Towards deciphering the principles underlying an mRNA recognition code

Serganov, Alexander; Patel, Dinshaw J.

doi:10.1016/j.sbi.2007.12.006

Cited by 24 publications

(26 citation statements)

References 61 publications

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“…These changes may trigger rearrangements in additional expression platform structures located outside the aptamer, giving two alternative conformations. Riboswitches are able to interconvert between these ligand-bound and ligand-free structures in the context of the full-length RNA (25,405,406). The crystal structure of the FMN riboswitch controlling the putative RF transporter encoded by impX in Fusobacterium nucleatum bound with FMN, RF, and roseoflavin has been determined (404).…”

Section: Transcriptional Regulation In Bacteria Using the Riboswitch mentioning

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

324

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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Section: Transcriptional Regulation In Bacteria Using the Riboswitch mentioning

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

324

272

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“…These changes not only optimize intermolecular interactions, but they also serve to sense, process, and transmit chemical information. For example, structural changes triggered by ligand binding form the basis by which many RNA riboswitches both sense and respond to environmental factors in regulating gene expression (Mandal and Breaker 2004;Montange and Batey 2008;Serganov and Patel 2008). Multistep RNA structural transitions can help order the sequence of transactions underlying assembly of ribonucleoproteins and catalysis (Liu et al 2007;Stone et al 2007;Williamson 2008;Woodson 2008).…”

Section: Introductionmentioning

confidence: 99%

Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition

Zhang

Al‐Hashimi

2009

RNA

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By simplifying the interpretation of nuclear magnetic resonance spin relaxation and residual dipolar couplings data, recent developments involving the elongation of RNA helices are providing new atomic insights into the dynamical properties that allow RNA structures to change functionally and adaptively. Domain elongation, in concert with spin relaxation measurements, has allowed the detailed characterization of a hierarchical network of local and collective motional modes occurring at nanosecond timescale that mirror the structural rearrangements that take place following adaptive recognition. The combination of domain elongation with residual dipolar coupling measurements has allowed the experimental threedimensional visualization of very large amplitude rigid-body helix motions in HIV-1 transactivation response element (TAR) that trace out a highly choreographed trajectory in which the helices twist and bend in a correlated manner. The dynamic trajectory allows unbound TAR to sample many of its ligand bound conformations, indicating that adaptive recognition occurs by ''conformational selection'' rather than ''induced fit.'' These studies suggest that intrinsic flexibility plays essential roles directing RNA conformational changes along specific pathways.

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“…Although post-transcriptional processes are sometimes mediated by RNA secondary structure, most mRNA-specific interactions require a primary nucleotide sequence component (Rabani et al 2008;Serganov and Patel 2008;Gilligan et al 2011). The conservation of such primary sequence elements is typically easier to interpret because similarity in secondary structure is often a result of nucleotide composition (Rivas and Eddy 2000) and, even when constrained structure can be identified via covariance, these structures are difficult to generalize across the genes that harbor them (McGuire and Galagan 2008;Rabani et al 2008).…”

Section: Introductionmentioning

confidence: 99%

Known and novel post-transcriptional regulatory sequences are conserved across plant families

Vaughn¹,

Ellingson²,

Mignone³

et al. 2012

RNA

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The sequence elements that mediate post-transcriptional gene regulation often reside in the 59 and 39 untranslated regions (UTRs) of mRNAs. Using six different families of dicotyledonous plants, we developed a comparative transcriptomics pipeline for the identification and annotation of deeply conserved regulatory sequences in the 59 and 39 UTRs. Our approach was robust to confounding effects of poor UTR alignability and rampant paralogy in plants. In the 39 UTR, motifs resembling PUMILIObinding sites form a prominent group of conserved motifs. Additionally, Expansins, one of the few plant mRNA families known to be localized to specific subcellular sites, possess a core conserved RCCCGC motif. In the 59 UTR, one major subset of motifs consists of purine-rich repeats. A distinct and substantial fraction possesses upstream AUG start codons. Half of the AUG containing motifs reveal hidden protein-coding potential in the 59 UTR, while the other half point to a peptideindependent function related to translation. Among the former, we added four novel peptides to the small catalog of conserved-peptide uORFs. Among the latter, our case studies document patterns of uORF evolution that include gain and loss of uORFs, switches in uORF reading frame, and switches in uORF length and position. In summary, nearly three hundred posttranscriptional elements show evidence of purifying selection across the eudicot branch of flowering plants, indicating a regulatory function spanning at least 70 million years. Some of these sequences have experimental precedent, but many are novel and encourage further exploration.

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Towards deciphering the principles underlying an mRNA recognition code

Cited by 24 publications

References 61 publications

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

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

Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition

Known and novel post-transcriptional regulatory sequences are conserved across plant families

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