Riboswitch effectors as protein enzyme cofactors

Cochrane, Jesse C.; Strobel, Scott A.

doi:10.1261/rna.908408

Cited by 47 publications

(34 citation statements)

References 84 publications

(107 reference statements)

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“…In addition, divalent cations such as Mg 2+ and backbone phosphate oxygens also play key functional roles in catalysis of many ribozymes (Cochrane and Strobel 2008a;Donghi and Schnabl 2011). Biochemical roles of cofactors and metal ions in RNA biochemistry have been studied elsewhere (for review, see Cochrane and Strobel 2008b;Donghi and Schnabl 2011). Furthermore, as indicated above, chemical modifications of nucleobases (such as the ones observed in tRNA and rRNA) are also known to contribute to an increased chemical versatility of RNA, as detailed in Björk et al (1999) and Czerwoniec et al (2009).…”

Section: Biochemical Functions and Mechanisms Of Chemical Diversificamentioning

confidence: 99%

Role of tautomerism in RNA biochemistry

Singh

Fedeles

Essigmann

2014

RNA

126

116

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Heterocyclic nucleic acid bases and their analogs can adopt multiple tautomeric forms due to the presence of multiple solventexchangeable protons. In DNA, spontaneous formation of minor tautomers has been speculated to contribute to mutagenic mispairings during DNA replication, whereas in RNA, minor tautomeric forms have been proposed to enhance the structural and functional diversity of RNA enzymes and aptamers. This review summarizes the role of tautomerism in RNA biochemistry, specifically focusing on the role of tautomerism in catalysis of small self-cleaving ribozymes and recognition of ligand analogs by riboswitches. Considering that the presence of multiple tautomers of nucleic acid bases is a rare occurrence, and that tautomers typically interconvert on a fast time scale, methods for studying rapid tautomerism in the context of nucleic acids under biologically relevant aqueous conditions are also discussed.

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Section: Biochemical Functions and Mechanisms Of Chemical Diversificamentioning

confidence: 99%

Role of tautomerism in RNA biochemistry

Singh

Fedeles

Essigmann

2014

RNA

126

116

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“…Riboswitches are found in many classes of eubacteria but only a few archaea and eukaryotes (25). Riboswitches involved in vitamin and coenzyme synthesis constitute the most abundant class of untranslated mRNA regions capable of direct sensing of cellular metabolites (75,325,378,405). Riboswitches are the nontranslated mRNAs that bind effectors (low-molecular-weight metabolites) using selective binding domains (otherwise called ligand-binding pockets or aptamers) without a requirement for any proteins.…”

Section: Transcriptional Regulation In Bacteria Using the Riboswitchmentioning

confidence: 99%

“…For example, exponentially growing wild-type cells of E. coli, B. subtilis, and Pseudomonas fluorescens secrete into the medium VOL. 75,2011 RF AND FLAVIN NUCLEOTIDE BIOSYNTHESIS AND TRANSPORT 343…”

Section: Flavin Synthesis By Flavinogenic Microorganismsmentioning

confidence: 99%

Genetic Control of Biosynthesis and Transport of Riboflavin and Flavin Nucleotides and Construction of Robust Biotechnological Producers

Abbas

Sibirny

2011

Microbiol Mol Biol Rev

325

272

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SUMMARY Riboflavin [7,8-dimethyl-10-(1′- d -ribityl)isoalloxazine, vitamin B 2 ] is an obligatory component of human and animal diets, as it serves as the precursor of flavin coenzymes, flavin mononucleotide, and flavin adenine dinucleotide, which are involved in oxidative metabolism and other processes. Commercially produced riboflavin is used in agriculture, medicine, and the food industry. Riboflavin synthesis starts from GTP and ribulose-5-phosphate and proceeds through pyrimidine and pteridine intermediates. Flavin nucleotides are synthesized in two consecutive reactions from riboflavin. Some microorganisms and all animal cells are capable of riboflavin uptake, whereas many microorganisms have distinct systems for riboflavin excretion to the medium. Regulation of riboflavin synthesis in bacteria occurs by repression at the transcriptional level by flavin mononucleotide, which binds to nascent noncoding mRNA and blocks further transcription (named the riboswitch). In flavinogenic molds, riboflavin overproduction starts at the stationary phase and is accompanied by derepression of enzymes involved in riboflavin synthesis, sporulation, and mycelial lysis. In flavinogenic yeasts, transcriptional repression of riboflavin synthesis is exerted by iron ions and not by flavins. The putative transcription factor encoded by SEF1 is somehow involved in this regulation. Most commercial riboflavin is currently produced or was produced earlier by microbial synthesis using special selected strains of Bacillus subtilis , Ashbya gossypii , and Candida famata . Whereas earlier RF overproducers were isolated by classical selection, current producers of riboflavin and flavin nucleotides have been developed using modern approaches of metabolic engineering that involve overexpression of structural and regulatory genes of the RF biosynthetic pathway as well as genes involved in the overproduction of the purine precursor of riboflavin, GTP.

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“…It has been explicitly noted that such experimental systems might, in fact, model the amplification and propagation of the first replicators in primordial environmental settings [57,351,354]. Further indications of primeval RNA life might be the participation of tRNA molecules as catalysts in several metabolic reactions (see [23] and references therein) and interactions of RNA molecules with metabolites [379,380], in particular in the case of riboswitches [381,382].…”

Section: Colonization Wavesmentioning

confidence: 99%