Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803

Pei, Guangsheng; Sun, Tao; Chen, Shawn; Chen, Lei; Zhang, Weiwen

doi:10.1186/s13068-017-0743-y

Cited by 23 publications

(24 citation statements)

References 72 publications

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“…For example, sRNA Nc117 in Synechocystis sp. PCC 6803 (Pei et al, 2017) as well as OLE RNA in Bacillus halodurans C-125 (Wallace et al, 2012) both appear to protect the cells from ethanol toxicity. However, the mRNA and/or protein targets of these sRNAs are unknown (Nc117) or limited in number (OLE RNA).…”

Section: Introductionmentioning

confidence: 98%

Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis

Han

Haning

Gonzalez-Rivera

et al. 2020

Front. Bioeng. Biotechnol.

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sRNAs represent a powerful class of regulators that influences multiple mRNA targets in response to environmental changes. However, very few direct sRNA-sRNA interactions have been deeply studied in any organism. Zymomonas mobilis is a bacterium with unique ethanol-producing metabolic pathways in which multiple small RNAs (sRNAs) have recently been identified, some of which show differential expression in ethanol stress. In this study, we show that two sRNAs (Zms4 and Zms6) are upregulated under ethanol stress and have significant impacts on ethanol tolerance and production in Z. mobilis. We conducted multi-omics analysis (combining transcriptomics and sRNAimmunoprecipitation) to map gene networks under the influence of their regulation. We confirmed that Zms4 and Zms6 bind multiple RNA targets and regulate their expressions, influencing many downstream pathways important to ethanol tolerance and production. In particular, Zms4 and Zms6 interact with each other as well as many other sRNAs, forming a novel sRNA-sRNA direct interaction network. This study thus uncovers a sRNA network that co-orchestrates multiple ethanol related pathways through a diverse set of mRNA targets and a large number of sRNAs. To our knowledge, this study represents one of the largest sRNA-sRNA direct interactions uncovered so far.

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Section: Introductionmentioning

confidence: 98%

Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis

Han

Haning

Gonzalez-Rivera

et al. 2020

Front. Bioeng. Biotechnol.

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“…As different sRNA species were identified to be involved in the stress response of Synechocystis, the overexpression of the sRNA Nc117 enhanced the ethanol tolerance. Other sRNA identified in the same experiment led to a reduced growth phenotype during ethanol stress compared to the wild type when overexpressed in the same manner [65]. These data underline on the one hand the great opportunities for the development of cyanobacterial cell factories offered by now available so called "-omics" technologies, but on the other hand prove the big knowledge gap in the cellular regulation mechanisms.…”

Section: Bioethanol Production In Cyanobacteriamentioning

confidence: 64%

“…In general, there are two different mechanisms described for their regulatory function. Either, longer sRNAs bind their counter mRNA over a long anti-sense sequence and, thereby, mediate the degradation via a cellular RNase, or short sRNAs compete with the 16S rRNA for the Shine-Dalgarno sequence and thus prevent translation initiation [61][62][63][64][65][66]. Further RNA based regulatory elements are riboswitches.…”

Section: Post-transcriptional Control Elementsmentioning

confidence: 99%

Evaluation of New Genetic Toolkits and Their Role for Ethanol Production in Cyanobacteria

2019

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Since the public awareness for climate change has risen, increasing scientific effort has been made to find and develop alternative resources and production processes to reduce the dependency on petrol-based fuels and chemicals of our society. Among others, the biotechnological fuel production, as for example fermenting sugar-rich crops to ethanol, is one of the main strategies. For this purpose, various classical production systems like Escherichia coli or Saccharomyces cerevisiae are used and have been optimized via genetic modifications. Despite the progress made, this strategy competes for nutritional resources and agricultural land. To overcome this problem, various attempts were made for direct photosynthetic driven ethanol synthesis with different microalgal species including cyanobacteria. However, compared to existing platforms, the development of cyanobacteria as photoautotrophic cell factories has just started, and accordingly, the ethanol yield of established production systems is still unreached. This is mainly attributed to low ethanol tolerance levels of cyanobacteria and there is still potential for optimizing the cyanobacteria towards alternative gene expression systems. Meanwhile, several improvements were made by establishing new toolboxes for synthetic biology offering new possibilities for advanced genetic modifications of cyanobacteria. Here, current achievements and innovations of those new molecular tools are discussed.

