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Living material assembly of bacteriogenic protocells. Nature 2022; 609:1029-1037. [DOI: 10.1038/s41586-022-05223-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/10/2022] [Indexed: 11/08/2022]
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2
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Braga A, Gomes D, Rainha J, Cardoso BB, Amorim C, Silvério SC, Fernández-Lobato M, Rodrigues JL, Rodrigues LR. Tailoring fructooligosaccharides composition with engineered Zymomonas mobilis ZM4. Appl Microbiol Biotechnol 2022; 106:4617-4626. [PMID: 35739346 DOI: 10.1007/s00253-022-12037-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 05/05/2022] [Accepted: 06/18/2022] [Indexed: 11/02/2022]
Abstract
Zymomonas mobilis ZM4 is an attractive host for the development of microbial cell factories to synthesize high-value compounds, including prebiotics. In this study, a straightforward process to produce fructooligosaccharides (FOS) from sucrose was established. To control the relative FOS composition, recombinant Z. mobilis strains secreting a native levansucrase (encoded by sacB) or a mutated β-fructofuranosidase (Ffase-Leu196) from Schwanniomyces occidentalis were constructed. Both strains were able to produce a FOS mixture with high concentration of 6-kestose. The best results were obtained with Z. mobilis ZM4 pB1-sacB that was able to produce 73.4 ± 1.6 g L-1 of FOS, with a productivity of 1.53 ± 0.03 g L-1 h-1 and a yield of 0.31 ± 0.03 gFOS gsucrose-1. This is the first report on the FOS production using a mutant Z. mobilis ZM4 strain in a one-step process. KEY POINTS: • Zymomonas mobilis was engineered to produce FOS in a one-step fermentation process. • Mutant strains produced FOS mixtures with high concentration of 6-kestose. • A new route to produce tailor-made FOS mixtures was presented.
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Affiliation(s)
- Adelaide Braga
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Daniela Gomes
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - João Rainha
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Beatriz B Cardoso
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Cláudia Amorim
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Sara C Silvério
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - María Fernández-Lobato
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry-Rocasolano (CSIC), 28006, Madrid, Spain
| | - Joana L Rodrigues
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal
| | - Lígia R Rodrigues
- CEB-Center of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal. .,LABBELS -Associate Laboratory, Braga/Guimarães, Portugal.
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Enhancing Secretion of Endoglucanase in Zymomonas mobilis by Disturbing Peptidoglycan Synthesis. Appl Environ Microbiol 2021; 88:e0216121. [PMID: 34818110 DOI: 10.1128/aem.02161-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Zymomonas mobilis (Z. mobilis) is a potential candidate for consolidated bioprocessing (CBP) strain in lignocellulosic biorefinery. However, the low-level secretion of cellulases limits this CBP process, and the mechanism of protein secretion affected by cell wall peptidoglycan is also not well understood. Here we constructed several Penicillin Binding Proteins (PBPs)-deficient strains derivated from Z. mobilis S192 to perturb the cell wall peptidoglycan network and investigated the effects of peptidoglycan on the endoglucanase secretion. Results showed that extracellular recombinant endoglucanase production was significantly enhanced in PBPs mutant strains, notably, △1089/0959 (4.09-fold) and △0959 (5.76-fold) in comparison to parent strains. Besides, for PBPs-deficient strains, the growth performance was not significantly inhibited but with enhanced antibiotic sensitivity and reduced inhibitor tolerance, otherwise, cell morphology was altered obviously. The concentration of intracellular soluble peptidoglycan was increased, especially for single gene deletion. Outer membrane permeability of PBPs-deficient strains was also improved, notably, △1089/0959 (1.14-fold) and △0959 (1.07-fold), which might explain the increased endoglucanase extracellular secretion. Our finding indicated that PBPs-deficient Z. mobilis is capable of increasing endoglucanase extracellular secretion via cell wall peptidoglycan disturbance and it will provide a foundation for the development of CBP technology in Z. mobilis in the future. IMPORTANCE Cell wall peptidoglycan has the function to maintain cell robustness, and also acts as the barrier to secret recombinant proteins from the cytoplasm to extracellular space in Z. mobilis and other bacterias. Herein, we perturb the peptidoglycan synthesis network via knocking out PBPs (ZMO0197, ZMO0959, ZMO1089) in order to enhance recombinant endoglycanase extracellular secretion in Z. mobilis S912. This study can not only lay the foundation for understanding the regulatory network of cell wall synthesis but also provide guidance for the construction of CBP strains in Z. mobilis.
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Lopes AMM, Martins M, Goldbeck R. Heterologous Expression of Lignocellulose-Modifying Enzymes in Microorganisms: Current Status. Mol Biotechnol 2021; 63:184-199. [PMID: 33484441 DOI: 10.1007/s12033-020-00288-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2020] [Indexed: 02/06/2023]
Abstract
Heterologous expression of the carbohydrate-active enzymes in microorganisms is a promising approach to produce bio-based compounds, such as fuels, nutraceuticals and other value-added products from sustainable lignocellulosic sources. Several microorganisms, including Saccharomyces cerevisiae, Escherichia coli, and the filamentous fungi Aspergillus nidulans, have unique characteristics desirable for a biorefinery production approach like well-known genetic tools, thermotolerance, high fermentative capacity and product tolerance, and high amount of recombinant enzyme secretion. These microbial factories are already stablished in the heterologous production of the carbohydrate-active enzymes to produce, among others, ethanol, xylooligosaccharides and the valuable coniferol. A complete biocatalyst able to heterologous express the CAZymes of glycoside hydrolases, carbohydrate esterases and auxiliary activities families could release these compounds faster, with higher yield and specificity. Recent advances in the synthetic biology tools could expand the number and diversity of enzymes integrated in these microorganisms, and also modify those already integrated. This review outlines the heterologous expression of carbohydrate-active enzymes in microorganisms, as well as recent updates in synthetic biology.
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Affiliation(s)
- Alberto Moura Mendes Lopes
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil
| | - Manoela Martins
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil
| | - Rosana Goldbeck
- Bioprocess and Metabolic Engineering Laboratory, School of Food Engineering, University of Campinas (UNICAMP), Rua Monteiro Lobato no 80, Cidade Universitária, Campinas, São Paulo, 13083-862, Brazil.
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Vadala BS, Deshpande S, Apte-Deshpande A. Soluble expression of recombinant active cellulase in E.coli using B.subtilis (natto strain) cellulase gene. J Genet Eng Biotechnol 2021; 19:7. [PMID: 33428026 PMCID: PMC7801579 DOI: 10.1186/s43141-020-00103-0] [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: 04/21/2020] [Accepted: 12/07/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Cellulases are well known for their various industrial applications. They are naturally produced by different species of bacteria and fungi. Fermentation process of cellulase producers has limitation due to the high substrate cost required for cellulase induction and challenges to maintain the suitable condition for the respective cellulase production. Recombinant cellulase production could be the potential solution to these problems. In the current study, we investigated recombinant cellulase expression in Escherichia coli using cellulase gene from Bacillus subtilis. RESULTS Extracellular cellulase production from B. subtilis strain was first confirmed on CMC agar and then the cellulase gene (1500 bp) was amplified from this strain and was further cloned in pET21a expression vector. In initial experimental studies, recombinant cellulase expression was achieved in inclusion bodies through shake flask level fermentation of transformed E. coli expression host BL21DE3. Attempts were made to express this 55 KDa His tagged recombinant cellulase into soluble form by modifications in fermentation conditions. Partially purified recombinant cellulase was obtained using Ni-NTA affinity chromatography. The activity of the purified enzyme was confirmed by 3,5-dinitrosalicylic acid (DNS) qualitative assay. CONCLUSION Soluble expression of active recombinant cellulase can be achieved by subtle alteration in the upstream process.
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Affiliation(s)
- Bhuvan Shankar Vadala
- Central Dogma Pvt. Ltd, A4, Gulmohar Residency, Baner Road, Baner, Pune, Maharashtra, 411045, India
| | - Sumedh Deshpande
- Central Dogma Pvt. Ltd, A4, Gulmohar Residency, Baner Road, Baner, Pune, Maharashtra, 411045, India
| | - Anjali Apte-Deshpande
- Central Dogma Pvt. Ltd, A4, Gulmohar Residency, Baner Road, Baner, Pune, Maharashtra, 411045, India.
