scholarly journals Extending the Spacing between the Shine–Dalgarno Sequence and P-Site Codon Reduces the Rate of mRNA Translocation

2020 ◽  
Vol 432 (16) ◽  
pp. 4612-4622
Author(s):  
Hironao Wakabayashi ◽  
Chandani Warnasooriya ◽  
Dmitri N. Ermolenko
Keyword(s):  
Shine Dalgarno Sequence

The malS-5′UTR regulates hisG, a key gene in the histidine biosynthetic pathway in Salmonella enterica serovar Typhi

2017 ◽  
Vol 63 (4) ◽  
pp. 287-295 ◽  
Author(s):  
Ying Zhang ◽  
Dongmei Yan ◽  
Lin Xia ◽  
Xin Zhao ◽  
George Osei-Adjei ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Rna Structure ◽  
Biosynthetic Pathway ◽  
Salmonella Typhi ◽  
Base Pairing ◽  
Salmonella Enterica Serovar Typhi ◽  
Cellular Processes ◽  
Invasive Capacity ◽  
Shine Dalgarno Sequence ◽  
Bax Gene

Bacterial noncoding RNAs (ncRNA) regulate diverse cellular processes, including virulence and environmental fitness. The malS 5′ untranslated region (named malS-5′UTR) was identified as a regulatory ncRNA that increases the invasive capacity of Salmonella enterica serovar Typhi. An IntaRNA search suggested base pairing between malS-5′UTR and hisG mRNA, a key gene in the histidine biosynthetic pathway. Overexpression of malS-5′UTR markedly reduced bacterial growth in minimal medium without histidine. Overexpression of malS-5′UTR increased mRNA from his operon genes, independently of the bax gene, and decreased HisG protein in Salmonella Typhi. RNA structure analysis showed base pairing of the malS-5′UTR RNA with the hisG mRNA across the ribosome binding site. Thus, we propose that malS-5′UTR inhibited hisG translation, probably by base pairing to the Shine–Dalgarno sequence.

scholarly journals Mutational analysis of the mRNA operator for T4 DNA polymerase.

Genetics ◽  
1991 ◽  
Vol 128 (2) ◽  
pp. 203-213 ◽  
Author(s):  
M D Andrake ◽  
J D Karam
Keyword(s):  
Dna Polymerase ◽  
Mutational Analysis ◽  
Bacteriophage T4 ◽  
Spatial Arrangement ◽  
Loop Sequence ◽  
Shine Dalgarno Sequence ◽  
In Vitro Effects ◽  
Rna Hairpin

Abstract Biosynthesis of bacteriophage T4 DNA polymerase is autogenously regulated at the translational level. The enzyme, product of gene 43, represses its own translation by binding to its mRNA 5' to the initiator AUG at a 36-40 nucleotide segment that includes the Shine-Dalgarno sequence and a putative RNA hairpin structure consisting of a 5-base-pair stem and an 8-base loop. We constructed mutations that either disrupted the stem or altered specific loop residues of the hairpin and found that many of these mutations, including single-base changes in the loop sequence, diminished binding of purified T4 DNA polymerase to its RNA in vitro (as measured by a gel retardation assay) and derepressed synthesis of the enzyme in vivo (as measured in T4 infections and by recombinant-plasmid-mediated expression). In vitro effects, however, were not always congruent with in vivo effects. For example, stem pairing with a sequence other than wild-type resulted in normal protein binding in vitro but derepression of protein synthesis in vivo. Similarly, a C----A change in the loop had a small effect in vitro and a strong effect in vivo. In contrast, an A----U change near the base of the hairpin that was predicted to increase the length of the base-paired stem had small effects both in vitro and in vivo. The results suggest that interaction of T4 DNA polymerase with its structured RNA operator depends on the spatial arrangement of specific nucleotide residues and is subject to modulation in vivo.

scholarly journals Protein S1 counteracts the inhibitory effect of the extended Shine???Dalgarno sequence on translation

