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Riboswitches for the Alarmone Ppgpp Expand the Collection of RNA-Based Signaling Systems

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Riboswitches for the Alarmone Ppgpp Expand the Collection of RNA-Based Signaling Systems Riboswitches for the alarmone ppGpp expand the collection of RNA-based signaling systems Madeline E. Sherlocka, Narasimhan Sudarsanb, and Ronald R. Breakera,b,c,1 aDepartment of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103; bHoward Hughes Medical Institute, Yale University, New Haven, CT 06520-8103; and cDepartment of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8103 Contributed by Ronald R. Breaker, April 20, 2018 (sent for review November 27, 2017; reviewed by Daniel A. Lafontaine and Jörg Vogel) Riboswitches are noncoding portions of certain mRNAs that bind mononucleotide are consistent with an ancient RNA World or- metabolite, coenzyme, signaling molecule, or inorganic ion ligands igin (5). Given these characteristics, we previously speculated and regulate gene expression. Most known riboswitches sense de- that ppGpp would be an ideal ligand candidate for a riboswitch rivatives of RNA monomers. This bias in ligand chemical composition class that had yet to be discovered (5, 6, 10, 12). Thus, we were is consistent with the hypothesis that widespread riboswitch classes well positioned to test ppGpp as a candidate ligand when we first emerged during the RNA World, which is proposed to have recently (23) identified a riboswitch subtype (Fig. 1B) of un- existed before proteins were present. Here we report the discovery known function that commonly associates with genes for BCAA and biochemical validation of a natural riboswitch class that selectively metabolism (Fig. 1C). The ppGpp riboswitch candidates were “ ” binds guanosine tetraphosphate (ppGpp), a widespread signaling recognized as subtype 2a variants of what we originally called a molecule and bacterial “alarmone” derived from the ribonucleotide GTP. ykkC motif RNAs (24). Riboswitches for ppGpp are predicted to regulate genes involved in The predominant members (subtype 1) of the ykkC motif branched-chain amino acid biosynthesis and transport, as well as other collection were recently determined to function as guanidine- sensing RNAs, which are collectively called guanidine-I riboswitches gene classes that previously had not been implicated to be part of its (23). In this same study, it was discovered that certain ykkC signaling network. This newfound riboswitch–alarmone partnership motif RNAs (subtype 2) carry distinctive mutations at nucleo- supports the hypothesis that prominent RNA World signaling pathways tide positions found directly in the binding pocket (25, 26). have been retained by modern cells to control key biological processes. Members of the ykkC subtype 2 collection do not bind guani- dine, confirming that the binding site differences indeed alter branched chain amino acid | guanosine tetraphosphate | logic gate | riboswitch specificity. stringent response | ykkC motif RNA Although ppGpp had previously been tested for binding to ykkC RNAs (27), it was determined in retrospect that the specific mong the 38 distinct riboswitch (1–3) classes validated RNA sequences tested belong to the guanidine-I riboswitch Apreviously (4), five respond to RNA-derived signaling class. After further separation of the subtypes into four addi- molecules that might have emerged in an RNA World, but have tional classes, called subtype 2a through 2d (based on distinctive been retained to trigger regulatory processes in modern cells. We gene associations and aptamer sequence variations), ppGpp have proposed (5, 6) that riboswitches for the RNA-derived became a likely candidate ligand because of the association of molecules c-di-GMP (7, 8), c-di-AMP (9), ZTP (10), and c- many subtype 2a representatives with genes for BCAA bio- AMP-GMP (11, 12) represent modern versions of primordial synthesis. Furthermore, BCAA biosynthesis is activated during the stringent response in Firmicutes, which are the predominant signaling processes built entirely from RNA. organisms that contain subtype 2a ykkC motif variants. A widely distributed RNA signaling molecule that is essential for many bacteria is ppGpp (Fig. 1A), a guanosine tetraphosphate alarmone originally called magic spot (13). This compound, along Significance with its natural precursor pppGpp, is widely implicated in regulating RNA polymerase and other protein factors to control metabolic Bacteria and other organisms make extensive use of signaling and physiological responses to various stresses (14–16), including molecules that are derived from ribonucleotides or their de- the long-studied stringent response. The stringent response is a rivatives. Previously, five riboswitch classes had been discov- major starvation-induced adaptation that can be triggered by amino ered that sense the four RNA-derived signaling molecules: c-di- acid depletion (17–19). In Proteobacteria, this adaptation is ac- GMP, c-di-AMP, c-AMP-GMP, and