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Chander AM, de Melo Teixeira M, Singh NK, Williams MP, Parker CW, Leo P, Stajich JE, Torok T, Tighe S, Mason CE, Venkateswaran K. Genomic and morphological characterization of Knufia obscura isolated from the Mars 2020 spacecraft assembly facility. Sci Rep 2024; 14:12249. [PMID: 38806503 PMCID: PMC11133487 DOI: 10.1038/s41598-024-61115-1] [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: 09/21/2023] [Accepted: 05/02/2024] [Indexed: 05/30/2024] Open
Abstract
Members of the family Trichomeriaceae, belonging to the Chaetothyriales order and the Ascomycota phylum, are known for their capability to inhabit hostile environments characterized by extreme temperatures, oligotrophic conditions, drought, or presence of toxic compounds. The genus Knufia encompasses many polyextremophilic species. In this report, the genomic and morphological features of the strain FJI-L2-BK-P2 presented, which was isolated from the Mars 2020 mission spacecraft assembly facility located at the Jet Propulsion Laboratory in Pasadena, California. The identification is based on sequence alignment for marker genes, multi-locus sequence analysis, and whole genome sequence phylogeny. The morphological features were studied using a diverse range of microscopic techniques (bright field, phase contrast, differential interference contrast and scanning electron microscopy). The phylogenetic marker genes of the strain FJI-L2-BK-P2 exhibited highest similarities with type strain of Knufia obscura (CBS 148926T) that was isolated from the gas tank of a car in Italy. To validate the species identity, whole genomes of both strains (FJI-L2-BK-P2 and CBS 148926T) were sequenced, annotated, and strain FJI-L2-BK-P2 was confirmed as K. obscura. The morphological analysis and description of the genomic characteristics of K. obscura FJI-L2-BK-P2 may contribute to refining the taxonomy of Knufia species. Key morphological features are reported in this K. obscura strain, resembling microsclerotia and chlamydospore-like propagules. These features known to be characteristic features in black fungi which could potentially facilitate their adaptation to harsh environments.
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Affiliation(s)
- Atul Munish Chander
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Marcus de Melo Teixeira
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
- School of Medicine, University of Brasilia, Brasília, DF, Brazil
| | - Nitin K Singh
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Michael P Williams
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Ceth W Parker
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Patrick Leo
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of CA-Riverside, Riverside, CA, USA
| | - Tamas Torok
- Ecology Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Scott Tighe
- Vermont Integrative Genomics Lab, University of Vermont, Burlington, VT, USA
| | - Christopher E Mason
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, 1305 York Avenue, Room Y-13.15, New York, NY, 10021, USA.
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, M/S 89-2, 4800 Oak Grove Dr., Pasadena, CA, 91109, USA.
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Kayalvizhi R, Sanjana J, Jacob S, Kumar V. An Eclectic Review on Dicarboxylic Acid Production Through Yeast Cell Factories and Its Industrial Prominence. Curr Microbiol 2024; 81:147. [PMID: 38642080 DOI: 10.1007/s00284-024-03654-4] [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: 04/27/2023] [Accepted: 02/29/2024] [Indexed: 04/22/2024]
Abstract
Dicarboxylic acid (DCA) is a multifaceted chemical intermediate, recoursed to produce many industrially important products such as adhesives, plasticizers, lubricants, polymers, etc. To bypass the shortcomings of the chemical methods of synthesis of DCA and to reduce fossil fuel footprints, bio-based synthesis is gaining attention. In pursuit of an eco-friendly sustainable alternative method of DCA production, microbial cell factories, and renewable organic resources are gaining popularity. Among the plethora of microbial communities, yeast is being favored industrially compared to bacterial fermentation due to its hyperosmotic and low pH tolerance and flexibility for gene manipulations. By application of rapidly evolving genetic manipulation techniques, the bio-based DCA production could be made more precise and economical. To bridge the gap between supply and demand of DCA, many strategies are employed to improve the fermentation. This review briefly outlines the advancements in DCA production using yeast cell factories with the exemplification of strain improvement strategies.
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Affiliation(s)
- Ramalingam Kayalvizhi
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu Dist., Kattankulathur, Tamil Nadu, 603203, India
| | - Jayacumar Sanjana
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu Dist., Kattankulathur, Tamil Nadu, 603203, India
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Chengalpattu Dist., Kattankulathur, Tamil Nadu, 603203, India.
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK.
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Nwaefuna AE, Garcia-Aloy M, Loeto D, Ncube T, Gombert AK, Boekhout T, Alwasel S, Zhou N. Dung beetle-associated yeasts display multiple stress tolerance: a desirable trait of potential industrial strains. BMC Microbiol 2023; 23:309. [PMID: 37884896 PMCID: PMC10601127 DOI: 10.1186/s12866-023-03044-z] [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: 07/08/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Stress-tolerant yeasts are highly desirable for cost-effective bioprocessing. Several strategies have been documented to develop robust yeasts, such as genetic and metabolic engineering, artificial selection, and natural selection strategies, among others. However, the significant drawbacks of such techniques have motivated the exploration of naturally occurring stress-tolerant yeasts. We previously explored the biodiversity of non-conventional dung beetle-associated yeasts from extremophilic and pristine environments in Botswana (Nwaefuna AE et.al., Yeast, 2023). Here, we assessed their tolerance to industrially relevant stressors individually, such as elevated concentrations of osmolytes, organic acids, ethanol, and oxidizing agents, as well as elevated temperatures. RESULTS Our findings suggest that these dung beetle-associated yeasts tolerate various stresses comparable to those of the robust bioethanol yeast strain, Saccharomyces cerevisiae (Ethanol Red™). Fifty-six percent of the yeast isolates were tolerant of temperatures up to 42 °C, 12.4% of them could tolerate ethanol concentrations up to 9% (v/v), 43.2% of them were tolerant to formic acid concentrations up to 20 mM, 22.7% were tolerant to acetic acid concentrations up to 45 mM, 34.0% of them could tolerate hydrogen peroxide up to 7 mM, and 44.3% of the yeasts could tolerate osmotic stress up to 1.5 M. CONCLUSION The ability to tolerate multiple stresses is a desirable trait in the selection of novel production strains for diverse biotechnological applications, such as bioethanol production. Our study shows that the exploration of natural diversity in the search for stress-tolerant yeasts is an appealing approach for the development of robust yeasts.
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Affiliation(s)
- Anita Ejiro Nwaefuna
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
| | - Mar Garcia-Aloy
- Metabolomics Unit, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38098, San Michele All'Adige, Italy
| | - Daniel Loeto
- Department of Biological Sciences, University of Botswana, Private Bag, 0022, Gaborone, Botswana
| | - Thembekile Ncube
- Department of Applied Biology and Biochemistry, National University of Science and Technology, P.O. Box AC 939, Ascot, Bulawayo, Zimbabwe
| | - Andreas K Gombert
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, Campinas, SP, 13083-862, Brazil
| | - Teun Boekhout
- Department of Zoology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Saleh Alwasel
- Department of Zoology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana.
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4
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Ting WW, Ng IS. Tunable T7 Promoter Orthogonality on T7RNAP for cis-Aconitate Decarboxylase Evolution via Base Editor and Screening from Itaconic Acid Biosensor. ACS Synth Biol 2023; 12:3020-3029. [PMID: 37750409 PMCID: PMC10595973 DOI: 10.1021/acssynbio.3c00344] [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: 06/05/2023] [Indexed: 09/27/2023]
Abstract
The deaminase-fused T7 RNA polymerase (T7RNAP) presents a promising toolkit for in vivo target-specific enzyme evolution, offering the unique advantage of simultaneous DNA modification and screening. Previous studies have reported the mutation efficiency of base editors relying on different resources. In contrast, the mechanism underlying the T7RNAP/T7 system is well-understood. Therefore, this study aimed to establish a new platform, termed dT7-Muta, by tuning the binding efficiency between T7RNAP and the T7 promoter for gene mutagenesis. The strategy for proof-of-concept involves alterations in the fluorescence distribution through dT7-Muta and screening of the mutants via flow cytometry. The cis-aconitate decarboxylase from Aspergillus terreus (AtCadA) was evolved and screened via an itaconate-induced biosensor as proof-of-function of enzyme evolution. First, the degenerated codons were designed within the binding and initial region of T7 promoters (dT7s), including upstream (U), central (C), and downstream (D) regions. Three strength variants of dT7 promoter from each design, i.e., strong (S), medium (M), and weak (W), were used for evaluation. Mutation using dT7s of varying strength resulted in a broader fluorescence distribution in sfGFP mutants from the promoters CW and DS. On the other hand, broader fluorescence distribution was observed in the AtCadA mutants from the original promoter T7, UW, and DS, with the highest fluorescence and itaconic acid titer at 860 a.u. and 0.51 g/L, respectively. The present platform introduces a novel aspect of the deaminase-based mutagenesis, emphasizing the potential of altering the binding efficiency between T7RNAP and the T7 promoter for further efforts in enzyme evolution.
