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.

scholarly journals RGS4 RNA Secondary Structure Mediates Staufen2 RNP Assembly in Neurons

2021 ◽  
Vol 22 (23) ◽  
pp. 13021
Author(s):  
Sandra M. Fernández-Moya ◽  
Janina Ehses ◽  
Karl E. Bauer ◽  
Rico Schieweck ◽  
Anob M. Chakrabarti ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Rna Secondary Structure ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Underlying Mechanism ◽  
Secondary Structures ◽  
Rna Granules ◽  
Rna Hairpins ◽  
Sequence Elements ◽  
Rna Hairpin

RNA-binding proteins (RBPs) act as posttranscriptional regulators controlling the fate of target mRNAs. Unraveling how RNAs are recognized by RBPs and in turn are assembled into neuronal RNA granules is therefore key to understanding the underlying mechanism. While RNA sequence elements have been extensively characterized, the functional impact of RNA secondary structures is only recently being explored. Here, we show that Staufen2 binds complex, long-ranged RNA hairpins in the 3′-untranslated region (UTR) of its targets. These structures are involved in the assembly of Staufen2 into RNA granules. Furthermore, we provide direct evidence that a defined Rgs4 RNA duplex regulates Staufen2-dependent RNA localization to distal dendrites. Importantly, disrupting the RNA hairpin impairs the observed effects. Finally, we show that these secondary structures differently affect protein expression in neurons. In conclusion, our data reveal the importance of RNA secondary structure in regulating RNA granule assembly, localization and eventually translation. It is therefore tempting to speculate that secondary structures represent an important code for cells to control the intracellular fate of their mRNAs.

scholarly journals Thiamine pyrophosphate riboswitch regulation: a new possible mechanism involved in the action of nalidixic acid

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Sahar Shahidi ◽  
Seyed Sadegh Shahraeini ◽  
Yekta Farmahini Farahani ◽  
Soroush Sardari
Keyword(s):  
Minimum Inhibitory Concentration ◽  
Binding Energy ◽  
Nalidixic Acid ◽  
Inhibitory Concentration ◽  
Thiamine Pyrophosphate ◽  
E Coli ◽  
Expression Platform ◽  
Antibiotic Compounds ◽  
Aptamer Domain

AbstractObjectivesThe development of novel antibiotic compounds requires riboswitches; in fact, riboswitches are RNA elements present in the 5′ untranslated region of bacterial mRNA and have a metabolite-binding aptamer domain and an expression platform regulating the expression of vital genes. In the present research, one riboswitch, namely thi-box riboswitch with distinct regulatory mechanisms, was studied. It recognizes Thiamine Pyrophosphates (TPP) regulating TPP-biosynthesis genes in Escherichiacoli.MethodsFirst, the compounds similar to riboswitch ligands were studied, and their binding with the riboswitch and nucleosides was investigated by molecular docking. Then, compounds containing high binding energy were chosen, and their minimum inhibitory concentration in E. coli was determined by the MIC test. Finally, the binding of compounds to nucleotides and RNA was investigated by measuring the absorbance spectrum through NanoDrop and circular dichroism (CD).ResultsIn the thi-box riboswitch, nalidixic acid was found to have the best binding energy (−5.31 kJ/mol), and it inhibited E. coli growth at the minimum inhibitory concentration of 125 μg/mL, and it could bind to ribonucleosides and RNA in vitro.ConclusionsOne possible mechanism involved in the action of nalidixic acid in inhibiting the E. coli growth is to influence thi-box riboswitch.

scholarly journals Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch

2021 ◽  
Author(s):  
Junyan Ma ◽  
Nabanita Saikia ◽  
Subash Godar ◽  
George L. Hamilton ◽  
Feng Ding ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Single Molecule ◽  
Conformational Changes ◽  
Thiamine Pyrophosphate ◽  
Switching Sequence ◽  
Expression Platform ◽  
Domains Of Life ◽  
Order Of Magnitude ◽  
Dynamics Simulations ◽  
Aptamer Domain

