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Schwardmann LS, Benninghaus L, Lindner SN, Wendisch VF. Prospects of formamide as nitrogen source in biotechnological production processes. Appl Microbiol Biotechnol 2024; 108:105. [PMID: 38204134 PMCID: PMC10781810 DOI: 10.1007/s00253-023-12962-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/27/2023] [Accepted: 10/05/2023] [Indexed: 01/12/2024]
Abstract
This review presents an analysis of formamide, focussing on its occurrence in nature, its functional roles, and its promising applications in the context of the bioeconomy. We discuss the utilization of formamide as an innovative nitrogen source achieved through metabolic engineering. These approaches underscore formamide's potential in supporting growth and production in biotechnological processes. Furthermore, our review illuminates formamide's role as a nitrogen source capable of safeguarding cultivation systems against contamination in non-sterile conditions. This attribute adds an extra layer of practicality to its application, rendering it an attractive candidate for sustainable and resilient industrial practices. Additionally, the article unveils the versatility of formamide as a potential carbon source that could be combined with formate or CO2 assimilation pathways. However, its attributes, i.e., enriched nitrogen content and comparatively limited energy content, led to conclude that formamide is more suitable as a co-substrate and that its use as a sole source of carbon for biomass and bio-production is limited. Through our exploration of formamide's properties and its applications, this review underscores the significance of formamide as valuable resource for a large spectrum of industrial applications. KEY POINTS: • Formidases enable access to formamide as source of nitrogen, carbon, and energy • The formamide/formamidase system supports non-sterile fermentation • The nitrogen source formamide supports production of nitrogenous compounds.
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Affiliation(s)
- Lynn S Schwardmann
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
- , Aminoverse B.V., Daelderweg 9, 6361 HK, Nuth, Beekdaelen, The Netherlands
| | - Leonie Benninghaus
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Steffen N Lindner
- Department of Biochemistry, Charite Universitatsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, Berlin, Germany
| | - Volker F Wendisch
- Genetics of Prokaryotes, Faculty of Biology and CeBiTec, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
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2
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Yang Z, Li B, Bu R, Wang Z, Xin Z, Li Z, Zhang L, Wang W. A highly efficient method for genomic deletion across diverse lengths in thermophilic Parageobacillus thermoglucosidasius. Synth Syst Biotechnol 2024; 9:658-666. [PMID: 38817825 PMCID: PMC11137367 DOI: 10.1016/j.synbio.2024.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/07/2024] [Accepted: 05/16/2024] [Indexed: 06/01/2024] Open
Abstract
Parageobacillus thermoglucosidasius is emerging as a highly promising thermophilic organism for metabolic engineering. The utilization of CRISPR-Cas technologies has facilitated programmable genetic manipulation in P. thermoglucosidasius. However, the absence of thermostable NHEJ enzymes limited the capability of the endogenous type I CRISPR-Cas system to generate a variety of extensive genomic deletions. Here, two thermophilic NHEJ enzymes were identified and combined with the endogenous type I CRISPR-Cas system to develop a genetic manipulation tool that can achieve long-range genomic deletion across various lengths. By optimizing this tool-through adjusting the expression level of NHEJ enzymes and leveraging our discovery of a negative correlation between GC content of the guide RNA (gRNA) and deletion efficacy-we streamlined a comprehensive gRNA selection manual for whole-genome editing, achieving a 100 % success rate in randomly selecting gRNAs. Notably, using just one gRNA, we achieved genomic deletions spanning diverse length, exceeding 200 kilobases. This tool will facilitate the genomic manipulation of P. thermoglucosidasius for both fundamental research and applied engineering studies, further unlocking its potential as a thermophilic cell factory.
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Affiliation(s)
- Zhiheng Yang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
| | - Bixiao Li
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Cluster Science, Ministry of Education, Frontiers Science Center for High Energy Material, Advanced Research Institute of Multidisciplinary Science, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Ruihong Bu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhengduo Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
| | - Zhenguo Xin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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3
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Phaneuf PV, Kim SH, Rychel K, Rode C, Beulig F, Palsson BO, Yang L. Meta-analysis Driven Strain Design for Mitigating Oxidative Stresses Important in Biomanufacturing. ACS Synth Biol 2024. [PMID: 38934464 DOI: 10.1021/acssynbio.3c00572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2024]
Abstract
As the availability of data sets increases, meta-analysis leveraging aggregated and interoperable data types is proving valuable. This study leveraged a meta-analysis workflow to identify mutations that could improve robustness to reactive oxygen species (ROS) stresses using an industrially important melatonin production strain as an example. ROS stresses often occur during cultivation and negatively affect strain performance. Cellular response to ROS is also linked to the SOS response and resistance to pH fluctuations, which is important to strain robustness in large-scale biomanufacturing. This work integrated more than 7000 E. coli adaptive laboratory evolution (ALE) mutations across 59 experiments to statistically associate mutated genes to 2 ROS tolerance ALE conditions from 72 unique conditions. Mutant oxyR, fur, iscR, and ygfZ were significantly associated and hypothesized to contribute fitness in ROS stress. Across these genes, 259 total mutations were inspected in conjunction with transcriptomics from 46 iModulon experiments. Ten mutations were chosen for reintroduction based on mutation clustering and coinciding transcriptional changes as evidence of fitness impact. Strains with mutations reintroduced into oxyR, fur, iscR, and ygfZ exhibited increased tolerance to H2O2 and acid stress and reduced SOS response, all of which are related to ROS. Additionally, new evidence was generated toward understanding the function of ygfZ, an uncharacterized gene. This meta-analysis approach utilized aggregated and interoperable multiomics data sets to identify mutations conferring industrially relevant phenotypes with the least drawbacks, describing an approach for data-driven strain engineering to optimize microbial cell factories.
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Affiliation(s)
- P V Phaneuf
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - S H Kim
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - K Rychel
- Department of Bioengineering, University of California, San Diego, La Jolla ,California92093-0412 ,United States
| | - C Rode
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - F Beulig
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
| | - B O Palsson
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
- Department of Bioengineering, University of California, San Diego, La Jolla ,California92093-0412 ,United States
- Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla ,California92093-0021, United States
- Department of Pediatrics, University of California, San Diego, La Jolla ,California 92093-0412, United States
| | - L Yang
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220. Kongens Lyngby 2800, Denmark
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Makopa TP, Ncube T, Alwasel S, Boekhout T, Zhou N. Yeast-insect interactions in southern Africa: Tapping the diversity of yeasts for modern bioprocessing. Yeast 2024; 41:330-348. [PMID: 38450792 DOI: 10.1002/yea.3935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/31/2024] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
Yeast-insect interactions are one of the most interesting long-standing relationships whose research has contributed to our understanding of yeast biodiversity and their industrial applications. Although insect-derived yeast strains are exploited for industrial fermentations, only a limited number of such applications has been documented. The search for novel yeasts from insects is attractive to augment the currently domesticated and commercialized production strains. More specifically, there is potential in tapping the insects native to southern Africa. Southern Africa is home to a disproportionately high fraction of global biodiversity with a cluster of biomes and a broad climate range. This review presents arguments on the roles of the mutualistic relationship between yeasts and insects, the presence of diverse pristine environments and a long history of spontaneous food and beverage fermentations as the potential source of novelty. The review further discusses the recent advances in novelty of industrial strains of insect origin, as well as various ancient and modern-day industries that could be improved by use yeasts from insect origin. The major focus of the review is on the relationship between insects and yeasts in southern African ecosystems as a potential source of novel industrial yeast strains for modern bioprocesses.
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Affiliation(s)
- Tawanda P Makopa
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Thembekile Ncube
- Department of Biology and Biochemistry, Faculty of Applied Science, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Saleh Alwasel
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Teun Boekhout
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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Xie L, Yu W, Gao J, Wang H, Zhou YJ. Ogataea polymorpha as a next-generation chassis for industrial biotechnology. Trends Biotechnol 2024:S0167-7799(24)00086-6. [PMID: 38622041 DOI: 10.1016/j.tibtech.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
Ogataea (Hansenula) polymorpha is a nonconventional yeast with some unique characteristics, including fast growth, thermostability, and broad substrate spectrum. Other than common applications for protein production, O. polymorpha is attracting interest for chemical and protein production from methanol; a promising feedstock for the next-generation biomanufacturing due to its abundant sources and excellent characteristics. Benefiting from the development of synthetic biology, it has been engineered to produce value-added chemicals by extensively rewiring cellular metabolism. This Review discusses recently developed synthetic biology tools of O. polymorpha. The advances of chemicals production and systems biology were reviewed comprehensively. Finally, we look ahead to the developments of biomanufacturing in O. polymorpha to make an overall understanding of this chassis for academia and industry.
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Affiliation(s)
- Linfeng Xie
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, China
| | - Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, China
| | - Haoyu Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China; Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, CAS, 457 Zhongshan Road, Dalian 116023, China.
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6
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Gan L, Huang X, He Z, He T. Exopolysaccharide production by salt-tolerant bacteria: Recent advances, current challenges, and future prospects. Int J Biol Macromol 2024; 264:130731. [PMID: 38471615 DOI: 10.1016/j.ijbiomac.2024.130731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/27/2024] [Accepted: 03/06/2024] [Indexed: 03/14/2024]
Abstract
Natural biopolymers derived from exopolysaccharides (EPSs) are considered eco-friendly and sustainable alternatives to available traditional synthetic counterparts. Salt-tolerant bacteria inhabiting harsh ecological niches have evolved a number of unique adaptation strategies allowing them to maintain cellular integrity and assuring their long-term survival; among these, producing EPSs can be adopted as an effective strategy to thrive under high-salt conditions. A great diversity of EPSs from salt-tolerant bacteria have attracted widespread attention recently. Because of factors such as their unique structural, physicochemical, and functional characteristics, EPSs are commercially valuable for the global market and their application potential in various sectors is promising. However, large-scale production and industrial development of these biopolymers are hindered by their low yields and high costs. Consequently, the research progress and future prospects of salt-tolerant bacterial EPSs must be systematically reviewed to further promote their application and commercialization. In this review, the structure and properties of EPSs produced by a variety of salt-tolerant bacterial strains isolated from different sources are summarized. Further, feasible strategies for solving production bottlenecks are discussed, which provides a scientific basis and direct reference for more scientific and rational EPS development.
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Affiliation(s)
- Longzhan Gan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou Province, China.
| | - Xin Huang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Zhicheng He
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou Province, China
| | - Tengxia He
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 550025, Guizhou Province, China.
