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Wang J, Liu S, Huang J, Ren K, Zhu Y, Yang S. Alginate: Microbial production, functionalization, and biomedical applications. Int J Biol Macromol 2023; 242:125048. [PMID: 37236570 DOI: 10.1016/j.ijbiomac.2023.125048] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/21/2023] [Accepted: 05/22/2023] [Indexed: 05/28/2023]
Abstract
Alginates are natural polysaccharides widely participating in food, pharmaceutical, and environmental applications due to their excellent gelling capacity. Their excellent biocompatibility and biodegradability further extend their application to biomedical fields. The low consistency in molecular weight and composition of algae-based alginates may limit their performance in advanced biomedical applications. It makes microbial alginate production more attractive due to its potential for customizing alginate molecules with stable characteristics. Production costs remain the primary factor limiting the commercialization of microbial alginates. However, carbon-rich wastes from sugar, dairy, and biodiesel industries may serve as potential substitutes for pure sugars for microbial alginate production to reduce substrate costs. Fermentation parameter control and genetic engineering strategies may further improve the production efficiency and customize the molecular composition of microbial alginates. To meet the specific needs of biomedical applications, alginates may need functionalization, such as functional group modifications and crosslinking treatments, to achieve enhanced mechanical properties and biochemical activities. The development of alginate-based composites incorporated with other polysaccharides, gelatin, and bioactive factors can integrate the advantages of each component to meet multiple requirements in wound healing, drug delivery, and tissue engineering applications. This review provided a comprehensive insight into the sustainable production of high-value microbial alginates. It also discussed recent advances in alginate modification strategies and alginate-based composites for representative biomedical applications.
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Affiliation(s)
- Jianfei Wang
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Shijie Liu
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States.
| | - Jiaqi Huang
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States; The Center for Biotechnology & Interdisciplinary Studies (CBIS) at Rensselaer Polytechnic Institute, Troy, NY 12180, United States
| | - Kexin Ren
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Yan Zhu
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
| | - Siying Yang
- Department of Chemical Engineering, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, United States
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2
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Ferreira D, Venceslau SS, Bernardino R, Preto A, Zhang L, Waldbauer JR, Leavitt WD, Pereira IAC. DsrC is involved in fermentative growth and interacts directly with the FlxABCD-HdrABC complex in Desulfovibrio vulgaris Hildenborough. Environ Microbiol 2023; 25:962-976. [PMID: 36602077 DOI: 10.1111/1462-2920.16335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023]
Abstract
DsrC is a key protein in dissimilatory sulfur metabolism, where it works as co-substrate of the dissimilatory sulfite reductase DsrAB. DsrC has two conserved cysteines in a C-terminal arm that are converted to a trisulfide upon reduction of sulfite. In sulfate-reducing bacteria, DsrC is essential and previous works suggested additional functions beyond sulfite reduction. Here, we studied whether DsrC also plays a role during fermentative growth of Desulfovibrio vulgaris Hildenborough, by studying two strains where the functionality of DsrC is impaired by a lower level of expression (IPFG07) and additionally by the absence of one conserved Cys (IPFG09). Growth studies coupled with metabolite and proteomic analyses reveal that fermentation leads to lower levels of DsrC, but impairment of its function results in reduced growth by fermentation and a shift towards more fermentative metabolism during sulfate respiration. In both respiratory and fermentative conditions, there is increased abundance of the FlxABCD-HdrABC complex and Adh alcohol dehydrogenase in IPFG09 versus the wild type, which is reflected in higher production of ethanol. Pull-down experiments confirmed a direct interaction between DsrC and the FlxABCD-HdrABC complex, through the HdrB subunit. Dissimilatory sulfur metabolism, where sulfur compounds are used for energy generation, is a key process in the ecology of anoxic environments, and is more widespread among bacteria than previously believed. Two central proteins for this type of metabolism are DsrAB dissimilatory sulfite reductase and its co-substrate DsrC. Using physiological, proteomic and biochemical studies of Desulfovibrio vulgaris Hildenborough and mutants affected in DsrC functionality, we show that DsrC is also relevant for fermentative growth of this model organism and that it interacts directly with the soluble FlxABCD-HdrABC complex that links the NAD(H) pool with dissimilatory sulfite reduction.
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Affiliation(s)
- Delfim Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sofia S Venceslau
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Raquel Bernardino
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - André Preto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lichun Zhang
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - Jacob R Waldbauer
- Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois, USA
| | - William D Leavitt
- Department of Earth Sciences, Dartmouth College, Hanover, New Hampshire, USA
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire, USA
| | - Inês A C Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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3
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Gleason CB, Beckett LM, White RR. Rumen fermentation and epithelial gene expression responses to diet ingredients designed to differ in ruminally degradable protein and fiber supplies. Sci Rep 2022; 12:2933. [PMID: 35190602 PMCID: PMC8861106 DOI: 10.1038/s41598-022-06890-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/08/2022] [Indexed: 12/02/2022] Open
Abstract
Although numerous studies exist relating ruminal volatile fatty acid (VFA) concentrations to diet composition and animal performance, minimal information is available describing how VFA dynamics respond to diets within the context of the whole rumen environment. The objective of this study was to characterize how protein and fiber sources affect dry matter intake, rumen pH, fluid dynamics, fermentation parameters, and epithelial gene expression. Four diet treatments (soybean meal or heat-treated soybean meal and beet pulp or timothy hay) were delivered to 10 wethers. The soybean meals served as crude protein (CP) sources while the beet pulp and timothy hay represented neutral detergent fiber (NDF) sources. Feed intake, rumen pH, fluid pool size, and fluid passage rate were unaffected by treatment. Butyrate synthesis and absorption were greater on the beet pulp treatment whereas synthesis and absorption of other VFA remained unchanged. Both CP and NDF treatment effects were associated with numerous VFA interconversions. Expression levels of rumen epithelial genes were not altered by diet treatment. These results indicate that rumen VFA dynamics are altered by changes in dietary sources of nutrients but that intake, rumen environmental parameters, and the rumen epithelium may be less responsive to such changes.
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Affiliation(s)
- C B Gleason
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - L M Beckett
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - R R White
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, 24061, USA.
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4
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Mendoza SN, Saa PA, Teusink B, Agosin E. Metabolic Modeling of Wine Fermentation at Genome Scale. Methods Mol Biol 2022; 2399:395-454. [PMID: 35604565 DOI: 10.1007/978-1-0716-1831-8_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wine fermentation is an ancient biotechnological process mediated by different microorganisms such as yeast and bacteria. Understanding of the metabolic and physiological phenomena taking place during this process can be now attained at a genome scale with the help of metabolic models. In this chapter, we present a detailed protocol for modeling wine fermentation using genome-scale metabolic models. In particular, we illustrate how metabolic fluxes can be computed, optimized and interpreted, for both yeast and bacteria under winemaking conditions. We also show how nutritional requirements can be determined and simulated using these models in relevant test cases. This chapter introduces fundamental concepts and practical steps for applying flux balance analysis in wine fermentation, and as such, it is intended for a broad microbiology audience as well as for practitioners in the metabolic modeling field.
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Affiliation(s)
| | - Pedro A Saa
- Laboratory of Biotechnology, Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Bas Teusink
- Systems Biology Lab, AIMMS, Vrije Universiteit, Amsterdam, The Netherlands
| | - Eduardo Agosin
- Laboratory of Biotechnology, Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile.
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5
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Liu J, Chen Y, Wang WQ, Liu JH, Zhu CQ, Zhong YP, Zhang HQ, Liu XF, Yin XR. Transcription factors AcERF74/75 respond to waterlogging stress and trigger alcoholic fermentation-related genes in kiwifruit. Plant Sci 2022; 314:111115. [PMID: 34895544 DOI: 10.1016/j.plantsci.2021.111115] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/04/2021] [Accepted: 11/08/2021] [Indexed: 06/14/2023]
Abstract
Kiwifruit plants have a fleshy, shallow root system which is sensitive to waterlogging stress, which results in a decrease in crop yield or even plants death. Although the waterlogging stress responses in kiwifruit have attracted much attention, the underlying molecular mechanism remains unclear. In this study, waterlogging led to drastic inhibition of root growth of 'Donghong' kiwifruit (Actinidia chinensis) plants grown in vitro, which was accompanied by significant elevation of endogenous acetaldehyde and ethanol contents. RNA-seq of roots of plants waterlogged for 0, 1 and 2 days revealed that a total of 149 genes were up- or down-regulated, including seven biosynthetic genes related to the glycolysis/gluconeogenesis pathway and 10 transcription factors. Analyses with real-time PCR, dual-luciferase assays and EMSA demonstrated that AcERF74 and AcERF75, two members of the ERF-VII subfamily, directly upregulated AcADH1 (alcohol dehydrogenase). Moreover, the overexpression of AcERF74/75 in transgenic calli resulted in dramatic increase of endogenous ethanol contents through the triggering of AcADH1 and AcADH2 expression. Although the AcPDC2 (pyruvate decarboxylase) expression was also enhanced in transgenic lines, the endogenous acetaldehyde contents showed no significant changes. These results illustrated that AcERF74/75 are two transcriptional activators on alcoholic fermentation related genes and are responsive to waterlogging stress in kiwifruit.
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Affiliation(s)
- Jiao Liu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Yue Chen
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Wen-Qiu Wang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Ji-Hong Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, PR China
| | - Chang-Qing Zhu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
| | - Yun-Peng Zhong
- Key Laboratory for Fruit Tree Growth, Development and Quality Control, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, PR China
| | - Hui-Qin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, PR China.
| | - Xiao-Fen Liu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China.
| | - Xue-Ren Yin
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China; The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, PR China
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6
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Tsuchiya Y, Nakamura T, Izumi Y, Okazaki K, Shinano T, Kubo Y, Katsuhara M, Sasaki T, Yamamoto Y. Physiological Role of Aerobic Fermentation Constitutively Expressed in an Aluminum-Tolerant Cell Line of Tobacco (Nicotiana tabacum). Plant Cell Physiol 2021; 62:1460-1477. [PMID: 34184745 PMCID: PMC8981456 DOI: 10.1093/pcp/pcab098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 06/12/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
Aluminum (Al)-tolerant tobacco cell line ALT301 derived from SL (wild-type) hardly exhibits Al-triggered reactive oxygen species (ROS) compared with SL. Molecular mechanism leading to this phenotype was investigated comparatively with SL. Under normal growth condition, metabolome data suggested the activation of glycolysis and lactate fermentation but the repression of the tricarboxylic acid (TCA) cycle in ALT301, namely aerobic fermentation, which seemed to be transcriptionally controlled partly by higher expression of genes encoding lactate dehydrogenase and pyruvate dehydrogenase kinase. Microarray and gene ontology analyses revealed the upregulation of the gene encoding related to APETALA2.3 (RAP2.3)-like protein, one of the group VII ethylene response factors (ERFVIIs), in ALT301. ERFVII transcription factors are known to be key regulators for hypoxia response that promotes substrate-level ATP production by glycolysis and fermentation. ERFVIIs are degraded under normoxia by the N-end rule pathway of proteolysis depending on both oxygen and nitric oxide (NO), and NO is produced mainly by nitrate reductase (NR) in plants. In ALT301, levels of the NR gene expression (NIA2), NR activity and NO production were all lower compared with SL. Consistently, the known effects of NO on respiratory pathways were also repressed in ALT301. Under Al-treatment condition, NO level increased in both lines but was lower in ALT301. These results suggest that the upregulation of the RAP2.3-like gene and the downregulation of the NIA2 gene and resultant NO depletion in ALT301 coordinately enhance aerobic fermentation, which seems to be related to a higher capacity to prevent ROS production in mitochondria under Al stress.