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Chettri D, Verma AK, Verma AK. Innovations in CAZyme gene diversity and its modification for biorefinery applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2020; 28:e00525. [PMID: 32963975 PMCID: PMC7490808 DOI: 10.1016/j.btre.2020.e00525] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/04/2020] [Accepted: 08/30/2020] [Indexed: 02/07/2023]
Abstract
For sustainable growth, concept of biorefineries as recourse to the "fossil derived" energy source is important. Here, the Carbohydrate Active enZymes (CAZymes) play decisive role in generation of biofuels and related sugar-based products utilizing lignocellulose as a carbon source. Given their industrial significance, extensive studies on the evolution of CAZymes have been carried out. Various bacterial and fungal organisms have been scrutinized for the development of CAZymes, where advance techniques for strain enhancement such as CRISPR and analysis of specific expression systems have been deployed. Specific Omic-based techniques along with protein engineering have been adopted to unearth novel CAZymes and improve applicability of existing enzymes. In-Silico computational research and functional annotation of new CAZymes to synergy experiments are being carried out to devise cocktails of enzymes for use in biorefineries. Thus, with the establishment of these technologies, increased diversity of CAZymes with broad span of functions and applications is seen.
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Bioethanol production from cereal crops and lignocelluloses rich agro-residues: prospects and challenges. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-03471-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Kurumbang NP, Vera JM, Hebert AS, Coon JJ, Landick R. Heterologous expression of a glycosyl hydrolase and cellular reprogramming enable Zymomonas mobilis growth on cellobiose. PLoS One 2020; 15:e0226235. [PMID: 32797046 PMCID: PMC7428164 DOI: 10.1371/journal.pone.0226235] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 07/14/2020] [Indexed: 11/19/2022] Open
Abstract
Plant-derived fuels and chemicals from renewable biomass have significant potential to replace reliance on petroleum and improve global carbon balance. However, plant biomass contains significant fractions of oligosaccharides that are not usable natively by many industrial microorganisms, including Escherichia coli, Saccharomyces cerevisiae, and Zymomonas mobilis. Even after chemical or enzymatic hydrolysis, some carbohydrate remains as non-metabolizable oligosaccharides (e.g., cellobiose or longer cellulose-derived oligomers), thus reducing the efficiency of conversion to useful products. To begin to address this problem for Z. mobilis, we engineered a strain (Z. mobilis GH3) that expresses a glycosyl hydrolase (GH) with β-glucosidase activity from a related α-proteobacterial species, Caulobacter crescentus, and subjected it to an adaptation in cellobiose medium. Growth on cellobiose was achieved after a prolonged lag phase in cellobiose medium that induced changes in gene expression and cell composition, including increased expression and extracellular release of GH. These changes were reversible upon growth in glucose-containing medium, meaning they did not result from genetic mutation but could be retained upon transfer of cells to fresh cellobiose medium. After adaptation to cellobiose, our GH-expressing strain was able to convert about 50% of cellobiose to glucose within 24 h and use it for growth and ethanol production. Alternatively, pre-growth of Z. mobilis GH3 in sucrose medium enabled immediate growth on cellobiose. Proteomic analysis of cellobiose- and sucrose-adapted strains revealed upregulation of secretion-, transport-, and outer membrane-related proteins, which may aid release or surface display of GHs, entry of cellobiose into the periplasm, or both. Our two key findings are that Z. mobilis can be reprogrammed to grow on cellobiose as a sole carbon source and that this reprogramming is related to a natural response of Z. mobilis to sucrose that promotes sucrase production.
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Affiliation(s)
- Nagendra P. Kurumbang
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jessica M. Vera
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Alexander S. Hebert
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Robert Landick
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Departments of Biochemistry and Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- * E-mail:
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Todhanakasem T, Wu B, Simeon S. Perspectives and new directions for bioprocess optimization using Zymomonas mobilis in the ethanol production. World J Microbiol Biotechnol 2020; 36:112. [PMID: 32656581 DOI: 10.1007/s11274-020-02885-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 06/29/2020] [Indexed: 12/28/2022]
Abstract
Zymomonas mobilis is an ethanologenic microbe that has a demonstrated potential for use in lignocellulosic biorefineries for bioethanol production. Z. mobilis exhibits a number of desirable characteristics for use as an ethanologenic microbe, with capabilities for metabolic engineering and bioprocess modification. Many advanced genetic tools, including mutation techniques, screening methods and genome editing have been successively performed to improve various Z. mobilis strains as potential consolidated ethanologenic microbes. Many bioprocess strategies have also been applied to this organism for bioethanol production. Z. mobilis biofilm reactors have been modified with various benefits, including high bacterial populations, less fermentation times, high productivity, high cell stability, resistance to the high concentration of substrates and toxicity, and higher product recovery. We suggest that Z. mobilis biofilm reactors could be used in bioethanol production using lignocellulosic substrates under batch, continuous and repeated batch processes.
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Affiliation(s)
- Tatsaporn Todhanakasem
- Department of Agro- Industry, Faculty of Biotechnology, Assumption University, Ramkhamhaeng Road, Bangkapi, Bangkok, 10240, Thailand.
| | - Bo Wu
- Biomass Energy Technology Research Center, Biogas Institute of Ministry of Agriculture and Rural Affairs, Renmin Rd. S 4-13, Chengdu, 610041, China
| | - Saw Simeon
- Absolute Clean Energy Public Company Limited, ITF Tower 7th Floor, Silom Road, Bang Rak, Bangkok, 10500, Thailand
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Green Production and Biotechnological Applications of Cell Wall Lytic Enzymes. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9235012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
: Energy demand is constantly growing, and, nowadays, fossil fuels still play a dominant role in global energy production, despite their negative effects on air pollution and the emission of greenhouse gases, which are the main contributors to global warming. An alternative clean source of energy is represented by the lignocellulose fraction of plant cell walls, the most abundant carbon source on Earth. To obtain biofuels, lignocellulose must be efficiently converted into fermentable sugars. In this regard, the exploitation of cell wall lytic enzymes (CWLEs) produced by lignocellulolytic fungi and bacteria may be considered as an eco-friendly alternative. These organisms evolved to produce a variety of highly specific CWLEs, even if in low amounts. For an industrial use, both the identification of novel CWLEs and the optimization of sustainable CWLE-expressing biofactories are crucial. In this review, we focus on recently reported advances in the heterologous expression of CWLEs from microbial and plant expression systems as well as some of their industrial applications, including the production of biofuels from agricultural feedstock and of value-added compounds from waste materials. Moreover, since heterologous expression of CWLEs may be toxic to plant hosts, genetic strategies aimed in converting such a deleterious effect into a beneficial trait are discussed.
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Physiological effects of overexpressed sigma factors on fermentative stress response of Zymomonas mobilis. Braz J Microbiol 2019; 51:65-75. [PMID: 31701383 DOI: 10.1007/s42770-019-00158-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/11/2019] [Indexed: 01/04/2023] Open
Abstract
Zymomonas mobilis is a bacterium of industrial interest due to its high ethanol productivity and high tolerance to stresses. Although the physiological parameters of fermentation are well characterized, there are few studies on the molecular mechanisms that regulate the response to fermentative stress. Z. mobilis ZM4 presents five different sigma factors identified in the genome annotation, but the absence of sigma 38 leads to the questioning of which sigma factors are responsible for its mechanism of fermentative stress response. Thus, in this study, factors sigma 32 and sigma 24, traditionally related to heat shock, were tested for their influence on the response to osmotic and ethanol stress. The overexpression of these sigma factors in Z. mobilis ZM4 strain confirmed that both are associated with heat shock response, as described in other bacteria. Moreover, sigma 32 has also a role in the adaptation to osmotic stress, increasing both growth rate and glucose influx rate. The same strain that overexpresses sigma 32 also showed a decrease in ethanol tolerance, suggesting an antagonism between these two mechanisms. It was not possible to conclude if sigma 24 really affects ethanol tolerance in Z. mobilis, but the overexpression of this sigma factor led to a decrease in ethanol productivity.