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Atasoy M, Álvarez Ordóñez A, Cenian A, Djukić-Vuković A, Lund PA, Ozogul F, Trček J, Ziv C, De Biase D. Exploitation of microbial activities at low pH to enhance planetary health. FEMS Microbiol Rev 2024; 48:fuad062. [PMID: 37985709 PMCID: PMC10963064 DOI: 10.1093/femsre/fuad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023] Open
Abstract
Awareness is growing that human health cannot be considered in isolation but is inextricably woven with the health of the environment in which we live. It is, however, under-recognized that the sustainability of human activities strongly relies on preserving the equilibrium of the microbial communities living in/on/around us. Microbial metabolic activities are instrumental for production, functionalization, processing, and preservation of food. For circular economy, microbial metabolism would be exploited to produce building blocks for the chemical industry, to achieve effective crop protection, agri-food waste revalorization, or biofuel production, as well as in bioremediation and bioaugmentation of contaminated areas. Low pH is undoubtedly a key physical-chemical parameter that needs to be considered for exploiting the powerful microbial metabolic arsenal. Deviation from optimal pH conditions has profound effects on shaping the microbial communities responsible for carrying out essential processes. Furthermore, novel strategies to combat contaminations and infections by pathogens rely on microbial-derived acidic molecules that suppress/inhibit their growth. Herein, we present the state-of-the-art of the knowledge on the impact of acidic pH in many applied areas and how this knowledge can guide us to use the immense arsenal of microbial metabolic activities for their more impactful exploitation in a Planetary Health perspective.
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Affiliation(s)
- Merve Atasoy
- UNLOCK, Wageningen University & Research and Technical University Delft, Droevendaalsesteeg 4, 6708 PB,Wageningen, the Netherlands
| | - Avelino Álvarez Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Adam Cenian
- Institute of Fluid Flow Machinery, Polish Academy of Sciences, Department of Physical Aspects of Ecoenergy, 14 Fiszera St., 80-231 Gdańsk, Poland
| | - Aleksandra Djukić-Vuković
- Department of Biochemical Engineering and Biotechnology, Faculty of Technology and Metallurgy, University of Belgrade, Karnegijeva 4, 11120 Belgrade, Serbia
| | - Peter A Lund
- Institute of Microbiology and Infection,School of Biosciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Fatih Ozogul
- Department of Seafood Processing and Technology, Faculty of Fisheries, Cukurova University, Balcali, 01330, Adana, Turkey
- Biotechnology Research and Application Center, Cukurova University, Balcali, 01330 Adana, Turkey
| | - Janja Trček
- Department of Biology, Faculty of Natural Sciences and Mathematics, University of Maribor, Koroška cesta 160, 2000 Maribor, Slovenia
| | - Carmit Ziv
- Department of Postharvest Science, Agricultural Research Organization – Volcani Center, 68 HaMaccabim Road , P.O.B 15159 Rishon LeZion 7505101, Israel
| | - Daniela De Biase
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Corso della Repubblica 79, 04100 Latina, Italy
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Dubinkina V, Bhogale S, Hsieh PH, Dibaeinia P, Nambiar A, Maslov S, Yoshikuni Y, Sinha S. A transcriptomic atlas of acute stress response to low pH in multiple Issatchenkia orientalis strains. Microbiol Spectr 2024; 12:e0253623. [PMID: 38018981 PMCID: PMC10783018 DOI: 10.1128/spectrum.02536-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/27/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Issatchenkia orientalis is a promising industrial chassis to produce biofuels and bioproducts due to its high tolerance to multiple environmental stresses such as low pH, heat, and other chemicals otherwise toxic for the most widely used microbes. Yet, little is known about specific mechanisms of such tolerance in this organism, hindering our ability to engineer this species to produce valuable biochemicals. Here, we report a comprehensive study of the mechanisms of acidic tolerance in this species via transcriptome profiling across variable pH for 12 different strains with different phenotypes. We found multiple regulatory mechanisms involved in tolerance to low pH in different strains of I. orientalis, marking potential targets for future gene editing and perturbation experiments.
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Affiliation(s)
- Veronika Dubinkina
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- The Gladstone Institute of Data Science and Biotechnology, San Francisco, California, USA
| | - Shounak Bhogale
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Ping-Hung Hsieh
- Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Payam Dibaeinia
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Ananthan Nambiar
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Sergei Maslov
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Yasuo Yoshikuni
- Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Global Institution for Collaborative Research and Education, Hokkaido University, Hokkaido, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Saurabh Sinha
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
- Department of Biomedical Engineering at Georgia Tech and Emory University, Atlanta, Georgia, USA
- Department of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
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Boob AG, Chen J, Zhao H. Enabling pathway design by multiplex experimentation and machine learning. Metab Eng 2024; 81:70-87. [PMID: 38040110 DOI: 10.1016/j.ymben.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/01/2023] [Accepted: 11/25/2023] [Indexed: 12/03/2023]
Abstract
The remarkable metabolic diversity observed in nature has provided a foundation for sustainable production of a wide array of valuable molecules. However, transferring the biosynthetic pathway to the desired host often runs into inherent failures that arise from intermediate accumulation and reduced flux resulting from competing pathways within the host cell. Moreover, the conventional trial and error methods utilized in pathway optimization struggle to fully grasp the intricacies of installed pathways, leading to time-consuming and labor-intensive experiments, ultimately resulting in suboptimal yields. Considering these obstacles, there is a pressing need to explore the enzyme expression landscape and identify the optimal pathway configuration for enhanced production of molecules. This review delves into recent advancements in pathway engineering, with a focus on multiplex experimentation and machine learning techniques. These approaches play a pivotal role in overcoming the limitations of traditional methods, enabling exploration of a broader design space and increasing the likelihood of discovering optimal pathway configurations for enhanced production of molecules. We discuss several tools and strategies for pathway design, construction, and optimization for sustainable and cost-effective microbial production of molecules ranging from bulk to fine chemicals. We also highlight major successes in academia and industry through compelling case studies.
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Affiliation(s)
- Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Junyu Chen
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, United States; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.
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10
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Li M, Chu Y, Dong X, Ji H. General mechanisms of weak acid-tolerance and current strategies for the development of tolerant yeasts. World J Microbiol Biotechnol 2023; 40:49. [PMID: 38133718 DOI: 10.1007/s11274-023-03875-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
Abstract
Yeast cells are often subjected to various types of weak acid stress in the process of industrial production, food processing, and preservation, resulting in growth inhibition and reduced fermentation performance. Under acidic conditions, weak acids enter the near-neutral yeast cytoplasm and dissociate into protons and anions, leading to cytoplasmic acidification and cell damage. Although some yeast strains have developed the ability to survive weak acids, the complexity and diversity of stresses during industrial production still require the application of appropriate strategies for phenotypes improvement. In this review, we summarized current knowledge concerning weak acid stress response and resistance, which may suggest important targets for further construction of more robust strains. We also highlight current feasible strategies for improving the weak acid resistance of yeasts, such as adaptive laboratory evolution, transcription factors engineering, and cell membrane/wall engineering. Moreover, the challenges and perspectives associated with improving the competitiveness of industrial strains are also discussed. This review provides effective strategies for improving the industrial phenotypes of yeast from multiple dimensions in future studies.
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Affiliation(s)
- Mengmeng Li
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Yunfei Chu
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Xiameng Dong
- Department of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang, 325006, PR China.
| | - Hao Ji
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China.
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China.
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11
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Hu L, Qiu H, Huang L, Zhang F, Tran VG, Yuan J, He N, Cao M. Emerging nonmodel eukaryotes for biofuel production. Curr Opin Biotechnol 2023; 84:103015. [PMID: 37913603 DOI: 10.1016/j.copbio.2023.103015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 10/07/2023] [Indexed: 11/03/2023]
Abstract
Microbial synthesis of biofuels offers a promising solution to the global environmental and energy concerns. However, the main challenge of microbial cell factories is their high fermentation costs. Model hosts, such as Escherichia coli and Saccharomyces cerevisiae, are typically used for proof-of-concept studies of producing different types of biofuels, however, they have a limited potential for biofuel production at an industrially relevant scale due to the weak stability/robustness and narrow substrate scope. With the advancements of synthetic biology and metabolic engineering, nonmodel eukaryotes, with naturally favorable phenotypic and metabolic features, have been emerging as promising biofuel producers. Here, we introduce the emerging nonmodel eukaryotes for the biofuel production and discuss their specific advantages, especially those with the capacity of producing cellulosic ethanol, higher alcohols, and fatty acid-/terpene-derived biofuel molecules. We also propose the challenges and prospects for developing nonmodel eukaryotic as the ideal hosts for future biofuel production.
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Affiliation(s)
- Lin Hu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China
| | - Huihui Qiu
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China
| | - Liuheng Huang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China
| | - Fenghui Zhang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China
| | - Vinh G Tran
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361102, China
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China.
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen University, Fujian 361005, China; Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Fujian 361005, China.
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12
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Gao J, Yu W, Li Y, Jin M, Yao L, Zhou YJ. Engineering co-utilization of glucose and xylose for chemical overproduction from lignocellulose. Nat Chem Biol 2023; 19:1524-1531. [PMID: 37620399 DOI: 10.1038/s41589-023-01402-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/10/2023] [Indexed: 08/26/2023]
Abstract
Bio-refining lignocellulose could provide a sustainable supply of fuels and fine chemicals; however, the challenges associated with the co-utilization of xylose and glucose typically compromise the efficiency of lignocellulose conversion. Here we engineered the industrial yeast Ogataea polymorpha (Hansenula polymorpha) for lignocellulose biorefinery by facilitating the co-utilization of glucose and xylose to optimize the production of free fatty acids (FFAs) and 3-hydroxypropionic acid (3-HP) from lignocellulose. We rewired the central metabolism for the enhanced supply of acetyl-coenzyme A and nicotinamide adenine dinucleotide phosphate hydrogen, obtaining 30.0 g l-1 of FFAs from glucose, with productivity of up to 0.27 g l-1 h-1. Strengthening xylose uptake and catabolism promoted the synchronous utilization of glucose and xylose, which enabled the production of 38.2 g l-1 and 7.0 g l-1 FFAs from the glucose-xylose mixture and lignocellulosic hydrolysates, respectively. Finally, this efficient cell factory was metabolically transformed for 3-HP production with the highest titer of 79.6 g l-1 in fed-batch fermentation in mixed glucose and xylose.
