and SAM biosynthesis and transport. Three distinct SAM riboswitches are known: SAM-I (originally called S-box), SAM-II and the SMK box riboswitch. SAM-I is widespread in bacteria, but SAM-II is found only in alpha-, beta- and a few gamma-proteobacteria. The SMK 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 riboswitches, appears to have a similar ligand-binding core to that of SAM-I riboswitches, but in the context of a distinct scaffold.
  • SAM-SAH riboswitches bind both SAM and SAH with similar affinities. Since they are always found in a position to regulate genes encoding methionine adenosyltransferase, it was proposed that only their binding to SAM is physiologically relevant.
  • TPP riboswitch (also THI-box) binds thiamin pyrophosphate (TPP) to regulate thiamin biosynthesis and transport, as well as transport of similar metabolites. It is the only riboswitch found so far in eukaryotes.[27]

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

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Riboswitches demonstrate that naturally occurring RNA can bind small molecules specifically, a capability that many previously believed was the domain of proteins or artificially constructed RNAs called aptamers. 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 ribozymes whose bindings domains are conserved.[12][28][29]


Riboswitches as antibiotic targets

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Riboswitches could be a target for novel antibiotics. Indeed, some antibiotics whose mechanism of action was unknown for decades have been shown to operate by targeting riboswitches.[30] 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.

Engineered riboswitches

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Since riboswitches are an effective method of controlling gene expression in natural organisms, there has been interest in engineering artificial riboswitches.[31]