RNA ◽  
2002 ◽  
Vol 8 (9) ◽  
pp. 1137-1147 ◽  
Author(s):  
ANASTASSIA V. KOMAROVA ◽  
LUDMILA S. TCHUFISTOVA ◽  
ELENA V. SUPINA ◽  
IRINA V. BONI
Keyword(s):  
Inhibitory Effect ◽  
Shine Dalgarno Sequence

scholarly journals Analysis of a preQ1-I riboswitch in effector-free and bound states reveals a metabolite-programmed nucleobase-stacking spine that controls gene regulation

2020 ◽  
Vol 48 (14) ◽  
pp. 8146-8164 ◽  
Author(s):  
Griffin M Schroeder ◽  
Debapratim Dutta ◽  
Chapin E Cavender ◽  
Jermaine L Jenkins ◽  
Elizabeth M Pritchett ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Bound States ◽  
Environmental Changes ◽  
Bound State ◽  
Yellow Mosaic Virus ◽  
Elastic Band ◽  
Rna Motifs ◽  
Shine Dalgarno Sequence ◽  
Effector Recognition ◽  
Molecular Framework

Abstract Riboswitches are structured RNA motifs that recognize metabolites to alter the conformations of downstream sequences, leading to gene regulation. To investigate this molecular framework, we determined crystal structures of a preQ1-I riboswitch in effector-free and bound states at 2.00 Å and 2.65 Å-resolution. Both pseudoknots exhibited the elusive L2 loop, which displayed distinct conformations. Conversely, the Shine-Dalgarno sequence (SDS) in the S2 helix of each structure remained unbroken. The expectation that the effector-free state should expose the SDS prompted us to conduct solution experiments to delineate environmental changes to specific nucleobases in response to preQ1. We then used nudged elastic band computational methods to derive conformational-change pathways linking the crystallographically-determined effector-free and bound-state structures. Pathways featured: (i) unstacking and unpairing of L2 and S2 nucleobases without preQ1—exposing the SDS for translation and (ii) stacking and pairing L2 and S2 nucleobases with preQ1—sequestering the SDS. Our results reveal how preQ1 binding reorganizes L2 into a nucleobase-stacking spine that sequesters the SDS, linking effector recognition to biological function. The generality of stacking spines as conduits for effector-dependent, interdomain communication is discussed in light of their existence in adenine riboswitches, as well as the turnip yellow mosaic virus ribosome sensor.

scholarly journals Nascent chain-monitored remodeling of the Sec machinery for salinity adaptation of marine bacteria

2015 ◽  
Vol 112 (40) ◽  
pp. E5513-E5522 ◽  
Author(s):  
Eiji Ishii ◽  
Shinobu Chiba ◽  
Narimasa Hashimoto ◽  
Seiji Kojima ◽  
Michio Homma ◽  
...  
Keyword(s):  
Marine Bacteria ◽  
Marine Bacterium ◽  
Life Cycles ◽  
Protein Export ◽  
Primary Role ◽  
Dependent Manner ◽  
Physiological Conditions ◽  
Low Salinity ◽  
Nascent Chain ◽  
Shine Dalgarno Sequence