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Affiliation(s)
- Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yunxia Li
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, PR China
| | - Lun Yao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
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13
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Zhao B, Zhao J, Wang M, Guo Y, Mehmood A, Wang W, Xiong Y, Luo S, Wei DQ, Zhao XQ, Wang Y. Exploring microproteins from various model organisms using the mip-mining database. BMC Genomics 2023; 24:661. [PMID: 37919660 PMCID: PMC10623795 DOI: 10.1186/s12864-023-09735-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 10/12/2023] [Indexed: 11/04/2023] Open
Abstract
Microproteins, prevalent across all kingdoms of life, play a crucial role in cell physiology and human health. Although global gene transcription is widely explored and abundantly available, our understanding of microprotein functions using transcriptome data is still limited. To mitigate this problem, we present a database, Mip-mining ( https://weilab.sjtu.edu.cn/mipmining/ ), underpinned by high-quality RNA-sequencing data exclusively aimed at analyzing microprotein functions. The Mip-mining hosts 336 sets of high-quality transcriptome data from 8626 samples and nine representative living organisms, including microorganisms, plants, animals, and humans, in our Mip-mining database. Our database specifically provides a focus on a range of diseases and environmental stress conditions, taking into account chemical, physical, biological, and diseases-related stresses. Comparatively, our platform enables customized analysis by inputting desired data sets with self-determined cutoff values. The practicality of Mip-mining is demonstrated by identifying essential microproteins in different species and revealing the importance of ATP15 in the acetic acid stress tolerance of budding yeast. We believe that Mip-mining will facilitate a greater understanding and application of microproteins in biotechnology. Moreover, it will be beneficial for designing therapeutic strategies under various biological conditions.
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Affiliation(s)
- Bowen Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Muyao Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yangfan Guo
- Central Laboratory of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, 650051, China
| | - Aamir Mehmood
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weibin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai, 200232, China
| | - Shenggan Luo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nayang, Henan, 473006, China.
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, 518055, Guangdong, China.
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Yanjing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Engineering Research Center of Cell & Therapeutic Antibody, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China.
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14
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Aminian-Dehkordi J, Rahimi S, Golzar-Ahmadi M, Singh A, Lopez J, Ledesma-Amaro R, Mijakovic I. Synthetic biology tools for environmental protection. Biotechnol Adv 2023; 68:108239. [PMID: 37619824 DOI: 10.1016/j.biotechadv.2023.108239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 08/17/2023] [Accepted: 08/20/2023] [Indexed: 08/26/2023]
Abstract
Synthetic biology transforms the way we perceive biological systems. Emerging technologies in this field affect many disciplines of science and engineering. Traditionally, synthetic biology approaches were commonly aimed at developing cost-effective microbial cell factories to produce chemicals from renewable sources. Based on this, the immediate beneficial impact of synthetic biology on the environment came from reducing our oil dependency. However, synthetic biology is starting to play a more direct role in environmental protection. Toxic chemicals released by industries and agriculture endanger the environment, disrupting ecosystem balance and biodiversity loss. This review highlights synthetic biology approaches that can help environmental protection by providing remediation systems capable of sensing and responding to specific pollutants. Remediation strategies based on genetically engineered microbes and plants are discussed. Further, an overview of computational approaches that facilitate the design and application of synthetic biology tools in environmental protection is presented.
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Affiliation(s)
| | - Shadi Rahimi
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden
| | - Mehdi Golzar-Ahmadi
- Norman B. Keevil Institute of Mining Engineering, University of British Columbia, Vancouver, Canada
| | - Amritpal Singh
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | - Javiera Lopez
- Department of Bioengineering, Imperial College London, London, SW72AZ, UK
| | | | - Ivan Mijakovic
- Department of Life Sciences, Chalmers University of Technology, Göteborg, Sweden; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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15
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Yang Z, Li Z, Li B, Bu R, Tan GY, Wang Z, Yan H, Xin Z, Zhang G, Li M, Xiang H, Zhang L, Wang W. A thermostable type I-B CRISPR-Cas system for orthogonal and multiplexed genetic engineering. Nat Commun 2023; 14:6193. [PMID: 37794017 PMCID: PMC10551041 DOI: 10.1038/s41467-023-41973-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
Thermophilic cell factories have remarkably broad potential for industrial applications, but are limited by a lack of genetic manipulation tools and recalcitrance to transformation. Here, we identify a thermophilic type I-B CRISPR-Cas system from Parageobacillus thermoglucosidasius and find it displays highly efficient transcriptional repression or DNA cleavage activity that can be switched by adjusting crRNA length to less than or greater than 26 bp, respectively, without ablating Cas3 nuclease. We then develop an orthogonal tool for genome editing and transcriptional repression using this type I-B system in both thermophile and mesophile hosts. Empowered by this tool, we design a strategy to screen the genome-scale targets involved in transformation efficiency and established dynamically controlled supercompetent P. thermoglucosidasius cells with high efficiency ( ~ 108 CFU/μg DNA) by temporal multiplexed repression. We also demonstrate the construction of thermophilic riboflavin cell factory with hitherto highest titers in high temperature fermentation by genome-scale identification and combinatorial manipulation of multiple targets. This work enables diverse high-efficiency genetic manipulation in P. thermoglucosidasius and facilitates the engineering of thermophilic cell factories.
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Affiliation(s)
- Zhiheng Yang
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Bixiao Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Ruihong Bu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- School of Medicine and Pharmacy, Ocean University of China, 266003, Qingdao, China
| | - Gao-Yi Tan
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
| | - Zhengduo Wang
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China
| | - Hao Yan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Zhenguo Xin
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Guojian Zhang
- School of Medicine and Pharmacy, Ocean University of China, 266003, Qingdao, China
| | - Ming Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, and School of Biotechnology, East China University of Science and Technology (ECUST), 200237, Shanghai, China.
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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16
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Huanca-Juarez J, Nascimento-Silva EA, Silva NH, Silva-Rocha R, Guazzaroni ME. Identification and functional analysis of novel protein-encoding sequences related to stress-resistance. Front Microbiol 2023; 14:1268315. [PMID: 37840709 PMCID: PMC10568318 DOI: 10.3389/fmicb.2023.1268315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
Currently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Thus, is essential developing robust bacteria for improved cell tolerance to process-specific parameters. In this context, metagenomic approaches from extreme environments can provide useful biological parts to improve bacterial robustness. Here, in order to build genetic constructs that increase bacterial resistance to diverse stress conditions, we recovered novel protein-encoding sequences related to stress-resistance from metagenomic databases using an in silico approach based on Hidden-Markov-Model profiles. For this purpose, we used metagenomic shotgun sequencing data from microbial communities of extreme environments to identify genes encoding chaperones and other proteins that confer resistance to stress conditions. We identified and characterized 10 novel protein-encoding sequences related to the DNA-binding protein HU, the ATP-dependent protease ClpP, and the chaperone protein DnaJ. By expressing these genes in Escherichia coli under several stress conditions (including high temperature, acidity, oxidative and osmotic stress, and UV radiation), we identified five genes conferring resistance to at least two stress conditions when expressed in E. coli. Moreover, one of the identified HU coding-genes which was retrieved from an acidic soil metagenome increased E. coli tolerance to four different stress conditions, implying its suitability for the construction of a synthetic circuit directed to expand broad bacterial resistance.
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Affiliation(s)
- Joshelin Huanca-Juarez
- Department of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, Brazil
| | - Edson Alexandre Nascimento-Silva
- Department of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, Brazil
| | - Ninna Hirata Silva
- Department of Cell and Molecular Biology, Ribeirão Preto School of Medicine (FMRP) – University of São Paulo (USP), São Paulo, Brazil
| | | | - María-Eugenia Guazzaroni
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP) – University of São Paulo (USP), São Paulo, Brazil
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17
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Zhang L, Lin Y, Yi X, Huang W, Hu Q, Zhang Z, Wu F, Ye JW, Chen GQ. Engineering low-salt growth Halomonas Bluephagenesis for cost-effective bioproduction combined with adaptive evolution. Metab Eng 2023; 79:146-158. [PMID: 37543135 DOI: 10.1016/j.ymben.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/07/2023]
Abstract
Halophilic Halomonas bluephagenesis has been engineered to produce various added-value bio-compounds with reduced costs. However, the salt-stress regulatory mechanism remained unclear. H. bluephagenesis was randomly mutated to obtain low-salt growing mutants via atmospheric and room temperature plasma (ARTP). The resulted H. bluephagenesis TDH4A1B5 was constructed with the chromosomal integration of polyhydroxyalkanoates (PHA) synthesis operon phaCAB and deletion of phaP1 gene encoding PHA synthesis associated protein phasin, forming H. bluephagenesis TDH4A1B5P, which led to increased production of poly(3-hydroxybutyrate) (PHB) and poly(3-hydroxybutyrate-co-4-hydrobutyrate) (P34HB) by over 1.4-fold. H. bluephagenesis TDH4A1B5P also enhanced production of ectoine and threonine by 50% and 77%, respectively. A total 101 genes related to salinity tolerance was identified and verified via comparative genomic analysis among four ARTP mutated H. bluephagenesis strains. Recombinant H. bluephagenesis TDH4A1B5P was further engineered for PHA production utilizing sodium acetate or gluconate as sole carbon source. Over 33% cost reduction of PHA production could be achieved using recombinant H. bluephagenesis TDH4A1B5P. This study successfully developed a low-salt tolerant chassis H. bluephagenesis TDH4A1B5P and revealed salt-stress related genes of halophilic host strains.
