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  1. Article ; Online: Discovering untapped biochemistry in microorganisms from hidden corners.

    Zhao, Zhiying / Yoshikuni, Yasuo

    Nature reviews. Microbiology

    2022  Volume 20, Issue 11, Page(s) 639

    Language English
    Publishing date 2022-09-09
    Publishing country England
    Document type Journal Article
    ZDB-ID 2139054-X
    ISSN 1740-1534 ; 1740-1526
    ISSN (online) 1740-1534
    ISSN 1740-1526
    DOI 10.1038/s41579-022-00795-w
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    Zs.A 5865: Show issues Location:
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  2. Article ; Online: Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes.

    Han, Sang-Woo / Yoshikuni, Yasuo

    Current opinion in microbiology

    2022  Volume 68, Page(s) 102172

    Abstract: Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because ...

    Abstract Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5'-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.
    MeSH term(s) Agriculture ; Crops, Agricultural/genetics ; Microbiota ; Nitrogen ; Prospective Studies ; Synthetic Biology
    Chemical Substances Nitrogen (N762921K75)
    Language English
    Publishing date 2022-06-16
    Publishing country England
    Document type Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2022.102172
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  3. Article ; Online: Metabolic engineering for valorization of macroalgae biomass.

    Sasaki, Yusuke / Yoshikuni, Yasuo

    Metabolic engineering

    2022  Volume 71, Page(s) 42–61

    Abstract: Marine macroalgae have huge potential as feedstocks for production of a wide spectrum of chemicals used in biofuels, biomaterials, and bioactive compounds. Harnessing macroalgae in these ways could promote wellbeing for people while mitigating climate ... ...

    Abstract Marine macroalgae have huge potential as feedstocks for production of a wide spectrum of chemicals used in biofuels, biomaterials, and bioactive compounds. Harnessing macroalgae in these ways could promote wellbeing for people while mitigating climate change and environmental destruction linked to use of fossil fuels. Microorganisms play pivotal roles in converting macroalgae into valuable products, and metabolic engineering technologies have been developed to extend their native capabilities. This review showcases current achievements in engineering the metabolisms of various microbial chassis to convert red, green, and brown macroalgae into bioproducts. Unique features of macroalgae, such as seasonal variation in carbohydrate content and salinity, provide the next challenges to advancing macroalgae-based biorefineries. Three emerging engineering strategies are discussed here: (1) designing dynamic control of metabolic pathways, (2) engineering strains of halophilic (salt-tolerant) microbes, and (3) developing microbial consortia for conversion. This review illuminates opportunities for future research communities by elucidating current approaches to engineering microbes so they can become cell factories for the utilization of macroalgae feedstocks.
    MeSH term(s) Biofuels ; Biomass ; Humans ; Metabolic Engineering ; Metabolic Networks and Pathways ; Seaweed/chemistry ; Seaweed/genetics ; Seaweed/metabolism
    Chemical Substances Biofuels
    Language English
    Publishing date 2022-01-22
    Publishing country Belgium
    Document type Journal Article ; Review ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 1470383-x
    ISSN 1096-7184 ; 1096-7176
    ISSN (online) 1096-7184
    ISSN 1096-7176
    DOI 10.1016/j.ymben.2022.01.005
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    Zs.A 6288: Show issues Location:
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  4. Article: Microbiome engineering for sustainable agriculture: using synthetic biology to enhance nitrogen metabolism in plant-associated microbes

    Han, Sang-Woo / Yoshikuni, Yasuo

    Current opinion in microbiology. 2022 May 16,

    2022  

    Abstract: Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because ...

    Abstract Plants benefit from symbiotic relationships with their microbiomes. Modifying these microbiomes to further promote plant growth and improve stress tolerance in crops is a promising strategy. However, such efforts have had limited success, perhaps because the original microbiomes quickly re-establish. Since the complex biological networks involved are little understood, progress through conventional means is time-consuming. Synthetic biology, with its practical successes in multiple industries, could speed up this research considerably. Some fascinating candidates for production by synthetic microbiomes are organic nitrogen metabolites and related pyridoxal-5′-phosphate-dependent enzymes, which have pivotal roles in microbe-microbe and plant-microbe interactions. This review summarizes recent studies of these metabolites and enzymes and discusses prospective synthetic biology platforms for sustainable agriculture.
    Keywords metabolites ; microbiome ; nitrogen metabolism ; organic nitrogen ; plant growth ; stress tolerance ; sustainable agriculture ; synthetic biology
    Language English
    Dates of publication 2022-0516
    Publishing place Elsevier Ltd
    Document type Article
    Note Pre-press version
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2022.102172
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  5. Article: Metabolic engineering for valorization of macroalgae biomass

    Sasaki, Yusuke / Yoshikuni, Yasuo

    Metabolic engineering. 2022 Jan. 12,

    2022  

    Abstract: Marine macroalgae have huge potential as feedstocks for production of a wide spectrum of chemicals used in biofuels, biomaterials, and bioactive compounds. Harnessing macroalgae in these ways could promote wellbeing for people while mitigating climate ... ...

