CRISPR/Cas9 editing genome of extremophile Halomonas spp.

Qin, Qin; Chen, Ling; Zhao, Yiqing; Yang, Tian; Yin, Jun; Guo, Yingying; Chen, Guo Qiang

doi:10.1016/j.ymben.2018.03.018

Cited by 120 publications

(77 citation statements)

References 65 publications

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“…Finally, the development of the rapid and efficient gene editing CRISPR/Cas9 system gave rise to new and extremely interesting research tools and strategies. A very recent example of this approach was reported for the halophile H. bluephagenesis designed to produce the microbial copolymer PHBHV …”

Section: Further Approaches To Reduce Pha Production Costsmentioning

confidence: 99%

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Improving polyhydroxyalkanoate production from inexpensive carbon sources by genetic approaches: a review

Favaro

Basaglia

Casella

2018

Biofuels Bioprod Bioref

132

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Polyhydroxyalkanoates (PHAs) are a family of biodegradable intracellular polyesters that a number of Eubacteria and Archaea can accumulate for energy and carbon storage. Most of the genetic modifications to the producing bacterial species have been accomplished to clarify basic biochemical, genetic, and metabolic aspects of PHA metabolism. However, due to its plastic‐like properties and complete biodegradability, this bio‐based polymer has attracted the attention of a variety of manufacturers. A number of genetic approaches have therefore been reported, aimed at improving the performance of the microorganisms with a potential for use in a production process. Indeed, genetic tools may find useful applications in all the phases of the PHA production chain, from the isolation and characterization of new microbial strains through all the production steps until they reach the downstream processes. The substrates generally used for PHA production are expensive, so the search for low‐cost feedstock is necessary. These materials, possibly deriving from agri‐food processes, are unfortunately not easily degraded or converted directly into PHAs. Thus, the development of engineered microbes is in progress to process waste streams and covert them to valuable polymers. This review will summarize the most relevant results obtained through genetic engineering tools for the production of PHAs from cheap carbon sources in view of possible industrial applications. © 2018 Society of Chemical Industry and John Wiley & Sons, Ltd.

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Section: Further Approaches To Reduce Pha Production Costsmentioning

confidence: 99%

“…A very recent example of this approach was reported for the halophile H. bluephagenesis designed to produce the microbial copolymer PHBHV. 190…”

Section: Further Approaches To Reduce Pha Production Costsmentioning

confidence: 99%

Improving polyhydroxyalkanoate production from inexpensive carbon sources by genetic approaches: a review

Favaro

Basaglia

Casella

2018

Biofuels Bioprod Bioref

132

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“…Endowed with the unique ability of rapid growth at high salt concentrations and alkaline pH, two halophiles, namely Halomonas bluephagenesis ( H. bluephagenesis ) and H. campaniensis , have been successfully developed as the platform strains for NGIB due to their ability to rapidly grow in a contamination‐free under open‐ and continuous‐fermentation process . H. bluephagenesis , isolated from Aydingol Lake of Xinjiang/China in the authors’ laboratory, has been studied with an available whole‐genome sequence and engineering tools to be reconstructed for the productions of various valuable chemicals and materials …”

Section: Next‐generation Industrial Biotechnologymentioning

confidence: 99%

“…A constitutive chromosomal expression system based on highly expressed porin protein gene porin and an inducible cassette named T7‐like expression system induced by isopropyl‐β‐ d ‐thiogalactoside (IPTG) via expressing RNA polymerases (RNAP) under a lacI‐controlled Ptac promoter have been exploited . As powerful tools for gene engineering in many model organisms, clustered regularly interspaced short palindromic repeats interference (CRISPRi) and CRISPR/Cas9 system have been successfully exploited and adopted in Halomonas spp. Other method such as morphology engineering, effective expression system for increasing oxygen availability, controlling of NADH/NAD + ratio, and promoter engineering for enhancing the accumulation of PHA in Halomonas spp.…”

Section: Next‐generation Industrial Biotechnologymentioning

confidence: 99%

Next‐Generation Industrial Biotechnology‐Transforming the Current Industrial Biotechnology into Competitive Processes

Chen

2019

Biotechnology Journal

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The chemical industry has made a contribution to modern society by providing cost‐competitive products for our daily use. However, it now faces a serious challenge regarding environmental pollutions and greenhouse gas emission. With the rapid development of molecular biology, biochemistry, and synthetic biology, industrial biotechnology has evolved to become more efficient for production of chemicals and materials. However, in contrast to chemical industries, current industrial biotechnology (CIB) is still not competitive for production of chemicals, materials, and biofuels due to their low efficiency and complicated sterilization processes as well as high‐energy consumption. It must be further developed into “next‐generation industrial biotechnology” (NGIB), which is low‐cost mixed substrates based on less freshwater consumption, energy‐saving, and long‐lasting open continuous intelligent processing, overcoming the shortcomings of CIB and transforming the CIB into competitive processes. Contamination‐resistant microorganism as chassis is the key to a successful NGIB, which requires resistance to microbial or phage contaminations, and available tools and methods for metabolic or synthetic biology engineering. This review proposes a list of contamination‐resistant bacteria and takes Halomonas spp. as an example for the production of a variety of products, including polyhydroxyalkanoates under open‐ and continuous‐processing conditions proposed for NGIB.

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“…Given the simplicity, the DNA-targeting effectors from Class 2, i.e. Type II CRISPR-Cas9 and Type V CRISPR-Cpf1, were developed as genome engineering tools right after their discovery and characterization and have now been widely applied in both eukaryotes and prokaryotes (9)(10)(11)(12)(13)(14). In particular, they have enabled rapid, easy yet accurate construction of strains for some production platform microorganisms, e.g.…”

Section: Introductionmentioning

confidence: 99%

Characterization and repurposing of the endogenous Type I-F CRISPR-Cas system ofZymomonas mobilisfor genome engineering

Zheng

Han

Liang

et al. 2019

Preprint

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Establishment of production platform organisms through prokaryotic engineering represents an efficient means to generate alternatives for yielding renewable biochemicals and biofuels from sustainable resources. Zymomonas mobilis, a natural facultative anaerobic ethanologen, possesses many attractive physiological attributes, making it an important industrial microorganism. To facilitate the broad applications of this strain for biorefinery, an efficient genome engineering toolkit for Z.mobilis was established in this study by repurposing the endogenous Type I-F CRISPR-Cas system upon its functional characterization, and further updated. This toolkit includes a series of genome engineering plasmids, each carrying an artificial self-targeting CRISPR and a donor DNA for the recovery of recombinants. Using the updated toolkit, genome engineering purposes were achieved with efficiencies of up to 100%, including knockout of cas3 gene, replacement of cas3 with the mCherry-encoding rfp gene, nucleotide substitutions in cas3, and deletion of two large genomic fragments up to 10 kb. This study established thus far the most efficient, straightforward and convenient genome engineering toolkit for Z. mobilis, and laid a foundation for further native CRISPRi studies in Z. mobilis, which extended the application scope of CRISPR-based technologies, and could also be applied to other industrial microorganisms with unexploited endogenous CRISPR-Cas systems.

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CRISPR/Cas9 editing genome of extremophile Halomonas spp.

Cited by 120 publications

References 65 publications

Improving polyhydroxyalkanoate production from inexpensive carbon sources by genetic approaches: a review

Improving polyhydroxyalkanoate production from inexpensive carbon sources by genetic approaches: a review

Next‐Generation Industrial Biotechnology‐Transforming the Current Industrial Biotechnology into Competitive Processes

Characterization and repurposing of the endogenous Type I-F CRISPR-Cas system ofZymomonas mobilisfor genome engineering

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