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Affiliation(s)
- Lizhan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yina Lin
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xueqing Yi
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wuzhe Huang
- PhaBuilder Biotech Co. Ltd., Shunyi District, Zhaoquan Ying, Beijing, 101309, China
| | - Qitiao Hu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zhongnan Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Fuqing Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jian-Wen Ye
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Guo-Qiang Chen
- School of Life Sciences, Tsinghua University, Beijing, 100084, China; Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing, China; MOE Key Lab of Industrial Biocatalysis, Dept Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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18
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Pyne ME, Bagley JA, Narcross L, Kevvai K, Exley K, Davies M, Wang Q, Whiteway M, Martin VJJ. Screening non-conventional yeasts for acid tolerance and engineering Pichia occidentalis for production of muconic acid. Nat Commun 2023; 14:5294. [PMID: 37652930 PMCID: PMC10471774 DOI: 10.1038/s41467-023-41064-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023] Open
Abstract
Saccharomyces cerevisiae is a workhorse of industrial biotechnology owing to the organism's prominence in alcohol fermentation and the suite of sophisticated genetic tools available to manipulate its metabolism. However, S. cerevisiae is not suited to overproduce many bulk bioproducts, as toxicity constrains production at high titers. Here, we employ a high-throughput assay to screen 108 publicly accessible yeast strains for tolerance to 20 g L-1 adipic acid (AA), a nylon precursor. We identify 15 tolerant yeasts and select Pichia occidentalis for production of cis,cis-muconic acid (CCM), the precursor to AA. By developing a genome editing toolkit for P. occidentalis, we demonstrate fed-batch production of CCM with a maximum titer (38.8 g L-1), yield (0.134 g g-1 glucose) and productivity (0.511 g L-1 h-1) that surpasses all metrics achieved using S. cerevisiae. This work brings us closer to the industrial bioproduction of AA and underscores the importance of host selection in bioprocessing.
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Affiliation(s)
- Michael E Pyne
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Department of Biology, University of Western Ontario, Ontario, Canada
| | - James A Bagley
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Lauren Narcross
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Amyris, Inc., Emeryville, CA, USA
| | - Kaspar Kevvai
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Pivot Bio, Berkeley, CA, USA
| | - Kealan Exley
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark
| | - Meghan Davies
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- BenchSci, Toronto, ON, Canada
| | | | - Malcolm Whiteway
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada.
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada.
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19
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Thorwall S, Trivedi V, Ottum E, Wheeldon I. Population genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis. Metab Eng 2023; 78:223-234. [PMID: 37369325 DOI: 10.1016/j.ymben.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 06/07/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023]
Abstract
The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets across the pangenome of a microbial population. This study leverages NGS data as well as existing molecular biology and bioinformatics tools to identify and validate genomic signatures for improving phenazine biosynthesis in Pseudomonas chlororaphis. We sequenced a diverse collection of 34 Pseudomonas isolates using short- and long-read sequencing techniques and assembled whole genomes using the NGS reads. In addition, we assayed three industrially relevant phenotypes (phenazine production, biofilm formation, and growth temperature) for these isolates in two different media conditions. We then provided the whole genomes and phenazine production data to a unitig-based microbial genome-wide association study (mGWAS) tool to identify novel genomic signatures responsible for phenazine production in P. chlororaphis. Post-processing of the mGWAS analysis results yielded 330 significant hits influencing the biosynthesis of one or more phenazine compounds. Based on a quantitative metric (called the phenotype score), we elucidated the most influential hits for phenazine production and experimentally validated them in vivo in the most optimal phenazine producing strain. Two genes significantly increased phenazine-1-carboxamide (PCN) production: a histidine transporter (ProY_1), and a putative carboxypeptidase (PS__04251). A putative MarR-family transcriptional regulator decreased PCN titer when overexpressed in a high PCN producing isolate. Overall, this work seeks to demonstrate the utility of a population genomics approach as an effective strategy in enabling the identification of targets for metabolic engineering of bioproduction hosts.
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Affiliation(s)
- Sarah Thorwall
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.
| | - Varun Trivedi
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA.
| | - Eva Ottum
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA 92521, USA; Center for Industrial Biotechnology, University of California, Riverside, CA 92521, USA; Integrative Institute for Genome Biology, University of California, Riverside, CA 92521, USA.
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20
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Ramesh A, Trivedi V, Lee S, Tafrishi A, Schwartz C, Mohseni A, Li M, Lonardi S, Wheeldon I. acCRISPR: an activity-correction method for improving the accuracy of CRISPR screens. Commun Biol 2023; 6:617. [PMID: 37291233 PMCID: PMC10250353 DOI: 10.1038/s42003-023-04996-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
High throughput CRISPR screens are revolutionizing the way scientists unravel the genetic underpinnings of engineered and evolved phenotypes. One of the critical challenges in accurately assessing screening outcomes is accounting for the variability in sgRNA cutting efficiency. Poorly active guides targeting genes essential to screening conditions obscure the growth defects that are expected from disrupting them. Here, we develop acCRISPR, an end-to-end pipeline that identifies essential genes in pooled CRISPR screens using sgRNA read counts obtained from next-generation sequencing. acCRISPR uses experimentally determined cutting efficiencies for each guide in the library to provide an activity correction to the screening outcomes via calculation of an optimization metric, thus determining the fitness effect of disrupted genes. CRISPR-Cas9 and -Cas12a screens were carried out in the non-conventional oleaginous yeast Yarrowia lipolytica and acCRISPR was used to determine a high-confidence set of essential genes for growth under glucose, a common carbon source used for the industrial production of oleochemicals. acCRISPR was also used in screens quantifying relative cellular fitness under high salt conditions to identify genes that were related to salt tolerance. Collectively, this work presents an experimental-computational framework for CRISPR-based functional genomics studies that may be expanded to other non-conventional organisms of interest.
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Affiliation(s)
- Adithya Ramesh
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Varun Trivedi
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Sangcheon Lee
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Aida Tafrishi
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Cory Schwartz
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
- iBio Inc., San Diego, CA, USA
| | - Amirsadra Mohseni
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
| | - Mengwan Li
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, 92521, USA
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Ian Wheeldon
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA.
- Integrative Institute for Genome Biology, University of California, Riverside, CA, 92521, USA.
- Center for Industrial Biotechnology, University of California, Riverside, CA, 92521, USA.
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Kim SJ, Oh MK. Minicell-forming Escherichia coli mutant with increased chemical production capacity and tolerance to toxic compounds. BIORESOURCE TECHNOLOGY 2023; 371:128586. [PMID: 36621693 DOI: 10.1016/j.biortech.2023.128586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
Minicell, a small spherical form of bacterium produced by abnormal fission, possesses cytoplasmic constituents similar to those of the parental cell, except for genomic DNA. E. coli strains were engineered to produce minicells and value-added chemicals. Minicell-forming mutants showed enhanced tolerance to toxic chemicals and a higher intracellular NADH/NAD+ ratio than the wild-type. When toxic chemicals such as isobutanol, isobutyraldehyde, and isobutyl acetate were produced in this mutant, the titers increased by 67 %, 175 %, and 214 %, respectively. In addition, morphological changes and membrane dispersion mechanisms in minicell-forming mutants improved lycopene production by 259 %. This increase in production capacity was more pronounced when biomass hydrolysate was used as the substrate. Isobutanol and lycopene production also increased by 92 % and 295 %, respectively, on using the substrate in the mutant. It suggests that minicell-forming mutants are an excellent platform for biochemical production.
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Affiliation(s)
- Seung-Jin Kim
- Department of Chemical and Biological Engineering, Korea University, Seongbuk-gu, Seoul 02841, South Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seongbuk-gu, Seoul 02841, South Korea.
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22
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Laboratory evolution reveals general and specific tolerance mechanisms for commodity chemicals. Metab Eng 2023; 76:179-192. [PMID: 36738854 DOI: 10.1016/j.ymben.2023.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/06/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Although strain tolerance to high product concentrations is a barrier to the economically viable biomanufacturing of industrial chemicals, chemical tolerance mechanisms are often unknown. To reveal tolerance mechanisms, an automated platform was utilized to evolve Escherichia coli to grow optimally in the presence of 11 industrial chemicals (1,2-propanediol, 2,3-butanediol, glutarate, adipate, putrescine, hexamethylenediamine, butanol, isobutyrate, coumarate, octanoate, hexanoate), reaching tolerance at concentrations 60%-400% higher than initial toxic levels. Sequencing genomes of 223 isolates from 89 populations, reverse engineering, and cross-compound tolerance profiling were employed to uncover tolerance mechanisms. We show that: 1) cells are tolerized via frequent mutation of membrane transporters or cell wall-associated proteins (e.g., ProV, KgtP, SapB, NagA, NagC, MreB), transcription and translation machineries (e.g., RpoA, RpoB, RpoC, RpsA, RpsG, NusA, Rho), stress signaling proteins (e.g., RelA, SspA, SpoT, YobF), and for certain chemicals, regulators and enzymes in metabolism (e.g., MetJ, NadR, GudD, PurT); 2) osmotic stress plays a significant role in tolerance when chemical concentrations exceed a general threshold and mutated genes frequently overlap with those enabling chemical tolerance in membrane transporters and cell wall-associated proteins; 3) tolerization to a specific chemical generally improves tolerance to structurally similar compounds whereas a tradeoff can occur on dissimilar chemicals, and 4) using pre-tolerized starting isolates can hugely enhance the subsequent production of chemicals when a production pathway is inserted in many, but not all, evolved tolerized host strains, underpinning the need for evolving multiple parallel populations. Taken as a whole, this study provides a comprehensive genotype-phenotype map based on identified mutations and growth phenotypes for 223 chemical tolerant isolates.
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23
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Singh B, Kumar A, Saini AK, Saini RV, Thakur R, Mohammed SA, Tuli HS, Gupta VK, Areeshi MY, Faidah H, Jalal NA, Haque S. Strengthening microbial cell factories for efficient production of bioactive molecules. Biotechnol Genet Eng Rev 2023:1-34. [PMID: 36809927 DOI: 10.1080/02648725.2023.2177039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 01/21/2023] [Indexed: 02/24/2023]
Abstract
High demand of bioactive molecules (food additives, antibiotics, plant growth enhancers, cosmetics, pigments and other commercial products) is the prime need for the betterment of human life where the applicability of the synthetic chemical product is on the saturation due to associated toxicity and ornamentations. It has been noticed that the discovery and productivity of such molecules in natural scenarios are limited due to low cellular yields as well as less optimized conventional methods. In this respect, microbial cell factories timely fulfilling the requirement of synthesizing bioactive molecules by improving production yield and screening more promising structural homologues of the native molecule. Where the robustness of the microbial host can be potentially achieved by taking advantage of cell engineering approaches such as tuning functional and adjustable factors, metabolic balancing, adapting cellular transcription machinery, applying high throughput OMICs tools, stability of genotype/phenotype, organelle optimizations, genome editing (CRISPER/Cas mediated system) and also by developing accurate model systems via machine-learning tools. In this article, we provide an overview from traditional to recent trends and the application of newly developed technologies, for strengthening the systemic approaches and providing future directions for enhancing the robustness of microbial cell factories to speed up the production of biomolecules for commercial purposes.