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Affiliation(s)
- Wan-Wen Ting
- Department of Chemical
Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - I-Son Ng
- Department of Chemical
Engineering, National Cheng Kung University, Tainan 70101, Taiwan
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Bagley JA, Pyne ME, Exley K, Kevvai K, Wang Q, Whiteway M, Martin VJJ. Genome sequencing of 15 acid-tolerant yeasts. Microbiol Resour Announc 2023; 12:e0033723. [PMID: 37747226 PMCID: PMC10586158 DOI: 10.1128/mra.00337-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/10/2023] [Indexed: 09/26/2023] Open
Abstract
We report draft genome sequences for 15 non-conventional Saccharomycotina yeast strains obtained from public culture repositories. Included in our collection are eight strains of Pichia with broad tolerance to dicarboxylic acids. The genome sequences of these strains will enable comparative genomics of acid-tolerant phenotypes and strain engineering of non-conventional hosts.
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Affiliation(s)
- James A. Bagley
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Michael E. Pyne
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Kealan Exley
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Kaspar Kevvai
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | | | - Malcolm Whiteway
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
| | - Vincent J. J. Martin
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
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6
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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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7
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Fatma Z, Tan SI, Boob AG, Zhao H. A landing pad system for multicopy gene integration in Issatchenkia orientalis. Metab Eng 2023; 78:200-208. [PMID: 37343658 DOI: 10.1016/j.ymben.2023.06.010] [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: 05/04/2023] [Revised: 06/18/2023] [Accepted: 06/18/2023] [Indexed: 06/23/2023]
Abstract
The robust nature of the non-conventional yeast Issatchenkia orientalis allows it to grow under highly acidic conditions and therefore, has gained increasing interest in producing organic acids using a variety of carbon sources. Recently, the development of a genetic toolbox for I. orientalis, including an episomal plasmid, characterization of multiple promoters and terminators, and CRISPR-Cas9 tools, has eased the metabolic engineering efforts in I. orientalis. However, multiplex engineering is still hampered by the lack of efficient multicopy integration tools. To facilitate the construction of large, complex metabolic pathways by multiplex CRISPR-Cas9-mediated genome editing, we developed a bioinformatics pipeline to identify and prioritize genome-wide intergenic loci and characterized 47 gRNAs located in 21 intergenic regions. These loci are screened for guide RNA cutting efficiency, integration efficiency of a gene cassette, the resulting cellular fitness, and GFP expression level. We further developed a landing pad system using components from these well-characterized loci, which can aid in the integration of multiple genes using single guide RNA and multiple repair templates of the user's choice. We have demonstrated the use of the landing pad for simultaneous integrations of 2, 3, 4, or 5 genes to the target loci with efficiencies greater than 80%. As a proof of concept, we showed how the production of 5-aminolevulinic acid can be improved by integrating five copies of genes at multiple sites in one step. We have further demonstrated the efficiency of this tool by constructing a metabolic pathway for succinic acid production by integrating five gene expression cassettes using a single guide RNA along with five different repair templates, leading to the production of 9 g/L of succinic acid in batch fermentations. This study demonstrates the effectiveness of a single gRNA-mediated CRISPR platform to build complex metabolic pathways in a non-conventional yeast. This landing pad system will be a valuable tool for the metabolic engineering of I. orientalis.
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Affiliation(s)
- Zia Fatma
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Aashutosh Girish Boob
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
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8
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Geng C, Jin Z, Gu M, Li J, Tang S, Guo Q, Zhang Y, Zhang W, Li Y, Huang X, Lu X. Microbial production of trans-aconitic acid. Metab Eng 2023; 78:183-191. [PMID: 37315711 DOI: 10.1016/j.ymben.2023.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 05/22/2023] [Accepted: 06/11/2023] [Indexed: 06/16/2023]
Abstract
Trans-aconitic acid (TAA) is a promising bio-based chemical with the structure of unsaturated tricarboxylic acid, and also has the potential to be a non-toxic nematicide as a potent inhibitor of aconitase. However, TAA has not been commercialized because the traditional production processes of plant extraction and chemical synthesis cannot achieve large-scale production at a low cost. The availability of TAA is a serious obstacle to its widespread application. In this study, we developed an efficient microbial synthesis and fermentation production process for TAA. An engineered Aspergillus terreus strain producing cis-aconitic acid and TAA was constructed by blocking itaconic acid biosynthesis in the industrial itaconic acid-producing strain. Through heterologous expression of exogenous aconitate isomerase, we further designed a more efficient cell factory to specifically produce TAA. Subsequently, the fermentation process was developed and scaled up step-by-step, achieving a TAA titer of 60 g L-1 at the demonstration scale of a 20 m3 fermenter. Finally, the field evaluation of the produced TAA for control of the root-knot nematodes was performed in a field trial, effectively reducing the damage of the root-knot nematode. Our work provides a commercially viable solution for the green manufacturing of TAA, which will significantly facilitate biopesticide development and promote its widespread application as a bio-based chemical.
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Affiliation(s)
- Ce Geng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
| | - Zhigang Jin
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China; Shandong Lukang Pharmaceutical Co. Ltd., Jining, 272021, Shandong, China
| | - Meng Gu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jibin Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Shen Tang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
| | - Qiang Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Yunpeng Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China
| | - Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, Shandong, China
| | - Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China; Shandong Energy Institute, Qingdao, 266101, Shandong, China; Qingdao New Energy Shandong Laboratory, Qingdao, 266101, Shandong, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, Shandong, China.
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9
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Diankristanti PA, Ng IS. Microbial itaconic acid bioproduction towards sustainable development: Insights, challenges, and prospects. BIORESOURCE TECHNOLOGY 2023:129280. [PMID: 37290713 DOI: 10.1016/j.biortech.2023.129280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/10/2023]
Abstract
Microbial biomanufacturing is a promising approach to produce high-value compounds with low-carbon footprint and significant economic benefits. Among twelve "Top Value-Added Chemicals from Biomass", itaconic acid (IA) stands out as a versatile platform chemical with numerous applications. IA is naturally produced by Aspergillus and Ustilago species through a cascade enzymatic reaction between aconitase (EC 4.2.1.3) and cis-aconitic acid decarboxylase (EC 4.1.1.6). Recently, non-native hosts such as Escherichia coli, Corynebacterium glutamicum, Saccharomyces cerevisiae, and Yarrowia lipolytica have been genetically engineered to produce IA through the introduction of key enzymes. This review provides an up-to-date summary of the progress made in IA bioproduction, from native to engineered hosts, covers in vivo and in vitro approaches, and highlights the prospects of combination tactics. Current challenges and recent endeavors are also addressed to envision comprehensive strategies for renewable IA production in the future towards sustainable development goals (SDGs).
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Affiliation(s)
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan.