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Banerjee S, Mishra G, Roy A. Metabolic Engineering of Bacteria for Renewable Bioethanol Production from Cellulosic Biomass. BIOTECHNOL BIOPROC E 2019. [DOI: 10.1007/s12257-019-0134-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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13
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Balodite E, Strazdina I, Martynova J, Galinina N, Rutkis R, Lasa Z, Kalnenieks U. Translocation of Zymomonas mobilis pyruvate decarboxylase to periplasmic compartment for production of acetaldehyde outside the cytosol. Microbiologyopen 2019; 8:e00809. [PMID: 30770675 PMCID: PMC6692523 DOI: 10.1002/mbo3.809] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/11/2019] [Accepted: 01/12/2019] [Indexed: 11/13/2022] Open
Abstract
Acetaldehyde, a valuable commodity chemical, is a volatile inhibitory byproduct of aerobic fermentation in Zymomonas mobilis and in several other microorganisms. Attempting to improve acetaldehyde production by minimizing its contact with the cell interior and facilitating its removal from the culture, we engineered a Z. mobilis strain with acetaldehyde synthesis reaction localized in periplasm. For that, the pyruvate decarboxylase (PDC) was transferred from the cell interior to the periplasmic compartment. This was achieved by the construction of a Z. mobilis Zm6 PDC‐deficient mutant, fusion of PDC with the periplasmic signal sequence of Z. mobilis gluconolactonase, and the following expression of this fusion protein in the PDC‐deficient mutant. The obtained recombinant strain PeriAc, with most of its PDC localized in periplasm, showed a twofold higher acetaldehyde yield, than the parent strain, and will be used for further improvement by directed evolution.
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Affiliation(s)
- Elina Balodite
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Inese Strazdina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | | | - Nina Galinina
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Reinis Rutkis
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Zane Lasa
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
| | - Uldis Kalnenieks
- Institute of Microbiology and Biotechnology, University of Latvia, Riga, Latvia
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Zhang K, Lu X, Li Y, Jiang X, Liu L, Wang H. New technologies provide more metabolic engineering strategies for bioethanol production in Zymomonas mobilis. Appl Microbiol Biotechnol 2019; 103:2087-2099. [PMID: 30661108 DOI: 10.1007/s00253-019-09620-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 02/06/2023]
Abstract
Bioethanol has been considered as a potentially renewable energy source, and metabolic engineering plays an important role in the production of biofuels. As an efficient ethanol-producing bacterium, Zymomonas mobilis has garnered special attention due to its high sugar uptake, ethanol yield, and tolerance. Different metabolic engineering strategies have been used to establish new metabolic pathways for Z. mobilis to broaden its substrate range, remove competing pathways, and enhance its tolerance to ethanol and lignocellulosic hydrolysate inhibitors. Recent advances in omics technology, computational modeling and simulation, system biology, and synthetic biology contribute to the efficient re-design and manipulation of microbes via metabolic engineering at the whole-cell level. In this review, we summarize the progress of some new technologies used for metabolic engineering to improve bioethanol production and tolerance in Z. mobilis. Some successful examples of metabolic engineering used to develop strains for ethanol production are described in detail. Lastly, some important strategies for future metabolic engineering efforts are also highlighted.
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Affiliation(s)
- Kun Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Xinxin Lu
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yi Li
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Xiaobing Jiang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Lei Liu
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Hailei Wang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.
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Todhanakasem T, Sowatad A, Kanokratana P, Havanapan PO, Champreda V. Expression and Extracellular Secretion of Endo-glucanase and Xylanase by Zymomonas mobilis. Appl Biochem Biotechnol 2018; 187:239-252. [PMID: 29923149 DOI: 10.1007/s12010-018-2821-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/11/2018] [Indexed: 12/27/2022]
Abstract
Recombinant Zymomonas mobilis (pGEX-4T-3 BI 120-2) was constructed to encode endo-glucanase (CelA) and endo-xylanase (Xyn11) from Z. mobilis ZM4 (ATCC 31821) and an uncultured bacterium. The recombinant was genetically engineered with the N-terminus of a predicted SecB-dependent (type II) secretion signal from phoC of Z. mobilis to translocate the enzymes extracellularly. Both the enzymes were characterized regarding their functional optimum pH and temperature, with the highest multi-enzyme activities at pH 6.0 and a temperature of 30 °C, which approximates the optimum conditions for ethanol production by Z. mobilis. The crude intracellular and extracellular fractions of the recombinant were characterized in terms of substrate specificity using carboxymethyl cellulose (CMC), beechwood xylan, filter paper, Avicel, and pretreated rice straw. The crude extracellular and intracellular enzymes with cellulolytic and xylanolytic activities were more robustly produced and secreted from the recombinant strain compared to the wild-type and ampicillin-sensitive strains, using CMC and beechwood xylan as the substrates. Ethanol production by the recombinant strain was greater than the production by the wild-type strain when pretreated rice straw was used as a sole carbon source.
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Affiliation(s)
- Tatsaporn Todhanakasem
- Department of Agro-Industry, Faculty of Biotechnology, Assumption University, Ramkhamhaeng Road, Bangkapi, Bangkok, 10240, Thailand.
| | - Apinya Sowatad
- Department of Agro-Industry, Faculty of Biotechnology, Assumption University, Ramkhamhaeng Road, Bangkapi, Bangkok, 10240, Thailand
| | - Pattanop Kanokratana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Phahonyothin Road, Klong Luang, Pathumthani, 12120, Thailand
| | - Phattara-Orn Havanapan
- Institute of Molecular Biosciences, Mahidol University, Phuttamonthon 4 Road, Salaya, Nakhon Pathom, 73170, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand Science Park, Phahonyothin Road, Klong Luang, Pathumthani, 12120, Thailand
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16
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Wang X, He Q, Yang Y, Wang J, Haning K, Hu Y, Wu B, He M, Zhang Y, Bao J, Contreras LM, Yang S. Advances and prospects in metabolic engineering of Zymomonas mobilis. Metab Eng 2018; 50:57-73. [PMID: 29627506 DOI: 10.1016/j.ymben.2018.04.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/31/2018] [Accepted: 04/01/2018] [Indexed: 12/22/2022]
Abstract
Biorefinery of biomass-based biofuels and biochemicals by microorganisms is a competitive alternative of traditional petroleum refineries. Zymomonas mobilis is a natural ethanologen with many desirable characteristics, which makes it an ideal industrial microbial biocatalyst for commercial production of desirable bioproducts through metabolic engineering. In this review, we summarize the metabolic engineering progress achieved in Z. mobilis to expand its substrate and product ranges as well as to enhance its robustness against stressful conditions such as inhibitory compounds within the lignocellulosic hydrolysates and slurries. We also discuss a few metabolic engineering strategies that can be applied in Z. mobilis to further develop it as a robust workhorse for economic lignocellulosic bioproducts. In addition, we briefly review the progress of metabolic engineering in Z. mobilis related to the classical synthetic biology cycle of "Design-Build-Test-Learn", as well as the progress and potential to develop Z. mobilis as a model chassis for biorefinery practices in the synthetic biology era.
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Affiliation(s)
- Xia Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Qiaoning He
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Yongfu Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jingwen Wang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Katie Haning
- Institute for Cellular and Molecular Biology, Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States.
| | - Yun Hu
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Bo Wu
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu 610041, China.
| | - Mingxiong He
- Key Laboratory of Development and Application of Rural Renewable Energy, Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, South Renmin Road, Chengdu 610041, China.
| | - Yaoping Zhang
- DOE-Great Lakes Bioenergy Research Center (GLBRC), University of Wisconsin-Madison, Madison, WI, United States.
| | - Jie Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Lydia M Contreras
- Institute for Cellular and Molecular Biology, Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, United States.
| | - Shihui Yang
- Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan 430062, China.