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Affiliation(s)
- Bharat Singh
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Ankit Kumar
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gurugram, India
| | - Adesh Kumar Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Reena Vohra Saini
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Rahul Thakur
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Shakeel A Mohammed
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Hardeep Singh Tuli
- Department of Biotechnology and Central Research Cell, MMEC, Maharishi Markandeshwar (Deemed to be University), Mullana-Ambala, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Mohammed Y Areeshi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
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Advances in the Application of the Non-Conventional Yeast Pichia kudriavzevii in Food and Biotechnology Industries. J Fungi (Basel) 2023; 9:jof9020170. [PMID: 36836285 PMCID: PMC9961021 DOI: 10.3390/jof9020170] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Pichia kudriavzevii is an emerging non-conventional yeast which has attracted increased attention for its application in food and biotechnology areas. It is widespread in various habitats and often occurs in the spontaneous fermentation process of traditional fermented foods and beverages. The contributions of P. kudriavzevii in degrading organic acid, releasing various hydrolase and flavor compounds, and displaying probiotic properties make it a promising starter culture in the food and feed industry. Moreover, its inherent characteristics, including high tolerance to extreme pH, high temperature, hyperosmotic stress and fermentation inhibitors, allow it the potential to address technical challenges in industrial applications. With the development of advanced genetic engineering tools and system biology techniques, P. kudriavzevii is becoming one of the most promising non-conventional yeasts. This paper systematically reviews the recent progress in the application of P. kudriavzevii to food fermentation, the feed industry, chemical biosynthesis, biocontrol and environmental engineering. In addition, safety issues and current challenges to its use are discussed.
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25
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Weihmann R, Kubicki S, Bitzenhofer NL, Domröse A, Bator I, Kirschen LM, Kofler F, Funk A, Tiso T, Blank LM, Jaeger KE, Drepper T, Thies S, Loeschcke A. The modular pYT vector series employed for chromosomal gene integration and expression to produce carbazoles and glycolipids in P. putida. FEMS MICROBES 2022; 4:xtac030. [PMID: 37333445 PMCID: PMC10117823 DOI: 10.1093/femsmc/xtac030] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 11/03/2022] [Accepted: 12/16/2022] [Indexed: 10/22/2023] Open
Abstract
The expression of biosynthetic genes in bacterial hosts can enable access to high-value compounds, for which appropriate molecular genetic tools are essential. Therefore, we developed a toolbox of modular vectors, which facilitate chromosomal gene integration and expression in Pseudomonas putida KT2440. To this end, we designed an integrative sequence, allowing customisation regarding the modes of integration (random, at attTn7, or into the 16S rRNA gene), promoters, antibiotic resistance markers as well as fluorescent proteins and enzymes as transcription reporters. We thus established a toolbox of vectors carrying integrative sequences, designated as pYT series, of which we present 27 ready-to-use variants along with a set of strains equipped with unique 'landing pads' for directing a pYT interposon into one specific copy of the 16S rRNA gene. We used genes of the well-described violacein biosynthesis as reporter to showcase random Tn5-based chromosomal integration leading to constitutive expression and production of violacein and deoxyviolacein. Deoxyviolacein was likewise produced after gene integration into the 16S rRNA gene of rrn operons. Integration in the attTn7 site was used to characterise the suitability of different inducible promoters and successive strain development for the metabolically challenging production of mono-rhamnolipids. Finally, to establish arcyriaflavin A production in P. putida for the first time, we compared different integration and expression modes, revealing integration at attTn7 and expression with NagR/PnagAa to be most suitable. In summary, the new toolbox can be utilised for the rapid generation of various types of P. putida expression and production strains.
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Affiliation(s)
- Robin Weihmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Sonja Kubicki
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Nora Lisa Bitzenhofer
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Andreas Domröse
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Isabel Bator
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Lisa-Marie Kirschen
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Franziska Kofler
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Aileen Funk
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Till Tiso
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Lars M Blank
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
- Institute of Bio-and Geosciences IBG 1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf at Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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Prospects of thermotolerant Kluyveromyces marxianus for high solids ethanol fermentation of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:134. [PMID: 36474296 PMCID: PMC9724321 DOI: 10.1186/s13068-022-02232-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/20/2022] [Indexed: 12/12/2022]
Abstract
Simultaneous saccharification and fermentation (SSF) is effective for minimizing sugar inhibition during high solids fermentation of biomass solids to ethanol. However, fungal enzymes used during SSF are optimal between 50 and 60 °C, whereas most fermentative yeast, such as Saccharomyces cerevisiae, do not tolerate temperatures above 37 °C. Kluyveromyces marxianus variant CBS 6556 is a thermotolerant eukaryote that thrives at 43 °C, thus potentially serving as a promising new host for SSF operation in biorefineries. Here, we attempt to leverage the thermotolerance of the strain to demonstrate the application of CBS 6556 in a high solids (up to 20 wt% insoluble solid loading) SSF configuration to understand its capabilities and limitations as compared to a proven SSF strain, S. cerevisiae D5A. For this study, we first pretreated hardwood poplar chips using Co-Solvent Enhanced Lignocellulosic Fractionation (CELF) to remove lignin and hemicellulose and to produce cellulose-enriched pretreated solids for SSF. Our results demonstrate that although CBS 6556 could not directly outperform D5A, it demonstrated similar tolerance to high gravity sugar solutions, superior growth rates at higher temperatures and higher early stage ethanol productivity. We discovered that CBS 6556's membrane was particularly sensitive to higher ethanol concentrations causing it to suffer earlier fermentation arrest than D5A. Cross-examination of metabolite data between CBS 6556 and D5A and cell surface imaging suggests that the combined stresses of high ethanol concentrations and temperature to CBS 6556's cell membrane was a primary factor limiting its ethanol productivity. Hence, we believe K. marxianus to be an excellent host for future genetic engineering efforts to improve membrane robustness especially at high temperatures in order to achieve higher ethanol productivity and titers, serving as a viable alternative to D5A.
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Biological production of xylitol by using nonconventional microbial strains. World J Microbiol Biotechnol 2022; 38:249. [DOI: 10.1007/s11274-022-03437-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/07/2022] [Indexed: 10/31/2022]
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28
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Lee JA, Kim HU, Na JG, Ko YS, Cho JS, Lee SY. Factors affecting the competitiveness of bacterial fermentation. Trends Biotechnol 2022; 41:798-816. [PMID: 36357213 DOI: 10.1016/j.tibtech.2022.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/05/2022] [Accepted: 10/12/2022] [Indexed: 11/09/2022]
Abstract
Sustainable production of chemicals and materials from renewable non-food biomass using biorefineries has become increasingly important in an effort toward the vision of 'net zero carbon' that has recently been pledged by countries around the world. Systems metabolic engineering has allowed the efficient development of microbial strains overproducing an increasing number of chemicals and materials, some of which have been translated to industrial-scale production. Fermentation is one of the key processes determining the overall economics of bioprocesses, but has recently been attracting less research attention. In this Review, we revisit and discuss factors affecting the competitiveness of bacterial fermentation in connection to strain development by systems metabolic engineering. Future perspectives for developing efficient fermentation processes are also discussed.
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Affiliation(s)
- Jong An Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Hyun Uk Kim
- Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea; Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, KAIST, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea
| | - Jeong-Geol Na
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul 04107, Republic of Korea
| | - Yoo-Sung Ko
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Jae Sung Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea.
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Wang XL, Zhou JJ, Liu S, Sun YQ, Xiu ZL. In situ carbon dioxide capture to co-produce 1,3-propanediol, biohydrogen and micro-nano calcium carbonate from crude glycerol by Clostridium butyricum. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:91. [PMID: 36057610 PMCID: PMC9440576 DOI: 10.1186/s13068-022-02190-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 08/26/2022] [Indexed: 11/30/2022]
Abstract
Background Climate change caused by greenhouse gas emission has become a global hot topic. Although biotechnology is considered as an environmentally friendly method to produce chemicals, almost all biochemicals face carbon dioxide emission from inevitable respiration and energy metabolism of most microorganisms. To cater for the broad prospect of biochemicals, bioprocess optimization of diverse valuable products is becoming increasingly important for environmental sustainability and cleaner production. Based on Ca(OH)2 as a CO2 capture agent and pH regulator, a bioprocess was proposed for co-production of 1,3-propanediol (1,3-PDO), biohydrogen and micro-nano CaCO3 by Clostridium butyricum DL07. Results In fed-batch fermentation, the maximum concentration of 1,3-PDO reached up to 88.6 g/L with an overall productivity of 5.54 g/L/h. This productivity is 31.9% higher than the highest value previously reports (4.20 g/L/h). In addition, the ratio of H2 to CO2 in exhaust gas showed a remarkable 152-fold increase in the 5 M Ca(OH)2 group compared to 5 M NaOH as the CO2 capture agent. Green hydrogen in exhaust gas ranged between 17.2% and 20.2%, with the remainder being N2 with negligible CO2 emissions. During CO2 capture in situ, micro-nano calcite particles of CaCO3 with sizes in the range of 300 nm to 20 µm were formed simultaneously. Moreover, when compared with 5M NaOH group, the concentrations of soluble salts and proteins in the fermentation broth of 5 M Ca(OH)2 group were notably reduced by 53.6% and 44.1%, respectively. The remarkable reduction of soluble salts and proteins would contribute to the separation of 1,3-PDO. Conclusions Ca(OH)2 was used as a CO2 capture agent and pH regulator in this study to promote the production of 1,3-PDO. Meanwhile, micro-nano CaCO3 and green H2 were co-produced. In addition, the soluble salts and proteins in the fermentation broth were significantly reduced. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02190-2.
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Liu X, Wang Z, Xiao J, Zhou X, Xu Y. Osmotic stress tolerance and transcriptome analysis of Gluconobacter oxydans to extra-high titers of glucose. Front Microbiol 2022; 13:977024. [PMID: 36033857 PMCID: PMC9412170 DOI: 10.3389/fmicb.2022.977024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Gluconobacter oxydans has been widely acknowledged as an ideal strain for industrial bio-oxidations with fantastic yield and productivity. Even 600 g/L xylose can be catalyzed efficiently in a sealed and compressed oxygen-supplying bioreactor. Therefore, the present study seeks to explore the osmotic stress tolerance against extra-high titer of representative lignocellulosic sugars like glucose. Gluconobacter oxydans can well adapted and fermented with initial 600 g/L glucose, exhibiting the highest bio-tolerance in prokaryotic strains and the comparability to the eukaryotic strain of Saccharomyces cerevisiae. 1,432 differentially expressed genes corresponding to osmotic pressure are detected through transcriptome analysis, involving several genes related to the probable compatible solutes (trehalose and arginine). Gluconobacter oxydans obtains more energy by enhancing the substrate-level phosphorylation, resulting in the increased glucose consumption rate after fermentation adaption phase. This study will provide insights into further investigation of biological tolerance and response to extra-high titers of glucose of G. oxydans.
