Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs

Chaudhary, Amit; Na, Dokyun; Lee, Eun Yeol

doi:10.1016/j.biotechadv.2015.05.009

Cited by 17 publications

(9 citation statements)

References 231 publications

(259 reference statements)

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“…Another alternative when gene knockouts can cause host instability or are lethal is to engineer RNA regulation using synthetic small regulatory sRNA to modulate chromosomal gene expression (Chaudhary et al , 2015, Na et al , 2013. One benefit of this strategy is the inhibition or knockdown of gene expression without the modification of the chromosomal sequence.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

White biotechnology: State of the art strategies for the development of biocatalysts for biorefining

Heux

Meynial-Salles

O’Donohue

et al. 2015

Biotechnology Advances

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Section: Accepted Manuscriptmentioning

confidence: 99%

White biotechnology: State of the art strategies for the development of biocatalysts for biorefining

Heux

Meynial-Salles

O’Donohue

et al. 2015

Biotechnology Advances

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“…Furthermore, the simplicity and universality of nucleic acid Watson–Crick complementarity makes antisense nucleic acids highly attractive for controlling gene expression (1,7–10) in biotechnological applications such as bacterial cellular engineering (11–14). Given the broad utility of RNA targeting via antisense binding, recent efforts to design effective synthetic asRNAs in bacteria have become more systematic, mimicking mechanisms of natural non-coding RNAs that downregulate their cognate messenger RNAs (mRNAs) by base-pairing (1,3,15). A more recent study in bacteria provided general guidelines for the design of asRNAs using large sets of gene-repression data (16).…”

Section: Introductionmentioning

confidence: 99%

Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions

Vazquez-Anderson

Mihailovic

Baldridge

et al. 2017

Nucleic Acids Research

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Current approaches to design efficient antisense RNAs (asRNAs) rely primarily on a thermodynamic understanding of RNA–RNA interactions. However, these approaches depend on structure predictions and have limited accuracy, arguably due to overlooking important cellular environment factors. In this work, we develop a biophysical model to describe asRNA–RNA hybridization that incorporates in vivo factors using large-scale experimental hybridization data for three model RNAs: a group I intron, CsrB and a tRNA. A unique element of our model is the estimation of the availability of the target region to interact with a given asRNA using a differential entropic consideration of suboptimal structures. We showcase the utility of this model by evaluating its prediction capabilities in four additional RNAs: a group II intron, Spinach II, 2-MS2 binding domain and glgC 5΄ UTR. Additionally, we demonstrate the applicability of this approach to other bacterial species by predicting sRNA–mRNA binding regions in two newly discovered, though uncharacterized, regulatory RNAs.

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“…Therefore, intracellular concentration of anthracycline in the bacterium is maintained below the lethal dose (Vasanthakumar et al 2013) by various regulators. Streptomyces species possess a large diversity of regulators encoding transcription factors, sigma factors and small regulatory RNAs (sRNAs) whose regulation and signal transduction mechanism is controlled by availability or depletion of signaling molecules (Pokhrel et al 2015;Chaudhary et al 2015a; Chaudhary et al 2015b). Beside resistant determinants and regulatory proteins the major unit responsible for the production of secondary metabolites is a biosynthetic gene cluster (Chaudhary et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Overexpression of a pathway specific negative regulator enhances production of daunorubicin in bldA deficient Streptomyces peucetius ATCC 27952

Pokhrel

Chaudhary

Nguyen

et al. 2016

Microbiological Research

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The dnrO gene is the first regulator to be activated in the daunorubicin (DNR) biosynthesis pathway of Streptomyces peucetius ATCC 27952. DnrO is known for its self-repression capability while it activates rest of the DNR biosynthesis pathway through cascades of regulatory events. S. peucetius was found to contain no functional copy of bldA-tRNA while a detailed examination of dnrO codons reveals the presence of TTA codon, which is rarely encoded by bldA-tRNA. Therefore, for evaluating the role of dnrO in DNR production, multiple engineered strains of S. peucetius were generated by heterologously expressing bldA, dnrO and combination of bldA and dnrO. Using these strains, the effects of heterologously expressed bldA and overexpressed dnrO were evaluated on pathway specific regulators, mycelial densities and production of DNR. The results showed that the transcription level of dnrO and master regulator dnrI, was found to be elevated in bldA containing strain in comparison to dnrO overexpressed strain. The bldA containing strain produces 45.7% higher DNR than bldA deficient wild type strain from culture broth with OD600 of 1.45 at 72h. Heterologous expression of bldA-tRNA is accounted for increased transcription levels of the DNR pathway specific regulators and enhanced DNR production.

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Rapid and high-throughput construction of microbial cell-factories with regulatory noncoding RNAs

Cited by 17 publications

References 231 publications

White biotechnology: State of the art strategies for the development of biocatalysts for biorefining

White biotechnology: State of the art strategies for the development of biocatalysts for biorefining

Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions

Overexpression of a pathway specific negative regulator enhances production of daunorubicin in bldA deficient Streptomyces peucetius ATCC 27952

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