ZTP. We now report the dis- complished at least in part via the direct inhibition of RNA poly- covery and biochemical validation of bacterial riboswitches for merase by ppGpp binding (16). the widespread alarmone guanosine tetraphosphate (ppGpp), In Firmicutes, transcription regulation by ppGpp is known to act which signals metabolic and physiological adaptations to star- indirectly. GTP levels drop as a result of (p)ppGpp synthesis to vation. These findings expand the number of natural partner- specifically down-regulate transcription of genes that initiate with a G ships between riboswitches and ribonucleotide-like signaling nucleotide, which affects the production of certain mRNAs and also molecules, and provide RNA-based sensors for detecting ppGpp rRNAs. GTP depletion still permits transcription of genes that ini- production in cells. tiate with an A nucleotide, such as those for branched-chain amino acid (BCAA) biosynthesis (20, 21). Specific gene activation also oc- Author contributions: M.E.S., N.S., and R.R.B. designed research; M.E.S. and N.S. per- curs by the dissociation of the CodY transcriptional repressor protein formed research; M.E.S., N.S., and R.R.B. analyzed data; and M.E.S. and R.R.B. wrote when GTP levels drop as a result of (p)ppGpp synthesis (22). This the paper. protein-based system thus allows ppGpp to indirectly activate CodY- Reviewers: D.A.L., Université de Sherbrooke; and J.V., Helmholtz Institute for RNA-Based controlled genes. Herein we describe another mechanism for ppGpp- Infection Research. triggeredregulationofgeneexpressioninFirmicutesmediatedby The authors declare no conflict of interest. numerous examples of selective ppGpp-sensing riboswitches. This open access article is distributed under Creative Commons Attribution-NonCommercial- NoDerivatives License 4.0 (CC BY-NC-ND). Results and Discussion 1To whom correspondence should be addressed. Email: [email protected]. Identification of ppGpp Riboswitch Candidates. The widespread This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. distribution of ppGpp in biology, its role in regulating funda- 1073/pnas.1720406115/-/DCSupplemental. mental biological processes, and its construction from an RNA Published online May 21, 2018. 6052–6057 | PNAS | June 5, 2018 | vol. 115 | no. 23 www.pnas.org/cgi/doi/10.1073/pnas.1720406115 Downloaded by guest on September 29, 2021 longer a conserved G nucleotide. It seemed plausible that the C O COG4587 A B Nucleotide identity covariation CCOG3694 N NH N 97% N 75% no covariation natA nucleotide (C71 in the T. oceani 112 ilvE RNA), which is in a O O N 90% R = A G Y = C U ilvB Nucleotide present variable -O P O P O N P1a gltBD O N NH2 G 97% 75% length region of reduced scission upon ligand binding in-line probing G - - C 90% 50% hairpin O O C G U UC G glxB ilvE reactions (Fig. 2A), might be available to base pair to the O OH U C A G C A A - P G R A gltS ppGpp O O A G nucleobase of ppGpp. Indeed, introducing a C to U mutation at G A G C O A G U Y P3 G C livF ilvC C G G Y this position (M8) (Fig. 3A) switches the specificity of the -O P O Y R livG R Y U livH - P1 G leuB O Y R GC livM aptamer from a G-containing ligand to an A-containing ligand, G C C G ilvH R C G leuD 5´ R G RAG R U A CA A RGUYC Y ilvD leuA R Y as demonstrated by ability of the mutant RNA to preferentially Y R P2 BCAA biosynthesis recognize pAp over pGp or ppGpp (Fig. 3B). YR BCAA transporters glutamate synthases In-line probing was also used to estimate the KD of pAp ABC transporters binding by the M8 RNA construct (Fig. 3C). The binding curve generated from these data (Fig. 3D) reveals a K of ∼50 μM for Fig. 1. ppGpp riboswitches and their regulatory network. (A)Thechemical D structure of ppGpp (guanosine-3′,5′-bisdiphosphate). (B) Consensus sequence one-to-one binding of pAp by M8 RNA. This KD is similar to and secondary structure model for ppGpp riboswitches derived from 115 unique that measured for pGp binding to the WT version of this same representatives. (C) Genes predicted to be regulated by ppGpp riboswitches. RNA (SI Appendix, Fig. S3B). These data suggest that this C nucleotide at position 71 of the 112 ilvE aptamer is the primary determinant of nucleobase recognition for the riboswitch ligand. Subtype 2a ykkC Motif RNAs Selectively Bind ppGpp. To test for Currently, we have no evidence for a naturally occurring aptamer ppGpp riboswitch function, we first arbitrarily chose to examine for ppApp (or a similar adenosine-containing molecule) because a BCAA-associated candidate RNA construct from the ilvE gene this position of the aptamer is conserved as a C nucleotide across of Thermosediminibacter oceani (Fig. 2A) by using in-line prob- all natural examples of the sequences resembling ppGpp riboswitches ing. This method exploits the differential instability of RNA examined to date. phosphoester bonds in unstructured versus structured regions, to provide evidence that ligand docking alters the folding state of Transcription Termination Regulated by a ppGpp Riboswitch.
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