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Affiliation(s)
- Xinlu Liu
- Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
- Jiangsu Province Key Laboratory of Green Biomass-based Fuels and Chemicals, Nanjing, China
| | - Zhiwei Wang
- Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
- Jiangsu Province Key Laboratory of Green Biomass-based Fuels and Chemicals, Nanjing, China
| | - Jianjian Xiao
- Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
- Jiangsu Province Key Laboratory of Green Biomass-based Fuels and Chemicals, Nanjing, China
| | - Xin Zhou
- Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
- Jiangsu Province Key Laboratory of Green Biomass-based Fuels and Chemicals, Nanjing, China
| | - Yong Xu
- Key Laboratory of Forestry Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
- Jiangsu Province Key Laboratory of Green Biomass-based Fuels and Chemicals, Nanjing, China
- *Correspondence: Yong Xu,
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Escherichia coli minicells with targeted enzymes as bioreactors for producing toxic compounds. Metab Eng 2022; 73:214-224. [PMID: 35970507 DOI: 10.1016/j.ymben.2022.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/05/2022] [Accepted: 08/06/2022] [Indexed: 11/20/2022]
Abstract
Formed by aberrant cell division, minicells possess functional metabolism despite their inability to grow and divide. Minicells exhibit not only superior stability when compared with bacterial cells but also exceptional tolerance-characteristics that are essential for a de novo bioreactor platform. Accordingly, we engineered minicells to accumulate protein, ensuring sufficient production capability. When tested with chemicals regarded as toxic against cells, the engineered minicells produced titers of C6-C10 alcohols and esters, far surpassing the corresponding production from bacterial cells. Additionally, microbial autoinducer production that is limited in expanding bacterial population was conducted in the minicells. Because bacterial population growth was nonexistent, the minicells produced autoinducers in constant amounts, which allowed precise control of the bacterial population having autoinducer-responsive gene circuits. When bacterial population growth was nonexistent, the minicells produced autoinducers in constant amounts, which allowed precise control of the bacterial population having autoinducer-based gene circuits with the minicells. This study demonstrates the potential of minicells as bioreactors suitable for products with known limitations in microbial production, thus providing new possibilities for bioreactor engineering.
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32
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Response and regulatory mechanisms of heat resistance in pathogenic fungi. Appl Microbiol Biotechnol 2022; 106:5415-5431. [PMID: 35941254 PMCID: PMC9360699 DOI: 10.1007/s00253-022-12119-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Abstract Both the increasing environmental temperature in nature and the defensive body temperature response to pathogenic fungi during mammalian infection cause heat stress during the fungal existence, reproduction, and pathogenic infection. To adapt and respond to the changing environment, fungi initiate a series of actions through a perfect thermal response system, conservative signaling pathways, corresponding transcriptional regulatory system, corresponding physiological and biochemical processes, and phenotypic changes. However, until now, accurate response and regulatory mechanisms have remained a challenge. Additionally, at present, the latest research progress on the heat resistance mechanism of pathogenic fungi has not been summarized. In this review, recent research investigating temperature sensing, transcriptional regulation, and physiological, biochemical, and morphological responses of fungi in response to heat stress is discussed. Moreover, the specificity thermal adaptation mechanism of pathogenic fungi in vivo is highlighted. These data will provide valuable knowledge to further understand the fungal heat adaptation and response mechanism, especially in pathogenic heat-resistant fungi. Key points • Mechanisms of fungal perception of heat pressure are reviewed. • The regulatory mechanism of fungal resistance to heat stress is discussed. • The thermal adaptation mechanism of pathogenic fungi in the human body is highlighted.
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Ribeiro RA, Bourbon-Melo N, Sá-Correia I. The cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts. Front Microbiol 2022; 13:953479. [PMID: 35966694 PMCID: PMC9366716 DOI: 10.3389/fmicb.2022.953479] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 07/11/2022] [Indexed: 01/18/2023] Open
Abstract
In industrial settings and processes, yeasts may face multiple adverse environmental conditions. These include exposure to non-optimal temperatures or pH, osmotic stress, and deleterious concentrations of diverse inhibitory compounds. These toxic chemicals may result from the desired accumulation of added-value bio-products, yeast metabolism, or be present or derive from the pre-treatment of feedstocks, as in lignocellulosic biomass hydrolysates. Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses, or on the microbiological stability and conservation of foods, beverages, and other goods. To sense, survive, and adapt to different stresses, yeasts rely on a network of signaling pathways to modulate the global transcriptional response and elicit coordinated changes in the cell. These pathways cooperate and tightly regulate the composition, organization and biophysical properties of the cell wall. The intricacy of the underlying regulatory networks reflects the major role of the cell wall as the first line of defense against a wide range of environmental stresses. However, the involvement of cell wall in the adaptation and tolerance of yeasts to multiple stresses of biotechnological relevance has not received the deserved attention. This article provides an overview of the molecular mechanisms involved in fine-tuning cell wall physicochemical properties during the stress response of Saccharomyces cerevisiae and their implication in stress tolerance. The available information for non-conventional yeast species is also included. These non-Saccharomyces species have recently been on the focus of very active research to better explore or control their biotechnological potential envisaging the transition to a sustainable circular bioeconomy.
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Affiliation(s)
- Ricardo A. Ribeiro
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno Bourbon-Melo
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Isabel Sá-Correia
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
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34
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La YH, Lee KS, Kim TW, Song JY. A bacteria-based carbon sequestration and waste recycling system. Sci Rep 2022; 12:10236. [PMID: 35764782 PMCID: PMC9240062 DOI: 10.1038/s41598-022-14239-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/03/2022] [Indexed: 11/30/2022] Open
Abstract
Achieving carbon neutrality requires a variety of technological approaches. In the present study, we confirmed the applicability of a carbon cycle system in several industrial fields using sulphur-oxidising bacteria. This system produces a nitrogen fertiliser, which decreases carbon emissions by recycling H2S and NH3 pollutants discharged into the atmosphere or wastewater. It should be considered in industrial fields as a carbon reduction strategy.
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Affiliation(s)
- Yeon Hwa La
- Environmental R&D Center, Institute of Environmental Science & Technology, SK Innovation, 325 Expo-ro, Yuseong-gu, Daejeon, 305-712, South Korea.
| | - Ki-Sung Lee
- Environmental R&D Center, Institute of Environmental Science & Technology, SK Innovation, 325 Expo-ro, Yuseong-gu, Daejeon, 305-712, South Korea
| | - Tae-Wan Kim
- Environmental R&D Center, Institute of Environmental Science & Technology, SK Innovation, 325 Expo-ro, Yuseong-gu, Daejeon, 305-712, South Korea
| | - Jae Yang Song
- Environmental R&D Center, Institute of Environmental Science & Technology, SK Innovation, 325 Expo-ro, Yuseong-gu, Daejeon, 305-712, South Korea
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35
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Li D, Liu L, Qin Z, Yu S, Zhou J. Combined evolutionary and metabolic engineering improve 2-keto-L-gulonic acid production in Gluconobacter oxydans WSH-004. BIORESOURCE TECHNOLOGY 2022; 354:127107. [PMID: 35381333 DOI: 10.1016/j.biortech.2022.127107] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 06/14/2023]
Abstract
The direct fermentation of the precursor of vitamin C, 2-keto-L-gulonic acid (2-KLG), has been a long-pursued goal. Previously, a strain of Gluconobacter oxydans WSH-004 was isolated that produced 2.5 g/L 2-KLG, and through adaptive evolution engineering, the strain G. oxydans MMC3 could tolerate 300 g/L D-sorbitol. This study verified that the sndh-sdh gene cluster encoded two key dehydrogenases for the 2-KLG biosynthesis pathway in this strain. Then G. oxydans MMC3 further evolved through adaptive evolution to G. oxydans 2-KLG5, which can tolerate high concentrations of D-sorbitol and 2-KLG. Finally, by increasing the gene expression levels of the sndh-sdh and terminal oxidase cyoBACD in G. oxydans 2-KLG5, the 2-KLG accumulation in the 5-L fermenter increased to 45.14 g/L by batch fermentation. The results showed that combined evolutionary and metabolic engineering efficiently improved the direct production of 2-KLG from D-sorbitol in G. oxydans.
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Affiliation(s)
- Dong Li
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Li Liu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Zhijie Qin
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Shiqin Yu
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China.
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36
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Rodriguez-Ocasio E, Khalid A, Truka CJ, Blenner MA, Jarboe LR. Survey of non-conventional yeasts for lipid and hydrocarbon biotechnology. J Ind Microbiol Biotechnol 2022; 49:6554550. [PMID: 35348703 PMCID: PMC9338885 DOI: 10.1093/jimb/kuac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/14/2022] [Indexed: 11/29/2022]
Abstract
Nonconventional yeasts have an untapped potential to expand biotechnology and enable process development necessary for a circular economy. They are especially convenient for the field of lipid and hydrocarbon biotechnology because they offer faster growth than plants and easier scalability than microalgae and exhibit increased tolerance relative to some bacteria. The ability of industrial organisms to import and metabolically transform lipids and hydrocarbons is crucial in such applications. Here, we assessed the ability of 14 yeasts to utilize 18 model lipids and hydrocarbons from six functional groups and three carbon chain lengths. The studied strains covered 12 genera from nine families. Nine nonconventional yeasts performed better than Saccharomyces cerevisiae, the most common industrial yeast. Rhodotorula toruloides, Candida maltosa, Scheffersomyces stipitis, and Yarrowia lipolytica were observed to grow significantly better and on more types of lipids and lipid molecules than other strains. They were all able to utilize mid- to long-chain fatty acids, fatty alcohols, alkanes, alkenes, and dicarboxylic acids, including 28 previously unreported substrates across the four yeasts. Interestingly, a phylogenetic analysis showed a short evolutionary distance between the R. toruloides, C. maltosa, and S. stipitis, even though R. toruloides is classified under a different phylum. This work provides valuable insight into the lipid substrate range of nonconventional yeasts that can inform species selection decisions and viability of lipid feedstocks.