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Kim ES, Kim BS, Kim KY, Woo HM, Lee SM, Um Y. Aerobic and anaerobic cellulose utilization by Paenibacillus sp. CAA11 and enhancement of its cellulolytic ability by expressing a heterologous endoglucanase. J Biotechnol 2018; 268:21-27. [PMID: 29339118 DOI: 10.1016/j.jbiotec.2018.01.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/09/2018] [Accepted: 01/12/2018] [Indexed: 12/21/2022]
Abstract
For cost-effective lignocellulosic biofuel/chemical production, consolidated bioprocessing (CBP)-enabling microorganisms utilizing cellulose as well as producing biofuel/chemical are required. A novel strain Paenibacillus sp. CAA11 isolated from sediment was found to be not only as a cellulose degrader under both aerobic and strict anaerobic conditions but also as a producer of cellulosic biofuel/chemicals. Paenibacillus sp. CAA11 secreted cellulolytic enzymes by its own secretion system and produced ethanol as well as short-chain organic acids (formic acid, acetic acid, lactic acid) from cellulose. Cellulolytic activity of the strain was significantly enhanced by expressing a heterologous endoglucanase 168Cel5 from Bacillus subtilis under both aerobic and anaerobic conditions. The strain harboring the 168cel5 gene revealed 2-fold bigger halo zone on Congo-red plate and 1.75-fold more aerobic cellulose utilization in liquid medium compared with the negative control. Notably, under anaerobic conditions, the recombinant strain expressing 168Cel5 consumed 1.83-fold more cellulose (5.10 g/L) and produced 5-fold more ethanol (0.65 g/L) along with 5-fold more total acids (1.6 g/L) compared with the control, resulting 2.73-fold higher yields. This result demonstrates the potential of Paenibacillus sp. CAA11 as a suitable aerobic and anaerobic CBP-enabling microbe with cellulolytic production of ethanol and short-chain organic acids.
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Affiliation(s)
- Eun Sook Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea
| | - Byeong-Soo Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Department of Chemical and Biological Engineering, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Ki-Yeon Kim
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea
| | - Han-Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Green School (Graduate School of Energy and Environment), Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; Clean Energy and Chemical Engineering, Korea University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon 34113, Republic of Korea.
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Abstract
For many years, industrial enzymes have played an important role in the benefit of our society due to their many useful properties and a wide range of applications. They are key elements in the progress of many industries including foods, beverages, pharmaceuticals, diagnostics, therapy, personal care, animal feed, detergents, pulp and paper, textiles, leather, chemicals and biofuels. During recent decades, microbial enzymes have replaced many plant and animal enzymes. This is because microbial enzymes are widely available and produced economically in short fermentations and inexpensive media. Screening is
simple, and strain improvement for increased production has been very successful. The advances in recombinant DNA technology have had a major effect on production levels of enzymes and represent a way to overproduce industrially important microbial, plant and animal enzymes. It has been calculated that 50-60% of the world enzyme market is supplied with recombinant enzymes. Molecular methods, including genomics and
metagenomics, are being used for the discovery of new enzymes from microbes. Also, directed evolution has allowed the design of enzyme specificities and better performance.
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Affiliation(s)
- Arnold L. Demain
- Research Institute for Scientists Emeriti (RISE), Drew University, Madison, New Jersey 07940, USA
| | - Sergio Sánchez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas. Universidad Nacional Autónoma de México
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Ma H, Delafield DG, Wang Z, You J, Wu S. Finding Biomass Degrading Enzymes Through an Activity-Correlated Quantitative Proteomics Platform (ACPP). JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:655-663. [PMID: 28083757 PMCID: PMC5373979 DOI: 10.1007/s13361-016-1569-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/29/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
The microbial secretome, known as a pool of biomass (i.e., plant-based materials) degrading enzymes, can be utilized to discover industrial enzyme candidates for biofuel production. Proteomics approaches have been applied to discover novel enzyme candidates through comparing protein expression profiles with enzyme activity of the whole secretome under different growth conditions. However, the activity measurement of each enzyme candidate is needed for confident "active" enzyme assignments, which remains to be elucidated. To address this challenge, we have developed an Activity-Correlated Quantitative Proteomics Platform (ACPP) that systematically correlates protein-level enzymatic activity patterns and protein elution profiles using a label-free quantitative proteomics approach. The ACPP optimized a high performance anion exchange separation for efficiently fractionating complex protein samples while preserving enzymatic activities. The detected enzymatic activity patterns in sequential fractions using microplate-based assays were cross-correlated with protein elution profiles using a customized pattern-matching algorithm with a correlation R-score. The ACPP has been successfully applied to the identification of two types of "active" biomass-degrading enzymes (i.e., starch hydrolysis enzymes and cellulose hydrolysis enzymes) from Aspergillus niger secretome in a multiplexed fashion. By determining protein elution profiles of 156 proteins in A. niger secretome, we confidently identified the 1,4-α-glucosidase as the major "active" starch hydrolysis enzyme (R = 0.96) and the endoglucanase as the major "active" cellulose hydrolysis enzyme (R = 0.97). The results demonstrated that the ACPP facilitated the discovery of bioactive enzymes from complex protein samples in a high-throughput, multiplexing, and untargeted fashion. Graphical Abstract ᅟ.
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Affiliation(s)
- Hongyan Ma
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Daniel G Delafield
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Zhe Wang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Jianlan You
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA.
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Duwe A, Tippkötter N, Ulber R. Lignocellulose-Biorefinery: Ethanol-Focused. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 166:177-215. [PMID: 29071401 DOI: 10.1007/10_2016_72] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development prospects of the world markets for petroleum and other liquid fuels are diverse and partly contradictory. However, comprehensive changes for the energy supply of the future are essential. Notwithstanding the fact that there are still very large deposits of energy resources from a geological point of view, the finite nature of conventional oil reserves is indisputable. To reduce our dependence on oil, the EU, the USA, and other major economic zones rely on energy diversification. For this purpose, alternative materials and technologies are being sought, and is most obvious in the transport sector. The objective is to progressively replace fossil fuels with renewable and more sustainable fuels. In this respect, biofuels have a pre-eminent position in terms of their capability of blending with fossil fuels and being usable in existing cars without substantial modification. Ethanol can be considered as the primary renewable liquid fuel. In this chapter enzymes, micro-organisms, and processes for ethanol production based on renewable resources are described.
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Affiliation(s)
- A Duwe
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany.
| | - N Tippkötter
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany
| | - R Ulber
- Institute of Bioprocess Engineering, University of Kaiserslautern, Gottlieb-Daimler-Str. 49, 67663, Kaiserslautern, Germany
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Yang S, Fei Q, Zhang Y, Contreras LM, Utturkar SM, Brown SD, Himmel ME, Zhang M. Zymomonas mobilis as a model system for production of biofuels and biochemicals. Microb Biotechnol 2016; 9:699-717. [PMID: 27629544 PMCID: PMC5072187 DOI: 10.1111/1751-7915.12408] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/03/2016] [Accepted: 08/05/2016] [Indexed: 12/04/2022] Open
Abstract
Zymomonas mobilis is a natural ethanologen with many desirable industrial biocatalyst characteristics. In this review, we will discuss work to develop Z. mobilis as a model system for biofuel production from the perspectives of substrate utilization, development for industrial robustness, potential product spectrum, strain evaluation and fermentation strategies. This review also encompasses perspectives related to classical genetic tools and emerging technologies in this context.
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Affiliation(s)
- Shihui Yang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA. .,Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Hubei Key Laboratory of Industrial Biotechnology, College of Life Sciences, Hubei University, Wuhan, 430062, China.
| | - Qiang Fei
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.,School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yaoping Zhang
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI, 53726, USA
| | - Lydia M Contreras
- McKetta Department of Chemical Engineering, University of Texas, Austin, TX, 78712, USA
| | - Sagar M Utturkar
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37919, USA
| | - Steven D Brown
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37919, USA.,BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Michael E Himmel
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA
| | - Min Zhang
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.
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Ali SS, Nugent B, Mullins E, Doohan FM. Fungal-mediated consolidated bioprocessing: the potential of Fusarium oxysporum for the lignocellulosic ethanol industry. AMB Express 2016; 6:13. [PMID: 26888202 PMCID: PMC4757592 DOI: 10.1186/s13568-016-0185-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 02/09/2016] [Indexed: 12/21/2022] Open
Abstract
Microbial bioprocessing of lignocellulose to bioethanol still poses challenges in terms of substrate catabolism. The most important challenge is to overcome substrate recalcitrance and to thus reduce the number of steps needed to biorefine lignocellulose. Conventionally, conversion involves chemical pretreatment of lignocellulose, followed by hydrolysis of biomass to monomer sugars that are subsequently fermented into bioethanol. Consolidated bioprocessing (CBP) has been suggested as an efficient and economical method of manufacturing bioethanol from lignocellulose. CBP integrates the hydrolysis and fermentation steps into a single process, thereby significantly reducing the amount of steps in the biorefining process. Filamentous fungi are remarkable organisms that are naturally specialised in deconstructing plant biomass and thus they have tremendous potential as components of CBP. The fungus Fusarium oxysporum has potential for CBP of lignocellulose to bioethanol. Here we discuss the complexity and potential of CBP, the bottlenecks in the process, and the potential influence of fungal genetic diversity, substrate complexity and new technologies on the efficacy of CPB of lignocellulose, with a focus on F. oxysporum.