    Abstract Marine macroalgae have huge potential as feedstocks for production of a wide spectrum of chemicals used in biofuels, biomaterials, and bioactive compounds. Harnessing macroalgae in these ways could promote wellbeing for people while mitigating climate change and environmental destruction linked to use of fossil fuels. Microorganisms play pivotal roles in converting macroalgae into valuable products, and metabolic engineering technologies have been developed to extend their native capabilities. This review showcases current achievements in engineering the metabolisms of various microbial chassis to convert red, green, and brown macroalgae into bioproducts. Unique features of macroalgae, such as seasonal variation in carbohydrate content and salinity, provide the next challenges to advancing macroalgae-based biorefineries. Three emerging engineering strategies are discussed here: (1) designing dynamic control of metabolic pathways, (2) engineering strains of halophilic (salt-tolerant) microbes, and (3) developing microbial consortia for conversion. This review illuminates opportunities for future research communities by elucidating current approaches to engineering microbes so they can become cell factories for the utilization of macroalgae feedstocks.
    Keywords biocompatible materials ; biofuels ; biomass ; biorefining ; carbohydrate content ; climate change ; feedstocks ; macroalgae ; people ; salinity ; salt tolerance ; seasonal variation
    Language English
    Dates of publication 2022-0112
    Publishing place Elsevier Inc.
    Document type Article
    Note Pre-press version
    ZDB-ID 1470383-x
    ISSN 1096-7184 ; 1096-7176
    ISSN (online) 1096-7184
    ISSN 1096-7176
    DOI 10.1016/j.ymben.2022.01.005
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  6. Article ; Online: Editorial overview: Energy biotechnology.

    Zhao, Huimin / Yoshikuni, Yasuo

    Current opinion in biotechnology

    2021  Volume 67, Page(s) iii–v

    MeSH term(s) Biotechnology
    Language English
    Publishing date 2021-02-10
    Publishing country England
    Document type Editorial
    ZDB-ID 1052045-4
    ISSN 1879-0429 ; 0958-1669
    ISSN (online) 1879-0429
    ISSN 0958-1669
    DOI 10.1016/j.copbio.2021.01.018
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    Zs.A 3071: Show issues Location:
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  7. Article ; Online: Chromosomal integration of complex DNA constructs using CRAGE and CRAGE-Duet systems.

    Zhao, Zhiying / Cheng, Jan-Fang / Yoshikuni, Yasuo

    STAR protocols

    2022  Volume 3, Issue 3, Page(s) 101546

    Abstract: Our recent development of the CRAGE (chassis-independent recombinase-assisted genome engineering) system enables single-step integration of large, complex DNA constructs directly into bacteria genomes across multiple phyla. This protocol describes the ... ...

    Abstract Our recent development of the CRAGE (chassis-independent recombinase-assisted genome engineering) system enables single-step integration of large, complex DNA constructs directly into bacteria genomes across multiple phyla. This protocol describes the details of the experimental design and procedures of CRAGE and extended CRAGE-Duet systems. It also describes a strategy that combines CRISPR with CRAGE, which allows implementation of CRISPR-Cas9, CRISPRa, and CRISPRi in diverse bacteria, overcoming major limitations to broaden the application of CRISPR in non-model bacterial genome engineering. For complete details on the use and execution of this protocol, please refer to Wang et al. (2019), Wang et al. (2020), and Liu et al. (2020).
    MeSH term(s) Bacteria ; DNA ; Genome, Bacterial ; Recombinases
    Chemical Substances Recombinases ; DNA (9007-49-2)
    Language English
    Publishing date 2022-07-16
    Publishing country United States
    Document type Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2666-1667
    ISSN (online) 2666-1667
    DOI 10.1016/j.xpro.2022.101546
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  8. Article: Multi-chassis engineering for heterologous production of microbial natural products

    Ke, Jing / Yoshikuni, Yasuo

    Current opinion in biotechnology. 2020 Apr., v. 62

    2020  

    Abstract: Microbial genomes encode numerous biosynthetic gene clusters (BGCs) that may produce natural products with diverse applications in medicine, agriculture, the environment, and materials science. With the advent of genome sequencing and bioinformatics, ... ...

