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Vasylyshyn R, Dmytruk O, Sybirnyy A, Ruchała J. Engineering of Ogataea polymorpha strains with ability for high-temperature alcoholic fermentation of cellobiose. FEMS Yeast Res 2024; 24:foae007. [PMID: 38400543 DOI: 10.1093/femsyr/foae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/30/2024] [Accepted: 02/22/2024] [Indexed: 02/25/2024] Open
Abstract
Successful conversion of cellulosic biomass into biofuels requires organisms capable of efficiently utilizing xylose as well as cellodextrins and glucose. Ogataea (Hansenula) polymorpha is the natural xylose-metabolizing organism and is one of the most thermotolerant yeasts known, with a maximum growth temperature above 50°C. Cellobiose-fermenting strains, derivatives of an improved ethanol producer from xylose O. polymorpha BEP/cat8∆, were constructed in this work by the introduction of heterologous genes encoding cellodextrin transporters (CDTs) and intracellular enzymes (β-glucosidase or cellobiose phosphorylase) that hydrolyze cellobiose. For this purpose, the genes gh1-1 of β-glucosidase, CDT-1m and CDT-2m of cellodextrin transporters from Neurospora crassa and the CBP gene coding for cellobiose phosphorylase from Saccharophagus degradans, were successfully expressed in O. polymorpha. Through metabolic engineering and mutagenesis, strains BEP/cat8∆/gh1-1/CDT-1m and BEP/cat8∆/CBP-1/CDT-2mAM were developed, showing improved parameters for high-temperature alcoholic fermentation of cellobiose. The study highlights the need for further optimization to enhance ethanol yields and elucidate cellobiose metabolism intricacies in O. polymorpha yeast. This is the first report of the successful development of stable methylotrophic thermotolerant strains of O. polymorpha capable of coutilizing cellobiose, glucose, and xylose under high-temperature alcoholic fermentation conditions at 45°C.
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Affiliation(s)
- Roksolana Vasylyshyn
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Olena Dmytruk
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Andriy Sybirnyy
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
| | - Justyna Ruchała
- Institute of Biotechnology, College of Natural Sciences, University of Rzeszow, Cwiklinskiej 2D Street, 35-601 Rzeszow, Poland
- Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAN of Ukraine, Drahomanov Street 14/16, 79005 Lviv, Ukraine
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Saxena A, Hussain A, Parveen F, Ashfaque M. Current status of metabolic engineering of microorganisms for bioethanol production by effective utilization of pentose sugars of lignocellulosic biomass. Microbiol Res 2023; 276:127478. [PMID: 37625339 DOI: 10.1016/j.micres.2023.127478] [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: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Lignocellulosic biomass, consisting of homo- and heteropolymeric sugars, acts as a substrate for the generation of valuable biochemicals and biomaterials. The readily available hexoses are easily utilized by microbes due to the presence of transporters and native metabolic pathways. But, utilization of pentose sugar viz., xylose and arabinose are still challenging due to several reasons including (i) the absence of the particular native pathways and transporters, (ii) the presence of inhibitors, and (iii) lower uptake of pentose sugars. These challenges can be overcome by manipulating metabolic pathways/glycosidic enzymes cascade by using genetic engineering tools involving inverse-metabolic engineering, ex-vivo isomerization, Adaptive Laboratory Evolution, Directed Metabolic Engineering, etc. Metabolic engineering of bacteria and fungi for the utilization of pentose sugars for bioethanol production is the focus area of research in the current decade. This review outlines current approaches to biofuel development and strategies involved in the metabolic engineering of different microbes that can uptake pentose for bioethanol production.
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Affiliation(s)
- Ayush Saxena
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Akhtar Hussain
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Fouziya Parveen
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Mohammad Ashfaque
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
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Going beyond E. coli: autotransporter based surface display on alternative host organisms. N Biotechnol 2015; 32:644-50. [PMID: 25579193 DOI: 10.1016/j.nbt.2014.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 12/19/2014] [Accepted: 12/31/2014] [Indexed: 11/21/2022]
Abstract
Autotransporters represent one of the most popular anchoring motifs used to display peptides, proteins or enzymes on the cell surface of a Gram-negative bacterium. Applications range from vaccine delivery to library screenings to biocatalysis and bioremediation. Although the underlying secretion mechanism is supposed to be available in most, if not all, Gram-negative bacteria, autotransporters have to date almost exclusively been used for surface display on Escherichia coli. However, for their utilisation beyond a laboratory scale, in particular for biocatalysis, host bacteria with specific features and industrial applicability are required. A few groups have addressed this issue and demonstrated that bacteria other than E. coli can also be used for autotransporter based surface display. We summarise these studies and discuss opportunities and challenges that arise from surface display of recombinant proteins using the autotransporter pathway in alternative hosts.