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Affiliation(s)
- Yoshiyuki Tsuchiya
- Institute of Plant Science and Resources, Okayama
University, Chuo 2-20-1, Kurashiki, Okayama 710-0046, Japan
| | - Takuji Nakamura
- Lowland Crop Rotation System Group, Division of
Lowland Farming Research, Hokkaido Agricultural Research Center (HARC),
NARO, 1 Hitsujigaoka, Toyohira-ku, Sapporo 062-8555, Japan
| | - Yohei Izumi
- Institute of Plant Science and Resources, Okayama
University, Chuo 2-20-1, Kurashiki, Okayama 710-0046, Japan
| | - Keiki Okazaki
- Central Region Agricultural Research Center, NARO
(CARC/NARO), 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8666, Japan
| | - Takuro Shinano
- Laboratory of Plant Nutrition, Graduate School of
Agriculture, Hokkaido University, N9, W9, Kitaku, Sapporo, Hokkaido
060-8589, Japan
| | - Yasutaka Kubo
- Graduate School of Environmental and Life
Science, Okayama University, Tsushima, Okayama 700-8530, Japan
| | - Maki Katsuhara
- Institute of Plant Science and Resources, Okayama
University, Chuo 2-20-1, Kurashiki, Okayama 710-0046, Japan
| | - Takayuki Sasaki
- Institute of Plant Science and Resources, Okayama
University, Chuo 2-20-1, Kurashiki, Okayama 710-0046, Japan
| | - Yoko Yamamoto
- Institute of Plant Science and Resources, Okayama
University, Chuo 2-20-1, Kurashiki, Okayama 710-0046, Japan
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7
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Vanmarcke G, Deparis Q, Vanthienen W, Peetermans A, Foulquié-Moreno MR, Thevelein JM. A novel AST2 mutation generated upon whole-genome transformation of Saccharomyces cerevisiae confers high tolerance to 5-Hydroxymethylfurfural (HMF) and other inhibitors. PLoS Genet 2021; 17:e1009826. [PMID: 34624020 PMCID: PMC8500407 DOI: 10.1371/journal.pgen.1009826] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/14/2021] [Indexed: 11/19/2022] Open
Abstract
Development of cell factories for conversion of lignocellulosic biomass hydrolysates into biofuels or bio-based chemicals faces major challenges, including the presence of inhibitory chemicals derived from biomass hydrolysis or pretreatment. Extensive screening of 2526 Saccharomyces cerevisiae strains and 17 non-conventional yeast species identified a Candida glabrata strain as the most 5-hydroxymethylfurfural (HMF) tolerant. Whole-genome (WG) transformation of the second-generation industrial S. cerevisiae strain MD4 with genomic DNA from C. glabrata, but not from non-tolerant strains, allowed selection of stable transformants in the presence of HMF. Transformant GVM0 showed the highest HMF tolerance for growth on plates and in small-scale fermentations. Comparison of the WG sequence of MD4 and GVM1, a diploid segregant of GVM0 with similarly high HMF tolerance, surprisingly revealed only nine non-synonymous SNPs, of which none were present in the C. glabrata genome. Reciprocal hemizygosity analysis in diploid strain GVM1 revealed AST2N406I as the only causative mutation. This novel SNP improved tolerance to HMF, furfural and other inhibitors, when introduced in different yeast genetic backgrounds and both in synthetic media and lignocellulose hydrolysates. It stimulated disappearance of HMF and furfural from the medium and enhanced in vitro furfural NADH-dependent reducing activity. The corresponding mutation present in AST1 (i.e. AST1D405I) the paralog gene of AST2, also improved inhibitor tolerance but only in combination with AST2N406I and in presence of high inhibitor concentrations. Our work provides a powerful genetic tool to improve yeast inhibitor tolerance in lignocellulosic biomass hydrolysates and other inhibitor-rich industrial media, and it has revealed for the first time a clear function for Ast2 and Ast1 in inhibitor tolerance.
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Affiliation(s)
- Gert Vanmarcke
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Quinten Deparis
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Ward Vanthienen
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Arne Peetermans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Maria R. Foulquié-Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
| | - Johan M. Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- Center for Microbiology, VIB, Leuven-Heverlee, Belgium
- NovelYeast bv, Open Bio-Incubator, Erasmus High School, Brussels (Jette), Belgium
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8
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Petrizzelli MS, de Vienne D, Nidelet T, Noûs C, Dillmann C. Data integration uncovers the metabolic bases of phenotypic variation in yeast. PLoS Comput Biol 2021; 17:e1009157. [PMID: 34264947 PMCID: PMC8315545 DOI: 10.1371/journal.pcbi.1009157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/27/2021] [Accepted: 06/07/2021] [Indexed: 12/13/2022] Open
Abstract
The relationship between different levels of integration is a key feature for understanding the genotype-phenotype map. Here, we describe a novel method of integrated data analysis that incorporates protein abundance data into constraint-based modeling to elucidate the biological mechanisms underlying phenotypic variation. Specifically, we studied yeast genetic diversity at three levels of phenotypic complexity in a population of yeast obtained by pairwise crosses of eleven strains belonging to two species, Saccharomyces cerevisiae and S. uvarum. The data included protein abundances, integrated traits (life-history/fermentation) and computational estimates of metabolic fluxes. Results highlighted that the negative correlation between production traits such as population carrying capacity (K) and traits associated with growth and fermentation rates (Jmax) is explained by a differential usage of energy production pathways: a high K was associated with high TCA fluxes, while a high Jmax was associated with high glycolytic fluxes. Enrichment analysis of protein sets confirmed our results. This powerful approach allowed us to identify the molecular and metabolic bases of integrated trait variation, and therefore has a broad applicability domain. The integration of data at different levels of cellular organization is an important goal in computational biology for understanding the way the genotypic variation translates into phenotypic variation. Novel profiling technologies and accurate high-throughput phenotyping now allows genomic, transcriptomic, metabolic and proteomic characterization of a large number of individuals under various environmental conditions. However, the metabolic fluxes remain difficult to measure. In this work, we take advantage of recent advances in genome-scale functional annotation and constraint-based metabolic modeling to provide a mathematical framework that allows to estimate internal cellular fluxes from protein abundances and elucidate the biological mechanisms underlying phenotypic variation. Applied to yeast as a model system, this approach highlights that the negative correlation between production traits such as maximum population size and growth and fermentation traits is explained by a differential usage of energy production pathways. The ability to identify molecular and metabolic bases of the variation of integrated traits through population studies has a broad applicability domain.
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Affiliation(s)
- Marianyela Sabina Petrizzelli
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE–Le Moulon, Gif-sur-Yvette, France
- Institut Curie, PSL Research University, Paris, France
- INSERM, U900, Paris, France
- CBIO-Centre for Computational Biology, MINES ParisTech, PSL Research University, Paris, France
- * E-mail:
| | - Dominique de Vienne
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE–Le Moulon, Gif-sur-Yvette, France
| | - Thibault Nidelet
- SPO, INRAE, Montpellier SupAgro, Université de Montpellier, Montpellier, France
| | | | - Christine Dillmann
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE–Le Moulon, Gif-sur-Yvette, France
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9
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Serrano R, González-Menéndez V, Martínez G, Toro C, Martín J, Genilloud O, Tormo JR. Metabolomic Analysis of The Chemical Diversity of South Africa Leaf Litter Fungal Species Using an Epigenetic Culture-Based Approach. Molecules 2021; 26:molecules26144262. [PMID: 34299537 PMCID: PMC8305139 DOI: 10.3390/molecules26144262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 11/16/2022] Open
Abstract
Microbial natural products are an invaluable resource for the biotechnological industry. Genome mining studies have highlighted the huge biosynthetic potential of fungi, which is underexploited by standard fermentation conditions. Epigenetic effectors and/or cultivation-based approaches have successfully been applied to activate cryptic biosynthetic pathways in order to produce the chemical diversity suggested in available fungal genomes. The addition of Suberoylanilide Hydroxamic Acid to fermentation processes was evaluated to assess its effect on the metabolomic diversity of a taxonomically diverse fungal population. Here, metabolomic methodologies were implemented to identify changes in secondary metabolite profiles to determine the best fermentation conditions. The results confirmed previously described effects of the epigenetic modifier on the metabolism of a population of 232 wide diverse South Africa fungal strains cultured in different fermentation media where the induction of differential metabolites was observed. Furthermore, one solid-state fermentation (BRFT medium), two classic successful liquid fermentation media (LSFM and YES) and two new liquid media formulations (MCKX and SMK-II) were compared to identify the most productive conditions for the different populations of taxonomic subgroups.
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10
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Zhang WJ, Zhang C, Zhou S, Li XG, Mangenot S, Fouteau S, Guerin T, Qi XQ, Yang J, Bartlett DH, Wu LF. Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench. Microb Genom 2021; 7:000591. [PMID: 34319226 PMCID: PMC8477399 DOI: 10.1099/mgen.0.000591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/20/2021] [Indexed: 01/19/2023] Open
Abstract
Hadal trenches are the deepest but underexplored ecosystems on the Earth. Inhabiting the trench bottom is a group of micro-organisms termed obligate piezophiles that grow exclusively under high hydrostatic pressures (HHP). To reveal the genetic and physiological characteristics of their peculiar lifestyles and microbial adaptation to extreme high pressures, we sequenced the complete genome of the obligately piezophilic bacterium Moritella yayanosii DB21MT-5 isolated from the deepest oceanic sediment at the Challenger Deep, Mariana Trench. Through comparative analysis against pressure sensitive and deep-sea piezophilic Moritella strains, we identified over a hundred genes that present exclusively in hadal strain DB21MT-5. The hadal strain encodes fewer signal transduction proteins and secreted polysaccharases, but has more abundant metal ion transporters and the potential to utilize plant-derived saccharides. Instead of producing osmolyte betaine from choline as other Moritella strains, strain DB21MT-5 ferments on choline within a dedicated bacterial microcompartment organelle. Furthermore, the defence systems possessed by DB21MT-5 are distinct from other Moritella strains but resemble those in obligate piezophiles obtained from the same geographical setting. Collectively, the intensive comparative genomic analysis of an obligately piezophilic strain Moritella yayanosii DB21MT-5 demonstrates a depth-dependent distribution of energy metabolic pathways, compartmentalization of important metabolism and use of distinct defence systems, which likely contribute to microbial adaptation to the bottom of hadal trench.
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Affiliation(s)
- Wei-Jia Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Institution of Deep-Sea Life Sciences, Hainan Deep-Sea Technology Laboratory, Sanya, PR China
| | - Chan Zhang
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- Present address: College of Horticulture, Hainan University, No. 58, Renmin Avenue, Haikou, PR China
| | - Siyu Zhou
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Xue-Gong Li
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Institution of Deep-Sea Life Sciences, Hainan Deep-Sea Technology Laboratory, Sanya, PR China
| | - Sophie Mangenot
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Stéphanie Fouteau
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Thomas Guerin
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Xiao-Qing Qi
- Laboratory of Deep-Sea Microbial Cell Biology, Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, PR China
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Institution of Deep-Sea Life Sciences, Hainan Deep-Sea Technology Laboratory, Sanya, PR China
| | - Jian Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, PR China
| | - Douglas H. Bartlett
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USA
| | - Long-Fei Wu
- France-China Joint Laboratory for Evolution and Development of Magnetotactic Multicellular Organisms (LIA-MagMC), Marseille, France / IDSSE-CAS, Sanya, PR China
- Aix-Marseille Université, CNRS, LCB UMR 7257, IMM, IM2B, Marseille, France
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Balabanova L, Averianova L, Marchenok M, Son O, Tekutyeva L. Microbial and Genetic Resources for Cobalamin (Vitamin B12) Biosynthesis: From Ecosystems to Industrial Biotechnology. Int J Mol Sci 2021; 22:ijms22094522. [PMID: 33926061 PMCID: PMC8123684 DOI: 10.3390/ijms22094522] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 12/12/2022] Open
Abstract
Many microbial producers of coenzyme B12 family cofactors together with their metabolically interdependent pathways are comprehensively studied and successfully used both in natural ecosystems dominated by auxotrophs, including bacteria and mammals, and in the safe industrial production of vitamin B12. Metabolic reconstruction for genomic and metagenomic data and functional genomics continue to mine the microbial and genetic resources for biosynthesis of the vital vitamin B12. Availability of metabolic engineering techniques and usage of affordable and renewable sources allowed improving bioprocess of vitamins, providing a positive impact on both economics and environment. The commercial production of vitamin B12 is mainly achieved through the use of the two major industrial strains, Propionobacterium shermanii and Pseudomonas denitrificans, that involves about 30 enzymatic steps in the biosynthesis of cobalamin and completely replaces chemical synthesis. However, there are still unresolved issues in cobalamin biosynthesis that need to be elucidated for future bioprocess improvements. In the present work, we review the current state of development and challenges for cobalamin (vitamin B12) biosynthesis, describing the major and novel prospective strains, and the studies of environmental factors and genetic tools effecting on the fermentation process are reported.