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Xun Z, Peter L. R, Kwon EE, Jeong SC, Jeon YJ. Growth Characteristics of a Pyruvate Decarboxylase Mutant Strain of Zymomonas mobilis. ACTA ACUST UNITED AC 2015. [DOI: 10.5352/jls.2015.25.11.1290] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Paulova L, Patakova P, Branska B, Rychtera M, Melzoch K. Lignocellulosic ethanol: Technology design and its impact on process efficiency. Biotechnol Adv 2015; 33:1091-107. [DOI: 10.1016/j.biotechadv.2014.12.002] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/01/2014] [Accepted: 12/03/2014] [Indexed: 12/27/2022]
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26
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Wang J, Gao G, Li Y, Yang L, Liang Y, Jin H, Han W, Feng Y, Zhang Z. Cloning, Expression, and Characterization of a Thermophilic Endoglucanase, AcCel12B from Acidothermus cellulolyticus 11B. Int J Mol Sci 2015; 16:25080-95. [PMID: 26506341 PMCID: PMC4632791 DOI: 10.3390/ijms161025080] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 09/29/2015] [Accepted: 10/13/2015] [Indexed: 12/23/2022] Open
Abstract
The gene ABK52392 from the thermophilic bacterium Acidothermus cellulolyticus 11B was predicted to be endoglucanase and classified into glycoside hydrolase family 12. ABK52392 encodes a protein containing a catalytic domain and a carbohydrate binding module. ABK52392 was cloned and functionally expressed in Escherichia coli. After purification by Ni-NTA agarose affinity chromatography and Q-Sepharose® Fast Flow chromatography, the properties of the recombinant protein (AcCel12B) were characterized. AcCel12B exhibited optimal activity at pH 4.5 and 75 °C. The half-lives of AcCel12B at 60 and 70 °C were about 90 and 2 h, respectively, under acidic conditions. The specific hydrolytic activities of AcCel12B at 70 °C and pH 4.5 for sodium carboxymethylcellulose (CMC) and regenerated amorphous cellulose (RAC) were 118.3 and 104.0 U·mg−1, respectively. The Km and Vmax of AcCel12B for CMC were 25.47 mg·mL−1 and 131.75 U·mg−1, respectively. The time course of hydrolysis for RAC was investigated by measuring reducing ends in the soluble and insoluble phases. The total hydrolysis rate rapidly decreased after the early stage of incubation and the generation of insoluble reducing ends decreased earlier than that of soluble reducing ends. High thermostability of the cellulase indicates its potential commercial significance and it could be exploited for industrial application in the future.
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Affiliation(s)
- Junling Wang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
- Department of Biotechnology, Jilin Agricultural Science and Technology College, Jilin 132101, China.
| | - Gui Gao
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Yuwei Li
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, China.
| | - Liangzhen Yang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Yanli Liang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Hanyong Jin
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Yan Feng
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
| | - Zuoming Zhang
- Key Laboratory for Molecular Enzymology & Engineering of the Ministry of Education, School of Life Science, Jilin University, Changchun 130012, China.
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Shivlata L, Satyanarayana T. Thermophilic and alkaliphilic Actinobacteria: biology and potential applications. Front Microbiol 2015; 6:1014. [PMID: 26441937 PMCID: PMC4585250 DOI: 10.3389/fmicb.2015.01014] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 09/07/2015] [Indexed: 11/13/2022] Open
Abstract
Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.
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Loaces I, Amarelle V, Muñoz-Gutierrez I, Fabiano E, Martinez A, Noya F. Improved ethanol production from biomass by a rumen metagenomic DNA fragment expressed in Escherichia coli MS04 during fermentation. Appl Microbiol Biotechnol 2015; 99:9049-60. [DOI: 10.1007/s00253-015-6801-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 10/23/2022]
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Simas-Rodrigues C, Villela HDM, Martins AP, Marques LG, Colepicolo P, Tonon AP. Microalgae for economic applications: advantages and perspectives for bioethanol. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:4097-108. [PMID: 25873683 DOI: 10.1093/jxb/erv130] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Renewable energy has attracted significant interest in recent years as a result of sustainability, environmental impact, and socio-economic considerations. Given existing technological knowledge and based on projections relating to biofuels derived from microalgae, microalgal feedstock is considered to be one of the most important renewable energy sources potentially available for industrial production. Therefore, this review examines microalgal bioethanol technology, which converts biomass from microalgae to fuel, the chemical processes involved, and possible ways of increasing the bioethanol yield, such as abiotic factors and genetic manipulation of fermenting organisms.
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Affiliation(s)
- Cíntia Simas-Rodrigues
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Professor Lineu Prestes, 748, 05508-000, São Paulo, Brazil
| | - Helena D M Villela
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Professor Lineu Prestes, 748, 05508-000, São Paulo, Brazil
| | - Aline P Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Professor Lineu Prestes, 748, 05508-000, São Paulo, Brazil
| | - Luiza G Marques
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Professor Lineu Prestes, 748, 05508-000, São Paulo, Brazil
| | - Pio Colepicolo
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Professor Lineu Prestes, 748, 05508-000, São Paulo, Brazil
| | - Angela P Tonon
- Los Alamos National Laboratory, Bioscience Division, PO Box M888, Los Alamos, NM 87545, USA
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Luo Z, Bao J. Secretive expression of heterologous β-glucosidase in Zymomonas mobilis. BIORESOUR BIOPROCESS 2015. [DOI: 10.1186/s40643-015-0053-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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Direct conversion of plant biomass to ethanol by engineered Caldicellulosiruptor bescii. Proc Natl Acad Sci U S A 2014; 111:8931-6. [PMID: 24889625 DOI: 10.1073/pnas.1402210111] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ethanol is the most widely used renewable transportation biofuel in the United States, with the production of 13.3 billion gallons in 2012 [John UM (2013) Contribution of the Ethanol Industry to the Economy of the United States]. Despite considerable effort to produce fuels from lignocellulosic biomass, chemical pretreatment and the addition of saccharolytic enzymes before microbial bioconversion remain economic barriers to industrial deployment [Lynd LR, et al. (2008) Nat Biotechnol 26(2):169-172]. We began with the thermophilic, anaerobic, cellulolytic bacterium Caldicellulosiruptor bescii, which efficiently uses unpretreated biomass, and engineered it to produce ethanol. Here we report the direct conversion of switchgrass, a nonfood, renewable feedstock, to ethanol without conventional pretreatment of the biomass. This process was accomplished by deletion of lactate dehydrogenase and heterologous expression of a Clostridium thermocellum bifunctional acetaldehyde/alcohol dehydrogenase. Whereas wild-type C. bescii lacks the ability to make ethanol, 70% of the fermentation products in the engineered strain were ethanol [12.8 mM ethanol directly from 2% (wt/vol) switchgrass, a real-world substrate] with decreased production of acetate by 38% compared with wild-type. Direct conversion of biomass to ethanol represents a new paradigm for consolidated bioprocessing, offering the potential for carbon neutral, cost-effective, sustainable fuel production.
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Bamboo: a new source of carbohydrate for biorefinery. Carbohydr Polym 2014; 111:645-54. [PMID: 25037399 DOI: 10.1016/j.carbpol.2014.05.025] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 04/08/2014] [Accepted: 05/03/2014] [Indexed: 01/08/2023]
Abstract
Bamboo is perennial woody grass, which distributed widely in the world and belonged to the Gramineae family and Bambuseae subfamily. It may be consider as a candidate lignocellulosic substrate for bio-ethanol production for its environmental benefits and higher annual biomass yield. The conversion of bamboo into bio-ethanol, bio-methane, natural food, flavonoids, and functional xylo-oligosaccharides production were reviewed in this paper. Future prospects for research include pretreatment, enzymatic hydrolysis and fermentation will also be performed to improve the whole process of ethanol production more economical. And revealing the molecular regulation mechanism of the fast growth of bamboo will provide chance for improving bamboo or other energy plants biomass yield through genetic engineering.