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10
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Nwaefuna AE, Boekhout T, Garcia-Aloy M, Vrhovsek U, Zhou N. Diversity of dung beetle-associated yeasts from pristine environments of Botswana. Yeast 2023. [PMID: 37096317 DOI: 10.1002/yea.3852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 04/06/2023] [Accepted: 04/08/2023] [Indexed: 04/26/2023] Open
Abstract
Yeast-insect interactions are increasingly becoming an attractive source of discovery for previously unknown, unique, diverse, and industrially relevant yeast species. Despite a wealth of studies that have recently focused on yeasts in symbiotic association with Hymenopteran insects, yeasts associated with Coleopteran insects, such as lignocellulosic-rich dung-dependent beetles, remain poorly studied. Trends in yeast discovery suggest that species richness and diversity can be attributed to the ecological niche of the insect. Here, we considered the potential of dung beetles inhabiting the extreme environments of Botswana, characterized by desert-like conditions (semi-arid to arid and hot) as well as protected pristine environments, as possible attribute niches that can shape the extremophilic and diverse life history strategies of yeasts. We obtained a total of 97 phylogenetically diverse yeast isolates from six species of dung beetles from Botswana's unexplored environments, representing 19 species belonging to 11 genera. The findings suggest that the guts of dung beetles are a rich niche for non-Saccharomyces yeast species. Meyerozyma and Pichia were the most dominant genera associated with dung beetles, representing 55% (53 out of 97) of the yeast isolates in our study. Trichosporon and Cutaneotrichosporon genera represented 32% (31 out of 97) of the isolates. The remaining isolates belonged to Apiotrichum, Candida, Diutina, Naganishia, Rhodotorula, and Wickerhamiella genera (12 out of 97). We found out that about 62% (60 out of 97) of the isolates were potentially new species because of their low internal transcribed spacer (ITS) sequence similarity when compared to the most recent optimal species delineation threshold. A single isolate was unidentifiable using the ITS sequences. Using an in silico polymerase chain reaction-restriction fragment length polymorphism approach, we revealed that there was genetic diversity within isolates of the same species. Our results contribute to the knowledge and understanding of the diversity of dung beetle-associated yeasts.
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Affiliation(s)
- Anita E Nwaefuna
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
| | - Teun Boekhout
- Westerdijk Institute of Fungal Biodiversity, Utrecht, The Netherlands
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mar Garcia-Aloy
- Metabolomics Unit, Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Urska Vrhovsek
- Metabolomics Unit, Food Quality and Nutrition Department, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Palapye, Botswana
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11
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Lertsriwong S, Boonvitthya N, Glinwong C. Schwanniomyces etchellsii, acid-thermotolerant yeasts from urban city soil. World J Microbiol Biotechnol 2023; 39:159. [PMID: 37067620 DOI: 10.1007/s11274-023-03602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/02/2023] [Indexed: 04/18/2023]
Abstract
Acid-tolerant yeasts are one of the important keys to producing ethanol from acidic substrates, especially from molasses and agricultural waste. In this study, selected cultivars of yeasts isolated from a variety of locations such as botanical gardens in Thailand urban areas, which are often found highly polluted in the air such as carbon dioxide which is a cause of acid rain. There is limited information about how tolerant yeasts, are or their functional properties related to the environment. Yeast species were determined by using the 18S rDNA sequence guide. The level of acid tolerance was evaluated by adding to the culture medium lactic acid (300-900 mM), acetic acid (100-400 mM), and propionic acid (25-100 mM). 18S rDNA analysis has shown a %similarity of the nucleotide sequence higher than 98.65% compared to the database. Schwanniomyces etchellsii strains found in urban city soil were notable for their tolerance of lactic acid up to 100 mM. There are two main types of yeasts in overall acid tolerance: S. etchellsii, which is recognized as an osmotic pressure-resistant species that is highly resistant to fermentation inhibitors and produces ethanol; and Schizosaccharomyces pombe, which cell wall has been reported to be characterized by accumulation of α-(1,3)-glucan and malic acid can be used in metabolic pathways. The results show that S. pombe, isolated from rice paddy fields, can grow efficiently in acetic and propionic acid up to 400 mM and 100 mM, respectively. This species could be cultured in ethanol at a concentration of 12.5% (v/v). Moreover, it presented high ethanol and acetic acid production of 14.5-15.9 g/L and 7-10 g/L, respectively, with or without acidic conditions. In comparison, S. etchellsii, isolated from the botanical garden soil, which is grown in acetic, propionic, and lactic acid, was also indicated to be an organic acid-tolerant species.
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Affiliation(s)
- Supattra Lertsriwong
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Biofuels By Biocatalysts Research Unit, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Chompunuch Glinwong
- Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
- Biofuels By Biocatalysts Research Unit, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.
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12
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Wu ZY, Sun W, Shen Y, Pratas J, Suthers PF, Hsieh PH, Dwaraknath S, Rabinowitz JD, Maranas CD, Shao Z, Yoshikuni Y. Metabolic engineering of low-pH-tolerant non-model yeast, Issatchenkia orientalis, for production of citramalate. Metab Eng Commun 2023; 16:e00220. [PMID: 36860699 PMCID: PMC9969067 DOI: 10.1016/j.mec.2023.e00220] [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: 11/29/2022] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Methyl methacrylate (MMA) is an important petrochemical with many applications. However, its manufacture has a large environmental footprint. Combined biological and chemical synthesis (semisynthesis) may be a promising alternative to reduce both cost and environmental impact, but strains that can produce the MMA precursor (citramalate) at low pH are required. A non-conventional yeast, Issatchenkia orientalis, may prove ideal, as it can survive extremely low pH. Here, we demonstrate the engineering of I. orientalis for citramalate production. Using sequence similarity network analysis and subsequent DNA synthesis, we selected a more active citramalate synthase gene (cimA) variant for expression in I. orientalis. We then adapted a piggyBac transposon system for I. orientalis that allowed us to simultaneously explore the effects of different cimA gene copy numbers and integration locations. A batch fermentation showed the genome-integrated-cimA strains produced 2.0 g/L citramalate in 48 h and a yield of up to 7% mol citramalate/mol consumed glucose. These results demonstrate the potential of I. orientalis as a chassis for citramalate production.
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Affiliation(s)
- Zong-Yen Wu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Wan Sun
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011-1027, USA,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yihui Shen
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Jimmy Pratas
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Patrick F. Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA,Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Ping-Hung Hsieh
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Sudharsan Dwaraknath
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA,Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08540, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, 16802, USA,Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Zengyi Shao
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011-1027, USA,Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA,NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, 50011, USA,Bioeconomy Institute, Iowa State University, Ames, IA, 50011, USA,The Ames Laboratory, Ames, IA, 50011, USA,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA,Corresponding author. Interdepartmental Microbiology Program, Iowa State University, Ames, IA, 50011-1027, USA.
| | - Yasuo Yoshikuni
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA,Center for Advanced Bioenergy and Bioproducts Innovation, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA,Global Center for Food, Land, and Water Resources, Hokkaido University, Hokkaido, 060-8589, Japan,Corresponding author. Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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13
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Ploessl D, Zhao Y, Shao Z. Engineering of non-model eukaryotes for bioenergy and biochemical production. Curr Opin Biotechnol 2023; 79:102869. [PMID: 36584447 DOI: 10.1016/j.copbio.2022.102869] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/14/2022] [Accepted: 11/23/2022] [Indexed: 12/29/2022]
Abstract
The prospect of leveraging naturally occurring phenotypes to overcome bottlenecks constraining the bioeconomy has marshalled increased exploration of nonconventional organisms. This review discusses the status of non-model eukaryotic species in bioproduction, the evaluation criteria for effectively matching a candidate host to a biosynthetic process, and the genetic engineering tools needed for host domestication. We present breakthroughs in genome editing and heterologous pathway design, delving into innovative spatiotemporal modulation strategies that potentiate more refined engineering capabilities. We cover current understanding of genetic instability and its ramifications for industrial scale-up, highlighting key factors and possible remedies. Finally, we propose future opportunities to expand the current collection of available hosts and provide guidance to benefit the broader bioeconomy.
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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; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 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; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA; Bioeconomy Institute, Iowa State University, Ames, IA, USA; The Ames Laboratory, Ames, IA, USA.