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Affiliation(s)
- Larissa Balabanova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- Laboratory of Marine Biochemistry, G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, 690022 Vladivostok, Russia
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
- Correspondence:
| | - Liudmila Averianova
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Maksim Marchenok
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Oksana Son
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
| | - Liudmila Tekutyeva
- Department of Bioeconomy and Food Security, School of Economics and Management, Far Eastern Federal University, 690922 Vladivostok, Russia; (L.A.); (M.M.); (O.S.); (L.T.)
- ARNIKA, Territory of PDA Nadezhdinskaya, 692481 Primorskiy Region, Russia
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Vichi J, Salazar E, Jacinto VJ, Rodriguez LO, Grande R, Dantán-González E, Morett E, Hernández-Mendoza A. High-throughput transcriptome sequencing and comparative analysis of Escherichia coli and Schizosaccharomyces pombe in respiratory and fermentative growth. PLoS One 2021; 16:e0248513. [PMID: 33730068 PMCID: PMC7968713 DOI: 10.1371/journal.pone.0248513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/26/2021] [Indexed: 12/13/2022] Open
Abstract
In spite of increased complexity in eukaryotes compared to prokaryotes, several basic metabolic and regulatory processes are conserved. Here we explored analogies in the eubacteria Escherichia coli and the unicellular fission yeast Schizosaccharomyces pombe transcriptomes under two carbon sources: 2% glucose; or a mix of 2% glycerol and 0.2% sodium acetate using the same growth media and growth phase. Overall, twelve RNA-seq libraries were constructed. A total of 593 and 860 genes were detected as differentially expressed for E. coli and S. pombe, respectively, with a log2 of the Fold Change ≥ 1 and False Discovery Rate ≤ 0.05. In aerobic glycolysis, most of the expressed genes were associated with cell proliferation in both organisms, including amino acid metabolism and glycolysis. In contrast in glycerol/acetate condition, genes related to flagellar assembly and membrane proteins were differentially expressed such as the general transcription factors fliA, flhD, flhC, and flagellum assembly genes were detected in E. coli, whereas in S. pombe genes for hexose transporters, integral membrane proteins, galactose metabolism, and ncRNAs related to cellular stress were overexpressed. In general, our study shows that a conserved "foraging behavior" response is observed in these eukaryotic and eubacterial organisms in gluconeogenic carbon sources.
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Affiliation(s)
- Joivier Vichi
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Emmanuel Salazar
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Verónica Jiménez Jacinto
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Leticia Olvera Rodriguez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Ricardo Grande
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Edgar Dantán-González
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Enrique Morett
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Armando Hernández-Mendoza
- Centro de Investigación en Dinámica Celular, Instituto de Investigación en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
- * E-mail:
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Mao B, Yin R, Li X, Cui S, Zhang H, Zhao J, Chen W. Comparative Genomic Analysis of Lactiplantibacillus plantarum Isolated from Different Niches. Genes (Basel) 2021; 12:genes12020241. [PMID: 33567604 PMCID: PMC7914981 DOI: 10.3390/genes12020241] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/31/2021] [Accepted: 02/03/2021] [Indexed: 11/16/2022] Open
Abstract
Lactiplantibacillus plantarum can adapt to a variety of niches and is widely distributed in many sources. We used comparative genomics to explore the differences in the genome and in the physiological characteristics of L. plantarum isolated from pickles, fermented sauce, and human feces. The relationships between genotypes and phenotypes were analyzed to address the effects of isolation source on the genetic variation of L. plantarum. The comparative genomic results indicate that the numbers of unique genes in the different strains were niche-dependent. L. plantarum isolated from fecal sources generally had more strain-specific genes than L. plantarum isolated from pickles. The phylogenetic tree and average nucleotide identity (ANI) results indicate that L. plantarum in pickles and fermented sauce clustered independently, whereas the fecal L. plantarum was distributed more uniformly in the phylogenetic tree. The pan-genome curve indicated that the L. plantarum exhibited high genomic diversity. Based on the analysis of the carbohydrate active enzyme and carbohydrate-use abilities, we found that L. plantarum strains isolated from different sources exhibited different expression of the Glycoside Hydrolases (GH) and Glycosyl Transferases (GT) families and that the expression patterns of carbohydrate active enzymes were consistent with the evolution relationships of the strains. L. plantarum strains exhibited niche-specific characteristicsand the results provided better understating on genetics of this species.
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Affiliation(s)
- Bingyong Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Ruimin Yin
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Xiaoshu Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Shumao Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Correspondence: ; Tel.: +86-510-8591-2155
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China; (B.M.); (R.Y.); (X.L.); (S.C.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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McCarthy GC, Morgan SC, Martiniuk JT, Newman BL, McCann SE, Measday V, Durall DM. An indigenous Saccharomyces uvarum population with high genetic diversity dominates uninoculated Chardonnay fermentations at a Canadian winery. PLoS One 2021; 16:e0225615. [PMID: 33539404 PMCID: PMC7861373 DOI: 10.1371/journal.pone.0225615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
Saccharomyces cerevisiae is the primary yeast species responsible for most fermentations in winemaking. However, other yeasts, including Saccharomyces uvarum, have occasionally been found conducting commercial fermentations around the world. S. uvarum is typically associated with white wine fermentations in cool-climate wine regions, and has been identified as the dominant yeast in fermentations from France, Hungary, northern Italy, and, recently, Canada. However, little is known about how the origin and genetic diversity of the Canadian S. uvarum population relates to strains from other parts of the world. In this study, a highly diverse S. uvarum population was found dominating uninoculated commercial fermentations of Chardonnay grapes sourced from two different vineyards. Most of the strains identified were found to be genetically distinct from S. uvarum strains isolated globally. Of the 106 strains of S. uvarum identified in this study, four played a dominant role in the fermentations, with some strains predominating in the fermentations from one vineyard over the other. Furthermore, two of these dominant strains were previously identified as dominant strains in uninoculated Chardonnay fermentations at the same winery two years earlier, suggesting the presence of a winery-resident population of indigenous S. uvarum. This research provides valuable insight into the diversity and persistence of non-commercial S. uvarum strains in North America, and a stepping stone for future work into the enological potential of an alternative Saccharomyces yeast species.
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Affiliation(s)
- Garrett C. McCarthy
- Department of Biology, Irfigving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Sydney C. Morgan
- Department of Biology, Irfigving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Jonathan T. Martiniuk
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Brianne L. Newman
- Department of Biology, Irfigving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Stephanie E. McCann
- Department of Biology, Irfigving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada
| | - Vivien Measday
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel M. Durall
- Department of Biology, Irfigving K. Barber School of Arts and Sciences, The University of British Columbia, Kelowna, British Columbia, Canada
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15
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Guo J, Wu Y, Tanaka T, Lin YH. Development of redox potential-driven fermentation process for recombinant protein expression. Biotechnol Lett 2020; 43:99-103. [PMID: 33064228 DOI: 10.1007/s10529-020-03030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022]
Abstract
OBJECTIVES A redox potential-driven fermentation, maintaining dissolved oxygen at a prescribed level while simultaneously monitoring the changes of fermentation redox potential, was developed to guide the cultivation progress of recombinant protein expression. RESULTS A recombinant E. coli harboring prolinase-expressing plasmid (pKK-PepR2) was cultivated using the developed process. Two distinct ORP valleys were noticeable based on recorded profile. The first ORP valley is equivalent to the timing for the addition of inducing agent, and the second ORP valley serves to guide the timing for cell harvesting. The final prolinase activity is 0.172 μmol/mg/min as compared to that of 0.154 μmol/mg/min where the optical density was employed to guide the timing of inducer addition and an empirically determined length of the cultivation. CONCLUSION The developed process can be further modified to become an automatic operation.
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Affiliation(s)
- Jingjie Guo
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, Canada
| | - Yixuan Wu
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, Canada
| | - Takuji Tanaka
- Department of Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Yen-Han Lin
- Department of Chemical and Biological Engineering, University of Saskatchewan, Saskatoon, Canada.
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Imrat, Labala RK, Velhal S, Bhagat S, Patel V, Jeyaram K. Small double-stranded RNA with anti-HIV activity abundantly produced by Bacillus subtilis MTCC5480 isolated from fermented soybean. Int J Biol Macromol 2020; 161:828-835. [PMID: 32553954 DOI: 10.1016/j.ijbiomac.2020.06.112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/27/2022]
Abstract
Anti-viral RNA therapy is on high demand nowadays due to the emergence of several new viral infections. The small non-coding regulatory RNAs (dsRNA) from the microbial sources are not yet explored for anti-viral activity. In this study, we assessed the anti-HIV activity of the small dsRNA produced by 12 different microbial species isolated from naturally fermented foods of North-East India. For this, we selectively extracted the dsRNA from the microbial culture, confirmed its double-stranded nature by immunoblotting, and deep sequenced the cDNA library using Illumina platform. Further, we used conventional algorithms to predict the potential targets of the dsRNA sequences within the 3'-UTR region of HIV-1. A small dsRNA fragment with 34 bases in size with a sequence of 3'-UUGGUACACGAGAUGGUUCGACUCGAUGAAGGGC-5' produced abundantly (9.17% of the total dsRNA fraction) by Bacillus subtilis MTCC5480 showed a much higher base complementarity values than previously reported miRNAs analysed against HIV-1. We separated the dsRNA fraction and validated the anti-HIV activity against human peripheral blood mononuclear cells (PBMC) infected with JRCSF strain of HIV-1 virus and the EC50 value ranges from 0.2-0.3 μM. This small dsRNA abundantly produced by B. subtilis could be studied further for its application as an anti-viral therapeutic agent.
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Affiliation(s)
- Imrat
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal 795001, Manipur, India; Department of Biotechnology, Gauhati University, Guwahati 781014, Assam, India
| | - Rajendra Kumar Labala
- Distributed Information Sub-Centre (DISC), Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal 795001, Manipur, India
| | - Shilpa Velhal
- Department of Biochemistry and Virology, National Institute for Research in Reproductive Health (ICMR), Mumbai 400012, India
| | - Sharad Bhagat
- Department of Biochemistry and Virology, National Institute for Research in Reproductive Health (ICMR), Mumbai 400012, India
| | - Vainav Patel
- Department of Biochemistry and Virology, National Institute for Research in Reproductive Health (ICMR), Mumbai 400012, India
| | - Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal 795001, Manipur, India; Institute of Bioresources and Sustainable Development (IBSD), Mizoram Center, Nursery Veng, Khatla, Aizawl 796005, Mizoram, India.
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Mao Y, Chen Z, Lu L, Jin B, Ma H, Pan Y, Chen T. Efficient solid-state fermentation for the production of 5-aminolevulinic acid enriched feed using recombinant Saccharomyces cerevisiae. J Biotechnol 2020; 322:29-32. [PMID: 32653638 DOI: 10.1016/j.jbiotec.2020.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/24/2020] [Accepted: 06/04/2020] [Indexed: 11/17/2022]
Abstract
Over the past decade, 5-aminolevulinic acid (5-ALA) has been highlighted as a promising functional feed additive and immunomodulator for improving the general health, immune response, and resistance to disease of livestock and poultry. However, it is very costly to produce 5-ALA using conventional chemical synthesis methods. Classical microbial fermentation fulfills the criteria of environmental friendliness, but the unsatisfactory titers still hinder actual industrial production. This study aimed to develop a solid-state fermentation (SSF) process that can be used to efficiently enrich feed with 5-ALA at a low cost. First, the endogenous 5-ALA synthase was overexpressed in Saccharomyces cerevisiae via integrating a copy of HEM1 gene into the chromosome and introducing a multi-copy plasmid pRS416-HEM1 which constitutively overexpresses HEM1 gene. The resulting strain ScA3 was able to produce 63.82 mg/L 5-ALA in shake-flask fermentation. After process optimization, a titer of 225.63 mg/kg dry materials, exceeding the usual effective dosage reported in animal trials, was achieved within 48 h through SSF of 20 kg feed in a 90-L steel drum. To our knowledge, this is the first report on combining microbial 5-ALA production with SSF in feed processing, which will hopefully promote the application and popularization of 5-ALA in the feed industry.