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Yang S, Pan C, Hurst GB, Dice L, Davison BH, Brown SD. Elucidation of Zymomonas mobilis physiology and stress responses by quantitative proteomics and transcriptomics. Front Microbiol 2014; 5:246. [PMID: 24904559 PMCID: PMC4033097 DOI: 10.3389/fmicb.2014.00246] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/06/2014] [Indexed: 11/13/2022] Open
Abstract
Zymomonas mobilis is an excellent ethanologenic bacterium. Biomass pretreatment and saccharification provides access to simple sugars, but also produces inhibitors such as acetate and furfural. Our previous work has identified and confirmed the genetic change of a 1.5-kb deletion in the sodium acetate tolerant Z. mobilis mutant (AcR) leading to constitutively elevated expression of a sodium proton antiporter encoding gene nhaA, which contributes to the sodium acetate tolerance of AcR mutant. In this study, we further investigated the responses of AcR and wild-type ZM4 to sodium acetate stress in minimum media using both transcriptomics and a metabolic labeling approach for quantitative proteomics the first time. Proteomic measurements at two time points identified about eight hundreds proteins, or about half of the predicted proteome. Extracellular metabolite analysis indicated AcR overcame the acetate stress quicker than ZM4 with a concomitant earlier ethanol production in AcR mutant, although the final ethanol yields and cell densities were similar between two strains. Transcriptomic samples were analyzed for four time points and revealed that the response of Z. mobilis to sodium acetate stress is dynamic, complex, and involved about one-fifth of the total predicted genes from all different functional categories. The modest correlations between proteomic and transcriptomic data may suggest the involvement of posttranscriptional control. In addition, the transcriptomic data of forty-four microarrays from four experiments for ZM4 and AcR under different conditions were combined to identify strain-specific, media-responsive, growth phase-dependent, and treatment-responsive gene expression profiles. Together this study indicates that minimal medium has the most dramatic effect on gene expression compared to rich medium followed by growth phase, inhibitor, and strain background. Genes involved in protein biosynthesis, glycolysis and fermentation as well as ATP synthesis and stress response play key roles in Z. mobilis metabolism with consistently strong expression levels under different conditions.
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Affiliation(s)
- Shihui Yang
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; BioEnergy Science Center, Oak Ridge National Laboratory Oak Ridge, TN, USA ; National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA
| | - Chongle Pan
- Computer Science and Mathematics Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Gregory B Hurst
- Chemical Sciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Lezlee Dice
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; BioEnergy Science Center, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Brian H Davison
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; BioEnergy Science Center, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; BioEnergy Science Center, Oak Ridge National Laboratory Oak Ridge, TN, USA
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Blumer-Schuette SE, Brown SD, Sander KB, Bayer EA, Kataeva I, Zurawski JV, Conway JM, Adams MWW, Kelly RM. Thermophilic lignocellulose deconstruction. FEMS Microbiol Rev 2014; 38:393-448. [DOI: 10.1111/1574-6976.12044] [Citation(s) in RCA: 128] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 08/20/2013] [Accepted: 08/28/2013] [Indexed: 11/28/2022] Open
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Wu B, He MX, Feng H, Shui ZX, Tang XY, Hu QC, Zhang YZ. Construction of a novel secretion expression system guided by native signal peptide of PhoD in Zymomonas mobilis. Biosci Biotechnol Biochem 2014; 78:708-13. [DOI: 10.1080/09168451.2014.896736] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Abstract
In the current study, three native signal peptides (SPs) from PhoC, PhoD, and ZMO0331were investigated and compared to construct novel secretion expression systems in Zymomonas mobilis. The secretion expression of target protein, α-amylase from Bacillus amyloliquefaciens (BAA), guided by PhoD’s SP resulted in more hydrolysis of starch than that by the other two SPs. Extracellular and intracellular α-amylase activities of the strain containing PhoD’s SP were also higher than the other two strains containing PhoC or ZMO0331’s SP. In addition, the evidence by alcohol dehydrogenase activity assay further confirmed that the starch hydrolysis was resulted from the secretion expression of BAA rather than the breakage of cells. Our results indicated that the SP of PhoD is able to serve as a promising candidate to assist secretion expression of heterogeneous genes in Z. mobilis. This will contribute to development of engineered Z. mobilis strains converting starch into ethanol.
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Affiliation(s)
- Bo Wu
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Ming-Xiong He
- Biomass Energy Technology and Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu, China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu, China
| | - Hong Feng
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Zong-Xia Shui
- Biomass Energy Technology and Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu, China
| | - Xiao-Yu Tang
- Biomass Energy Technology and Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu, China
| | - Qi-Chun Hu
- Biomass Energy Technology and Research Centre, Biogas Institute of Ministry of Agriculture, Chengdu, China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu, China
| | - Yi-Zheng Zhang
- College of Life Sciences, Sichuan University, Chengdu, China
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So LY, Chen WY, Lacap-Bugler DC, Seemann M, Watt RM. pZMO7-Derived shuttle vectors for heterologous protein expression and proteomic applications in the ethanol-producing bacterium Zymomonas mobilis. BMC Microbiol 2014; 14:68. [PMID: 24629064 PMCID: PMC4004385 DOI: 10.1186/1471-2180-14-68] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 03/06/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ethanol-producing bacterium Zymomonas mobilis has attracted considerable scientific and commercial interest due to its exceptional physiological properties. Shuttle vectors derived from native plasmids have previously been successfully used for heterologous gene expression in this bacterium for a variety of purposes, most notably for metabolic engineering applications. RESULTS A quantitative PCR (qPCR) approach was used to determine the copy numbers of two endogenous double stranded DNA plasmids: pZMO1A (1,647 bp) and pZMO7 (pZA1003; 4,551 bp) within the NCIMB 11163 strain of Z. mobilis. Data indicated pZMO1A and pZMO7 were present at ca. 3-5 and ca. 1-2 copies per cell, respectively. A ca. 1,900 bp fragment from plasmid pZMO7 was used to construct two Escherichia coli - Z. mobilis shuttle vectors (pZ7C and pZ7-184). The intracellular stabilities and copy numbers of pZ7C and pZ7-184 were characterized within the NCIMB 11163, ATCC 29191 and (ATCC 10988-derived) CU1 Rif2 strains of Z. mobilis. Both shuttle vectors could be stably maintained within the ATCC 29191 strain (ca. 20-40 copies per cell), and the CU1 Rif2 strain (ca. 2-3 copies per cell), for more than 50 generations in the absence of an antibiotic selectable marker. A selectable marker was required for shuttle vector maintenance in the parental NCIMB 11163 strain; most probably due to competition for replication with the endogenous pZMO7 plasmid molecules. N-terminal glutathione S-transferase (GST)-fusions of four endogenous proteins, namely the acyl-carrier protein (AcpP); 2-dehydro-3-deoxyphosphooctonate aldolase (KdsA); DNA polymerase III chi subunit (HolC); and the RNA chaperone protein Hfq; were successfully expressed from pZ7C-derived shuttle vectors, and their protein-protein binding interactions were analyzed in Z. mobilis ATCC 29191. Using this approach, proteins that co-purified with AcpP and KdsA were identified. CONCLUSIONS We show that a shuttle vector-based protein affinity 'pull-down' approach can be used to probe protein interaction networks in Z. mobilis cells. Our results demonstrate that protein expression plasmids derived from pZMO7 have significant potential for use in future biological or biotechnological applications within Z. mobilis.
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Affiliation(s)
| | | | | | | | - Rory M Watt
- Oral Biosciences Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Sai Ying Pun, Hong Kong.