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14
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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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15
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Recent Advances on the Production of Itaconic Acid via the Fermentation and Metabolic Engineering. FERMENTATION 2023. [DOI: 10.3390/fermentation9010071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Itaconic acid (ITA) is one of the top 12 platform chemicals. The global ITA market is expanding due to the rising demand for bio-based unsaturated polyester resin and its non-toxic qualities. Although bioconversion using microbes is the main approach in the current industrial production of ITA, ecological production of bio-based ITA faces several issues due to: low production efficiency, the difficulty to employ inexpensive raw materials, and high manufacturing costs. As metabolic engineering advances, the engineering of microorganisms offers a novel strategy for the promotion of ITA bio-production. In this review, the most recent developments in the production of ITA through fermentation and metabolic engineering are compiled from a variety of perspectives, including the identification of the ITA synthesis pathway, the metabolic engineering of natural ITA producers, the design and construction of the ITA synthesis pathway in model chassis, and the creation, as well as application, of new metabolic engineering strategies in ITA production. The challenges encountered in the bio-production of ITA in microbial cell factories are discussed, and some suggestions for future study are also proposed, which it is hoped offers insightful views to promote the cost-efficient and sustainable industrial production of ITA.
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16
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Itaconic acid production is regulated by LaeA in Aspergillus pseudoterreus. Metab Eng Commun 2022; 15:e00203. [PMID: 36065328 PMCID: PMC9440423 DOI: 10.1016/j.mec.2022.e00203] [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: 04/08/2022] [Revised: 07/08/2022] [Accepted: 08/15/2022] [Indexed: 11/22/2022] Open
Abstract
The global regulator LaeA controls secondary metabolism in diverse Aspergillus species. Here we explored its role in regulation of itaconic acid production in Aspergillus pseudoterreus. To understand its role in regulating metabolism, we deleted and overexpressed laeA, and assessed the transcriptome, proteome, and secreted metabolome prior to and during initiation of phosphate limitation induced itaconic acid production. We found that secondary metabolite clusters, including the itaconic acid biosynthetic gene cluster, are regulated by laeA and that laeA is required for high yield production of itaconic acid. Overexpression of LaeA improves itaconic acid yield at the expense of biomass by increasing the expression of key biosynthetic pathway enzymes and attenuating the expression of genes involved in phosphate acquisition and scavenging. Increased yield was observed in optimized conditions as well as conditions containing excess nutrients that may be present in inexpensive sugar containing feedstocks such as excess phosphate or complex nutrient sources. This suggests that global regulators of metabolism may be useful targets for engineering metabolic flux that is robust to environmental heterogeneity. The Itaconic acid biosynthetic gene cluster is regulated by laeA. LaeA is required for production of itaconic acid. Overexpression of laeA attenuates genes involved in phosphate acquisition. Global regulator engineering increases robustness of itaconic acid production.
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17
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Xie D. Continuous biomanufacturing with microbes - upstream progresses and challenges. Curr Opin Biotechnol 2022; 78:102793. [PMID: 36088736 DOI: 10.1016/j.copbio.2022.102793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/15/2022] [Accepted: 08/07/2022] [Indexed: 12/14/2022]
Abstract
Current biomanufacturing facilities are mainly built for batch or fed-batch operations, which are subject to low productivities and do not achieve the great bioconversion potential of the rewired cells generated via modern biotechnology. Continuous biomanufacturing should be the future directions for high-yield and low-cost manufacturing of various fermentation products. This review discusses the major challenges and the strategies for continuous biomanufacturing with microbes, which include minimizing contamination risk, enhancing genetic stability over a long-term continuous operation, achieving high product titer, rate, and yield simultaneously by decoupling cell growth from product formation, and using modeling approach to accelerate research and development of continuous biomanufacturing. New strain designs and process engineering strategies, including integration with artificial intelligence, are also discussed for intelligent and the next generation of continuous biomanufacturing.
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Affiliation(s)
- Dongming Xie
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, MA 01854, United States.
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18
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Ling X, Jie W, Qin X, Zhang S, Shi K, Li T, Guo J. Gut microbiome sheds light on the development and treatment of abdominal aortic aneurysm. Front Cardiovasc Med 2022; 9:1063683. [PMID: 36505348 PMCID: PMC9732037 DOI: 10.3389/fcvm.2022.1063683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/03/2022] [Indexed: 11/27/2022] Open
Abstract
Abdominal aortic aneurysm (AAA) is an inflammatory vascular disease with high disability and mortality. Its susceptible risk factors include old age, being male, smoking, hypertension, and aortic atherosclerosis. With the improvement of screening techniques, AAA incidence and number of deaths caused by aneurysm rupture increase annually, attracting much clinical attention. Due to the lack of non-invasive treatment, early detection and development of novel treatment of AAA is an urgent clinical concern. The pathophysiology and progression of AAA are characterized by inflammatory destruction. The gut microbiota is an "invisible organ" that directly or indirectly affects the vascular wall inflammatory cell infiltration manifested with enhanced arterial wall gut microbiota and metabolites, which plays an important role in the formation and progression of AAA. As such, the gut microbiome may become an important risk factor for AAA. This review summarizes the direct and indirect effects of the gut microbiome on the pathogenesis of AAA and highlights the gut microbiome-mediated inflammatory responses and discoveries of relevant therapeutic targets that may help manage the development and rupture of AAA.
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Affiliation(s)
- Xuebin Ling
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Department of Cardiovascular Medicine of the First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Wei Jie
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Department of Cardiovascular Medicine of the First Affiliated Hospital, Hainan Medical University, Haikou, China,Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou, China
| | - Xue Qin
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Department of Cardiovascular Medicine of the First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Shuya Zhang
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Department of Cardiovascular Medicine of the First Affiliated Hospital, Hainan Medical University, Haikou, China,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Kaijia Shi
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Department of Cardiovascular Medicine of the First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Tianfa Li
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Department of Cardiovascular Medicine of the First Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Junli Guo
- Key Laboratory of Tropical Cardiovascular Diseases Research of Hainan Province, Department of Cardiovascular Medicine of the First Affiliated Hospital, Hainan Medical University, Haikou, China,Key Laboratory of Emergency and Trauma of Ministry of Education, Hainan Medical University, Haikou, China,*Correspondence: Junli Guo
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19
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Nonconventional Yeasts Engineered Using the CRISPR-Cas System as Emerging Microbial Cell Factories. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8110656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Because the petroleum-based chemical synthesis of industrial products causes serious environmental and societal issues, biotechnological production using microorganisms is an alternative approach to achieve a more sustainable economy. In particular, the yeast Saccharomyces cerevisiae is widely used as a microbial cell factory to produce biofuels and valuable biomaterials. However, product profiles are often restricted due to the Crabtree-positive nature of S. cerevisiae, and ethanol production from lignocellulose is possibly enhanced by developing alternative stress-resistant microbial platforms. With desirable metabolic pathways and regulation in addition to strong resistance to diverse stress factors, nonconventional yeasts (NCY) may be considered an alternative microbial platform for industrial uses. Irrespective of their high industrial value, the lack of genetic information and useful gene editing tools makes it challenging to develop metabolic engineering-guided scaled-up applications using yeasts. The recently developed clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system is a powerful gene editing tool for NCYs. This review describes the current status of and recent advances in promising NCYs in terms of industrial and biotechnological applications, highlighting CRISPR-Cas9 system-based metabolic engineering strategies. This will serve as a basis for the development of novel yeast applications.
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20
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Lee YG, Kim C, Kuanyshev N, Kang NK, Fatma Z, Wu ZY, Cheng MH, Singh V, Yoshikuni Y, Zhao H, Jin YS. Cas9-Based Metabolic Engineering of Issatchenkia orientalis for Enhanced Utilization of Cellulosic Hydrolysates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12085-12094. [PMID: 36103687 DOI: 10.1021/acs.jafc.2c04251] [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] [Indexed: 06/15/2023]
Abstract
Issatchenkia orientalis, exhibiting high tolerance against harsh environmental conditions, is a promising metabolic engineering host for producing fuels and chemicals from cellulosic hydrolysates containing fermentation inhibitors under acidic conditions. Although genetic tools for I. orientalis exist, they require auxotrophic mutants so that the selection of a host strain is limited. We developed a drug resistance gene (cloNAT)-based genome-editing method for engineering any I. orientalis strains and engineered I. orientalis strains isolated from various sources for xylose fermentation. Specifically, xylose reductase, xylitol dehydrogenase, and xylulokinase from Scheffersomyces stipitis were integrated into an intended chromosomal locus in four I. orientalis strains (SD108, IO21, IO45, and IO46) through Cas9-based genome editing. The resulting strains (SD108X, IO21X, IO45X, and IO46X) efficiently produced ethanol from cellulosic and hemicellulosic hydrolysates even though the pH adjustment and nitrogen source were not provided. As they presented different fermenting capacities, selection of a host I. orientalis strain was crucial for producing fuels and chemicals using cellulosic hydrolysates.