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Affiliation(s)
- Yufeng Mao
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zetian Chen
- Henan Yihongshancheng Bio-Tech Co. Ltd., Yihongshancheng Park, South Gongye Road, Wuzhi, Henan 454950, China
| | - Lingxue Lu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Biao Jin
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hongwu Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yun Pan
- Henan Yihongshancheng Bio-Tech Co. Ltd., Yihongshancheng Park, South Gongye Road, Wuzhi, Henan 454950, China.
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of Ministry of Education, SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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Wei T, Jiao Z, Hu J, Lou H, Chen Q. Chinese Yellow Rice Wine Processing with Reduced Ethyl Carbamate Formation by Deleting Transcriptional Regulator Dal80p in Saccharomyces cerevisiae. Molecules 2020; 25:E3580. [PMID: 32781689 PMCID: PMC7464398 DOI: 10.3390/molecules25163580] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/26/2020] [Accepted: 08/04/2020] [Indexed: 11/16/2022] Open
Abstract
Ethyl carbamate (EC) is a potential carcinogen that forms spontaneously during Chinese rice wine fermentation. The primary precursor for EC formation is urea, which originates from both external sources and arginine degradation. Urea degradation is suppressed by nitrogen catabolite repression (NCR) in Saccharomyces cerevisiae. The regulation of NCR is mediated by two positive regulators (Gln3p, Gat1p/Nil1p) and two negative regulators (Dal80p/Uga43p, Deh1p/Nil2p/GZF3p). DAL80 revealed higher transcriptional level when yeast cells were cultivated under nitrogen-limited conditions. In this study, when DAL80-deleted yeast cells were compared to wild-type BY4741 cells, less urea was accumulated, and genes involved in urea utilization were up-regulated. Furthermore, Chinese rice wine fermentation was conducted using dal80Δ cells; the concentrations of urea and EC were both reduced when compared to the BY4741 and traditional fermentation starter. The findings of this work indicated Dal80p is involved in EC formation possibly through regulating urea metabolism and may be used as the potential target for EC reduction.
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Affiliation(s)
| | | | | | | | - Qihe Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (T.W.); (Z.J.); (J.H.); (H.L.)
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Szczerba H, Dudziak K, Krawczyk M, Targoński Z. A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production. Int J Mol Sci 2020; 21:ijms21144835. [PMID: 32650546 PMCID: PMC7402333 DOI: 10.3390/ijms21144835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/03/2020] [Accepted: 07/05/2020] [Indexed: 12/31/2022] Open
Abstract
Enterobacter sp. LU1, a wild-type bacterium originating from goat rumen, proved to be a potential succinic acid producer in previous studies. Here, the first complete genome of this strain was obtained and analyzed from a biotechnological perspective. A hybrid sequencing approach combining short (Illumina MiSeq) and long (ONT MinION) reads allowed us to obtain a single continuous chromosome 4,636,526 bp in size, with an average 55.6% GC content that lacked plasmids. A total of 4425 genes, including 4283 protein-coding genes, 25 ribosomal RNA (rRNA)-, 84 transfer RNA (tRNA)-, and 5 non-coding RNA (ncRNA)-encoding genes and 49 pseudogenes, were predicted. It has been shown that genes involved in transport and metabolism of carbohydrates and amino acids and the transcription process constitute the major group of genes, according to the Clusters of Orthologous Groups of proteins (COGs) database. The genetic ability of the LU1 strain to metabolize a wide range of industrially relevant carbon sources has been confirmed. The genome exploration indicated that Enterobacter sp. LU1 possesses all genes that encode the enzymes involved in the glycerol metabolism pathway. It has also been shown that succinate can be produced as an end product of fermentation via the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. The transport system involved in succinate excretion into the growth medium and the genes involved in the response to osmotic and oxidative stress have also been recognized. Furthermore, three intact prophage regions ~70.3 kb, ~20.9 kb, and ~49.8 kb in length, 45 genomic islands (GIs), and two clustered regularly interspaced short palindromic repeats (CRISPR) were recognized in the genome. Sequencing and genome analysis of Enterobacter sp. LU1 confirms many earlier results based on physiological experiments and provides insight into their genetic background. All of these findings illustrate that the LU1 strain has great potential to be an efficient platform for bio-based succinate production.
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Affiliation(s)
- Hubert Szczerba
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 20-704 Lublin, Poland;
- Correspondence: ; Tel.: +48-81-462-3402
| | - Karolina Dudziak
- Chair and Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland;
| | | | - Zdzisław Targoński
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 20-704 Lublin, Poland;
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20
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Lucena RM, Dolz-Edo L, Brul S, de Morais MA, Smits G. Extreme Low Cytosolic pH Is a Signal for Cell Survival in Acid Stressed Yeast. Genes (Basel) 2020; 11:genes11060656. [PMID: 32560106 PMCID: PMC7349538 DOI: 10.3390/genes11060656] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/18/2022] Open
Abstract
Yeast biomass is recycled in the process of bioethanol production using treatment with dilute sulphuric acid to control the bacterial population. This treatment can lead to loss of cell viability, with consequences on the fermentation yield. Thus, the aim of this study was to define the functional cellular responses to inorganic acid stress. Saccharomyces cerevisiae strains with mutation in several signalling pathways, as well as cells expressing pH-sensitive GFP derivative ratiometric pHluorin, were tested for cell survival and cytosolic pH (pHc) variation during exposure to low external pH (pHex). Mutants in calcium signalling and proton extrusion were transiently sensitive to low pHex, while the CWI slt2Δ mutant lost viability. Rescue of this mutant was observed when cells were exposed to extreme low pHex or glucose starvation and was dependent on the induced reduction of pHc. Therefore, a lowered pHc leads to a complete growth arrest, which protects the cells from lethal stress and keeps cells alive. Cytosolic pH is thus a signal that directs the growth stress-tolerance trade-off in yeast. A regulatory model was proposed to explain this mechanism, indicating the impairment of glucan synthesis as the primary cause of low pHex sensitivity.
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Affiliation(s)
- Rodrigo Mendonça Lucena
- Department of Genetics, Biosciences Centre, Federal University of Pernambuco, Recife 50670-901, Brazil;
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
| | - Laura Dolz-Edo
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
| | - Stanley Brul
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
| | - Marcos Antonio de Morais
- Department of Genetics, Biosciences Centre, Federal University of Pernambuco, Recife 50670-901, Brazil;
- Correspondence: (G.S.); (M.A.d.M.J.)
| | - Gertien Smits
- Molecular Biology and Microbial Food Safety, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, Netherlands; (L.D.-E.); (S.B.)
- Correspondence: (G.S.); (M.A.d.M.J.)
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21
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Watarai N, Yamamoto N, Sawada K, Yamada T. Evolution of Aspergillus oryzae before and after domestication inferred by large-scale comparative genomic analysis. DNA Res 2020; 26:465-472. [PMID: 31755931 PMCID: PMC6993814 DOI: 10.1093/dnares/dsz024] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 11/21/2019] [Indexed: 12/22/2022] Open
Abstract
Aspergillus oryzae is an industrially useful species, of which various strains have been identified; however, their genetic relationships remain unclear. A. oryzae was previously thought to be asexual and unable to undergo crossbreeding. However, recent studies revealed the sexual reproduction of Aspergillus flavus, a species closely related to A. oryzae. To investigate potential sexual reproduction in A. oryzae and evolutionary history among A. oryzae and A. flavus strains, we assembled 82 draft genomes of A. oryzae strains used practically. The phylogenetic tree of concatenated genes confirmed that A. oryzae was monophyletic and nested in one of the clades of A. flavus but formed several clades with different genomic structures. Our results suggest that A. oryzae strains have undergone multiple inter-genomic recombination events between A. oryzae ancestors, although sexual recombination among domesticated species did not appear to have occurred during the domestication process, at least in the past few decades. Through inter- and intra-cladal comparative analysis, we found that evolutionary pressure induced by the domestication of A. oryzae appears to selectively cause non-synonymous and gap mutations in genes involved in fermentation characteristics, as well as intra-genomic rearrangements, with the conservation of industrially useful catalytic enzyme-encoding genes.
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Affiliation(s)
- Naoki Watarai
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Nozomi Yamamoto
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | | | - Takuji Yamada
- Department of Life Science and Technology, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- To whom correspondence should be addressed. Tel. +81 3 5734 3591. Fax. +81 3 5734 3591.
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22
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Zhao C, Hu Y, Chen H, Li B, Cao L, Xia J, Yin Y. An in vitro evaluation of the effects of different statins on the structure and function of human gut bacterial community. PLoS One 2020; 15:e0230200. [PMID: 32214324 PMCID: PMC7098552 DOI: 10.1371/journal.pone.0230200] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 02/24/2020] [Indexed: 12/13/2022] Open
Abstract
Statins, a class of drugs that can effectively remove cholesterol from serum, are used to regulate plasma total cholesterol and reduce the risk of cardiovascular diseases, but it is still unclear whether the drug are modulated by gut microbiota or the structures of gut microbiota are shaped by statins. We investigated the interactions between statins and the human gut microbiota during the in vitro fermentation process by 16S rRNA gene sequencing, gas chromatography (GC), and high-performance liquid chromatography (HPLC) analyses. The presence of fluvastatin (FLU2) specifically promoted the growth of Escherichia/Shigella, Ruminococcaceae UCG 014, and Sutterella. However, the composition of the gut bacterial microbiota remained relatively static in samples treated with rosuvastatin (ROS), simvastatin (SIM), and atorvastatin (ATO). The PICRUSt program predicted moderate differences in the functional categories related to the biosynthesis of other secondary metabolites, cellular processes and signaling, and signal transduction in the FLU2 fermentation samples. Our study revealed substantial variation in the structure and function of microbiomes from the FLU2-treated samples. In addition, short-chain fatty acids (SCFAs) were also significantly decreased in FLU2-treated samples compared with the samples treated with other stains. Statins can be degraded by the human gut microbiota in vitro, and the degradation rate was approximately 7%–30% and 19%–48% after fermentation was allowed to proceed for 24 h and 48 h, respectively. Generally, FLU2 could largely shape the composition and function of human gut microbiota, which resulted in changes in the production of SCFAs. In turn, all statins could be degraded or modified by the gut microbiota. Our study paves the way for elucidating statin-gut microbiota interactions in vitro towards the improvement of the host health and personalized medicine.
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Affiliation(s)
- Changhui Zhao
- Key Lab of Biometallurgy of the Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Yunfei Hu
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Huahai Chen
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Baiyuan Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Linyan Cao
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
| | - Jinlan Xia
- Key Lab of Biometallurgy of the Ministry of Education of China, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China
- * E-mail: (JX); (YY)
| | - Yeshi Yin
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou, Hunan, China
- * E-mail: (JX); (YY)
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Ebeid HM, Mengwei L, Kholif AE, Hassan FU, Lijuan P, Xin L, Chengjian Y. Moringa Oleifera Oil Modulates Rumen Microflora to Mediate In Vitro Fermentation Kinetics and Methanogenesis in Total Mix Rations. Curr Microbiol 2020; 77:1271-1282. [PMID: 32130505 DOI: 10.1007/s00284-020-01935-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/24/2020] [Indexed: 01/16/2023]
Abstract
This study was conducted to evaluate potential of Moringa oleifera seed oil (MOSO) to modulate rumen microflora to mitigate methane (CH4) production in different total mixed rations (TMRs). Three TMRs with different roughage (R) to concentrate (C) ratio were used as substrates (R70:C30, R50:C50 and R30:C70) for in vitro fermentation study using batch culture technique. Results revealed that supplementation of MOSO in different rations with variable roughage to concentrates ratio altered (P < 0.05) CH4 production and fermentation parameters. M. oleifera seed oil at 3 and 4% increased (P < 0.01) microbial protein (MCP) and propionate concentration for all rations but decreased acetate concentration in R70:C30 TMR. Two levels of MOSO (3 and 4%) quadratically increased (P = 0.001) MCP and decreased acetate in R30:C70 while all levels increased propionate. For R30:C70 and R50:C50 rations, MOSO linearly and quadratically decreased (P < 0.001) protozoa and methanogen counts; however, protozoa, methanogens and bacteria were significantly increased in R70:C30 ration without any change in fungal counts. Supplementation of higher level of MOSO (4%) in high roughage ration (R70:C30) showed negative effects on diversity (Shannon index) and evenness of bacterial species as compared to control and lower oil level. Moreover, it also decreased Firmicutes to Bacteroidetes ratio in high roughage rations more obviously at lower levels. Moringa oil also stimulated Prevotella in both high and low roughages diets that indicates its potential to mediate rumen acidosis. Conclusively, MOSO enhanced fermentation kinetics and decreased CH4 production through effective modulation of rumen microbiome.