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He MX, Wu B, Qin H, Ruan ZY, Tan FR, Wang JL, Shui ZX, Dai LC, Zhu QL, Pan K, Tang XY, Wang WG, Hu QC. Zymomonas mobilis: a novel platform for future biorefineries. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:101. [PMID: 25024744 PMCID: PMC4094786 DOI: 10.1186/1754-6834-7-101] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 06/20/2014] [Indexed: 05/21/2023]
Abstract
Biosynthesis of liquid fuels and biomass-based building block chemicals from microorganisms have been regarded as a competitive alternative route to traditional. Zymomonas mobilis possesses a number of desirable characteristics for its special Entner-Doudoroff pathway, which makes it an ideal platform for both metabolic engineering and commercial-scale production of desirable bio-products as the same as Escherichia coli and Saccharomyces cerevisiae based on consideration of future biomass biorefinery. Z. mobilis has been studied extensively on both fundamental and applied level, which will provide a basis for industrial biotechnology in the future. Furthermore, metabolic engineering of Z. mobilis for enhancing bio-ethanol production from biomass resources has been significantly promoted by different methods (i.e. mutagenesis, adaptive laboratory evolution, specific gene knock-out, and metabolic engineering). In addition, the feasibility of representative metabolites, i.e. sorbitol, bionic acid, levan, succinic acid, isobutanol, and isobutanol produced by Z. mobilis and the strategies for strain improvements are also discussed or highlighted in this paper. Moreover, this review will present some guidelines for future developments in the bio-based chemical production using Z. mobilis as a novel industrial platform for future biofineries.
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Affiliation(s)
- Ming Xiong He
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu 610041, P. R. China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
| | - Han Qin
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
| | - Zhi Yong Ruan
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Fu Rong Tan
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
| | - Jing Li Wang
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
| | - Zong Xia Shui
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
| | - Li Chun Dai
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
| | - Qi Li Zhu
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
| | - Ke Pan
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
| | - Xiao Yu Tang
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
| | - Wen Guo Wang
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
| | - Qi Chun Hu
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, P. R. China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu 610041, P. R. China
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Wei H, Wang W, Alahuhta M, Vander Wall T, Baker JO, Taylor LE, Decker SR, Himmel ME, Zhang M. Engineering towards a complete heterologous cellulase secretome in Yarrowia lipolytica reveals its potential for consolidated bioprocessing. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:148. [PMID: 25337149 PMCID: PMC4203959 DOI: 10.1186/s13068-014-0148-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Accepted: 09/24/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Yarrowia lipolytica is an oleaginous yeast capable of metabolizing glucose to lipids, which then accumulate intracellularly. However, it lacks the suite of cellulolytic enzymes required to break down biomass cellulose and cannot therefore utilize biomass directly as a carbon source. Toward the development of a direct microbial conversion platform for the production of hydrocarbon fuels from cellulosic biomass, the potential for Y. lipolytica to function as a consolidated bioprocessing strain was investigated by first conducting a genomic search and functional testing of its endogenous glycoside hydrolases. Once the range of endogenous enzymes was determined, the critical cellulases from Trichoderma reesei were cloned into Yarrowia. RESULTS Initially, work to express T. reesei endoglucanase II (EGII) and cellobiohydrolase (CBH) II in Y. lipolytica resulted in the successful secretion of active enzymes. However, a critical cellulase, T. reesei CBHI, while successfully expressed in and secreted from Yarrowia, showed less than expected enzymatic activity, suggesting an incompatibility (probably at the post-translational level) for its expression in Yarrowia. This result prompted us to evaluate alternative or modified CBHI enzymes. Our subsequent expression of a T. reesei-Talaromyces emersonii (Tr-Te) chimeric CBHI, Chaetomium thermophilum CBHI, and Humicola grisea CBHI demonstrated remarkably improved enzymatic activities. Specifically, the purified chimeric Tr-Te CBHI showed a specific activity on Avicel that is comparable to that of the native T. reesei CBHI. Furthermore, the chimeric Tr-Te CBHI also showed significant synergism with EGII and CBHII in degrading cellulosic substrates, using either mixed supernatants or co-cultures of the corresponding Y. lipolytica transformants. The consortia system approach also allows rational volume mixing of the transformant cultures in accordance with the optimal ratio of cellulases required for efficient degradation of cellulosic substrates. CONCLUSIONS Taken together, this work demonstrates the first case of successful expression of a chimeric CBHI with essentially full native activity in Y. lipolytica, and supports the notion that Y. lipolytica strains can be genetically engineered, ultimately by heterologous expression of fungal cellulases and other enzymes, to directly convert lignocellulosic substrates to biofuels.
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Affiliation(s)
- Hui Wei
- />Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Wei Wang
- />Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Markus Alahuhta
- />Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Todd Vander Wall
- />Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - John O Baker
- />Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Larry E Taylor
- />Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Stephen R Decker
- />Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Michael E Himmel
- />Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
| | - Min Zhang
- />National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401 USA
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Garvey M, Klose H, Fischer R, Lambertz C, Commandeur U. Cellulases for biomass degradation: comparing recombinant cellulase expression platforms. Trends Biotechnol 2013; 31:581-93. [DOI: 10.1016/j.tibtech.2013.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 10/26/2022]
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Systems biology analysis of Zymomonas mobilis ZM4 ethanol stress responses. PLoS One 2013; 8:e68886. [PMID: 23874800 PMCID: PMC3712917 DOI: 10.1371/journal.pone.0068886] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 06/07/2013] [Indexed: 12/15/2022] Open
Abstract
Background Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular mechanisms of its ethanol stress response have not been elucidated fully. Methodology/Principal Findings In this study, ethanol stress responses were investigated using systems biology approaches. Medium supplementation with an initial 47 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 55% of the predicted ZM4 proteome. Proteins related to metabolism and stress response such as chaperones and key regulators were more abundant in the early ethanol stress condition. Transcriptomic studies indicated that the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Transcriptomic data were used to update Z. mobilis ZM4 operon models. Furthermore, correlations among the transcriptomic, proteomic and metabolic data were examined. Among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher. Conclusions Our study has provided insights into the responses of Z. mobilis to ethanol stress through an integrated “omics” approach for the first time. This systems biology study elucidated key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress.
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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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Reed B, Chen R. Biotechnological applications of bacterial protein secretion: from therapeutics to biofuel production. Res Microbiol 2013; 164:675-82. [PMID: 23541476 DOI: 10.1016/j.resmic.2013.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2012] [Accepted: 02/27/2013] [Indexed: 10/27/2022]
Abstract
Recent years have witnessed significant progresses in engineering of recombinant protein secretion. The relatively simple secretion mechanisms, Type I and Type V (autotransporters), are increasingly used for secretion of recombinant proteins. The secretion level of target proteins varied from milligrams to grams per liter. The range of proteins was significantly expanded beyond medical application. Notable additions include biofuel productions from renewable feedstock. Despite the progress, almost all successes in the engineering efforts come with significant trials and errors, highlighting the need for a better understanding of secretion systems and rational based methods.
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Affiliation(s)
- Ben Reed
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Melillo E, Setroikromo R, Quax WJ, Kayser O. Production of α-cuprenene in Xanthophyllomyces dendrorhous: a step closer to a potent terpene biofactory. Microb Cell Fact 2013; 12:13. [PMID: 23383605 PMCID: PMC3626582 DOI: 10.1186/1475-2859-12-13] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 01/28/2013] [Indexed: 11/15/2022] Open
Abstract
Background The red yeast Xanthophyllomyces dendrorhous is a natural producer of the carotenoid astaxanthin. Because of its high flux, the native terpene pathway leading to the production of the tetraterpene is of particular interest as it can be redirected toward the production of other terpene compounds. The genetic tools for the transformation of the yeast with the concurrent knock-out of genes involved in the astaxanthin biosynthesis are made available and here we show that the production of the sesquiterpene α-cuprenene is possible in mutant strains of X. dendrorhous transformed with the Cop6 gene originating from the fungus Coprinus cinereus. For the evaluation of the production levels, we chose to express the same gene and analyze the accumulation of α-cuprenene in Escherichia coli and Saccharomyces cerevisiae, as well. Here we propose that X. dendrorhous is a candidate in the search for the potential platform organism for the production of terpenes. Results All three X. dendrorhous mutants functionally express the Cop6 gene and accumulate α-cuprenene. The production of α-cuprenene in the red yeast reached 80 mg/L, which represents a far higher concentration compared to the levels obtained in the E. coli and S. cerevisiae mutants. At this expression levels the pool of terpene precursors has not become a limiting factor in the X. dendrorhous mutants since the expression of the Cop6 gene in the genomic rDNA of the yeast allows production of both α-cuprenene and astaxanthin without affecting the growth or the accumulation levels of both compounds. Conclusions We have shown that X. dendrorhous can produce α-cuprenene, and the results here presented, next to the capability of accumulating at least two more non-native sesquiterpenes, demonstrates the high potential of this yeast to become an interesting terpene-based drugs producer.
