CRISPR-mediated genome editing in non-conventional yeasts for biotechnological applications

Cai, Peng; Gao, Jiaoqi; Zhou, Yongjin J.

doi:10.1186/s12934-019-1112-2

Cited by 116 publications

(100 citation statements)

References 73 publications

(90 reference statements)

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“…It should be noted that different yeast species, and even strains, significantly differ in the products synthesised and in their production rates and yields (Rodríguez Madrera et al 2015;van Dijk et al 2019). Non-conventional yeasts have recently been in the focus of active and relevant research, their genome sequences are being released and suitable genetic engineering tools are either available or being developed for different purposes (Mira et al 2014;Palma et al 2017;Nambu-Nishida et al 2017;Lee et al 2018;Cai et al 2019;Protzko et al 2019; among several other examples). Thus, it is expected that, in the near future, the currently accepted designation of "non-conventional yeast" will no longer be adequate and non-Saccharomyces strains will successfully be used in the industry (Johnson 2013a;Radecka et al 2015;Kręgiel et al 2017;Siripong et al 2018).…”

Section: Introductionmentioning

confidence: 99%

Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges

Martins

Monteiro

Semedo

et al. 2020

Appl Microbiol Biotechnol

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Pectin-rich agro-industrial residues are feedstocks with potential for sustainable biorefineries. They are generated in high amounts worldwide from the industrial processing of fruits and vegetables. The challenges posed to the industrial implementation of efficient bioprocesses are however manyfold and thoroughly discussed in this review paper, mainly at the biological level. The most important yeast cell factory platform for advanced biorefineries is currently Saccharomyces cerevisiae, but this yeast species cannot naturally catabolise the main sugars present in pectin-rich agro-industrial residues hydrolysates, in particular Dgalacturonic acid and L-arabinose. However, there are non-Saccharomyces species (non-conventional yeasts) considered advantageous alternatives whenever they can express highly interesting metabolic pathways, natively assimilate a wider range of carbon sources or exhibit higher tolerance to relevant bioprocess-related stresses. For this reason, the interest in nonconventional yeasts for biomass-based biorefineries is gaining momentum. This review paper focuses on the valorisation of pectin-rich residues by exploring the potential of yeasts that exhibit vast metabolic versatility for the efficient use of the carbon substrates present in their hydrolysates and high robustness to cope with the multiple stresses encountered. The major challenges and the progresses made related with the isolation, selection, sugar catabolism, metabolic engineering and use of nonconventional yeasts and S. cerevisiae-derived strains for the bioconversion of pectin-rich residue hydrolysates are discussed. The reported examples of value-added products synthesised by different yeasts using pectin-rich residues are reviewed. Key Points • Review of the challenges and progresses made on the bioconversion of pectin-rich residues by yeasts. • Catabolic pathways for the main carbon sources present in pectin-rich residues hydrolysates. • Multiple stresses with potential to affect bioconversion productivity. • Yeast metabolic engineering to improve pectin-rich residues bioconversion.

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Section: Introductionmentioning

confidence: 99%

Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges

Martins

Monteiro

Semedo

et al. 2020

Appl Microbiol Biotechnol

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“…For example, nonmodel yeasts, such as Yarrowia lipolytica, Rhodosporidium toruloides, Pichia pastoris, Issatchenkia orientalis, and Candida albicans possess specific characteristics and can be exploited for various biotechnological applications. [6][7][8][9][10][11][12] Y. lipolytica and R. toruloides are oleaginous yeasts capable of storing lipids up to 70% of their dry cellular weights, which make them preferred hosts for production of lipid-based chemicals, such as oleochemicals and diesel-like fuels (alkanes, fatty alcohols, and fatty acid methyl esters). [13][14][15] Simple expression of a single gene encoding fatty acid reductase in R. toruloides yielded a strain capable of producing 8.4g/L fatty alcohols using fed-batch cultivation Zia Fatma and Carl Schultz contributed equally to this study.…”

Section: Introductionmentioning

confidence: 99%

“…Below, we highlight recent advances in gene editing of several prominent non-model yeasts. yeasts as well as led to impressive metabolic engineering outcomes 12,59. Y. lipolytica does not have an endogenous plasmid, but functional screening of Y. lipolytica genomic DNA fragments facilitated the discovery of ARS elements capable of plasmid maintenance, ARS18, and ARS6860 as well as YlARS1 and YlARS2 61.…”

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confidence: 99%

Recent advances in domesticating non‐model microorganisms

Fatma

Schultz

Zhao

2020

Biotechnology Progress

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Non-model microorganisms have been increasingly explored as microbial cell factories for production of chemicals, fuels, and materials owing to their unique physiology and metabolic capabilities. However, these microorganisms often lack facile genetic tools for strain development, which hinders their adoption as production hosts. In this review, we describe recent advances in domestication of non-model microorganisms, including bacteria, actinobacteria, cyanobacteria, yeast, and fungi, with a focus on the development of genetic tools. In addition, we highlight some successful applications of non-model microorganisms as microbial cell factories.

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“…CRISPR/Cas9 has also been used to simultaneously introduce multiple genomic alterations (Bao et al, ; Mans et al, ). For recent reviews of the application of CRISPR Cas9/gRNA technology in yeast, see Lian, Mishra, and Zhao (), Tarasava, Oh, Eckert, and Gill (), Lei, Liu, Wei, Lu, and Jiang (), and Cai, Gao, and Zhou () and references therein.…”

Section: Introductionmentioning

confidence: 99%

A CRISPR/Cas9 method to generate heterozygous alleles in Saccharomyces cerevisiae

EauClaire

Webb

2019

Yeast

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Saccharomyces cerevisiae is a genetically facile organism, yet multiple CRISPR/Cas9 techniques are widely used to edit its genome more efficiently and cost effectively than conventional methods. The absence of selective markers makes CRISPR/Cas9 editing particularly useful when making mutations within genes or regulatory sequences. Heterozygous mutations within genes frequently arise in the winners of evolution experiments. The genetic dissection of heterozygous alleles can be important to understanding gene structure and function. Unfortunately, the high efficiency of genome cutting and repair makes the introduction of heterozygous alleles by standard CRISPR/Cas9 technique impossible. To be able to quickly and reliably determine the individual phenotypes of the thousands of heterozygous mutations that can occur during directed evolutions is of particular interest to industrial strain improvement research. In this report, we describe a CRISPR/Cas9 method that introduces specific heterozygous mutations into the S. cerevisiae genome. This method relies upon creating silent point mutations in the protospacer adjacent motif site or removing the protospacer adjacent motif site entirely to stop the multiple rounds of genome editing that prevent heterozygous alleles from being generated. This technique should be able to create heterozygous alleles in other diploid yeasts and different allelic copy numbers in polyploid cells.

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CRISPR-mediated genome editing in non-conventional yeasts for biotechnological applications

Cited by 116 publications

References 73 publications

Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges

Valorisation of pectin-rich agro-industrial residues by yeasts: potential and challenges

Recent advances in domesticating non‐model microorganisms

A CRISPR/Cas9 method to generate heterozygous alleles in Saccharomyces cerevisiae

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