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Affiliation(s)
- Hossam M Ebeid
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
- Dairy Science Department, National Research Centre, 33 Bohouth St. Dokki, Giza, 12622, Egypt
| | - Li Mengwei
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
| | - Ahmed E Kholif
- Dairy Science Department, National Research Centre, 33 Bohouth St. Dokki, Giza, 12622, Egypt
| | - Faiz-Ul Hassan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Peng Lijuan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
| | - Liang Xin
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China
| | - Yang Chengjian
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Ministry of Agriculture and Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, 530001, China.
- Animal Nutrition and Feed Science, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, 24-1 Yongwu Road, Nanning, 530001, Guangxi, People's Republic of China.
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24
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Varela JA, Puricelli M, Ortiz-Merino RA, Giacomobono R, Braun-Galleani S, Wolfe KH, Morrissey JP. Origin of Lactose Fermentation in Kluyveromyces lactis by Interspecies Transfer of a Neo-functionalized Gene Cluster during Domestication. Curr Biol 2019; 29:4284-4290.e2. [PMID: 31813610 PMCID: PMC6926475 DOI: 10.1016/j.cub.2019.10.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/15/2019] [Accepted: 10/21/2019] [Indexed: 11/18/2022]
Abstract
Humans have used yeasts to make cheese and kefir for millennia, but the ability to ferment the milk sugar lactose is found in only a few yeast species, of which the foremost is Kluyveromyces lactis [1]. Two genes, LAC12 (lactose permease) and LAC4 (lactase), are sufficient for lactose uptake and hydrolysis to glucose and galactose [2]. Here, we show that these genes have a complex evolutionary history in the genus Kluyveromyces that is likely the result of human activity during domestication. We show that the ancestral Lac12 was bifunctional, able to import both lactose and cellobiose into the cell. These disaccharides were then hydrolyzed by Lac4 in the case of lactose or Cel2 in the case of cellobiose. A second cellobiose transporter, Cel1, was also present ancestrally. In the K. lactis lineage, the ancestral LAC12 and LAC4 were lost and a separate upheaval in the sister species K. marxianus resulted in loss of CEL1 and quadruplication of LAC12. One of these LAC12 genes became neofunctionalized to encode an efficient lactose transporter capable of supporting fermentation, specifically in dairy strains of K. marxianus, where it formed a LAC4-LAC12-CEL2 gene cluster, although another remained a cellobiose transporter. Then, the ability to ferment lactose was acquired very recently by K. lactis var. lactis by introgression of LAC12 and LAC4 on a 15-kb subtelomeric region from a dairy strain of K. marxianus. The genomic history of the LAC genes shows that strong selective pressures were imposed on yeasts by early dairy farmers.
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Affiliation(s)
- Javier A Varela
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Ireland, University College Cork, Cork T12YN60, Ireland
| | - Martina Puricelli
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Ireland, University College Cork, Cork T12YN60, Ireland
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 Delft, the Netherlands
| | - Romina Giacomobono
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Ireland, University College Cork, Cork T12YN60, Ireland
| | | | - Kenneth H Wolfe
- UCD Conway Institute, School of Medicine, University College Dublin, Dublin 4 D04 C7X2, Ireland
| | - John P Morrissey
- School of Microbiology, Centre for Synthetic Biology and Biotechnology, Environmental Research Institute, APC Microbiome Ireland, University College Cork, Cork T12YN60, Ireland.
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25
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Gil-Monreal M, Giuntoli B, Zabalza A, Licausi F, Royuela M. ERF-VII transcription factors induce ethanol fermentation in response to amino acid biosynthesis-inhibiting herbicides. J Exp Bot 2019; 70:5839-5851. [PMID: 31384925 PMCID: PMC6812701 DOI: 10.1093/jxb/erz355] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 07/22/2019] [Indexed: 05/17/2023]
Abstract
Herbicides inhibiting either aromatic or branched-chain amino acid biosynthesis trigger similar physiological responses in plants, despite their different mechanism of action. Both types of herbicides are known to activate ethanol fermentation by inducing the expression of fermentative genes; however, the mechanism of such transcriptional regulation has not been investigated so far. In plants exposed to low-oxygen conditions, ethanol fermentation is transcriptionally controlled by the ethylene response factors-VII (ERF-VIIs), whose stability is controlled in an oxygen-dependent manner by the Cys-Arg branch of the N-degron pathway. In this study, we investigated the role of ERF-VIIs in the regulation of the ethanol fermentation pathway in herbicide-treated Arabidopsis plants grown under aerobic conditions. Our results demonstrate that these transcriptional regulators are stabilized in response to herbicide treatment and are required for ethanol fermentation in these conditions. We also observed that mutants with reduced fermentative potential exhibit higher sensitivity to herbicide treatments, thus revealing the existence of a mechanism that mimics oxygen deprivation to activate metabolic pathways that enhance herbicide tolerance. We speculate that this signaling pathway may represent a potential target in agriculture to affect tolerance to herbicides that inhibit amino acid biosynthesis.
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Affiliation(s)
- Miriam Gil-Monreal
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Pamplona, Spain
| | - Beatrice Giuntoli
- Department of Biology, University of Pisa, Via Ghini, Pisa, Italy
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Guidiccioni, Pisa, Italy
| | - Ana Zabalza
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Pamplona, Spain
| | - Francesco Licausi
- Department of Biology, University of Pisa, Via Ghini, Pisa, Italy
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant’Anna, Via Guidiccioni, Pisa, Italy
| | - Mercedes Royuela
- Institute for Multidisciplinary Research in Applied Biology (IMAB), Universidad Pública de Navarra, Pamplona, Spain
- Correspondence:
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26
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Li Z, Liu B, Cui H, Ding J, Li H, Xie G, Ren N, Xing D. The complete genome sequence of Ethanoligenens harbinense reveals the metabolic pathway of acetate-ethanol fermentation: A novel understanding of the principles of anaerobic biotechnology. Environ Int 2019; 131:105053. [PMID: 31357089 DOI: 10.1016/j.envint.2019.105053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 05/05/2023]
Abstract
Ethanol-type fermentation is one of three main fermentation types in the acidogenesis of anaerobic treatment systems. Non-spore-forming Ethanoligenens is as a typical genus capable of ethanol-type fermentation in mixed culture (i.e. acetate-ethanol fermentation). This genus can produce ethanol, acetate, CO2, and H2 using carbohydrates, and has application potential in anaerobic bioprocesses. Here, the complete genome sequences and methylome of Ethanoligenens harbinense strains with different autoaggregative and coaggregative abilities were obtained using the PacBio single-molecule real-time sequencing platform. The genome size of E. harbinense strains was about 2.97-3.10 Mb with 55.5% G+C content. 3020-3153 genes were annotated, most of which were methylated at specific sites or motifs. The methylation types included 6mA, 4mC, and unknown types. Comparative genomic analysis demonstrated low levels of genetic similarity between E. harbinense and other well-known hydrogen-producing bacteria (i.e., Clostridium and Thermoanaerobacter) in phylogenesis. Hydrogen production of E. harbinense was catalyzed by genes that encode [FeFe]‑hydrogenases and that were synthesized by three maturases of [FeFe]-H2ase. The metabolic mechanism of H2-ethanol co-production fermentation, catalyzed by pyruvate ferredoxin oxidoreductase was proposed. This study provides genetic and evolutionary information of a model genus for the further investigation of the metabolic pathway and regulatory network of ethanol-type fermentation and anaerobic bioprocesses for waste or wastewater treatment.
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Affiliation(s)
- Zhen Li
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Bingfeng Liu
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Han Cui
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Jie Ding
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Huahua Li
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Guojun Xie
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Nanqi Ren
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China
| | - Defeng Xing
- State Key Lab of Urban Water Resources and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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27
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Berbegal C, Borruso L, Fragasso M, Tufariello M, Russo P, Brusetti L, Spano G, Capozzi V. A Metagenomic-Based Approach for the Characterization of Bacterial Diversity Associated with Spontaneous Malolactic Fermentations in Wine. Int J Mol Sci 2019; 20:ijms20163980. [PMID: 31443334 PMCID: PMC6721008 DOI: 10.3390/ijms20163980] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/13/2023] Open
Abstract
This study reports the first application of a next generation sequencing (NGS) analysis. The analysis was designed to monitor the effect of the management of microbial resources associated with alcoholic fermentation on spontaneous malolactic consortium. Together with the analysis of 16S rRNA genes from the metagenome, we monitored the principal parameters linked to MLF (e.g., malic and lactic acid concentration, pH). We encompass seven dissimilar concrete practices to manage microorganisms associated with alcoholic fermentation: Un-inoculated must (UM), pied-de-cuve (PdC), Saccharomyces cerevisiae (SC), S. cerevisiae and Torulaspora delbrueckii co-inoculated and sequentially inoculated, as well as S. cerevisiae and Metschnikowia pulcherrima co-inoculated and sequentially inoculated. Surprisingly, each experimental modes led to different taxonomic composition of the bacterial communities of the malolactic consortia, in terms of prokaryotic phyla and genera. Our findings indicated that, uncontrolled AF (UM, PdC) led to heterogeneous consortia associated with MLF (with a relevant presence of the genera Acetobacter and Gluconobacter), when compared with controlled AF (SC) (showing a clear dominance of the genus Oenococcus). Effectively, the SC trial malic acid was completely degraded in about two weeks after the end of AF, while, on the contrary, malic acid decarboxylation remained uncomplete after 7 weeks in the case of UM and PdC. In addition, for the first time, we demonstrated that both (i) the inoculation of different non-Saccharomyces (T. delbrueckii and M. pulcherrima) and, (ii) the inoculation time of the non-Saccharomyces with respect to S. cerevisiae resources (co-inoculated and sequentially inoculated) influence the composition of the connected MLF consortia, modulating MLF performance. Finally, we demonstrated the first findings of delayed and inhibited MLF when M. pulcherrima, and T. delbrueckii were inoculated, respectively. In addition, as a further control test, we also assessed the effect of the inoculation with Oenococcus oeni and Lactobacillus plantarum at the end of alcoholic fermentation, as MLF starter cultures. Our study suggests the potential interest in the application of NGS analysis, to monitor the effect of alcoholic fermentation on the spontaneous malolactic consortium, in relation to wine.
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Affiliation(s)
- Carmen Berbegal
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
- EnolabERI BioTecMed, Universitat de València, 46100 Valencia, Spain
| | - Luigimaria Borruso
- Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bozen-Bolzano, Italy
| | - Mariagiovanna Fragasso
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Maria Tufariello
- Istituto di Scienze delle Produzioni Alimentari, Consiglio Nazionale delle Ricerche, Unità Operativa di Supporto di Lecce, 73100 Lecce, Italy
| | - Pasquale Russo
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Lorenzo Brusetti
- Faculty of Science and Technology, Free University of Bozen-Bolzano, 39100 Bozen-Bolzano, Italy
| | - Giuseppe Spano
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | - Vittorio Capozzi
- Department of Agriculture, Food and Environment Sciences, University of Foggia, Via Napoli 25, 71122 Foggia, Italy.