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Affiliation(s)
- Ye-Gi Lee
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 02707, South Korea
| | - Chanwoo Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Nurzhan Kuanyshev
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
| | - Nam Kyu Kang
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, South Korea
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zong-Yen Wu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Ming-Hsun Cheng
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Vijay Singh
- Department of Agricultural and Biological Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yasuo Yoshikuni
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, Illinois 61801, United States
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21
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Fujie N, Ito M, Kishida M, Hirata Y, Kondo A, Tanaka T. Metabolic engineering of Schizosaccharomyces pombe for itaconic acid production. J Biotechnol 2022; 358:111-117. [PMID: 36122598 DOI: 10.1016/j.jbiotec.2022.09.006] [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: 06/09/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 10/31/2022]
Abstract
The economical production of value-added chemicals from renewable biomass is a promising aspect of producing a sustainable economy. Itaconic acid (IA) is a high value-added compound that is expected to be an alternative to petroleum-based chemicals. In this study, we developed a metabolic engineering strategy for the large-scale production of IA from glucose using the fission yeast Schizosaccharomyces pombe. Heterologous expression of the cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus, which encodes cis-aconitate decarboxylase in the cytosol, led to the production of 0.132 g/L of IA. We demonstrated that mitochondrial localization of CAD enhanced the production of IA. To prevent the leakage of carbon flux from the TCA cycle, we generated a strain in which the endogenous malate exporter, citrate lyase, and citrate transporter genes were disrupted. A titer of 1.110 g/L of IA was obtained from a culture of this strain started with 50 g/L of glucose. By culturing the multiple mutant strain at increased cell density, we succeeded in enhancing the IA production to 1.555 g/L. The metabolic engineering strategies presented in this study have the potential to improve the titer of the biosynthesis of derivatives of intermediates of the TCA cycle.
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Affiliation(s)
- Naofumi Fujie
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Miki Ito
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Mayumi Kishida
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Yuuki Hirata
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tsutomu Tanaka
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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22
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Fentie EG, Jeong M, Emire SA, Demsash HD, Kim MC, Lim K, Shin JH. Development of mixed starter culture for the fermentation of Ethiopian honey wine, Tej. Sci Rep 2022; 12:13431. [PMID: 35927420 PMCID: PMC9352660 DOI: 10.1038/s41598-022-17594-1] [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: 02/14/2022] [Accepted: 07/27/2022] [Indexed: 11/09/2022] Open
Abstract
Ethiopian honey wine is one of the country's most popular spontaneously fermented traditional alcoholic beverages. However, the final product of this natural fermentation system is frequently of poor and inconsistent quality. Furthermore, it makes the process difficult to predict, control, and correct. Thus, the main aim of this study was to develop a direct fermentation system for Ethiopian honey wine, Tej. After isolating fermentative microbial strains from Tej samples, they were subjected to intensive screening to fit to its purpose. Later, phenotypic and genotypic characterization, and inoculation of isolates to honey-must were performed sequentially. Finally, microbial interaction and physicochemical analysis, including volatile compounds profiling, were done for the inoculated samples. The identified isolates were strains of Saccharomycetaceae and Lactobacillaceae families. These strains showed a good ability to tolerate osmotic stress and a lower pH environment. Tej sample produced by mixed culture inoculation of Saccharomyces and Lactobacillus species showed similar physicochemical, volatile compounds, and sensory attributes values with that of the control sample. Thus, a mixture of Saccharomyces and Lactobacillus strains could be used as a starter culture to produce Ethiopian honey, Tej, without scarifying of its major quality attributes.
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Affiliation(s)
- Eskindir Getachew Fentie
- College of Biological and Chemical Engineering, Addis Ababa Science and Technology University, 16417, Addis Ababa, Ethiopia.,School of Chemical and Bio-Engineering, Addis Ababa Institute of Technology, Addis Ababa University, King George VI Street, P.O. Box 385, 16417, Addis Ababa, Ethiopia
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Shimelis Admassu Emire
- School of Chemical and Bio-Engineering, Addis Ababa Institute of Technology, Addis Ababa University, King George VI Street, P.O. Box 385, 16417, Addis Ababa, Ethiopia
| | - Hundessa Dessalegn Demsash
- School of Chemical and Bio-Engineering, Addis Ababa Institute of Technology, Addis Ababa University, King George VI Street, P.O. Box 385, 16417, Addis Ababa, Ethiopia
| | - Min-Chul Kim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Kyeongmo Lim
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea.
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23
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Hsiang CC, Diankristanti PA, Tan SI, Ke YC, Chen YC, Effendi SSW, Ng IS. Tailoring key enzymes for renewable and high-level itaconic acid production using genetic Escherichia coli via whole-cell bioconversion. Enzyme Microb Technol 2022; 160:110087. [DOI: 10.1016/j.enzmictec.2022.110087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/14/2022] [Accepted: 06/16/2022] [Indexed: 11/29/2022]
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24
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Rong L, Miao L, Wang S, Wang Y, Liu S, Lu Z, Zhao B, Zhang C, Xiao D, Pushpanathan K, Wong A, Yu A. Engineering Yarrowia lipolytica to Produce Itaconic Acid From Waste Cooking Oil. Front Bioeng Biotechnol 2022; 10:888869. [PMID: 35547171 PMCID: PMC9083544 DOI: 10.3389/fbioe.2022.888869] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
Itaconic acid (IA) is a high-value organic acid with a plethora of industrial applications. In this study, we seek to develop a microbial cell factory that could utilize waste cooking oil (WCO) as raw material for circular and cost-effective production of the abovementioned biochemical. Specifically, we expressed cis-aconitic acid decarboxylase (CAD) gene from Aspergillus terreus in either the cytosol or peroxisome of Yarrowia lipolytica and assayed for production of IA on WCO. To further improve production yield, the 10 genes involved in the production pathway of acetyl-CoA, an intermediate metabolite necessary for the synthesis of cis-aconitic acid, were individually overexpressed and investigated for their impact on IA production. To minimize off-target flux channeling, we had also knocked out genes related to competing pathways in the peroxisome. Impressively, IA titer up to 54.55 g/L was achieved in our engineered Y. lipolytica in a 5 L bioreactor using WCO as the sole carbon source.
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Affiliation(s)
- Lanxin Rong
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Lin Miao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shuhui Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yaping Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Shiqi Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Zhihui Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Baixiang Zhao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Cuiying Zhang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Dongguang Xiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Krithi Pushpanathan
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Dover, Singapore
| | - Adison Wong
- Food, Chemical and Biotechnology Cluster, Singapore Institute of Technology, Dover, Singapore
- *Correspondence: Adison Wong, ; Aiqun Yu,
| | - Aiqun Yu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Fermentation Microbiology of the Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- *Correspondence: Adison Wong, ; Aiqun Yu,
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25
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Yi X, Alper HS. Considering Strain Variation and Non-Type Strains for Yeast Metabolic Engineering Applications. Life (Basel) 2022; 12:life12040510. [PMID: 35455001 PMCID: PMC9032683 DOI: 10.3390/life12040510] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 03/24/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022] Open
Abstract
A variety of yeast species have been considered ideal hosts for metabolic engineering to produce value-added chemicals, including the model organism Saccharomyces cerevisiae, as well as non-conventional yeasts including Yarrowia lipolytica, Kluyveromyces marxianus, and Pichia pastoris. However, the metabolic capacity of these microbes is not simply dictated or implied by genus or species alone. Within the same species, yeast strains can display distinct variations in their phenotypes and metabolism, which affect the performance of introduced pathways and the production of interesting compounds. Moreover, it is unclear how this metabolic potential corresponds to function upon rewiring these organisms. These reports thus point out a new consideration for successful metabolic engineering, specifically: what are the best strains to utilize and how does one achieve effective metabolic engineering? Understanding such questions will accelerate the host selection and optimization process for generating yeast cell factories. In this review, we survey recent advances in studying yeast strain variations and utilizing non-type strains in pathway production and metabolic engineering applications. Additionally, we highlight the importance of employing portable methods for metabolic rewiring to best access this metabolic diversity. Finally, we conclude by highlighting the importance of considering strain diversity in metabolic engineering applications.