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Affiliation(s)
- Efrain Rodriguez-Ocasio
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Ammara Khalid
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Charles J Truka
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
- Griswold Undergraduate Internship Program, Ames, IA, 50011, USA
| | - Mark A Blenner
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE, 19716, USA
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
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37
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Huang C, Wang C, Luo Y. Research progress of pathway and genome evolution in microbes. Synth Syst Biotechnol 2022; 7:648-656. [PMID: 35224232 PMCID: PMC8857405 DOI: 10.1016/j.synbio.2022.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/23/2021] [Accepted: 01/06/2022] [Indexed: 12/16/2022] Open
Abstract
Microbes can produce valuable natural products widely applied in medicine, food and other important fields. Nevertheless, it is usually challenging to achieve ideal industrial yields due to low production rate and poor toxicity tolerance. Evolution is a constant mutation and adaptation process used to improve strain performance. Generally speaking, the synthesis of natural products in microbes is often intricate, involving multiple enzymes or multiple pathways. Individual evolution of a certain enzyme often fails to achieve the desired results, and may lead to new rate-limiting nodes that affect the growth of microbes. Therefore, it is inevitable to evolve the biosynthetic pathways or the whole genome. Here, we reviewed the pathway-level evolution including multi-enzyme evolution, regulatory elements engineering, and computer-aided engineering, as well as the genome-level evolution based on several tools, such as genome shuffling and CRISPR/Cas systems. Finally, we also discussed the major challenges faced by in vivo evolution strategies and proposed some potential solutions.
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Affiliation(s)
- Chaoqun Huang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Chang Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
| | - Yunzi Luo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China
- Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen, 518071, China
- Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
- Corresponding author. Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
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38
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Jayakody LN, Chinmoy B, Turner TL. Trends in valorization of highly-toxic lignocellulosic biomass derived-compounds via engineered microbes. BIORESOURCE TECHNOLOGY 2022; 346:126614. [PMID: 34954359 DOI: 10.1016/j.biortech.2021.126614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 05/26/2023]
Abstract
Lignocellulosic biomass-derived fuels, chemicals, and materials are promising sustainable solutions to replace the current petroleum-based production. The direct microbial conversion of thermos-chemically pretreated lignocellulosic biomass is hampered by the presence of highly toxic chemical compounds. Also, thermo-catalytic upgrading of lignocellulosic biomass generates wastewater that contains heterogeneous toxic chemicals, a mixture of unutilized carbon. Metabolic engineering efforts have primarily focused on the conversion of carbohydrates in lignocellulose biomass; substantial opportunities exist to harness value from toxic lignocellulose-derived toxic compounds. This article presents the comprehensive metabolic routes and tolerance mechanisms to develop robust synthetic microbial cell factories to valorize the highly toxic compounds to advanced-platform chemicals. The obtained platform chemicals can be used to manufacture high-value biopolymers and biomaterials via a hybrid biochemical approach for replacing petroleum-based incumbents. The proposed strategy enables a sustainable bio-based materials economy by microbial biofunneling of lignocellulosic biomass-derived toxic molecules, an untapped biogenic carbon.
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Affiliation(s)
- Lahiru N Jayakody
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA; Fermentation Science Institute, Southern Illinois University Carbondale, Carbondale, IL, USA.
| | - Baroi Chinmoy
- Illinois Sustainable Technology Center, University of Illinois Urbana Champaign, IL, USA
| | - Timothy L Turner
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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39
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Rin Kim S, Kim SJ, Kim SK, Seo SO, Park S, Shin J, Kim JS, Park BR, Jin YS, Chang PS, Park YC. Yeast metabolic engineering for carbon dioxide fixation and its application. BIORESOURCE TECHNOLOGY 2022; 346:126349. [PMID: 34800639 DOI: 10.1016/j.biortech.2021.126349] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/09/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
As numerous industrial bioprocesses rely on yeast fermentation, developing CO2-fixing yeast strains can be an attractive option toward sustainable industrial processes and carbon neutrality. Recent studies have shown that the expression of ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) in yeasts, such as Saccharomyces cerevisiae and Kluyveromyces marxianus, enables mixotrophic CO2 fixation and production of biofuels. Also, the expression of a synthetic Calvin-Benson-Bassham (CBB) cycle including RuBisCO in Pichia pastoris enables autotrophic growth on CO2. This review highlights recent advances in metabolic engineering strategies to enable CO2 fixation in yeasts. Also, we discuss the potentials of other natural and synthetic metabolic pathways independent of RuBisCO for developing CO2-fixing yeast strains capable of producing value-added biochemicals.
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Affiliation(s)
- Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sun-Ki Kim
- Department of Food Science and Technology, Chung-Ang University, Anseong, Gyeonggi 17546, Republic of Korea
| | - Seung-Oh Seo
- Department of Food Science and Nutrition, The Catholic University of Korea, Bucheon 14662, Republic of Korea
| | - Sujeong Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jamin Shin
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Bo-Ram Park
- Department of Agro-food Resources, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pahn-Shick Chang
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Cheol Park
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, Republic of Korea.
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40
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Microbial cell surface engineering for high-level synthesis of bio-products. Biotechnol Adv 2022; 55:107912. [PMID: 35041862 DOI: 10.1016/j.biotechadv.2022.107912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/28/2021] [Accepted: 01/09/2022] [Indexed: 02/08/2023]
Abstract
Microbial cell surface layers, which mainly include the cell membrane, cell wall, periplasmic space, outer membrane, capsules, S-layers, pili, and flagella, control material exchange between the cell and the extracellular environment, and have great impact on production titers and yields of various bio-products synthesized by microbes. Recent research work has made exciting achievements in metabolic engineering using microbial cell surface components as novel regulation targets without direct modifications of the metabolic pathways of the desired products. This review article will summarize the accomplishments obtained in this emerging field, and will describe various engineering strategies that have been adopted in bacteria and yeasts for the enhancement of mass transfer across the cell surface, improvement of protein expression and folding, modulation of cell size and shape, and re-direction of cellular resources, all of which contribute to the construction of more efficient microbial cell factories toward the synthesis of a variety of bio-products. The existing problems and possible future directions will also be discussed.
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41
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Strategies to increase tolerance and robustness of industrial microorganisms. Synth Syst Biotechnol 2022; 7:533-540. [PMID: 35024480 PMCID: PMC8718811 DOI: 10.1016/j.synbio.2021.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 01/06/2023] Open
Abstract
The development of a cost-competitive bioprocess requires that the cell factory converts the feedstock into the product of interest at high rates and yields. However, microbial cell factories are exposed to a variety of different stresses during the fermentation process. These stresses can be derived from feedstocks, metabolism, or industrial production processes, limiting production capacity and diminishing competitiveness. Improving stress tolerance and robustness allows for more efficient production and ultimately makes a process more economically viable. This review summarises general trends and updates the most recent developments in technologies to improve the stress tolerance of microorganisms. We first look at evolutionary, systems biology and computational methods as examples of non-rational approaches. Then we review the (semi-)rational approaches of membrane and transcription factor engineering for improving tolerance phenotypes. We further discuss challenges and perspectives associated with these different approaches.
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42
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Dekker WJC, Jürgens H, Ortiz-Merino RA, Mooiman C, van den Berg R, Kaljouw A, Mans R, Pronk JT. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6523363. [PMID: 35137036 PMCID: PMC8862043 DOI: 10.1093/femsyr/foac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/26/2022] [Accepted: 02/03/2022] [Indexed: 11/13/2022] Open
Abstract
While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha showed its minimum oxygen requirements to be an order of magnitude larger than those reported for the thermotolerant yeast Kluyveromyces marxianus. High oxygen requirements of O. parapolymorpha coincided with a near absence of glycerol, a key NADH/NAD+ redox-cofactor-balancing product in many other yeasts, in oxygen-limited cultures. Genome analysis indicated absence of orthologs of the Saccharomyces cerevisiae glycerol-3-phosphate-phosphatase genes GPP1 and GPP2. Co-feeding of acetoin, whose conversion to 2,3-butanediol enables reoxidation of cytosolic NADH, supported a 2.5-fold increase of the biomass concentration in oxygen-limited cultures. An O. parapolymorpha strain in which key genes involved in mitochondrial reoxidation of NADH were inactivated did produce glycerol, but transcriptome analysis did not reveal a clear candidate for a responsible phosphatase. Expression of S. cerevisiae GPD2, which encodes NAD+-dependent glycerol-3-phosphate dehydrogenase, and GPP1 supported increased glycerol production by oxygen-limited chemostat cultures of O. parapolymorpha. These results identify dependence on respiration for NADH reoxidation as a key contributor to unexpectedly high oxygen requirements of O. parapolymorpha.
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Affiliation(s)
- Wijbrand J C Dekker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Hannes Jürgens
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Remon van den Berg
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Astrid Kaljouw
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Corresponding author: Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands. Tel: +31 15 2783214; E-mail:
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43
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Ploessl D, Zhao Y, Cao M, Ghosh S, Lopez C, Sayadi M, Chudalayandi S, Severin A, Huang L, Gustafson M, Shao Z. A repackaged CRISPR platform increases homology-directed repair for yeast engineering. Nat Chem Biol 2022; 18:38-46. [PMID: 34711982 DOI: 10.1038/s41589-021-00893-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022]
Abstract
Inefficient homology-directed repair (HDR) constrains CRISPR-Cas9 genome editing in organisms that preferentially employ nonhomologous end joining (NHEJ) to fix DNA double-strand breaks (DSBs). Current strategies used to alleviate NHEJ proficiency involve NHEJ disruption. To confer precision editing without NHEJ disruption, we identified the shortcomings of the conventional CRISPR platforms and developed a CRISPR platform-lowered indel nuclease system enabling accurate repair (LINEAR)-which enhanced HDR rates (to 67-100%) compared to those in previous reports using conventional platforms in four NHEJ-proficient yeasts. With NHEJ preserved, we demonstrate its ability to survey genomic landscapes, identifying loci whose spatiotemporal genomic architectures yield favorable expression dynamics for heterologous pathways. We present a case study that deploys LINEAR precision editing and NHEJ-mediated random integration to rapidly engineer and optimize a microbial factory to produce (S)-norcoclaurine. Taken together, this work demonstrates how to leverage an antagonizing pair of DNA DSB repair pathways to expand the current collection of microbial factories.