ABSTRACTThiamine pyrophosphate (TPP) riboswitches regulate thiamine metabolism by inhibiting the translation of enzymes essential to thiamine synthesis pathways upon binding to thiamine pyrophosphate in cells across all domains of life. Recent work on theArabidopsis thalianaTPP riboswitch suggests a multi-step TPP binding process involving multiple riboswitch conformational ensembles and that Mg2+dependence underlies the mechanism of TPP recognition and subsequent transition to the translation-inhibiting state of the switching sequence followed by changes in the expression platform. However, details of the relationship between TPP riboswitch conformational changes and interactions with TPP and Mg2+in the aptamer domain constituting this mechanism are unknown. Therefore, we integrated single-molecule multiparameter fluorescence and force spectroscopy with atomistic molecular dynamics simulations and found that conformational transitions within the aptamer domain associated with TPP and Mg2+ligand binding occurred between at least five different ensembles on timescales ranging from μs to ms. These dynamics are at least an order of magnitude faster than folding and unfolding kinetics associated with translation-state switching in the switching sequence. Moreover, we propose that two pathways exist for ligand recognition. Together, our results suggest a dynamic ensemble switching of the aptamer domain that may lead to the translation-inhibiting state of the riboswitch. Additionally, our results suggest that multiple configurations could enable inhibitory tuning manifested through ligand-dependent changes via ensemble switching and kinetic rheostat-like behavior of theArabidopsis thalianaTPP riboswitch.

Phosphate-Group Recognition by the Aptamer Domain of the Thiamine Pyrophosphate Sensing Riboswitch

ChemBioChem ◽  
2006 ◽  
Vol 7 (9) ◽  
pp. 1451-1456 ◽  
Author(s):  
Jonas Noeske ◽  
Christian Richter ◽  
Elke Stirnal ◽  
Harald Schwalbe ◽  
Jens Wöhnert
Keyword(s):  
Phosphate Group ◽  
Thiamine Pyrophosphate ◽  
Aptamer Domain

An Integrated Approach for a Knowledge-based Clinical Workstation: Architecture and Experience

1998 ◽  
Vol 37 (01) ◽  
pp. 16-25 ◽  
Author(s):  
P. Ringleb ◽  
T. Steiner ◽  
P. Knaup ◽  
W. Hacke ◽  
R. Haux ◽  
...  
Keyword(s):  
Decision Support ◽  
Information Systems ◽  
Patient Care ◽  
Hospital Information Systems ◽  
Medical Decision ◽  
Daily Routine ◽  
Functional Requirements ◽  
Support Functions ◽  
Knowledge Based ◽  
Clinical Workstation

Abstract:Today, the demand for medical decision support to improve the quality of patient care and to reduce costs in health services is generally recognized. Nevertheless, decision support is not yet established in daily routine within hospital information systems which often show a heterogeneous architecture but offer possibilities of interoperability. Currently, the integration of decision support functions into clinical workstations is the most promising way. Therefore, we first discuss aspects of integrating decision support into clinical workstations including clinical needs, integration of database and knowledge base, knowledge sharing and reuse and the role of standardized terminology. In addition, we draw up functional requirements to support the physician dealing with patient care, medical research and administrative tasks. As a consequence, we propose a general architecture of an integrated knowledge-based clinical workstation. Based on an example application we discuss our experiences concerning clinical applicability and relevance. We show that, although our approach promotes the integration of decision support into hospital information systems, the success of decision support depends above all on an adequate transformation of clinical needs.

Unravelling a microbial synergy to boost caproate production via carboxylates chain elongation with ethanol

2019 ◽  
Vol 26 (2) ◽  
pp. 63-71
Author(s):  
Ling Leng ◽  
Ying Wang ◽  
Peixian Yang ◽  
Takashi Narihiro ◽  
Masaru Konishi Nobu ◽  
...  
Keyword(s):  
Fatty Acids ◽  
Volatile Fatty Acids ◽  
Microbial Consortia ◽  
Chain Elongation ◽  
Desulfovibrio Vulgaris ◽  
Rrna Gene ◽  
Selective Enrichment ◽  
Microbial Network ◽  
Cost Efficient ◽  
Rrna Gene Sequencing

Chain elongation of volatile fatty acids for medium chain fatty acids production (e.g. caproate) is an attractive approach to treat wastewater anaerobically and recover resource simultaneously. Undefined microbial consortia can be tailored to achieve chain elongation process with selective enrichment from anaerobic digestion sludge, which has advantages over pure culture approach for cost-efficient application. Whilst the metabolic pathway of the dominant caproate producer, Clostridium kluyveri, has been annotated, the role of other coexisting abundant microbiomes remained unclear. To this end, an ethanol-acetate fermentation inoculated with fresh digestion sludge at optimal conditions was conducted. Also, physiological study, thermodynamics and 16 S rRNA gene sequencing to elucidate the biological process by linking the system performance and dominant microbiomes were integrated. Results revealed a possible synergistic network in which C. kluyveri and three co-dominant species, Desulfovibrio vulgaris, Fusobacterium varium and Acetoanaerobium sticklandii coexisted. D. vulgaris and A. sticklandii (F. varium) were likely to boost the carboxylates chain elongation by stimulating ethanol oxidation and butyrate production through a syntrophic partnership with hydrogen (H2) serving as an electron messenger. This study unveils a synergistic microbial network to boost caproate production in mixed culture carboxylates chain elongation.

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