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Direct ethanol production from cellulosic materials by Zymobacter palmae carrying Cellulomonas endoglucanase and Ruminococcus β-glucosidase genes. Appl Microbiol Biotechnol 2013; 97:5137-47. [DOI: 10.1007/s00253-013-4874-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Revised: 03/20/2013] [Accepted: 03/21/2013] [Indexed: 10/26/2022]
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Yamada R, Hasunuma T, Kondo A. Endowing non-cellulolytic microorganisms with cellulolytic activity aiming for consolidated bioprocessing. Biotechnol Adv 2013; 31:754-63. [PMID: 23473971 DOI: 10.1016/j.biotechadv.2013.02.007] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 02/19/2013] [Accepted: 02/24/2013] [Indexed: 11/17/2022]
Abstract
With the exhaustion of fossil fuels and with the environmental issues they pose, utilization of abundant lignocellulosic biomass as a feedstock for biofuels and bio-based chemicals has recently become an attractive option. Lignocellulosic biomass is primarily composed of cellulose, hemicellulose, and lignin and has a very rigid and complex structure. It is accordingly much more expensive to process than starchy grains because of the need for extensive pretreatment and relatively large amounts of cellulases for efficient hydrolysis. Efficient and cost-effective methods for the production of biofuels and chemicals from lignocellulose are required. A consolidated bioprocess (CBP), which integrates all biological steps consisting of enzyme production, saccharification, and fermentation, is considered a promising strategy for reducing production costs. Establishing an efficient CBP using lignocellulosic biomass requires both lignocellulose degradation into glucose and efficient production of biofuels or chemicals from glucose. With this aim, many researchers are attempting to endow selected microorganisms with lignocellulose-assimilating ability. In this review, we focus on studies aimed at conferring lignocellulose-assimilating ability not only to yeast strains but also to bacterial strains by recombinant technology. Recent developments in improvement of enzyme productivity by microorganisms and in improvement of the specific activity of cellulase are emphasized.
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Affiliation(s)
- Ryosuke Yamada
- Organization of Advanced Science and Technology, Kobe University, 1-1 Rokkodaicho, Nada, Kobe 657-8501, Japan
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Kojima M, Akahoshi T, Okamoto K, Yanase H. Expression and surface display of Cellulomonas endoglucanase in the ethanologenic bacterium Zymobacter palmae. Appl Microbiol Biotechnol 2012; 96:1093-104. [DOI: 10.1007/s00253-012-4424-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 09/06/2012] [Accepted: 09/07/2012] [Indexed: 11/29/2022]
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Argandoña M, Vargas C, Reina-Bueno M, Rodríguez-Moya J, Salvador M, Nieto JJ. An extended suite of genetic tools for use in bacteria of the Halomonadaceae: an overview. Methods Mol Biol 2012; 824:167-201. [PMID: 22160899 DOI: 10.1007/978-1-61779-433-9_9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Halophilic gammaproteobacteria of the family Halomonadaceae (including the genera Aidingimonas, Carnimonas, Chromohalobacter, Cobetia, Halomonas, Halotalea, Kushneria, Modicisalibacter, Salinicola, and Zymobacter) have current and promising applications in biotechnology mainly as a source of compatible solutes (powerful stabilizers of biomolecules and cells, with exciting potentialities in biomedicine), salt-tolerant enzymes, biosurfactants, and extracellular polysaccharides, among other products. In addition, they display a number of advantages to be used as cell factories, alternative to conventional prokaryotic hosts like Escherichia coli or Bacillus, for the production of recombinant proteins: (1) their high salt tolerance decreases to a minimum the necessity for aseptic conditions, resulting in cost-reducing conditions, (2) they are very easy to grow and maintain in the laboratory, and their nutritional requirements are simple, and (3) the majority can use a large range of compounds as a sole carbon and energy source. In the last 15 years, the efforts of our group and others have made possible the genetic manipulation of this bacterial group. In this review, the most relevant and recent tools for their genetic manipulation are described, with emphasis on nucleic acid isolation procedures, cloning and expression vectors, genetic exchange mechanisms, mutagenesis approaches, reporter genes, and genetic expression analyses. Complementary sections describing the influence of salinity on the susceptibility of these bacteria to antimicrobials, as well as the growth media most routinely used and culture conditions, for these microorganisms, are also included.