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Borelli G, Fiamenghi MB, dos Santos LV, Carazzolle MF, Pereira GAG, José J. Positive Selection Evidence in Xylose-Related Genes Suggests Methylglyoxal Reductase as a Target for the Improvement of Yeasts' Fermentation in Industry. Genome Biol Evol 2019; 11:1923-1938. [PMID: 31070742 PMCID: PMC6637916 DOI: 10.1093/gbe/evz036] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2019] [Indexed: 12/12/2022] Open
Abstract
Xylose assimilation and fermentation are important traits for second generation ethanol production. However, some genomic features associated with this pentose sugar's metabolism remain unknown in yeasts. Comparative genomics studies have led to important insights in this field, but we are still far from completely understanding endogenous yeasts' xylose metabolism. In this work, we carried out a deep evolutionary analysis suited for comparative genomics of xylose-consuming yeasts, searching for of positive selection on genes associated with glucose and xylose metabolism in the xylose-fermenters' clade. Our investigation detected positive selection fingerprints at this clade not only among sequences of important genes for xylose metabolism, such as xylose reductase and xylitol dehydrogenase, but also in genes expected to undergo neutral evolution, such as the glycolytic gene phosphoglycerate mutase. In addition, we present expansion, positive selection marks, and convergence as evidence supporting the hypothesis that natural selection is shaping the evolution of the little studied methylglyoxal reductases. We propose a metabolic model suggesting that selected codons among these proteins caused a putative change in cofactor preference from NADPH to NADH that alleviates cellular redox imbalance. These findings provide a wider look into pentose metabolism of yeasts and add this previously overlooked piece into the intricate puzzle of oxidative imbalance. Although being extensively discussed in evolutionary works the awareness of selection patterns is recent in biotechnology researches, rendering insights to surpass the reached status quo in many of its subareas.
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Affiliation(s)
- Guilherme Borelli
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
| | - Mateus Bernabe Fiamenghi
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
| | - Leandro Vieira dos Santos
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
- Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, Brazil
| | - Juliana José
- Genomics and bioEnergy Laboratory (LGE), Institute of Biology, Unicamp, São Paulo, Campinas, Brazil
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Tesnière C, Bessière C, Pradal M, Sanchez I, Blondin B, Bigey F. Relief from nitrogen starvation entails quick unexpected down-regulation of glycolytic/lipid metabolism genes in enological Saccharomyces cerevisiae. PLoS One 2019; 14:e0215870. [PMID: 31022239 PMCID: PMC6483528 DOI: 10.1371/journal.pone.0215870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/09/2019] [Indexed: 11/24/2022] Open
Abstract
Nitrogen composition of the grape must has an impact on yeast growth and fermentation kinetics as well as on the organoleptic properties of the final product. In some technological processes, such as white wine/rosé winemaking, the yeast-assimilable nitrogen content is sometimes insufficient to cover yeast requirements, which can lead to slow or sluggish fermentations. Growth is nevertheless quickly restored upon relief from nutrient starvation, e.g. through the addition of ammonium nitrogen, allowing fermentation completion. The aim of this study was to determine how nitrogen repletion affected the transcriptional response of a Saccharomyces cerevisiae wine yeast strain, in particular within the first hour after nitrogen addition. We found almost 4800 genes induced or repressed, sometimes within minutes after nutrient changes. Some of these responses to nitrogen depended on the TOR pathway, which controls positively ribosomal protein genes, amino acid and purine biosynthesis or amino acid permease genes and negatively stress-response genes, and genes related to the retrograde response (RTG) specific to the tricarboxylic acid (TCA) cycle and nitrogen catabolite repression (NCR). Some unexpected transcriptional responses concerned all the glycolytic genes, carbohydrate metabolism and TCA cycle-related genes that were down-regulated, as well as genes from the lipid metabolism.
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Affiliation(s)
| | - Chloé Bessière
- SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Martine Pradal
- SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Isabelle Sanchez
- SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Bruno Blondin
- SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Frédéric Bigey
- SPO, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
- * E-mail:
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Čadež N, Bellora N, Ulloa R, Hittinger CT, Libkind D. Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina. PLoS One 2019; 14:e0210792. [PMID: 30699175 PMCID: PMC6353571 DOI: 10.1371/journal.pone.0210792] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 01/03/2019] [Indexed: 11/19/2022] Open
Abstract
A novel yeast species was isolated from the sugar-rich stromata of Cyttaria hariotii collected from two different Nothofagus tree species in the Andean forests of Patagonia, Argentina. Phylogenetic analyses of the concatenated sequence of the rRNA gene sequences and the protein-coding genes for actin and translational elongation factor-1α indicated that the novel species belongs to the genus Hanseniaspora. De novo genome assembly of the strain CRUB 1928T yielded a 10.2-Mbp genome assembly predicted to encode 4452 protein-coding genes. The genome sequence data were compared to the genomes of other Hanseniaspora species using three different methods, an alignment-free distance measure, Kr, and two model-based estimations of DNA-DNA homology values, of which all provided indicative values to delineate species of Hanseniaspora. Given its potential role in a rare indigenous alcoholic beverage in which yeasts ferment sugars extracted from the stromata of Cytarria sp., we searched for the genes that may suggest adaptation of novel Hanseniaspora species to fermenting communities. The SSU1-like gene encoding a sulfite efflux pump, which, among Hanseniaspora, is present only in close relatives to the new species, was detected and analyzed, suggesting that this gene might be one factor that characterizes this novel species. We also discuss several candidate genes that likely underlie the physiological traits used for traditional taxonomic identification. Based on these results, a novel yeast species with the name Hanseniaspora gamundiae sp. nov. is proposed with CRUB 1928T (ex-types: ZIM 2545T = NRRL Y-63793T = PYCC 7262T; MycoBank number MB 824091) as the type strain. Furthermore, we propose the transfer of the Kloeckera species, K. hatyaiensis, K. lindneri and K. taiwanica to the genus Hanseniaspora as Hanseniaspora hatyaiensis comb. nov. (MB 828569), Hanseniaspora lindneri comb. nov. (MB 828566) and Hanseniaspora taiwanica comb. nov. (MB 828567).
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Affiliation(s)
- Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, Ljubljana, Slovenia
| | - Nicolas Bellora
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medio-ambiente, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
| | - Ricardo Ulloa
- Laboratorio de Bioprocesos, Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Neuquén, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Diego Libkind
- Laboratorio de Microbiología Aplicada y Biotecnología, Instituto de Investigaciones en Biodiversidad y Medio-ambiente, Consejo Nacional de Investigaciones, Científicas y Técnicas (CONICET)-Universidad Nacional del Comahue, Bariloche, Argentina
- * E-mail:
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Johnson JM, Hays FA. High-Throughput Protein Production of Membrane Proteins in Saccharomyces cerevisiae. Methods Mol Biol 2019; 2025:227-259. [PMID: 31267456 DOI: 10.1007/978-1-4939-9624-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
This chapter outlines a protocol to assess viability for large-scale protein production and purification for selected targets from an initial medium-throughput cloning strategy. Thus, one can assess a broad number of potential candidate proteins, mutants, or expression variants using an empirically minimalistic approach. In addition, a key output from this protocol is utilization of Saccharomyces cerevisiae as a means for the efficient screening and production of purified proteins. The primary focus in this protocol is overexpression of polytopic integral membrane proteins though methods can be equally applied to soluble proteins. The protocol starts with outlining high-throughput (sans robotics) cloning of expression proteins into a dual-tag yeast expression plasmid. These membrane proteins are then screened for expression level, detergent solubilization, initial purity, and chromatography characteristics. Both small- and large-scale expression methods are discussed along with fermentation.
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Affiliation(s)
- Jennifer M Johnson
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Franklin A Hays
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
- Harold Hamm Diabetes Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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Baker EP, Peris D, Moriarty RV, Li XC, Fay JC, Hittinger CT. Mitochondrial DNA and temperature tolerance in lager yeasts. Sci Adv 2019; 5:eaav1869. [PMID: 30729163 PMCID: PMC6353617 DOI: 10.1126/sciadv.aav1869] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/03/2019] [Indexed: 06/01/2023]
Abstract
A growing body of research suggests that the mitochondrial genome (mtDNA) is important for temperature adaptation. In the yeast genus Saccharomyces, species have diverged in temperature tolerance, driving their use in high- or low-temperature fermentations. Here, we experimentally test the role of mtDNA in temperature tolerance in synthetic and industrial hybrids (Saccharomyces cerevisiae × Saccharomyces eubayanus or Saccharomyces pastorianus), which cold-brew lager beer. We find that the relative temperature tolerances of hybrids correspond to the parent donating mtDNA, allowing us to modulate lager strain temperature preferences. The strong influence of mitotype on the temperature tolerance of otherwise identical hybrid strains provides support for the mitochondrial climactic adaptation hypothesis in yeasts and demonstrates how mitotype has influenced the world's most commonly fermented beverage.
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Affiliation(s)
- EmilyClare P. Baker
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
| | - David Peris
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
- Department of Food Biotechnology, Institute of Agrochemistry and Food Technology (IATA), CSIC, Paterna, Valencia, Spain
| | - Ryan V. Moriarty
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
| | - Xueying C. Li
- Molecular Genetics and Genomics Program, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
- Center for Genome Sciences and System Biology, Washington University, St. Louis, MO, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Justin C. Fay
- Molecular Genetics and Genomics Program, Washington University, St. Louis, MO, USA
- Department of Genetics, Washington University, St. Louis, MO, USA
- Center for Genome Sciences and System Biology, Washington University, St. Louis, MO, USA
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, Genome Center of Wisconsin, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin–Madison, Madison, WI, USA
- Microbiology Doctoral Training Program, University of Wisconsin–Madison, Madison, WI, USA
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin–Madison, Madison, WI, USA
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Tack ILMM, Nimmegeers P, Akkermans S, Logist F, Van Impe JFM. A low-complexity metabolic network model for the respiratory and fermentative metabolism of Escherichia coli. PLoS One 2018; 13:e0202565. [PMID: 30157229 PMCID: PMC6114798 DOI: 10.1371/journal.pone.0202565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/06/2018] [Indexed: 01/01/2023] Open
Abstract
Over the last decades, predictive microbiology has made significant advances in the mathematical description of microbial spoiler and pathogen dynamics in or on food products. Recently, the focus of predictive microbiology has shifted from a (semi-)empirical population-level approach towards mechanistic models including information about the intracellular metabolism in order to increase model accuracy and genericness. However, incorporation of this subpopulation-level information increases model complexity and, consequently, the required run time to simulate microbial cell and population dynamics. In this paper, results of metabolic flux balance analyses (FBA) with a genome-scale model are used to calibrate a low-complexity linear model describing the microbial growth and metabolite secretion rates of Escherichia coli as a function of the nutrient and oxygen uptake rate. Hence, the required information about the cellular metabolism (i.e., biomass growth and secretion of cell products) is selected and included in the linear model without incorporating the complete intracellular reaction network. However, the applied FBAs are only representative for microbial dynamics under specific extracellular conditions, viz., a neutral medium without weak acids at a temperature of 37℃. Deviations from these reference conditions lead to metabolic shifts and adjustments of the cellular nutrient uptake or maintenance requirements. This metabolic dependency on extracellular conditions has been taken into account in our low-complex metabolic model. In this way, a novel approach is developed to take the synergistic effects of temperature, pH, and undissociated acids on the cell metabolism into account. Consequently, the developed model is deployable as a tool to describe, predict and control E. coli dynamics in and on food products under various combinations of environmental conditions. To emphasize this point,three specific scenarios are elaborated: (i) aerobic respiration without production of weak acid extracellular metabolites, (ii) anaerobic fermentation with secretion of mixed acid fermentation products into the food environment, and (iii) respiro-fermentative metabolic regimes in between the behaviors at aerobic and anaerobic conditions.