    Abstract Microbial genomes encode numerous biosynthetic gene clusters (BGCs) that may produce natural products with diverse applications in medicine, agriculture, the environment, and materials science. With the advent of genome sequencing and bioinformatics, heterologous expression of BGCs is of increasing interest in bioactive natural product (NP) discovery. However, this approach has had limited success because expression of BGCs relies heavily on the physiology of just a few commonly available host chassis. Expanding and diversifying the chassis portfolio for heterologous BGC expression may greatly increase the chances for successful NP production. In this review, we first discuss genetic and genome engineering technologies used to clone, modify, and transform BGCs into multiple strains and to engineer chassis strains. We then highlight studies that employed the multi-chassis approach successfully to optimize NP production, discover previously uncharacterized NPs, and better understand BGC function.
    Keywords bioinformatics ; biosynthesis ; engineering ; genetic engineering ; heterologous gene expression ; multigene family ; sequence analysis
    Language English
    Dates of publication 2020-04
    Size p. 88-97.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1052045-4
    ISSN 1879-0429 ; 0958-1669
    ISSN (online) 1879-0429
    ISSN 0958-1669
    DOI 10.1016/j.copbio.2019.09.005
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  9. Article: Microbiome Engineering: Synthetic Biology of Plant-Associated Microbiomes in Sustainable Agriculture

    Ke, Jing / Wang, Bing / Yoshikuni, Yasuo

    Trends in biotechnology. 2021 Mar., v. 39, no. 3

    2021  

    Abstract: To support an ever-increasing population, modern agriculture faces numerous challenges that pose major threats to global food and energy security. Plant-associated microbes, with their many plant growth-promoting (PGP) traits, have enormous potential in ... ...

    Abstract To support an ever-increasing population, modern agriculture faces numerous challenges that pose major threats to global food and energy security. Plant-associated microbes, with their many plant growth-promoting (PGP) traits, have enormous potential in helping to solve these challenges. However, the results of their use in agriculture have been variable, probably because of poor colonization. Phytomicrobiome engineering is an emerging field of synthetic biology that may offer ways to alleviate this limitation. This review highlights recent advances in both bottom-up and top-down approaches to engineering non-model bacteria and microbiomes to promote beneficial plant–microbe interactions, as well as advances in strategies to evaluate these interactions. Biosafety, biosecurity, and biocontainment strategies to address the environmental concerns associated with field use of synthetic microbes are also discussed.
    Keywords biocontainment ; biosecurity ; biotechnology ; energy ; microbiome ; phytobiome ; sustainable agriculture ; synthetic biology
    Language English
    Dates of publication 2021-03
    Size p. 244-261.
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 47474-5
    ISSN 1879-3096 ; 0167-7799
    ISSN (online) 1879-3096
    ISSN 0167-7799
    DOI 10.1016/j.tibtech.2020.07.008
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  10. Article ; Online: Pathway and Gene Discovery from Natural Hosts and Organisms.

    Ke, Jing / Yoshikuni, Yasuo

    Methods in molecular biology (Clifton, N.J.)

    2019  Volume 1927, Page(s) 1–9

    Abstract: Information in public sequence databases on the genomes and metagenomes of microbes and plants has grown rapidly. In conjunction with technological developments in computational identification of biosynthetic gene clusters, molecular biology, synthetic ... ...

    Abstract Information in public sequence databases on the genomes and metagenomes of microbes and plants has grown rapidly. In conjunction with technological developments in computational identification of biosynthetic gene clusters, molecular biology, synthetic biology, and analytical tools, this has revealed genes for enzymes with optimal and targeted function, as well as a rich pool of uncharacterized metabolic pathways. This chapter discusses different approaches to discovery of genes and metabolic pathways in microbes and plants in nature, such as genomic mining, transcriptome analysis, and metabolite profiling.
    MeSH term(s) Bacteria/genetics ; Bacteria/metabolism ; Computational Biology/methods ; Databases, Genetic ; Fungi/genetics ; Fungi/metabolism ; Genetic Association Studies/methods ; Genome ; Genomics/methods ; Metabolic Networks and Pathways/genetics ; Molecular Sequence Annotation ; Multigene Family ; Plants/genetics ; Plants/metabolism
    Language English
    Publishing date 2019-02-20
    Publishing country United States
    Document type Journal Article
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-4939-9142-6_1
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