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Affiliation(s)
- Xiunan Yi
- Interdisciplinary Life Sciences, The University of Texas at Austin, Austin, TX 78712, USA;
| | - Hal S. Alper
- Interdisciplinary Life Sciences, The University of Texas at Austin, Austin, TX 78712, USA;
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
- Correspondence:
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26
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Nascimento MF, Marques N, Correia J, Faria NT, Mira NP, Ferreira FC. Integrated perspective on microbe-based production of itaconic acid: from metabolic and strain engineering to upstream and downstream strategies. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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27
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State of the Art on the Microbial Production of Industrially Relevant Organic Acids. Catalysts 2022. [DOI: 10.3390/catal12020234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The industrial relevance of organic acids is high; because of their chemical properties, they can be used as building blocks as well as single-molecule agents with a huge annual market. Organic acid chemical platforms can derive from fossil sources by petrochemical refining processes, but most of them also represent natural metabolites produced by many cells. They are the products, by-products or co-products of many primary metabolic processes of microbial cells. Thanks to the potential of microbial cell factories and to the development of industrial biotechnology, from the last decades of the previous century, the microbial-based production of these molecules has started to approach the market. This was possible because of a joint effort of microbial biotechnologists and biochemical and process engineers that boosted natural production up to the titer, yield and productivity needed to be industrially competitive. More recently, the possibility to utilize renewable residual biomasses as feedstock not only for biofuels, but also for organic acids production is further augmenting the sustainability of their production, in a logic of circular bioeconomy. In this review, we briefly present the latest updates regarding the production of some industrially relevant organic acids (citric fumaric, itaconic, lactic and succinic acid), discussing the challenges and possible future developments of successful production.
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28
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Bangar SP, Suri S, Trif M, Ozogul F. Organic acids production from lactic acid bacteria: A preservation approach. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101615] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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29
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Kawaguchi H, Takada K, Elkasaby T, Pangestu R, Toyoshima M, Kahar P, Ogino C, Kaneko T, Kondo A. Recent advances in lignocellulosic biomass white biotechnology for bioplastics. BIORESOURCE TECHNOLOGY 2022; 344:126165. [PMID: 34695585 DOI: 10.1016/j.biortech.2021.126165] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 06/13/2023]
Abstract
Lignocellulosic biomass has great potential as an inedible feedstock for bioplastic synthesis, although its use is still limited compared to current edible feedstocks of glucose and starch. This review focuses on recent advances in the production of biopolymers and biomonomers from lignocellulosic feedstocks with downstream processing and chemical polymer syntheses. In microbial production, four routes composed of existing poly (lactic acid) and polyhydroxyalkanoates (PHAs) and the emerging biomonomers of itaconic acid and aromatic compounds were presented to review present challenges and future perspectives, focusing on the use of lignocellulosic feedstocks. Recently, advances in purification technologies decreased the number of processes and their environmental burden. Additionally, the unique structures and high-performance of emerging lignocellulose-based bioplastics have expanded the possibilities for the use of bioplastics. The sequence of processes provides insight into the emerging technologies that are needed for the practical use of bioplastics made from lignocellulosic biomass.
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Affiliation(s)
- Hideo Kawaguchi
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kenji Takada
- Energy and Environmental Area, Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Taghreed Elkasaby
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Botany Department, Faculty of Science, Mansoura University, 60 Elgomhoria st, Mansoura 35516, Egypt
| | - Radityo Pangestu
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Research Center for Biotechnology, Indonesian Institute of Sciences, Cibinong, West Java 16911, Indonesia
| | - Masakazu Toyoshima
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Prihardi Kahar
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Chiaki Ogino
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tatsuo Kaneko
- Energy and Environmental Area, Graduate School of Advanced Science and Technology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Biomass Engineering Research Division, RIKEN, 1-7-22 Suehiro, Turumi, Yokohama, Kanagawa 230-0045, Japan.
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30
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Liao B, Chen X, Zhou X, Zhou Y, Shi Y, Ye X, Liao M, Zhou Z, Cheng L, Ren B. Applications of CRISPR/Cas gene-editing technology in yeast and fungi. Arch Microbiol 2021; 204:79. [DOI: 10.1007/s00203-021-02723-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/20/2021] [Accepted: 12/09/2021] [Indexed: 12/12/2022]
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31
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McNaughton AD, Bredeweg EL, Manzer J, Zucker J, Munoz Munoz N, Burnet MC, Nakayasu ES, Pomraning KR, Merkley ED, Dai Z, Chrisler WB, Baker SE, St. John PC, Kumar N. Bayesian Inference for Integrating Yarrowia lipolytica Multiomics Datasets with Metabolic Modeling. ACS Synth Biol 2021; 10:2968-2981. [PMID: 34636549 DOI: 10.1021/acssynbio.1c00267] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Optimizing the metabolism of microbial cell factories for yields and titers is a critical step for economically viable production of bioproducts and biofuels. In this process, tuning the expression of individual enzymes to obtain the desired pathway flux is a challenging step, in which data from separate multiomics techniques must be integrated with existing biological knowledge to determine where changes should be made. Following a design-build-test-learn strategy, building on recent advances in Bayesian metabolic control analysis, we identify key enzymes in the oleaginous yeast Yarrowia lipolytica that correlate with the production of itaconate by integrating a metabolic model with multiomics measurements. To this extent, we quantify the uncertainty for a variety of key parameters, known as flux control coefficients (FCCs), needed to improve the bioproduction of target metabolites and statistically obtain key correlations between the measured enzymes and boundary flux. Based on the top five significant FCCs and five correlated enzymes, our results show phosphoglycerate mutase, acetyl-CoA synthetase (ACSm), carbonic anhydrase (HCO3E), pyrophosphatase (PPAm), and homoserine dehydrogenase (HSDxi) enzymes in rate-limiting reactions that can lead to increased itaconic acid production.
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Affiliation(s)
- Andrew D. McNaughton
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Erin L. Bredeweg
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - James Manzer
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Jeremy Zucker
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Nathalie Munoz Munoz
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Meagan C. Burnet
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ernesto S. Nakayasu
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Kyle R. Pomraning
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric D. Merkley
- National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ziyu Dai
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - William B. Chrisler
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Scott E. Baker
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Peter C. St. John
- Biosciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Neeraj Kumar
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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32
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Shan L, Dai Z, Wang Q. Advances and Opportunities of CRISPR/Cas Technology in Bioengineering Non-conventional Yeasts. Front Bioeng Biotechnol 2021; 9:765396. [PMID: 34708030 PMCID: PMC8542773 DOI: 10.3389/fbioe.2021.765396] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022] Open
Abstract
Non-conventional yeasts have attracted a growing interest on account of their excellent characteristics. In recent years, the emerging of CRISPR/Cas technology has improved the efficiency and accuracy of genome editing. Utilizing the advantages of CRISPR/Cas in bioengineering of non-conventional yeasts, quite a few advancements have been made. Due to the diversity in their genetic background, the ways for building a functional CRISPR/Cas system of various species non-conventional yeasts were also species-specific. Herein, we have summarized the different strategies for optimizing CRISPR/Cas systems in different non-conventional yeasts and their biotechnological applications in the construction of cell factories. In addition, we have proposed some potential directions for broadening and improving the application of CRISPR/Cas technology in non-conventional yeasts.