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Affiliation(s)
| | | | - Simen Akkermans
- BioTeC+, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
| | - Filip Logist
- BioTeC+, Department of Chemical Engineering, KU Leuven, Ghent, Belgium
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Pereira B, Miguel J, Vilaça P, Soares S, Rocha I, Carneiro S. Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z. BMC Syst Biol 2018; 12:61. [PMID: 29843739 PMCID: PMC5975692 DOI: 10.1186/s12918-018-0585-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 05/14/2018] [Indexed: 12/23/2022]
Abstract
BACKGROUND Actinobacillus succinogenes is a promising bacterial catalyst for the bioproduction of succinic acid from low-cost raw materials. In this work, a genome-scale metabolic model was reconstructed and used to assess the metabolic capabilities of this microorganism under producing conditions. RESULTS The model, iBP722, was reconstructed based on the functional reannotation of the complete genome sequence of A. succinogenes 130Z and manual inspection of metabolic pathways, covering 1072 enzymatic reactions associated with 722 metabolic genes that involve 713 metabolites. The highly curated model was effective in capturing the growth of A. succinogenes on various carbon sources, as well as the SA production under various growth conditions with fair agreement between experimental and predicted data. Calculated flux distributions under different conditions show that a number of metabolic pathways are affected by the activity of some metabolic enzymes at key nodes in metabolism, including the transport mechanism of carbon sources and the ability to fix carbon dioxide. CONCLUSIONS The established genome-scale metabolic model can be used for model-driven strain design and medium alteration to improve succinic acid yields.
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Affiliation(s)
- Bruno Pereira
- SilicoLife Lda, Rua do Canastreiro 15, 4715-387 Braga, Portugal
| | - Joana Miguel
- SilicoLife Lda, Rua do Canastreiro 15, 4715-387 Braga, Portugal
| | - Paulo Vilaça
- SilicoLife Lda, Rua do Canastreiro 15, 4715-387 Braga, Portugal
| | - Simão Soares
- SilicoLife Lda, Rua do Canastreiro 15, 4715-387 Braga, Portugal
| | - Isabel Rocha
- CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Sónia Carneiro
- SilicoLife Lda, Rua do Canastreiro 15, 4715-387 Braga, Portugal
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Abstract
Microalgae are simple chlorophyll containing organisms, they have high photosynthetic efficiency and can synthesize and accumulate large quantities of carbohydrate biomass. They can be cultivated in fresh water, seawater and wastewater. They have been used as feedstock for producing biodiesel, bioethanol and biogas. The production of these biofuels can be integrated with CO2 mitigation, wastewater treatment, and the production of high-value chemicals. Biohydrogen from microalgae is renewable. Microalgae have several advantages compared to terrestrial plants, such as higher growth rate with superior CO2 fixation capacity; they do not need arable land to grow; they do not contain lignin. In this review, the biology of microalgae and the chemical composition of microalgae were briefly introduced, the advantages and disadvantages of hydrogen production from microalgae were discussed, and the pretreatment of microalgal biomass and the fermentative hydrogen production from microalgal biomass pretreated by different methods (including physical, chemical, biological and combined methods) were summarized and evaluated. For the production of biohydrogen from microalgae, the economic feasibility remains the most important aspect to consider. Several technological and economic issues must be addressed to achieve success on a commercial scale.
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Affiliation(s)
- Jianlong Wang
- Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Energy Science Building, Tsinghua University, Beijing, 100084 People’s Republic of China
- Beijing Key Laboratory of Radioactive Waste Treatment, Tsinghua University, Beijing, 100084 People’s Republic of China
| | - Yanan Yin
- Collaborative Innovation Center for Advanced Nuclear Energy Technology, INET, Energy Science Building, Tsinghua University, Beijing, 100084 People’s Republic of China
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Goncerzewicz A, Kamińska-Wojteczek K, Młynarczyk I, Misiewicz A. Expression of GPD1 and SIP18 genes during rehydration in active dry industrial Saccharomyces cerevisiae cider-making yeast strains (ADY). Acta Biochim Pol 2017; 64:287-294. [PMID: 28600909 DOI: 10.18388/abp.2016_1404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 02/22/2017] [Accepted: 02/25/2017] [Indexed: 11/10/2022]
Abstract
In this study we determined the influence of different sugar concentration in media, time of rehydration and type of strain on relative expression level of GPD1 and SIP18 genes of active dry cider-making yeast strains, followed by the assessment of the impact of rehydration on the fermentation process. High expression of SIP18 at the beginning of rehydration was shown to be due to high transcription of the gene during the drying process. High sugar concentrations of media initiated transcription of the GPD1 gene and triggered the cellular glycerol biosynthesis pathway in examined strains. Rehydration time and type of strain showed to have no statistically significant impact on the course of the fermentation; RT qPCR results depended mainly on the time of rehydration and sugar concentration of the medium. This is the first attempt to confront rehydration time and molecular mechanisms acting upon rehydration with the course of the fermentation process.
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Affiliation(s)
- Anna Goncerzewicz
- Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology, Department of Microbiology, Culture Collection of Industrial Microorganisms, Warsaw, Poland
| | - Karolina Kamińska-Wojteczek
- Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology, Department of Microbiology, Culture Collection of Industrial Microorganisms, Warsaw, Poland
| | - Izabella Młynarczyk
- Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology, Department of Microbiology, Culture Collection of Industrial Microorganisms, Warsaw, Poland
| | - Anna Misiewicz
- Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology, Department of Microbiology, Culture Collection of Industrial Microorganisms, Warsaw, Poland
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Acevedo A, Conejeros R, Aroca G. Ethanol production improvement driven by genome-scale metabolic modeling and sensitivity analysis in Scheffersomyces stipitis. PLoS One 2017; 12:e0180074. [PMID: 28658270 PMCID: PMC5489217 DOI: 10.1371/journal.pone.0180074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 06/11/2017] [Indexed: 11/18/2022] Open
Abstract
The yeast Scheffersomyces stipitis naturally produces ethanol from xylose, however reaching high ethanol yields is strongly dependent on aeration conditions. It has been reported that changes in the availability of NAD(H/+) cofactors can improve fermentation in some microorganisms. In this work genome-scale metabolic modeling and phenotypic phase plane analysis were used to characterize metabolic response on a range of uptake rates. Sensitivity analysis was used to assess the effect of ARC on ethanol production indicating that modifying ARC by inhibiting the respiratory chain ethanol production can be improved. It was shown experimentally in batch culture using Rotenone as an inhibitor of the mitochondrial NADH dehydrogenase complex I (CINADH), increasing ethanol yield by 18%. Furthermore, trajectories for uptakes rates, specific productivity and specific growth rate were determined by modeling the batch culture, to calculate ARC associated to the addition of CINADH inhibitor. Results showed that the increment in ethanol production via respiratory inhibition is due to excess in ARC, which generates an increase in ethanol production. Thus ethanol production improvement could be predicted by a change in ARC.
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Affiliation(s)
- Alejandro Acevedo
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
| | - Raúl Conejeros
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
- * E-mail:
| | - Germán Aroca
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Av. Brasil 2085, Valparaíso, Chile
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Deed RC, Fedrizzi B, Gardner RC. Saccharomyces cerevisiae FLO1 Gene Demonstrates Genetic Linkage to Increased Fermentation Rate at Low Temperatures. G3 (Bethesda) 2017; 7:1039-1048. [PMID: 28143947 PMCID: PMC5345705 DOI: 10.1534/g3.116.037630] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/25/2017] [Indexed: 01/14/2023]
Abstract
Low fermentation temperatures are of importance to food and beverage industries working with Saccharomyces cerevisiae Therefore, the identification of genes demonstrating a positive impact on fermentation kinetics is of significant interest. A set of 121 mapped F1 progeny, derived from a cross between haploid strains BY4716 (a derivative of the laboratory yeast S288C) and wine yeast RM11-1a, were fermented in New Zealand Sauvignon Blanc grape juice at 12.5°. Analyses of five key fermentation kinetic parameters among the F1 progeny identified a quantitative trait locus (QTL) on chromosome I with a significant degree of linkage to maximal fermentation rate (Vmax) at low temperature. Independent deletions of two candidate genes within the region, FLO1 and SWH1, were constructed in the parental strains (with S288C representing BY4716). Fermentation of wild-type and deletion strains at 12.5 and 25° confirmed that the genetic linkage to Vmax corresponds to the S288C version of the FLO1 allele, as the absence of this allele reduced Vmax by ∼50% at 12.5°, but not at 25°. Reciprocal hemizygosity analysis (RHA) between S288C and RM11-1a FLO1 alleles did not confirm the prediction that the S288C version of FLO1 was promoting more rapid fermentation in the opposing strain background, suggesting that the positive effect on Vmax derived from S288C FLO1 may only provide an advantage in haploids, or is dependent on strain-specific cis or trans effects. This research adds to the growing body of evidence demonstrating the role of FLO1 in providing stress tolerance to S. cerevisiae during fermentation.
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Affiliation(s)
- Rebecca C Deed
- School of Chemical Sciences, University of Auckland, 1010, New Zealand
- School of Biological Sciences, University of Auckland, 1010, New Zealand
| | - Bruno Fedrizzi
- School of Chemical Sciences, University of Auckland, 1010, New Zealand
| | - Richard C Gardner
- School of Biological Sciences, University of Auckland, 1010, New Zealand
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Martí-Raga M, Peltier E, Mas A, Beltran G, Marullo P. Genetic Causes of Phenotypic Adaptation to the Second Fermentation of Sparkling Wines in Saccharomyces cerevisiae. G3 (Bethesda) 2017; 7:399-412. [PMID: 27903630 PMCID: PMC5295589 DOI: 10.1534/g3.116.037283] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/14/2016] [Indexed: 01/12/2023]
Abstract
Hybridization is known to improve complex traits due to heterosis and phenotypic robustness. However, these phenomena have been rarely explained at the molecular level. Here, the genetic determinism of Saccharomyces cerevisiae fermentation performance was investigated using a QTL mapping approach on an F1-progeny population. Three main QTL were detected, with positive alleles coming from both parental strains. The heterosis effect found in the hybrid was partially explained by three loci showing pseudooverdominance and dominance effects. The molecular dissection of those QTL revealed that the adaptation to second fermentation is related to pH, lipid, or osmotic regulation. Our results suggest that the stressful conditions of second fermentation have driven the selection of rare genetic variants adapted to maintain yeast cell homeostasis and, in particular, to low pH conditions.
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Affiliation(s)
- Maria Martí-Raga
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
- Unité de recherche OEnologie, EA 4577, ISVV, Université Bordeaux, 33882 Villenave d'Ornon, France
| | - Emilien Peltier
- Unité de recherche OEnologie, EA 4577, ISVV, Université Bordeaux, 33882 Villenave d'Ornon, France
- Biolaffort, 33100 Bordeaux, France
| | - Albert Mas
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Gemma Beltran
- Departament de Bioquímica i Biotecnologia, Facultat d'Enologia, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Philippe Marullo
- Unité de recherche OEnologie, EA 4577, ISVV, Université Bordeaux, 33882 Villenave d'Ornon, France
- Biolaffort, 33100 Bordeaux, France
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Fujita Y, Tsuno H, Nakayama J. Fermented Papaya Preparation Restores Age-Related Reductions in Peripheral Blood Mononuclear Cell Cytolytic Activity in Tube-Fed Patients. PLoS One 2017; 12:e0169240. [PMID: 28060858 PMCID: PMC5218495 DOI: 10.1371/journal.pone.0169240] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 12/14/2016] [Indexed: 12/16/2022] Open
Abstract
Tube-fed elderly patients are generally supplied with the same type of nutrition over long periods, resulting in an increased risk for micronutrient deficiencies. Dietary polyphenols promote immunity and have anti-inflammatory, anti-carcinogenic, and anti-oxidative properties. Carica papaya Linn. is rich in several polyphenols; however, these polyphenols are poorly absorbed from the digestive tract in their original polymerized form. Therefore, we determined the molecular components of a fermented Carica papaya Linn. preparation, as well as its effects on immunity and the composition of gut microbiota in tube-fed patients. Different doses of the fermented C. papaya L. preparation were administered to three groups of tube-fed patients for 30 days. Its effects on fecal microbiota composition and immunity were assessed by 16S rRNA gene sequencing and immune-marker analysis, respectively. The chemical composition of the fermented C. papaya L. preparation was analyzed by capillary electrophoresis- and liquid chromatography- time of flight mass spectrometry. The fermented C. papaya L. preparation restored peripheral blood mononuclear cell (PBMC) cytolytic activity; however, no other biomarkers of immunity were observed. Treatment with the preparation (9 g/day) significantly reduced the abundance of Firmicutes in the fecal microbiota. In particular, treatment reduced Clostridium scindens and Eggerthella lenta in most patients receiving 9 g/day. Chemical analysis identified low-molecular-weight phenolic acids as polyphenol metabolites; however, no polymerized, large-molecular-weight molecules were detected. Our study indicates that elderly patients who are tube-fed over the long-term have decreased PBMC cytolytic activity. In addition, low-molecular-weight polyphenol metabolites fermented from polymerized polyphenols restore PBMC cytolytic activity and modulate the composition of gut microbiota in tube-fed patients.