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Affiliation(s)
- Montserrat Argandoña
- Department of Microbiology and Parasitology, University of Seville, Seville, Spain
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Simultaneous utilization of d-cellobiose, d-glucose, and d-xylose by recombinant Corynebacterium glutamicum under oxygen-deprived conditions. Appl Microbiol Biotechnol 2008; 81:691-9. [DOI: 10.1007/s00253-008-1703-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 09/02/2008] [Accepted: 09/03/2008] [Indexed: 10/21/2022]
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Ito J, Sahara H, Kaya M, Hata Y, Shibasaki S, Kawata K, Ishida S, Ogino C, Fukuda H, Kondo A. Characterization of yeast cell surface displayed Aspergillus oryzae β-glucosidase 1 high hydrolytic activity for soybean isoflavone. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.molcatb.2008.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wang Z, Chen M, Xu Y, Li S, Lu W, Ping S, Zhang W, Lin M. An ethanol-tolerant recombinant Escherichia coli expressing Zymomonas mobilis pdc and adhB genes for enhanced ethanol production from xylose. Biotechnol Lett 2007; 30:657-63. [DOI: 10.1007/s10529-007-9597-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 10/25/2007] [Accepted: 10/30/2007] [Indexed: 11/29/2022]
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Ito J, Ebe T, Shibasaki S, Fukuda H, Kondo A. Production of alkyl glucoside from cellooligosaccharides using yeast strains displaying Aspergillus aculeatus β-glucosidase 1. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.molcatb.2007.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Yanase H, Sato D, Yamamoto K, Matsuda S, Yamamoto S, Okamoto K. Genetic engineering of Zymobacter palmae for production of ethanol from xylose. Appl Environ Microbiol 2007; 73:2592-9. [PMID: 17308178 PMCID: PMC1855588 DOI: 10.1128/aem.02302-06] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 02/12/2007] [Indexed: 11/20/2022] Open
Abstract
Its metabolic characteristics suggest that Zymobacter palmae gen. nov., sp. nov. could serve as a useful new ethanol-fermenting bacterium, but its biotechnological exploitation will require certain genetic modifications. We therefore engineered Z. palmae so as to broaden the range of its fermentable sugar substrates to include the pentose sugar xylose. The Escherichia coli genes encoding the xylose catabolic enzymes xylose isomerase, xylulokinase, transaldolase, and transketolase were introduced into Z. palmae, where their expression was driven by the Zymomonas mobilis glyceraldehyde-3-phosphate dehydrogenase promoter. When cultured with 40 g/liter xylose, the recombinant Z. palmae strain was able to ferment 16.4 g/liter xylose within 5 days, producing 91% of the theoretical yield of ethanol with no accumulation of organic acids as metabolic by-products. Notably, xylose acclimation enhanced both the expression of xylose catabolic enzymes and the rate of xylose uptake into recombinant Z. palmae, which enabled the acclimated organism to completely and simultaneously ferment a mixture of 40 g/liter glucose and 40 g/liter xylose within 8 h, producing 95% of the theoretical yield of ethanol. Thus, efficient fermentation of a mixture of glucose and xylose to ethanol can be accomplished by using Z. palmae expressing E. coli xylose catabolic enzymes.
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Affiliation(s)
- Hideshi Yanase
- Department of Biotechnology, Faculty of Engineering, Tottori University, 4-101 Koyamacho-Minami, Tottori, Tottori, Japan.
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Hong J, Wang Y, Kumagai H, Tamaki H. Construction of thermotolerant yeast expressing thermostable cellulase genes. J Biotechnol 2007; 130:114-23. [PMID: 17433483 DOI: 10.1016/j.jbiotec.2007.03.008] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 02/22/2007] [Accepted: 03/06/2007] [Indexed: 11/26/2022]
Abstract
Kluyveromyces marxianus NBRC1777 was identified as a thermotolerant yeast and was developed as a host for the expression of thermostable cellulase genes. The previously isolated genes for thermostable endo-beta-1,4-glucanase, cellobiohydrolase, and beta-glucosidase were introduced into the chromosome of K. marxianus and successfully expressed under the control of high-expression promoters. The recombinant K. marxianus expressing cellulase genes became able to grow in synthetic medium containing cellobiose or carboxymethyl-cellulose as the single carbon source. Moreover, the recombinant strain produced 43.4 g/L ethanol from 10% cellobiose. These results suggest that K. marxianus may afford a useful host system, which may be applicable to the simultaneous saccharification and fermentation and the foundation of cellulose consolidated bioprocessing.
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Affiliation(s)
- Jiong Hong
- Laboratory of Applied Microbiology, Research Institute of Natural Resources, Ishikawa Prefectural University, Nonoichi-cho, Ishikawa 921-8836, Japan
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