Thermozymes

Saragliadis, Athanasios; Krajewski, Stefanie; Rehm, Charlotte; Narberhaus, Franz; Hartig, Jörg S.

doi:10.4161/rna.24482

Cited by 34 publications

(14 citation statements)

References 42 publications

(60 reference statements)

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“…Synthetic biology approaches developed empirical guidelines based on naturally occurring RNAT motifs to create a variety of functional RNATs with specific regulatory properties ( 69 , 70 ). Yet, the unexpected behaviour of many in silico designed sequences necessitates experimental screening and additional directed evolution approaches ( 69 , 71 ).…”

Section: Discussionmentioning

confidence: 99%

Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution

Wagner

Rinnenthal

Narberhaus

et al. 2015

Nucleic Acids Research

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The cyanobacterial hsp17 ribonucleicacid thermometer (RNAT) is one of the smallest naturally occurring RNAT. It forms a single hairpin with an internal 1×3-bulge separating the start codon in stem I from the ribosome binding site (RBS) in stem II. We investigated the temperature-dependent regulation of hsp17 by mapping individual base-pair stabilities from solvent exchange nuclear magnetic resonance (NMR) spectroscopy. The wild-type RNAT was found to be stabilized by two critical CG base pairs (C14-G27 and C13-G28). Replacing the internal 1×3 bulge by a stable CG base pair in hsp17rep significantly increased the global stability and unfolding cooperativity as evidenced by circular dichroism spectroscopy. From the NMR analysis, remote stabilization and non-nearest neighbour effects exist at the base-pair level, in particular for nucleotide G28 (five nucleotides apart from the side of mutation). Individual base-pair stabilities are coupled to the stability of the entire thermometer within both the natural and the stabilized RNATs by enthalpy–entropy compensation presumably mediated by the hydration shell. At the melting point the Gibbs energies of the individual nucleobases are equalized suggesting a consecutive zipper-type unfolding mechanism of the RBS leading to a dimmer-like function of hsp17 and switch-like regulation behaviour of hsp17rep. The data show how minor changes in the nucleotide sequence not only offset the melting temperature but also alter the mode of temperature sensing. The cyanobacterial thermosensor demonstrates the remarkable adjustment of natural RNATs to execute precise temperature control.

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Section: Discussionmentioning

confidence: 99%

Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution

Wagner

Rinnenthal

Narberhaus

et al. 2015

Nucleic Acids Research

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“…Therefore, at higher temperature, the self-cleavage activity of the thermometer structure is impaired and the gene expression is silenced. This is the opposite of the natural behavior of thermosensors [68]. …”

Section: Introductionmentioning

confidence: 93%

Natural antisense RNAs as mRNA regulatory elements in bacteria: a review on function and applications

et al. 2016

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Naturally occurring antisense RNAs are small, diffusible, untranslated transcripts that pair to target RNAs at specific regions of complementarity to control their biological function by regulating gene expression at the post-transcriptional level. This review focuses on known cases of antisense RNA control in prokaryotes and provides an overview of some natural RNA-based mechanisms that bacteria use to modulate gene expression, such as mRNA sensors, riboswitches and antisense RNAs. We also highlight recent advances in RNA-based technology. The review shows that studies on both natural and synthetic systems are reciprocally beneficial.

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“…[2a] There are many natural and engineered versions of gene switches that respond to an enormous variety of chemical input signals (e.g.a ntibiotics, [19] metabolites, [20] and other disease-related signals [21] ), biological signals (proteins [22] and nucleic acids [23] ), and even physical signals (light [24] and temperature; [25] Table 2). [2a] There are many natural and engineered versions of gene switches that respond to an enormous variety of chemical input signals (e.g.a ntibiotics, [19] metabolites, [20] and other disease-related signals [21] ), biological signals (proteins [22] and nucleic acids [23] ), and even physical signals (light [24] and temperature; [25] Table 2).…”

Section: Gene Switchesmentioning

confidence: 99%

“…Gene expression is the process of decoding functional genetic information into RNAa nd protein products.T his process,c alled transcription, involves the production of messenger RNA( mRNA) molecules where the genetic information encoded in DNAi st ranscribed into mRNA molecules.I nt he next step,m RNAm olecules serve as templates for the synthesis of protein products.Gene switches have the capacity to intervene in this process at different levels in asignal-responsive manner and enable living cells to adapt to environmental changes.B ased on the level of intervention, ad istinction is made between transcriptional, post-transcriptional, and post-translational gene switches.A typical gene switch consists of asensor unit that is capable of detecting as ignal of interest (input) and influencing ar egulatory unit, which controls the production of agene of interest (output). [2a] There are many natural and engineered versions of gene switches that respond to an enormous variety of chemical input signals (e.g.a ntibiotics, [19] metabolites, [20] and other disease-related signals [21] ), biological signals (proteins [22] and nucleic acids [23] ), and even physical signals (light [24] and temperature; [25] Table 2). Applications of gene switches range from basic research, biotechnology,a nd metabolic engineering, to diagnostics and cell-based therapies,and are discussed in Sections 4a nd 5.…”

Section: Gene Switchesmentioning

confidence: 99%

Synthetic Biology—The Synthesis of Biology

2017

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Synthetic biology concerns the engineering of man-made living biomachines from standardized components that can perform predefined functions in a (self-)controlled manner. Different research strategies and interdisciplinary efforts are pursued to implement engineering principles to biology. The "top-down" strategy exploits nature's incredible diversity of existing, natural parts to construct synthetic compositions of genetic, metabolic, or signaling networks with predictable and controllable properties. This mainly application-driven approach results in living factories that produce drugs, biofuels, biomaterials, and fine chemicals, and results in living pills that are based on engineered cells with the capacity to autonomously detect and treat disease states in vivo. In contrast, the "bottom-up" strategy seeks to be independent of existing living systems by designing biological systems from scratch and synthesizing artificial biological entities not found in nature. This more knowledge-driven approach investigates the reconstruction of minimal biological systems that are capable of performing basic biological phenomena, such as self-organization, self-replication, and self-sustainability. Moreover, the syntheses of artificial biological units, such as synthetic nucleotides or amino acids, and their implementation into polymers inside living cells currently set the boundaries between natural and artificial biological systems. In particular, the in vitro design, synthesis, and transfer of complete genomes into host cells point to the future of synthetic biology: the creation of designer cells with tailored desirable properties for biomedicine and biotechnology.

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Thermozymes

Cited by 34 publications

References 42 publications

Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution

Mechanistic insights into temperature-dependent regulation of the simple cyanobacterial hsp17 RNA thermometer at base-pair resolution

Natural antisense RNAs as mRNA regulatory elements in bacteria: a review on function and applications

Synthetic Biology—The Synthesis of Biology

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