Characterization of the full-length btuB riboswitch from Klebsiella pneumoniae

Palou-Mir, Joana; Musiari, Anastasia; Sigel, Roland K. O.; Barceló‐Oliver, Miquel

doi:10.1016/j.jinorgbio.2015.12.012

Cited by 6 publications

(5 citation statements)

References 36 publications

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“…In contrast, these parts are not yet exploited as regulatory SynBio tools for non-model hosts. Moreover, the first riboswitches and RNA thermometers have only recently been characterized in vivo in non-traditional bacteria 70 – 73 , except for B. subtilis for which riboswitch research is more mature 69 . The trans -acting counterparts of riboswitches are called translation riboregulators or antisense RNAs and can be used for multiplexed genome-wide knock-down of gene expression 39 , but their utilization as biological parts in non-traditional hosts is still limited.…”

Section: Constructing Novel Genetic Circuits: the Sum Is More Than Itmentioning

confidence: 99%

Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria

2020

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Non-model bacteria like Pseudomonas putida, Lactococcus lactis and other species have unique and versatile metabolisms, offering unique opportunities for Synthetic Biology (SynBio). However, key genome editing and recombineering tools require optimization and large-scale multiplexing to unlock the full SynBio potential of these bacteria. In addition, the limited availability of a set of characterized, species-specific biological parts hampers the construction of reliable genetic circuitry. Mining of currently available, diverse bacteriophages could complete the SynBio toolbox, as they constitute an unexplored treasure trove for fully adapted metabolic modulators and orthogonally-functioning parts, driven by the longstanding co-evolution between phage and host.

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Section: Constructing Novel Genetic Circuits: the Sum Is More Than Itmentioning

confidence: 99%

Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria

2020

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“…To date, there are about 15 riboswitch classes reported as shown in Table 1, and more of it is still unknown [35]. Among all classes of riboswitches, TPP riboswitches are the most ubiquitous in three life domains [36].…”

Section: Thiamine Pyrophosphate: the Dominant Class Of Riboswitchmentioning

confidence: 99%

The Role of Thiamine in Plants and Current Perspectives in Crop Improvement

Subki¹,

Abidin²,

Yusof³

2018

B Group Vitamins - Current Uses and Perspectives

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Current research is focusing on selecting potential genes that can alleviate stress and produce disease-tolerant crop variety. The novel paradigm is to investigate the potential of thiamine as a crop protection molecule in plants. Thiamine or vitamin B 1 is important for primary metabolism for all living organisms. The active form, thiamine pyrophosphate (TPP), is a cofactor for the enzymes involved in the synthesis of amino acids, tricarboxylic acid cycle and pentose phosphate pathway. Recently, thiamine is shown to have a role in the processes underlying protection of plants against biotic and abiotic stresses. The aim of this chapter is to review the role of thiamine in plant growth and disease protection and also to highlight that TPP and its intermediates are involved in management of stress. The perspectives on its potential for manipulating the biosynthesis pathway in crop improvement will also be discussed.

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“…Indeed, several studies have reported negative ΔC p values for RNA-small molecule and RNApeptide interactions in which the complex is thought to undergo a conformational change resulting in an increased level of burial of nonpolar surface area. 87,[89][90][91]96,[103][104][105][106] Due to the several factors that may contribute to ΔC p , however, it is important to note that interpretation of ΔC p data is not always straightforward. In addition to hydration, ΔC p calculations include contributions from vibrational motion, from the conformational entropy of the biomolecule, and from the mere coupling of conformational equilibria to binding equilibria.…”

Section: Heat Capacity Changementioning

confidence: 99%

“…The unfavorable entropy change was thought to correspond to the RNA conformational changes associated with ligand binding. This trend might be a general trait of riboswitch ligand binding, although the presence of dications in some cases stabilizes the RNA, leading to a favorable entropy change. − Ligand design for riboswitch targets may therefore benefit from optimizing molecular properties that give an enthalpy change that is large enough to offset the unfavorable entropy change.…”

Section: Thermodynamic Analysis Of Rna–small Molecule Interactionsmentioning

confidence: 99%

“…Changes in heat capacity upon complex formation and biomolecular folding are often described as originating from differential hydration of the molecules before and after the binding or folding process. − Because hydration of nonpolar groups increases the heat capacity of the solution through strengthened water hydrogen bonds, an RNA–small molecule interaction that decreases the total solvent-accessible nonpolar surface area may lead to a negative Δ C p . Indeed, several studies have reported negative Δ C p values for RNA–small molecule and RNA–peptide interactions in which the complex is thought to undergo a conformational change resulting in an increased level of burial of nonpolar surface area. ,− ,,− Due to the several factors that may contribute to Δ C p , however, it is important to note that interpretation of Δ C p data is not always straightforward. In addition to hydration, Δ C p calculations include contributions from vibrational motion, from the conformational entropy of the biomolecule, and from the mere coupling of conformational equilibria to binding equilibria. , While definite conclusions about the meaning of Δ C p data often require additional experimentation, large changes can provide insight into the importance or degree of the conformational change in ligand binding.…”

Section: Thermodynamic Analysis Of Rna–small Molecule Interactionsmentioning

confidence: 99%

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Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA–Small Molecule Interactions

Juru

Hargrove

2019

ACS Chem. Biol.

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The implication of RNA in multiple cellular processes beyond protein coding has revitalized interest in the development of small molecules for therapeutically targeting RNA and for further probing its cellular biology. However, the process of rationally designing such small molecule probes is hampered by the paucity of information about fundamental molecular recognition principles of RNA. In this Review, we summarize two important and often underappreciated aspects of RNA-small molecule recognition: RNA conformational dynamics and the biophysical properties of interactions of small molecules with RNA, specifically thermodynamics and kinetics. While conformational flexibility is often said to impede RNA ligand development, the ability of small molecules to influence the RNA conformational landscape can have a significant effect on the cellular functions of RNA. An analysis of the conformational landscape of RNA and the interactions of individual conformations with ligands can thus guide the development of new small molecule probes, which needs to be investigated further. Additionally, while it is common practice to quantify the binding affinities (K a or K d) of small molecules for biomacromolecules as a measure of their activity, further biophysical characterization of their interaction can provide a deeper understanding. Studies that focus on the thermodynamic and kinetic parameters for interaction between RNA and ligands are next discussed. Finally, this Review provides the reader with a perspective on how such in-depth analysis of biophysical characteristics of the interaction of RNA and small molecules can impact our understanding of these interactions and how they will benefit the future design of small molecule probes.

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Characterization of the full-length btuB riboswitch from Klebsiella pneumoniae

Cited by 6 publications

References 36 publications

Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria

Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria

The Role of Thiamine in Plants and Current Perspectives in Crop Improvement

Understanding the Contributions of Conformational Changes, Thermodynamics, and Kinetics of RNA–Small Molecule Interactions

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