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“…The two-step RT-PCR analysis was performed according to the previous report (41), in order to determine the transcriptional direction of the potential small RNA sr8384. In brief, the total RNA of C. acetobutylicum was isolated by TRIzol extraction.…”

Section: Methodsmentioning

confidence: 99%

The small noncoding RNA sr8384 determines solvent synthesis and cell growth in industrial solventogenic clostridia

Yang

Lang

Zhang

et al. 2019

Preprint

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20Small noncoding RNAs (sncRNAs) are crucial regulatory molecules in organisms and 21 are well known not only for their roles in the control of diverse essential biological 22 processes but also for their value in genetic modification. However, to date, in 23 gram-positive anaerobic solventogenic clostridia (which are a group of important 24 industrial bacteria with exceptional substrate and product diversity), sncRNAs remain 25 minimally explored, leading to a lack of detailed understanding regarding these 26 important molecules and their use as targets for genetic improvement. Here, we 27 performed large-scale phenotypic screens of a transposon-mediated mutant library of 28 Clostridium acetobutylicum, a typical solventogenic clostridial species, and 29 discovered a novel sncRNA (sr8384) that functions as a determinant positive regulator 30 of growth and solvent synthesis. Comparative transcriptomic data combined with 31 genetic and biochemical analyses revealed that sr8384 acts as a pleiotropic regulator 32and controls multiple targets that are associated with crucial biological processes, 33 through direct or indirect interactions. Notably, modulation of the expression level of 34 either sr8384 or its core target genes significantly increased the growth rate, solvent 35 titer and productivity of the cells, indicating the importance of sr8384-mediated 36 regulatory network in C. acetobutylicum. Furthermore, a homolog of sr8384 was 37 discovered and proven to be functional in another important Clostridium species, C. 38 beijerinckii, suggesting the potential broad role of this sncRNA in clostridia. Our 39 work showcases a previously unknown potent and complex role of sncRNAs in 40 clostridia, providing new opportunities for understanding and engineering these 41 3 anaerobes, including pathogenic Clostridium species.42 4 IMPORTANCE 43The discovery of sncRNAs as new resources for functional studies and strain 44 modifications are promising strategies in microorganisms. However, these crucial 45 regulatory molecules have hardly been explored in industrially important 46 solventogenic clostridia. Here, we identified sr8384 as a novel determinant sncRNA 47 controlling cellular performance of solventogenic Clostridium acetobutylicum and 48 performed detailed functional analysis, which is the most in-depth study of sncRNAs 49 in clostridia to date. We reveal the pleiotropic function of sr8384 and its multiple 50 direct and indirect crucial targets, which represents a valuable source for 51 understanding and optimizing this anaerobe. Of note, manipulation of these targets 52 leads to improved cell growth and solvent synthesis. Our findings provide a new 53 perspective for future studies on regulatory sncRNAs in clostridia. 54 5 93 importance of this sncRNA as well as the related gene network in genetic 94 improvement. Furthermore, we also identified a functional sr8384 homolog in C. 95 beijerinckii, another important Clostridium species that is widely used in the 96 fermentation of lignocellulose hydrolysates, indica...

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Systematic and functional identification of small non-coding RNAs associated with exogenous biofuel stress in cyanobacterium Synechocystis sp. PCC 6803

Cited by 23 publications

References 72 publications

Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis

Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance in Zymomonas mobilis

Evaluation of New Genetic Toolkits and Their Role for Ethanol Production in Cyanobacteria

The small noncoding RNA sr8384 determines solvent synthesis and cell growth in industrial solventogenic clostridia

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