Riboswitches and the role of noncoding RNAs in bacterial metabolic control

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Microorganisms use a plethora of genetic strategies to regulate expression of their genes. In recent years there has been an increase in the discovery and characterization of riboswitches, cis-acting regulatory RNAs that function as direct receptors for intracellular metabolites. Nine classes have been uncovered that together regulate many essential biochemical pathways. Two classes, responding to either glucosamine-6-phosphate (GlcN6P) or glycine, have been found to employ novel mechanisms of genetic control. Additionally, progress has been achieved in elucidating molecular details for regulation by the other riboswitches, via X-ray crystallography and biochemical analyses of riboswitch–metabolite interactions. The complete repertoire of metabolite-sensing RNAs and extent of their usage in modern organisms remains to be determined; however, these current data assist in establishing a foundation from which to build future expectations.

Introduction

The recent wealth of genomic information has empowered bacterial biologists from numerous research disciplines and has accelerated the comprehensive cataloging of biochemical activities, biological functions, and the genes that are responsible for them. One can also envisage a complete analysis of genetic circuitry, which would undoubtedly reveal greater complexity than was imagined while current genetic paradigms were being established. Control of transcription initiation through protein-based activators and repressors will certainly comprise a large portion of this hypothetical catalog; however, thorough analyses of the diverse roles of cellular RNA polymers will also be required. To that end, there is an escalating awareness that RNAs perform tasks in addition to serving as passive templates for the translation apparatus. These newfound abilities include recently described examples of catalytic RNAs and burgeoning roles for cis- and trans-acting RNAs in post-transcriptional genetic regulation. No longer the occasional anomaly, RNA-mediated regulatory mechanisms have been found to exert control over a substantial portion of the typical microbial genome. A recent survey of published literature revealed that greater than 4% of the Bacillus subtilis genome is thought to be regulated through cis-acting regulatory RNAs, a value that is certain to be an underestimate [1]. Similar results have demonstrated extensive regulation of Escherichia coli expression by trans-acting small RNAs (sRNAs) [2, 3], although only cis-acting RNAs are discussed herein.

In general, cis-acting regulatory RNAs are almost always located in the 5′-untranslated region (5′-UTR) and can form mutually exclusive alternate conformations, wherein one configuration leads to greater expression of the associated genes (Figure 1). Changes in metabolic or environmental conditions are primarily transduced through intermediate effector molecules that associate with the 5′-UTR and stabilize a conformational state. These effector moieties can be in the form of proteins, physical stimuli, structured or unstructured RNAs, and small-molecule metabolites (Figure 1). Metabolite-sensing RNAs (riboswitches) have been identified within evolutionarily diverse bacterial species [4] and associate with chemicals that are believed to have been derived from ancient origins [5], circumstantially suggesting they are modern relics from primordial organisms. Given their importance in metabolisms of extant and extinct organisms, and their usage as tools for general study of RNA structure, riboswitches have recently become subjects of intensive biochemical and structural analyses [6••, 7••]. Additionally, studies of the kinetics of RNA–metabolite interactions have recently provided important insights into their genetic mechanisms [8].

In addition to these advancements, several important new classes and examples of noncoding RNAs have been uncovered [9•, 10, 11••, 12, 13, 14, 15, 16]. Interestingly, two classes that respond to either gluosamine-6-phosphate [11••] or glycine [17] use entirely novel mechanisms for genetic regulation. Additionally, a riboswitch example has been found to function in eukaryotes, most likely through control of splicing [18]. In total, the past several years have led to rapid and significant advancements on the study of RNA-mediated genetic control. Much of this progress has resulted from the continued search for additional riboswitch RNAs and investigations into the biochemical principles that underlie their molecular mechanisms.

Section snippets

Riboswitches as chemical sensors: new classes and structural insights

Before 2004, riboswitches had been demonstrated to bind adenosylcobalamin (AdoCbl), thiamine pyrophosphate (TPP), flavin mononucleotide (FMN), S-adenosylmethionine (SAM), lysine, guanine, and adenine [19, 20, 21, 22]. Upon binding of the appropriate metabolite, these 5′-UTRs are conformationally altered such that expression of the associated genes is modified. Metabolite-binding regions (aptamers) of riboswitches exhibit a high degree of primary sequence and secondary structure conservation and

The importance of kinetics

Over half of putative riboswitches are predicted to regulate expression through transcription attenuation (see Figure 1 for an example). They must rapidly adopt their aptamer structures as the nascent transcript emerges, which then has until RNA polymerase (RNAP) nears completion of the expression platform to attain productive interactions with its target ligand. These mechanisms are likely to require synchronization of multiple processes, including RNA folding, kinetics of ligand binding, and

Conclusions

Recent investigations into RNA-mediated genetic control have led to significant advancements in our understanding of the role of RNA polymers in biology. In particular, new computational methods have been successfully employed for identification of regulatory RNAs, which hint at a broader role for noncoding RNAs than previously anticipated. In particular, metabolite-sensing riboswitches have been discovered to be commonly used for regulation of fundamental biochemical pathways in bacteria. The

References and recommended reading

Papers of particular interest, published within the annual period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgements

In an effort to narrow the focus of this manuscript and limit citations, I have undoubtedly omitted important research articles that would have enriched these discussions. In particular, I encourage readers to pursue specialized review articles on the functional roles of bacterial sRNAs as well as recent advancements in transcription attenuation and pausing. I thank the editors and Charles Dann III for helpful suggestions. Research in the Winkler laboratory is funded by the Searle Scholars

References (47)

  • J. Johansson et al.

    An RNA thermosensor controls expression of virulence genes in Listeria monocytogenes

    Cell

    (2002)
  • W.C. Winkler

    Metabolic monitoring by bacterial mRNAs

    Arch Microbiol

    (2005)
  • S. Gottesman

    The small RNA regulators of Escherichia coli: roles and mechanisms

    Annu Rev Microbiol

    (2004)
  • G. Storz et al.

    An abundance of RNA regulators

    Annu Rev Biochem

    (2005)
  • HB. White

    Coenzymes as fossils of an earlier metabolic state

    J Mol Evol

    (1976)
  • R.T. Batey et al.

    Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine

    Nature

    (2004)
  • A. Serganov et al.

    Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

    Chem Biol

    (2004)
  • J.E. Barrick et al.

    New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control

    Proc Natl Acad Sci USA

    (2004)
  • W.C. Winkler et al.

    Control of gene expression by a natural metabolite-responsive ribozyme

    Nature

    (2004)
  • M. Mandal et al.

    Adenine riboswitches and gene activation by disruption of a transcription terminator

    Nat Struct Mol Biol

    (2004)
  • T. Kubodera et al.

    Thiamine-regulated gene expression of Aspergillus oryzae thiA requires splicing of the intron containing a riboswitch-like domain in the 5′-UTR

    FEBS Lett

    (2003)
  • J.E. Barrick et al.

    6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter

    RNA

    (2005)
  • A.E. Trotochaud et al.

    A highly conserved 6S RNA structure is required for regulation of transcription

    Nat Struct Mol Biol

    (2005)
  • Cited by (0)

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