SecDF interacts with the SecYEG translocon in bacteria and enhances protein export in a proton-motive-force-dependent manner.Vibrio alginolyticus, a marine-estuarine bacterium, contains two SecDF paralogs, V.SecDF1 and V.SecDF2. Here, we show that the export-enhancing function of V.SecDF1 requires Na+instead of H+, whereas V.SecDF2 is Na+-independent, presumably requiring H+. In accord with the cation-preference difference, V.SecDF2 was only expressed under limited Na+concentrations whereas V.SecDF1 was constitutive. However, it is not the decreased concentration of Na+per se that the bacterium senses to up-regulate the V.SecDF2 expression, because marked up-regulation of the V.SecDF2 synthesis was observed irrespective of Na+concentrations under certain genetic/physiological conditions: (i) when thesecDF1VAgene was deleted and (ii) whenever the Sec export machinery was inhibited. VemP (Vibrioexport monitoring polypeptide), a secretory polypeptide encoded by the upstream ORF ofsecDF2VA,plays the primary role in this regulation by undergoing regulated translational elongation arrest, which leads to unfolding of the Shine–Dalgarno sequence for translation ofsecDF2VA.Genetic analysis ofV. alginolyticusestablished that the VemP-mediated regulation of SecDF2 is essential for the survival of this marine bacterium in low-salinity environments. These results reveal that a class of marine bacteria exploits nascent-chain ribosome interactions to optimize their protein export pathways to propagate efficiently under different ionic environments that they face in their life cycles.

Secondary structures and functional requirements for thiM riboswitches from Desulfovibrio vulgaris, Erwinia carotovora and Rhodobacter spheroides

2008 ◽  
Vol 389 (2) ◽  
pp. 127-134 ◽  
Author(s):  
Andrea Rentmeister ◽  
Günter Mayer ◽  
Nicole Kuhn ◽  
Michael Famulok
Keyword(s):  
Erwinia Carotovora ◽  
Secondary Structures ◽  
Thiamine Pyrophosphate ◽  
Desulfovibrio Vulgaris ◽  
Functional Requirements ◽  
Expression Domain ◽  
Rna Hairpins ◽  
Broad Variety ◽  
Shine Dalgarno Sequence ◽  
Aptamer Domain

Abstract Bacterial thiM riboswitches contain aptamer domains that bind the metabolite thiamine pyrophosphate (TPP). Binding of TPP to the aptamer domain induces structural rearrangements that are relayed to the expression domain, thereby interfering with gene expression. Here, we report identification of three putative thiM riboswitches from different bacteria and analysis of their secondary structures. Chemical probing revealed that the riboswitches share similar secondary structures in their aptamer domains that can communicate with the highly variant expression domains in a mechanism likely involving sequestration of the Shine-Dalgarno sequence. Remarkably, the aptamer domain of the thiM gene of Desulfovibrio vulgaris binds TPP with similar affinity and selectivity as that of Escherichia coli, although nucleotides previously shown to form direct contacts to the metabolite are mutated. We also designed small RNA hairpins for each riboswitch that bind the RNA only in the absence of the metabolite. Our study shows that aptamer domains in riboswitches with high similarity in their secondary structures can communicate with a broad variety of non-related expression domains by similar mechanisms.

EVOLUTIONARY OPTIMIZATION OF SEQUENCE KERNELS FOR DETECTION OF BACTERIAL GENE STARTS

2007 ◽  
Vol 17 (05) ◽  
pp. 369-381 ◽  
Author(s):  
BRITTA MERSCH ◽  
TOBIAS GLASMACHERS ◽  
PETER MEINICKE ◽  
CHRISTIAN IGEL
Keyword(s):  
Cross Validation ◽  
Classification Performance ◽  
Sequence Classification ◽  
Biological Sequence ◽  
Bacterial Gene ◽  
Covariance Matrix Adaptation ◽  
Multiple Kernel ◽  
Specific Choice ◽  
Shine Dalgarno Sequence ◽  
Adaptation Evolution

Oligo kernels for biological sequence classification have a high discriminative power. A new parameterization for the K-mer oligo kernel is presented, where all oligomers of length K are weighted individually. The task specific choice of these parameters increases the classification performance and reveals information about discriminative features. For adapting the multiple kernel parameters based on cross-validation the covariance matrix adaptation evolution strategy is proposed. It is applied to optimize the trimer oligo kernels for the detection of bacterial gene starts. The resulting kernels lead to higher classification rates, and the adapted parameters reveal the importance of particular triplets for classification, for example of those occurring in the Shine-Dalgarno Sequence.