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Affiliation(s)
- Deon Ploessl
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Yuxin Zhao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Saptarshi Ghosh
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Carmen Lopez
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.,Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA
| | - Maryam Sayadi
- The Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Siva Chudalayandi
- The Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Andrew Severin
- The Genome Informatics Facility, Iowa State University, Ames, IA, USA
| | - Lei Huang
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Marissa Gustafson
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA. .,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA. .,Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA. .,Bioeconomy Institute, Iowa State University, Ames, IA, USA. .,The Ames Laboratory, Ames, IA, USA. .,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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44
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Keasling J, Garcia Martin H, Lee TS, Mukhopadhyay A, Singer SW, Sundstrom E. Microbial production of advanced biofuels. Nat Rev Microbiol 2021; 19:701-715. [PMID: 34172951 DOI: 10.1038/s41579-021-00577-w] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Concerns over climate change have necessitated a rethinking of our transportation infrastructure. One possible alternative to carbon-polluting fossil fuels is biofuels produced by engineered microorganisms that use a renewable carbon source. Two biofuels, ethanol and biodiesel, have made inroads in displacing petroleum-based fuels, but their uptake has been limited by the amounts that can be used in conventional engines and by their cost. Advanced biofuels that mimic petroleum-based fuels are not limited by the amounts that can be used in existing transportation infrastructure but have had limited uptake due to costs. In this Review, we discuss engineering metabolic pathways to produce advanced biofuels, challenges with substrate and product toxicity with regard to host microorganisms and methods to engineer tolerance, and the use of functional genomics and machine learning approaches to produce advanced biofuels and prospects for reducing their costs.
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Affiliation(s)
- Jay Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA. .,Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Center for Biosustainability, Danish Technical University, Lyngby, Denmark. .,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
| | - Hector Garcia Martin
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,DOE Agile BioFoundry, Emeryville, CA, USA.,BCAM,Basque Center for Applied Mathematics, Bilbao, Spain.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eric Sundstrom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, USA
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45
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Chang D, Wang C, Ndayisenga F, Yu Z. Mutations in adaptively evolved Escherichia coli LGE2 facilitated the cost-effective upgrading of undetoxified bio-oil to bioethanol fuel. BIORESOUR BIOPROCESS 2021; 8:105. [PMID: 38650237 PMCID: PMC10991953 DOI: 10.1186/s40643-021-00459-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 10/11/2021] [Indexed: 11/10/2022] Open
Abstract
Levoglucosan is a promising sugar present in the lignocellulose pyrolysis bio-oil, which is a renewable and environment-friendly source for various value-added productions. Although many microbial catalysts have been engineered to produce biofuels and chemicals from levoglucosan, the demerits that these biocatalysts can only utilize pure levoglucosan while inhibited by the inhibitors co-existing with levoglucosan in the bio-oil have greatly limited the industrial-scale application of these biocatalysts in lignocellulose biorefinery. In this study, the previously engineered Escherichia coli LGE2 was evolved for enhanced inhibitor tolerance using long-term adaptive evolution under the stress of multiple inhibitors and finally, a stable mutant E. coli-H was obtained after ~ 374 generations' evolution. In the bio-oil media with an extremely acidic pH of 3.1, E. coli-H with high inhibitor tolerance exhibited remarkable levoglucosan consumption and ethanol production abilities comparable to the control, while the growth of the non-evolved strain was completely blocked even when the pH was adjusted to 7.0. Finally, 8.4 g/L ethanol was achieved by E. coli-H in the undetoxified bio-oil media with ~ 2.0% (w/v) levoglucosan, reaching 82% of the theoretical yield. Whole-genome re-sequencing to monitor the acquisition of mutations identified 4 new mutations within the globally regulatory genes rssB, yqhA, and basR, and the - 10 box of the putative promoter of yqhD-dgkA operon. Especially, yqhA was the first time to be revealed as a gene responsible for inhibitor tolerance. The mutations were all responsible for improved fitness, while basR mutation greatly contributed to the fitness improvement of E. coli-H. This study, for the first time, generated an inhibitor-tolerant levoglucosan-utilizing strain that could produce cost-effective bioethanol from the toxic bio-oil without detoxification process, and provided important experimental evidence and valuable genetic/proteinic information for the development of other robust microbial platforms involved in lignocellulose biorefining processes.
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Affiliation(s)
- Dongdong Chang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Cong Wang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
- RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing, 100085, People's Republic of China.
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46
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Kayastha S, Sagwan-Barkdoll L, Anterola A, Jayakody LN. Developing synthetic microbes to produce indirubin-derivatives. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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47
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Lopez C, Cao M, Yao Z, Shao Z. Revisiting the unique structure of autonomously replicating sequences in Yarrowia lipolytica and its role in pathway engineering. Appl Microbiol Biotechnol 2021; 105:5959-5972. [PMID: 34357429 DOI: 10.1007/s00253-021-11399-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 11/26/2022]
Abstract
Production of industrially relevant compounds in microbial cell factories can employ either genomes or plasmids as an expression platform. Selection of plasmids as pathway carriers is advantageous for rapid demonstration but poses a challenge of stability. Yarrowia lipolytica has attracted great attention in the past decade for the biosynthesis of chemicals related to fatty acids at titers attractive to industry, and many genetic tools have been developed to explore its oleaginous potential. Our recent studies on the autonomously replicating sequences (ARSs) of nonconventional yeasts revealed that the ARSs from Y. lipolytica showcase a unique structure that includes a previously unannotated sequence (spacer) linking the origin of replication (ORI) and the centromeric (CEN) element and plays a critical role in modulating plasmid behavior. Maintaining a native 645-bp spacer yielded a 2.2-fold increase in gene expression and 1.7-fold higher plasmid stability compared to a more universally employed minimized ARS. Testing the modularity of the ARS sub-elements indicated that plasmid stability exhibits a pronounced cargo dependency. Instability caused both plasmid loss and intramolecular rearrangements. Altogether, our work clarifies the appropriate application of various ARSs for the scientific community and sheds light on a previously unexplored DNA element as a potential target for engineering Y. lipolytica.
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Affiliation(s)
- Carmen Lopez
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011, USA
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA
| | - Mingfeng Cao
- Department of Chemical and Biological Engineering, University of Illinois, Urbana, IL, 60801, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA.
| | - Zhanyi Yao
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Zengyi Shao
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011, USA.
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA.
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA.
- The Ames Laboratory, Ames, IA, 50011, USA.
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48
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Montaño López J, Duran L, Avalos JL. Physiological limitations and opportunities in microbial metabolic engineering. Nat Rev Microbiol 2021; 20:35-48. [PMID: 34341566 DOI: 10.1038/s41579-021-00600-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2021] [Indexed: 11/10/2022]
Abstract
Metabolic engineering can have a pivotal role in increasing the environmental sustainability of the transportation and chemical manufacturing sectors. The field has already developed engineered microorganisms that are currently being used in industrial-scale processes. However, it is often challenging to achieve the titres, yields and productivities required for commercial viability. The efficiency of microbial chemical production is usually dependent on the physiological traits of the host organism, which may either impose limitations on engineered biosynthetic pathways or, conversely, boost their performance. In this Review, we discuss different aspects of microbial physiology that often create obstacles for metabolic engineering, and present solutions to overcome them. We also describe various instances in which natural or engineered physiological traits in host organisms have been harnessed to benefit engineered metabolic pathways for chemical production.
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Affiliation(s)
- José Montaño López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Lisset Duran
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - José L Avalos
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA. .,Department of Molecular Biology, Princeton University, Princeton, NJ, USA. .,Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, USA. .,Princeton Environmental Institute, Princeton University, Princeton, NJ, USA.
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49
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Towards robust Pseudomonas cell factories to harbour novel biosynthetic pathways. Essays Biochem 2021; 65:319-336. [PMID: 34223620 PMCID: PMC8314020 DOI: 10.1042/ebc20200173] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 05/01/2021] [Accepted: 05/24/2021] [Indexed: 02/07/2023]
Abstract
Biotechnological production in bacteria enables access to numerous valuable chemical compounds. Nowadays, advanced molecular genetic toolsets, enzyme engineering as well as the combinatorial use of biocatalysts, pathways, and circuits even bring new-to-nature compounds within reach. However, the associated substrates and biosynthetic products often cause severe chemical stress to the bacterial hosts. Species of the Pseudomonas clade thus represent especially valuable chassis as they are endowed with multiple stress response mechanisms, which allow them to cope with a variety of harmful chemicals. A built-in cell envelope stress response enables fast adaptations that sustain membrane integrity under adverse conditions. Further, effective export machineries can prevent intracellular accumulation of diverse harmful compounds. Finally, toxic chemicals such as reactive aldehydes can be eliminated by oxidation and stress-induced damage can be recovered. Exploiting and engineering these features will be essential to support an effective production of natural compounds and new chemicals. In this article, we therefore discuss major resistance strategies of Pseudomonads along with approaches pursued for their targeted exploitation and engineering in a biotechnological context. We further highlight strategies for the identification of yet unknown tolerance-associated genes and their utilisation for engineering next-generation chassis and finally discuss effective measures for pathway fine-tuning to establish stable cell factories for the effective production of natural compounds and novel biochemicals.
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50
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Dekker WJC, Ortiz-Merino RA, Kaljouw A, Battjes J, Wiering FW, Mooiman C, Torre PDL, Pronk JT. Engineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth. Metab Eng 2021; 67:347-364. [PMID: 34303845 DOI: 10.1016/j.ymben.2021.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae, these yeasts cannot grow in the absence of oxygen. Responses of K. marxianus and S. cerevisiae to different oxygen-limitation regimes were analyzed in chemostats. Genome and transcriptome analysis, physiological responses to sterol supplementation and sterol-uptake measurements identified absence of a functional sterol-uptake mechanism as a key factor underlying the oxygen requirement of K. marxianus. Heterologous expression of a squalene-tetrahymanol cyclase enabled oxygen-independent synthesis of the sterol surrogate tetrahymanol in K. marxianus. After a brief adaptation under oxygen-limited conditions, tetrahymanol-expressing K. marxianus strains grew anaerobically on glucose at temperatures of up to 45 °C. These results open up new directions in the development of thermotolerant yeast strains for anaerobic industrial applications.
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Affiliation(s)
- Wijbrand J C Dekker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Astrid Kaljouw
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Julius Battjes
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Frank W Wiering
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Pilar de la Torre
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands.
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