References

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  1. ^ Tucker BJ, Breaker RR (2005). "Riboswitches as versatile gene control elements". Curr Opin Struct Biol. 15 (3): 342–8. doi:10.1016/j.sbi.2005.05.003. PMID 15919195.
  2. ^ Vitreschak AG, Rodionov DA, Mironov AA, Gelfand MS (2004). "Riboswitches: the oldest mechanism for the regulation of gene expression?". Trends Genet. 20 (1): 44–50. doi:10.1016/j.tig.2003.11.008. PMID 14698618.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. ^ Batey RT (2006). "Structures of regulatory elements in mRNAs". Curr Opin Struct Biol. 16 (3): 299–306. doi:10.1016/j.sbi.2006.05.001. PMID 16707260.
  4. ^ a b Nahvi A, Sudarsan N, Ebert MS, Zou X, Brown KL, Breaker RR (2002). "Genetic control by a metabolite binding mRNA". Chem Biol. 9 (9): 1043. doi:10.1016/S1074-5521(02)00224-7. PMID 12323379.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ Sudarsan N, Barrick JE, Breaker RR (2003). "Metabolite-binding RNA domains are present in the genes of eukaryotes". RNA. 9 (6): 644–7. doi:10.1261/rna.5090103. PMC 1370431. PMID 12756322.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ Nou X, Kadner RJ (June 2000). "Adenosylcobalamin inhibits ribosome binding to btuB RNA". Proc. Natl. Acad. Sci. U.S.A. 97 (13): 7190–5. doi:10.1073/pnas.130013897. PMC 16521. PMID 10852957.{{cite journal}}: CS1 maint: date and year (link)
  7. ^ Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA (November 1999). "A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends Genet. 15 (11): 439–42. doi:10.1016/s0168-9525(99)01856-9. PMID 10529804.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  8. ^ Miranda-Ríos J, Navarro M, Soberón M (August 2001). "A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria". Proc. Natl. Acad. Sci. U.S.A. 98 (17): 9736–41. doi:10.1073/pnas.161168098. PMC 55522. PMID 11470904.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
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  10. ^ Gold L, Brown D, He Y, Shtatland T, Singer BS, Wu Y (January 1997). "From oligonucleotide shapes to genomic SELEX: novel biological regulatory loops". Proc. Natl. Acad. Sci. U.S.A. 94 (1): 59–64. doi:10.1073/pnas.94.1.59. PMC 19236. PMID 8990161.{{cite journal}}: CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  11. ^ Mironov AS, Gusarov I, Rafikov R, Lopez LE, Shatalin K, Kreneva RA, Perumov DA, Nudler E (2002). "Sensing small molecules by nascent RNA: a mechanism to control transcription in bacteria". Cell. 111 (5): 747–56. doi:10.1016/S0092-8674(02)01134-0. PMID 12464185.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  12. ^ a b Winkler W, Nahvi A, Breaker RR (2002). "Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression". Nature. 419 (6910): 890–1. doi:10.1038/nature01145. PMID 12410317.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  13. ^ Winkler WC, Cohen-Chalamish S, Breaker RR (2002). "An mRNA structure that controls gene expression by binding FMN". Proc Natl Acad Sci USA. 99 (25): 15908–13. doi:10.1073/pnas.212628899. PMC 138538. PMID 12456892.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  14. ^ Grundy FJ, Henkin TM (1998). "The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria". Mol Microbiol. 30 (4): 737–49. doi:10.1046/j.1365-2958.1998.01105.x. PMID 10094622.
  15. ^ Miranda-Ríos J, Navarro M, Soberón M (2001). "A conserved RNA structure (thi box) is involved in regulation of thiamin biosynthetic gene expression in bacteria". Proc Natl Acad Sci USA. 98 (17): 9736–41. doi:10.1073/pnas.161168098. PMC 55522. PMID 11470904.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  16. ^ Gelfand MS, Mironov AA, Jomantas J, Kozlov YI, Perumov DA (1999). "A conserved RNA structure element involved in the regulation of bacterial riboflavin synthesis genes". Trends Genet. 15 (11): 439–42. doi:10.1016/S0168-9525(99)01856-9. PMID 10529804.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  17. ^ Franklund CV, Kadner RJ (June 1997). "Multiple transcribed elements control expression of the Escherichia coli btuB gene". J. Bacteriol. 179 (12): 4039–42. doi:10.1128/jb.179.12.4039-4042.1997. PMC 179215. PMID 9190822.{{cite journal}}: CS1 maint: date and year (link)
  18. ^ Barrick JE, Corbino KA, Winkler WC, Nahvi A, Mandal M, Collins J, Lee M, Roth A, Sudarsan N, Jona I, Wickiser JK, Breaker RR (2004). "New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control". Proc Natl Acad Sci USA. 101 (17): 6421–6. doi:10.1073/pnas.0308014101. PMC 404060. PMID 15096624.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  19. ^ Corbino KA, Barrick JE, Lim J, Welz R, Tucker BJ, Puskarz I, Mandal M, Rudnick ND, Breaker RR (2005). "Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria". Genome Biol. 6 (8): R70. doi:10.1186/gb-2005-6-8-r70. PMC 1273637. PMID 16086852.{{cite journal}}: CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  20. ^ 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 (2007). "Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline". Nucleic Acids Res. 35 (14): 4809–4819. doi:10.1093/nar/gkm487. PMC 1950547. PMID 17621584.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  21. ^ Weinberg Z, Wang JX, Bogue J; et al. (March 2010). "Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea and their metagenomes". Genome Biol. 11 (3): R31. doi:10.1186/gb-2010-11-3-r31. PMC 2864571. PMID 20230605. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  22. ^ Cheah MT, Wachter A, Sudarsan N, Breaker RR (2007). "Control of alternative RNA splicing and gene expression by eukaryotic riboswitches". Nature. 447 (7143): 497–500. doi:10.1038/nature05769. PMID 17468745.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  23. ^ Wachter A, Tunc-Ozdemir M, Grove BC, Green PJ, Shintani DK, Breaker RR (2007). "Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs". Plant Cell. 19 (11): 3437–50. doi:10.1105/tpc.107.053645. PMC 2174889. PMID 17993623.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  24. ^ Bocobza S, Adato A, Mandel T, Shapira M, Nudler E, Aharoni A (2007). "Riboswitch-dependent gene regulation and its evolution in the plant kingdom". Genes Dev. 21 (22): 2874–9. doi:10.1101/gad.443907. PMC 2049190. PMID 18006684.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  25. ^ André G, Even S, Putzer H; et al. (October 2008). "S-box and T-box riboswitches and antisense RNA control a sulfur metabolic operon of Clostridium acetobutylicum". Nucleic Acids Res. 36 (18): 5955–69. doi:10.1093/nar/gkn601. PMC 2566862. PMID 18812398. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  26. ^ Loh E, Dussurget O, Gripenland J; et al. (November 2009). "A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes". Cell. 139 (4): 770–9. doi:10.1016/j.cell.2009.08.046. PMID 19914169. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: date and year (link) CS1 maint: multiple names: authors list (link)
  27. ^ Switching the light on plant riboswitches. Samuel Bocobza and Asaph Aharoni Trends in Plant Science Volume 13, Issue 10, October 2008, Pages 526-533 doi:10.1016/j.tplants.2008.07.004
  28. ^ Corbino KA, Barrick JE, Lim J; et al. (2005). "Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria". Genome Biol. 6 (8): R70. doi:10.1186/gb-2005-6-8-r70. PMC 1273637. PMID 16086852. {{cite journal}}: Explicit use of et al. in: |author= (help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link)
  29. ^ Cochrane JC, Strobel SA (April 2008). "Riboswitch effectors as protein enzyme cofactors". RNA. 14 (6): 993–1002. doi:10.1261/rna.908408. PMC 2390802. PMID 18430893.{{cite journal}}: CS1 maint: date and year (link)
  30. ^ Blount KF, Breaker RR (2006). "Riboswitches as antibacterial drug targets". Nat Biotechnol. 24 (12): 1558–64. doi:10.1038/nbt1268. PMID 17160062.
  31. ^ Bauer G, Suess B (June 2006). "Engineered riboswitches as novel tools in molecular biology". Journal of Biotechnology. 124 (1): 4–11. doi:10.1016/j.jbiotec.2005.12.006. PMID 16442180.{{cite journal}}: CS1 maint: date and year (link)
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