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Affiliation(s)
- Lu Shan
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Zongjie Dai
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
| | - Qinhong Wang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,National Center of Technology Innovation for Synthetic Biology, Tianjin, China
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33
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Gopaliya D, Kumar V, Khare SK. Recent advances in itaconic acid production from microbial cell factories. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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34
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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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35
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Microbial production of chemicals driven by CRISPR-Cas systems. Curr Opin Biotechnol 2021; 73:34-42. [PMID: 34303184 DOI: 10.1016/j.copbio.2021.07.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 02/07/2023]
Abstract
Microorganisms have provided an attractive route for biosynthesis of various chemicals from renewable resources. CRISPR-Cas systems have served as powerful mechanisms for generating cell factories with desirable properties by manipulating nucleic acids quickly and efficiently. The CRISPR-Cas system provides a toolbox with excellent opportunities for identifying better biocatalysts, multiplexed fine-tuning of metabolic flux, efficient utilization of low-cost substrates, and improvement of metabolic robustness. The overall goal of this review highlights recent advances in the development of microbial cell factories for chemical production using various CRISPR-Cas systems. The perspectives for further development or applications of CRISPR-Cas systems for strain improvement are also discussed.
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36
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Xi Y, Zhan T, Xu H, Chen J, Bi C, Fan F, Zhang X. Characterization of JEN family carboxylate transporters from the acid-tolerant yeast Pichia kudriavzevii and their applications in succinic acid production. Microb Biotechnol 2021; 14:1130-1147. [PMID: 33629807 PMCID: PMC8085920 DOI: 10.1111/1751-7915.13781] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/26/2021] [Accepted: 02/09/2021] [Indexed: 12/20/2022] Open
Abstract
The unconventional yeast Pichia kudriavzevii is renowned for its ability to survive at low pH and has been exploited for the industrial production of various organic acids, especially succinic acid (SA). However, P. kudriavzevii can also utilize the di- and tricarboxylate intermediates of the Krebs cycle as the sole carbon sources for cell growth, which may adversely affect the extracellular accumulation of SA. Because the carboxylic acid transport machinery of P. kudriavzevii remains poorly understood, here, we focused on studying its SA transportation process from the perspective of mining and characterization of dicarboxylate transporters in a newly isolated acid-tolerant P. kudriavzevii strain CY902. Through genome sequencing and transcriptome analysis, two JEN family carboxylate transporters (PkJEN2-1 and PkJEN2-2) were found to be involved in SA transport. Substrate specificity analysis revealed that both PkJEN proteins are active dicarboxylate transporters, that can effectively import succinate, fumarate and L-malate into the cell. In addition, PkJEN2-1 can transport α-ketoglutarate, while PkJEN2-2 cannot. Since PkJEN2-1 shows higher transcript abundance than PkJEN2-2, its role in dicarboxylate transport is more important than PkJEN2-2. In addition, PKJEN2-2 is also responsible for the uptake of citrate. To our best knowledge, this is the first study to show that a JEN2 subfamily transporter is involved in tricarboxylate transport in yeast. A combination of model-based structure analysis and rational mutagenesis further proved that amino acid residues 392-403 of the tenth transmembrane span (TMS-X) of PkJEN2-2 play an important role in determining the specificity of the tricarboxylate substrate. Moreover, these two PkJEN transporters only exhibited inward transport activity for SA, and simultaneous inactivation of both PkJEN transporters reduced the SA influx, resulting in enhanced extracellular accumulation of SA in the late stage of fermentation. This work provides useful information on the mechanism of di-/tricarboxylic acid utilization in P. kudriavzevii, which will help improve the organic acid production performance of this microbial chassis.
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Affiliation(s)
- Yongyan Xi
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- University of Chinese Academy of SciencesBeijingChina
| | - Tao Zhan
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Hongtao Xu
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Jing Chen
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
| | - Changhao Bi
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Feiyu Fan
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
| | - Xueli Zhang
- Tianjin Institute of Industrial BiotechnologyChinese Academy of Sciences32 West 7th Ave, Tianjin Airport Economic ParkTianjin300308China
- Key Laboratory of Systems Microbial BiotechnologyChinese Academy of SciencesTianjinChina
- National Technology Innovation Center of Synthetic BiologyTianjinChina
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Adhesion Properties, Biofilm Forming Potential, and Susceptibility to Disinfectants of Contaminant Wine Yeasts. Microorganisms 2021; 9:microorganisms9030654. [PMID: 33809953 PMCID: PMC8004283 DOI: 10.3390/microorganisms9030654] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/15/2021] [Accepted: 03/18/2021] [Indexed: 12/15/2022] Open
Abstract
In this study, yeasts isolated from filter membranes used for the quality control of bottled wines were identified and tested for their resistance to some cleaning agents and potassium metabisulphite, adhesion to polystyrene and stainless-steel surfaces, and formation of a thin round biofilm, referred to as a MAT. A total of 40 strains were identified by rRNA internal transcribed spacer (ITS) restriction analysis and sequence analysis of D1/D2 domain of 26S rRNA gene. Strains belong to Pichia manshurica (12), Pichia kudriavzevii (9), Pichia membranifaciens (1), Candida sojae (6), Candida parapsilosis (3), Candida sonorensis (1), Lodderomyces elongisporus (2), Sporopachydermia lactativora (3), and Clavispora lusitaniae (3) species. Regarding the adhesion properties, differences were observed among species. Yeasts preferred planktonic state when tested on polystyrene plates. On stainless-steel supports, adhered cells reached values of about 6 log CFU/mL. MAT structures were formed only by yeasts belonging to the Pichia genus. Yeast species showed different resistance to sanitizers, with peracetic acid being the most effective and active at low concentrations, with minimum inhibitory concentration (MIC) values ranging from 0.08% (v/v) to 1% (v/v). C. parapsilosis was the most sensible species. Data could be exploited to develop sustainable strategies to reduce wine contamination and establish tailored sanitizing procedures.
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Martínez-Avila O, Muñoz-Torrero P, Sánchez A, Font X, Barrena R. Valorization of agro-industrial wastes by producing 2-phenylethanol via solid-state fermentation: Influence of substrate selection on the process. WASTE MANAGEMENT (NEW YORK, N.Y.) 2021; 121:403-411. [PMID: 33445113 DOI: 10.1016/j.wasman.2020.12.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 12/07/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
2-phenylethanol (2-PE) is a value-added compound widely used in industry due to its rose-like odor and antibacterial properties that can be bioproduced using wastes as raw materials. This study presents the valorization of nine agro-industrial wastes as potential substrates for 2-PE production using an isolated 2-PE producer Pichia kudriavzevii, and the solid-state fermentation (SSF) technology as an alternative approach. The assessed substrates comprised wastes of varied traits such that each of them provided different characteristics to the fermentation. Thus, by using a principal component analysis (PCA), it was possible to identify the most significant characteristics associated with the substrates affecting the 2-PE production. Results show that L-phenylalanine biotransformation was more efficient than de novo synthesis for producing 2-PE. Besides, from the evaluated set, the maximum 2-PE production was achieved with red apple pomace, reaching 1.7 and 25.2 mg2PE per gram of used waste through de novo and L-phenylalanine biotransformation, respectively. In that scenario, volumetric productivity and precursor yield were 39.6 mg2PE L-1h-1 and 0.69 g2PE per gram of L-phenylalanine added, respectively. From the PCA, it was identified that the reducing sugars content of the substrate, the air-filled porosity of the bed and the L-phenylalanine availability were the most critical parameters (associated with the substrates) influencing the microbial activity and 2-PE production. These results suggest that the desirable traits a solid media needs for promoting 2-PE production via SSF could be reached by using a combination of wastes in a synergistic approach.
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Affiliation(s)
- Oscar Martínez-Avila
- Composting Research Group, Department of Chemical, Biological and Environmental Engineering. Escola d'Enginyeria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Patricia Muñoz-Torrero
- Composting Research Group, Department of Chemical, Biological and Environmental Engineering. Escola d'Enginyeria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Antoni Sánchez
- Composting Research Group, Department of Chemical, Biological and Environmental Engineering. Escola d'Enginyeria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Xavier Font
- Composting Research Group, Department of Chemical, Biological and Environmental Engineering. Escola d'Enginyeria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain.
| | - Raquel Barrena
- Composting Research Group, Department of Chemical, Biological and Environmental Engineering. Escola d'Enginyeria, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, 08193 Barcelona, Spain.