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Affiliation(s)
- Elena Melillo
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, A, Deusinglaan 1, Groningen 9713AV, The Netherlands
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He MX, Wu B, Shui ZX, Hu QC, Wang WG, Tan FR, Tang XY, Zhu QL, Pan K, Li Q, Su XH. Transcriptome profiling of Zymomonas mobilis under ethanol stress. BIOTECHNOLOGY FOR BIOFUELS 2012; 5:75. [PMID: 23057803 PMCID: PMC3495753 DOI: 10.1186/1754-6834-5-75] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 10/02/2012] [Indexed: 05/12/2023]
Abstract
BACKGROUND High tolerance to ethanol is a desirable characteristics for ethanologenic strains used in industrial ethanol fermentation. A deeper understanding of the molecular mechanisms underlying ethanologenic strains tolerance of ethanol stress may guide the design of rational strategies to increase process performance in industrial alcoholic production. Many extensive studies have been performed in Saccharomyces cerevisiae and Escherichia coli. However, the physiological basis and genetic mechanisms involved in ethanol tolerance for Zymomonas mobilis are poorly understood on genomic level. To identify the genes required for tolerance to ethanol, microarray technology was used to investigate the transcriptome profiling of the ethanologenic Z. mobilis in response to ethanol stress. RESULTS We successfully identified 127 genes which were differentially expressed in response to ethanol. Ethanol up- or down-regulated genes related to cell wall/membrane biogenesis, metabolism, and transcription. These genes were classified as being involved in a wide range of cellular processes including carbohydrate metabolism, cell wall/membrane biogenesis, respiratory chain, terpenoid biosynthesis, DNA replication, DNA recombination, DNA repair, transport, transcriptional regulation, some universal stress response, etc. CONCLUSION In this study, genome-wide transcriptional responses to ethanol were investigated for the first time in Z. mobilis using microarray analysis.Our results revealed that ethanol had effects on multiple aspects of cellular metabolism at the transcriptional level and that membrane might play important roles in response to ethanol. Although the molecular mechanism involved in tolerance and adaptation of ethanologenic strains to ethanol is still unclear, this research has provided insights into molecular response to ethanol in Z. mobilis. These data will also be helpful to construct more ethanol resistant strains for cellulosic ethanol production in the future.
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Affiliation(s)
- Ming-xiong He
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu 610041, P. R. China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
| | - Zong-xia Shui
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
| | - Qi-chun Hu
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu 610041, P. R. China
| | - Wen-guo Wang
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
| | - Fu-rong Tan
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
| | - Xiao-yu Tang
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
| | - Qi-li Zhu
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
| | - Ke Pan
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
| | - Qing Li
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
| | - Xiao-hong Su
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu 610041, China
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Cloning and expression of amyE gene from Bacillus subtilis in Zymomonas mobilis and direct production of ethanol from soluble starch. BIOTECHNOL BIOPROC E 2012. [DOI: 10.1007/s12257-011-0490-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Heterologous expression of plant cell wall degrading enzymes for effective production of cellulosic biofuels. J Biomed Biotechnol 2012; 2012:405842. [PMID: 22911272 PMCID: PMC3403577 DOI: 10.1155/2012/405842] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 05/20/2012] [Indexed: 11/17/2022] Open
Abstract
A major technical challenge in the cost-effective production of cellulosic biofuel is the need to lower the cost of plant cell wall degrading enzymes (PCDE), which is required for the production of sugars from biomass. Several competitive, low-cost technologies have been developed to produce PCDE in different host organisms such as Escherichia coli, Zymomonas mobilis, and plant. Selection of an ideal host organism is very important, because each host organism has its own unique features. Synthetic biology-aided tools enable heterologous expression of PCDE in recombinant E. coli or Z. mobilis and allow successful consolidated bioprocessing (CBP) in these microorganisms. In-planta expression provides an opportunity to simplify the process of enzyme production and plant biomass processing and leads to self-deconstruction of plant cell walls. Although the future of currently available technologies is difficult to predict, a complete and viable platform will most likely be available through the integration of the existing approaches with the development of breakthrough technologies.
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He MX, Wu B, Shui ZX, Hu QC, Wang WG, Tan FR, Tang XY, Zhu QL, Pan K, Li Q, Su XH. Transcriptome profiling of Zymomonas mobilis under furfural stress. Appl Microbiol Biotechnol 2012; 95:189-99. [PMID: 22592554 DOI: 10.1007/s00253-012-4155-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 05/03/2012] [Accepted: 05/03/2012] [Indexed: 11/24/2022]
Abstract
Furfural from lignocellulosic hydrolysates is the prevalent inhibitor to microorganisms during cellulosic ethanol production, but the molecular mechanisms of tolerance to this inhibitor in Zymomonas mobilis are still unclear. In this study, genome-wide transcriptional responses to furfural were investigated in Z. mobilis using microarray analysis. We found that 433 genes were differentially expressed in response to furfural. Furfural up- or down-regulated genes related to cell wall/membrane biogenesis, metabolism, and transcription. However, furfural has a subtle negative effect on Entner-Doudoroff pathway mRNAs. Our results revealed that furfural had effects on multiple aspects of cellular metabolism at the transcriptional level and that membrane might play important roles in response to furfural. This research has provided insights into the molecular response to furfural in Z. mobilis, and it will be helpful to construct more furfural-resistant strains for cellulosic ethanol production.
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Affiliation(s)
- Ming-xiong He
- Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renming Nanlu, Chengdu 610041, China.
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Galinina N, Lasa Z, Strazdina I, Rutkis R, Kalnenieks U. Effect of ADH II deficiency on the intracellular redox homeostasis in Zymomonas mobilis. ScientificWorldJournal 2012; 2012:742610. [PMID: 22629192 PMCID: PMC3354707 DOI: 10.1100/2012/742610] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 12/07/2011] [Indexed: 01/11/2023] Open
Abstract
Mutant strain of the facultatively anaerobic, ethanol-producing bacterium Zymomonas mobilis, deficient in the Fe-containing alcohol dehydrogenase isoenzyme (ADH II), showed impaired homeostasis of the intracellular NAD(P)H during transition from anaerobic to aerobic conditions, and also in steady-state continuous cultures at various oxygen supplies. At the same time, ADH II deficiency in aerobically grown cells was accompanied by a threefold increase of catalase activity and by about 50% increase of hydrogen peroxide excretion. It is concluded that ADH II under aerobic conditions functions to maintain intracellular redox homeostasis and to protect the cells from endogenous hydrogen peroxide.
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Affiliation(s)
- Nina Galinina
- Institute of Microbiology and Biotechnology, University of Latvia, Kronvalda Boulevard 4, 1586 Riga, Latvia
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Jeon YJ, Xun Z, Su P, Rogers PL. Genome-wide transcriptomic analysis of a flocculent strain of Zymomonas mobilis. Appl Microbiol Biotechnol 2012; 93:2513-8. [PMID: 22350321 DOI: 10.1007/s00253-012-3948-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Revised: 02/06/2012] [Accepted: 02/06/2012] [Indexed: 11/28/2022]
Abstract
ZM401, a flocculent mutant strain of Zymomonas mobilis ZM4 was studied using genome-wide transcriptomic analysis for evidence related to phenotypic changes associated with its cell-cell attachment behaviour. Batch fermentation studies with ZM401 and its parent strain ZM4 demonstrated that similar ethanol yields and productivities could be achieved with both strains indicating the potential of the flocculent strains for cost-effective cell biomass recycling with resultant high ethanol volumetric productivities. The results showed that twofold or greater differential expression occurred for 26 genes of ZM401 when compared to those of ZM4. Among these, significant over-expression was evident for the genes ZMO1083 and ZMO1084 which are associated with bacterial cellulose synthesis, while reduced expression was found for ZMO0614, ZMO0613, and ZMO0635 which are all associated with synthesis of flagella-related proteins. Both enhanced cellulose production and reduced flagella activity are likely to facilitate more stable flocculent behaviour in ZM401. From comparative DNA sequence analysis of these 26 genes, only one single point mutation was identified. This occurred at the amino acid position A525V of ZMO1055 which encodes for diguanyl cyclase/phosphoesterase which may be related to cell motility and cellulose synthesis in Z. mobilis.
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Affiliation(s)
- Young Jae Jeon
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Kensington, Australia
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