scholarly journals Processing and Stability of Inducibly Expressed rpsO mRNA Derivatives in Bacillus subtilis

2009 ◽  
Vol 191 (18) ◽  
pp. 5680-5689 ◽  
Author(s):  
Shiyi Yao ◽  
David H. Bechhofer
Keyword(s):  
Bacillus Subtilis ◽  
Early Step ◽  
Stem Loop ◽  
Processing Event ◽  
Shine Dalgarno Sequence ◽  
Ribosomal Protein S15 ◽  
High Level ◽  
First Time ◽  
Derivatives Of

ABSTRACT The Bacillus subtilis rpsO gene specifies a small (388-nucleotide), monocistronic mRNA that encodes ribosomal protein S15. We showed earlier that rpsO mRNA decay intermediates accumulated to a high level in a strain lacking polynucleotide phosphorylase. Here, we used inducibly expressed derivatives of rpsO, encoding smaller RNAs that had the complex 5′ region deleted, to study aspects of mRNA processing in B. subtilis. An IPTG (isopropyl-β-d-thiogalactopyranoside)-inducible rpsO transcript that contained lac sequences at the 5′ end, called lac-rpsO RNA, was shown to undergo processing to result in an RNA that was 24 nucleotides shorter than full length. Such processing was dependent on the presence of an accessible 5′ terminus; a lac-rpsO RNA that contained a strong stem-loop at the 5′ end was not processed and was extremely stable. Interestingly, this stability depended also on ribosome binding to a nearby Shine-Dalgarno sequence but was independent of downstream translation. Either RNase J1 or RNase J2 was capable of processing lac-rpsO RNA, demonstrating for the first time a particular in vivo processing event that could be catalyzed by both enzymes. Decay intermediates were detected in the pnpA strain only for a lac-rpsO RNA that was untranslated. Analysis of processing of an untranslated lac-rpsO RNA in the pnpA strain shortly after induction of transcription suggested that endonuclease cleavage at 3′-proximal sites was an early step in turnover of mRNA.

scholarly journals Stationary-Phase Regulation of RpoS Translation in Escherichia coli

2005 ◽  
Vol 187 (21) ◽  
pp. 7204-7213 ◽  
Author(s):  
Matthew Hirsch ◽  
Thomas Elliott
Keyword(s):  
Escherichia Coli ◽  
Stationary Phase ◽  
Osmotic Shock ◽  
Transcriptional Response ◽  
Enteric Bacteria ◽  
Protein Activity ◽  
E Coli ◽  
Phase Regulation ◽  
Shine Dalgarno Sequence ◽  
Necessary And Sufficient

ABSTRACT In enteric bacteria, adaptation to a number of different stresses is mediated by the RpoS protein, one of several sigma factors that collectively allow a tailored transcriptional response to environmental cues. Stress stimuli including low temperature, osmotic shock, nutrient limitation, and growth to stationary phase (SP) all result in a substantial increase in RpoS abundance and activity. The mechanism of regulation depends on the specific signal but may occur at the level of transcription, translation, protein activity, or targeted proteolysis. In both Escherichia coli and Salmonella enterica, SP induction of RpoS in rich medium is >30 fold and includes effects on both transcription and translation. Recently, we found that SP control of rpoS transcription in S. enterica involves repression of the major rpoS promoter during exponential phase by the global transcription factor Fis. Working primarily with E. coli, we now show that 24 nucleotides of the rpoS ribosome-binding site (RBS) are necessary and sufficient for a large part of the increase in rpoS translation as cells grow to SP. Genetic evidence points to an essential role for the leader nucleotides just upstream of the Shine-Dalgarno sequence but is conflicted on the question of whether sequence or structure is important. SP regulation of rpoS is conserved between E. coli and S. enterica. When combined with an fis mutation to block transcriptional effects, replacement of the rpoS RBS sequence by the lacZ RBS eliminates nearly all SP induction of RpoS.

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