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Zwirzitz A, Alteio L, Sulzenbacher D, Atanasoff M, Selg M. Ethanol Production from Wheat Straw Hydrolysate by Issatchenkia Orientalis Isolated from Waste Cooking Oil. J Fungi (Basel) 2021; 7:jof7020121. [PMID: 33562172 PMCID: PMC7915885 DOI: 10.3390/jof7020121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 11/29/2022] Open
Abstract
The interest in using non-conventional yeasts to produce value-added compounds from low cost substrates, such as lignocellulosic materials, has increased in recent years. Setting out to discover novel microbial strains that can be used in biorefineries, an Issatchenkia orientalis strain was isolated from waste cooking oil (WCO) and its capability to produce ethanol from wheat straw hydrolysate (WSHL) was analyzed. As with previously isolated I. orientalis strains, WCO-isolated I. orientalis KJ27-7 is thermotolerant. It grows well at elevated temperatures up to 42 °C. Furthermore, spot drop tests showed that it is tolerant to various chemical fermentation inhibitors that are derived from the pre-treatment of lignocellulosic materials. I. orientalis KJ27-7 is particularly tolerant to acetic acid (up to 75 mM) and tolerates 10 mM formic acid, 5 mM furfural and 10 mM hydroxymethylfurfural. Important for biotechnological cellulosic ethanol production, I. orientalis KJ27-7 grows well on plates containing up to 10% ethanol and media containing up to 90% WSHL. As observed in shake flask fermentations, the specific ethanol productivity correlates with WSHL concentrations. In 90% WSHL media, I. orientalis KJ27-7 produced 10.3 g L−1 ethanol within 24 h. This corresponds to a product yield of 0.50 g g−1 glucose (97% of the theoretical maximum) and a volumetric productivity of 0.43 g L−1 h−1. Therefore, I. orientalis KJ27-7 is an efficient producer of lignocellulosic ethanol from WSHL.
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Affiliation(s)
- Alexander Zwirzitz
- Biosciences Research Group, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, 4600 Wels, Austria; (D.S.); (M.A.); (M.S.)
- Correspondence:
| | - Lauren Alteio
- Centre of Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, Division of Terrestrial Ecosystem Research, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria;
| | - Daniel Sulzenbacher
- Biosciences Research Group, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, 4600 Wels, Austria; (D.S.); (M.A.); (M.S.)
| | - Michael Atanasoff
- Biosciences Research Group, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, 4600 Wels, Austria; (D.S.); (M.A.); (M.S.)
| | - Manuel Selg
- Biosciences Research Group, University of Applied Sciences Upper Austria, Stelzhamerstraße 23, 4600 Wels, Austria; (D.S.); (M.A.); (M.S.)
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Lund PA, De Biase D, Liran O, Scheler O, Mira NP, Cetecioglu Z, Fernández EN, Bover-Cid S, Hall R, Sauer M, O'Byrne C. Understanding How Microorganisms Respond to Acid pH Is Central to Their Control and Successful Exploitation. Front Microbiol 2020; 11:556140. [PMID: 33117305 PMCID: PMC7553086 DOI: 10.3389/fmicb.2020.556140] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/21/2020] [Indexed: 12/20/2022] Open
Abstract
Microbes from the three domains of life, Bacteria, Archaea, and Eukarya, share the need to sense and respond to changes in the external and internal concentrations of protons. When the proton concentration is high, acidic conditions prevail and cells must respond appropriately to ensure that macromolecules and metabolic processes are sufficiently protected to sustain life. While, we have learned much in recent decades about the mechanisms that microbes use to cope with acid, including the unique challenges presented by organic acids, there is still much to be gained from developing a deeper understanding of the effects and responses to acid in microbes. In this perspective article, we survey the key molecular mechanisms known to be important for microbial survival during acid stress and discuss how this knowledge might be relevant to microbe-based applications and processes that are consequential for humans. We discuss the research approaches that have been taken to investigate the problem and highlight promising new avenues. We discuss the influence of acid on pathogens during the course of infections and highlight the potential of using organic acids in treatments for some types of infection. We explore the influence of acid stress on photosynthetic microbes, and on biotechnological and industrial processes, including those needed to produce organic acids. We highlight the importance of understanding acid stress in controlling spoilage and pathogenic microbes in the food chain. Finally, we invite colleagues with an interest in microbial responses to low pH to participate in the EU-funded COST Action network called EuroMicropH and contribute to a comprehensive database of literature on this topic that we are making publicly available.
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Affiliation(s)
- Peter A Lund
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Daniela De Biase
- Department of Medico-Surgical Sciences and Biotechnologies, Laboratory affiliated to the Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza University of Rome, Latina, Italy
| | - Oded Liran
- Department of Plant Sciences, MIGAL - Galilee Research Institute, Kiryat-Shemona, Israel
| | - Ott Scheler
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Nuno Pereira Mira
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Zeynep Cetecioglu
- Department of Chemical Engineering, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Sara Bover-Cid
- IRTA, Food Safety Programme, Finca Camps i Armet, Monells, Spain
| | - Rebecca Hall
- School of Biosciences, Kent Fungal Group, University of Kent, Canterbury, United Kingdom
| | - Michael Sauer
- Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
| | - Conor O'Byrne
- Bacterial Stress Response Group, Microbiology, School of Natural Sciences, NUI Galway, Galway, Ireland
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Srivastava RK, Akhtar N, Verma M, Imandi SB. Primary metabolites from overproducing microbial system using sustainable substrates. Biotechnol Appl Biochem 2020; 67:852-874. [PMID: 32294277 DOI: 10.1002/bab.1927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 04/12/2020] [Indexed: 02/06/2023]
Abstract
Primary (or secondary) metabolites are produced by animals, plants, or microbial cell systems either intracellularly or extracellularly. Production capabilities of microbial cell systems for many types of primary metabolites have been exploited at a commercial scale. But the high production cost of metabolites is a big challenge for most of the bioprocess industries and commercial production needs to be achieved. This issue can be solved to some extent by screening and developing the engineered microbial systems via reconstruction of the genome-scale metabolic model. The predicted genetic modification is applied for an increased flux in biosynthesis pathways toward the desired product. Wherein the resulting microbial strain is capable of converting a large amount of carbon substrate to the expected product with minimum by-product formation in the optimal operating conditions. Metabolic engineering efforts have also resulted in significant improvement of metabolite yields, depending on the nature of the products, microbial cell factory modification, and the types of substrate used. The objective of this review is to comprehend the state of art for the production of various primary metabolites by microbial strains system, focusing on the selection of efficient strain and genetic or pathway modifications, applied during strain engineering.
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Affiliation(s)
- Rajesh K Srivastava
- Department of Biotechnology, GIT, GITAM (Deemed to be University), Gandhi Nagar Campus, Rushikonda, Visakhapatnam, India
| | - Nasim Akhtar
- Department of Biotechnology, GIT, GITAM (Deemed to be University), Gandhi Nagar Campus, Rushikonda, Visakhapatnam, India
| | - Malkhey Verma
- Departments of Biochemistry and Microbial Sciences, Central University of Punjab, Bathinda, India
| | - Sarat Babu Imandi
- Department of Biotechnology, GIT, GITAM (Deemed to be University), Gandhi Nagar Campus, Rushikonda, Visakhapatnam, India
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42
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Fatma Z, Schultz JC, Zhao H. Recent advances in domesticating non‐model microorganisms. Biotechnol Prog 2020; 36:e3008. [DOI: 10.1002/btpr.3008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/14/2020] [Accepted: 04/18/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Zia Fatma
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - J. Carl Schultz
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Departments of Chemistry, Biochemistry, and Bioengineering University of Illinois at Urbana‐Champaign Urbana Illinois USA
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