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Affiliation(s)
- Yuhzo Fujita
- Yuno Onsen Hospital, Yuno, Syunan-shi, Yamaguchi, Japan
| | - Haruo Tsuno
- Yuno Onsen Hospital, Yuno, Syunan-shi, Yamaguchi, Japan
| | - Jiro Nakayama
- Laboratory of Microbial Technology, Division of Systems Bioengineering, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Hakozaki, Higashi-ku, Fukuoka, Japan
- * E-mail:
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Qi W, Guo HL, Wang CL, Hou LH, Cao XH, Liu JF, Lu FP. Comparative study on fermentation performance in the genome shuffled Candida versatilis and wild-type salt tolerant yeast strain. J Sci Food Agric 2017; 97:284-290. [PMID: 27012958 DOI: 10.1002/jsfa.7728] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 01/31/2016] [Accepted: 03/15/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND The fermentation performance of a genome-shuffled strain of Candida versatilis S3-5, isolated for improved tolerance to salt, and wild-type (WT) strain were analysed. The fermentation parameters, such as growth, reducing sugar, ethanol, organic acids and volatile compounds, were detected during soy sauce fermentation process. RESULTS The results showed that ethanol produced by the genome shuffled strain S3-5 was increasing at a faster rate and to a greater extent than WT. At the end of the fermentation, malic acid, citric acid and succinic acid formed in tricarboxylic acid cycle after S3-5 treatment elevated by 39.20%, 6.85% and 17.09% compared to WT, respectively. Moreover, flavour compounds such as phenethyl acetate, ethyl vanillate, ethyl acetate, isoamyl acetate, ethyl myristate, ethyl pentadecanoate, ethyl palmitate and phenylacetaldehyde produced by S3-5 were 2.26, 2.12, 2.87, 34.41, 6.32, 13.64, 2.23 and 78.85 times as compared to WT. CONCLUSIONS S3-5 exhibited enhanced metabolic ability as compared to the wild-type strain, improved conversion of sugars to ethanol, metabolism of organic acid and formation of volatile compounds, especially esters, Moreover, S3-5 might be an ester-flavour type salt-tolerant yeast. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Wei Qi
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
- National Engineering Laboratory for Industrial Enzymes (Tianjin University of Science & Technology), Tianjin, 300457, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology (Tianjin University of Science & Technology), Tianjin, 300457, P.R. China
| | - Hong-Lian Guo
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
| | - Chun-Ling Wang
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
| | - Li-Hua Hou
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
| | - Xiao-Hong Cao
- Key Laboratory of Food Nutrition and Safety (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
| | - Jin-Fu Liu
- Department of Food Science, Tianjin Agricultural University, Tianjin, 300384, P.R. China
| | - Fu-Ping Lu
- Key Laboratory of Industrial Fermentation Microbiology (Tianjin University of Science & Technology), Ministry of Education, Tianjin, 300457, P.R. China
- National Engineering Laboratory for Industrial Enzymes (Tianjin University of Science & Technology), Tianjin, 300457, P.R. China
- Tianjin Key Laboratory of Industrial Microbiology (Tianjin University of Science & Technology), Tianjin, 300457, P.R. China
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Zhang X, Li Y, Zhao X, Bai F. Constitutive cellulase production from glucose using the recombinant Trichoderma reesei strain overexpressing an artificial transcription activator. Bioresour Technol 2017; 223:317-322. [PMID: 27818160 DOI: 10.1016/j.biortech.2016.10.083] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 05/05/2023]
Abstract
The high cost of cellulase production presents biggest challenge in biomass deconstruction. Cellulase production by Trichoderma reesei using low cost carbon source is of great interest. In this study, an artificial transcription activator containing the Cre1 binding domain linked to the Xyr1 effector and binding domains was designed and constitutively overexpressed in T. reesei RUT C30. The recombinant strain T. reesei zxy-2 displayed constitutive cellulase production using glucose as a sole carbon source, and the production titer was 12.75-fold of that observed with T. reesei RUT C30 in shake flask culture. Moreover, FPase and xylanase titers of 2.63 and 108.72IU/mL, respectively, were achieved using glucose as sole carbon source within 48h in a 7-L fermenter by batch fermentation using T. reesei zxy-2. The crude enzyme obtained was used to hydrolyze alkali pretreated corn stover, and a high glucose yield of 99.18% was achieved.
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Affiliation(s)
- Xiaoyue Zhang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116023, China
| | - Yonghao Li
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116023, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism & School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Fengwu Bai
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116023, China; State Key Laboratory of Microbial Metabolism & School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Xia K, Li Y, Sun J, Liang X. Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu. PLoS One 2016; 11:e0162172. [PMID: 27611790 PMCID: PMC5017713 DOI: 10.1371/journal.pone.0162172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 08/18/2016] [Indexed: 11/21/2022] Open
Abstract
Acetobacter pasteurianus, an acetic acid resistant bacterium belonging to alpha-proteobacteria, has been widely used to produce vinegar in the food industry. To understand the mechanism of its high tolerance to acetic acid and robust ability of oxidizing ethanol to acetic acid (> 12%, w/v), we described the 3.1 Mb complete genome sequence (including 0.28 M plasmid sequence) with a G+C content of 52.4% of A. pasteurianus Ab3, which was isolated from the traditional Chinese rice vinegar (Meiguichu) fermentation process. Automatic annotation of the complete genome revealed 2,786 protein-coding genes and 73 RNA genes. The comparative genome analysis among A. pasteurianus strains revealed that A. pasteurianus Ab3 possesses many unique genes potentially involved in acetic acid resistance mechanisms. In particular, two-component systems or toxin-antitoxin systems may be the signal pathway and modulatory network in A. pasteurianus to cope with acid stress. In addition, the large numbers of unique transport systems may also be related to its acid resistance capacity and cell fitness. Our results provide new clues to understanding the underlying mechanisms of acetic acid resistance in Acetobacter species and guiding industrial strain breeding for vinegar fermentation processes.
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Affiliation(s)
- Kai Xia
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Yudong Li
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Jing Sun
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Xinle Liang
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310018, China
- * E-mail:
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Ji SD, Wang ZY, Fan HJ, Zhang RS, Yu ZY, Wang JJ, Liu ZH. Heterologous expression of the Hsp24 from Trichoderma asperellum improves antifungal ability of Populus transformant Pdpap-Hsp24 s to Cytospora chrysosperma and Alternaria alternate. J Plant Res 2016; 129:921-933. [PMID: 27193371 DOI: 10.1007/s10265-016-0829-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 11/27/2015] [Indexed: 05/02/2023]
Abstract
The tolerance of plants to biotic and abiotic stresses could be improved by transforming with fungal resistance-related genes. In this study, the cDNA sequence (GenBank Acc. No. KP337939) of the resistance-related gene Hsp24 encoding the 24 kD heat shock protein was obtained from the biocontrol fungus Trichoderma asperellum ACCC30536. The promoter region of Hsp24 contained many cis-regulators related to stresses response, such as "GCN4" and "GCR1" etc. Hsp24 transcription in T. asperellum was up-regulated under six different environmental stresses, compared with the control. Furthermore, following heterologous transformation into Populus davidiana × P. alba var. Pyramidalis (Pdpap), Hsp24 was successfully transcribed in transformant Pdpap-Hsp24s. Pathogen-related genes (PRs) in four Pdpap-Hsp24s were up-regulated compared with those in the control Pdpap (Pdpap-Con). After co-culture of Pdpap-Hsp24s with the weak parasite Cytospora chrysosperma, the transcription of genes related to hormone signal pathway (JA and SA) were up-regulated in Pdpap-Hsp24s, and ethidium bromide (EtBr) and Nitro-blue tetrazolium (NBT) staining assays indicated that the cell membrane permeability and the active oxygen content of Pdpap-Hsp24s leaves were lower than that of the control Pdpap-Con. And when the Pdpap-Hsp24s were under the Alternaria alternate stress, the activities of superoxide dismutase (SOD) and peroxidase (POD) got higher in Pdpap-Hsp24s than that in Pdpap-Con, and the disease spots in Pdpap-Con leaves were obviously larger than those in Pdpap-Hsp24s leaves. In summary, Hsp24 of T. asperellum ACCC30536 is an important defense response gene, and its heterologous expression improved the resistance of transformant Pdpap-Hsp24s to C. chrysosperma and A. alternate.
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Affiliation(s)
- S D Ji
- School of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China
| | - Z Y Wang
- School of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China
| | - H J Fan
- School of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China
| | - R S Zhang
- The College of Landscape, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China
| | - Z Y Yu
- School of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China
| | - J J Wang
- School of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China
| | - Z H Liu
- School of Forestry, Northeast Forestry University, 26 Hexing Road, 150040, Harbin, China.
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Guo W, Chen Y, Wei N, Feng X. Investigate the Metabolic Reprogramming of Saccharomyces cerevisiae for Enhanced Resistance to Mixed Fermentation Inhibitors via 13C Metabolic Flux Analysis. PLoS One 2016; 11:e0161448. [PMID: 27532329 PMCID: PMC4988770 DOI: 10.1371/journal.pone.0161448] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/07/2016] [Indexed: 11/18/2022] Open
Abstract
The fermentation inhibitors from the pretreatment of lignocellulosic materials, e.g., acetic acid and furfural, are notorious due to their negative effects on the cell growth and chemical production. However, the metabolic reprogramming of the cells under these stress conditions, especially metabolic response for resistance to mixed inhibitors, has not been systematically investigated and remains mysterious. Therefore, in this study, 13C metabolic flux analysis (13C-MFA), a powerful tool to elucidate the intracellular carbon flux distributions, has been applied to two Saccharomyces cerevisiae strains with different tolerances to the inhibitors under acetic acid, furfural, and mixed (i.e., acetic acid and furfural) stress conditions to unravel the key metabolic responses. By analyzing the intracellular carbon fluxes as well as the energy and cofactor utilization under different conditions, we uncovered varied metabolic responses to different inhibitors. Under acetate stress, ATP and NADH production was slightly impaired, while NADPH tended towards overproduction. Under furfural stress, ATP and cofactors (including both NADH and NADPH) tended to be overproduced. However, under dual-stress condition, production of ATP and cofactors was severely impaired due to synergistic stress caused by the simultaneous addition of two fermentation inhibitors. Such phenomenon indicated the pivotal role of the energy and cofactor utilization in resisting the mixed inhibitors of acetic acid and furfural. Based on the discoveries, valuable insights are provided to improve the tolerance of S. cerevisiae strain and further enhance lignocellulosic fermentation.
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Affiliation(s)
- Weihua Guo
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America
| | - Yingying Chen
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States of America
| | - Na Wei
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States of America
- * E-mail: (NW); (XF)
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States of America
- * E-mail: (NW); (XF)
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Krogerus K, Arvas M, De Chiara M, Magalhães F, Mattinen L, Oja M, Vidgren V, Yue JX, Liti G, Gibson B. Ploidy influences the functional attributes of de novo lager yeast hybrids. Appl Microbiol Biotechnol 2016; 100:7203-22. [PMID: 27183995 PMCID: PMC4947488 DOI: 10.1007/s00253-016-7588-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/03/2016] [Accepted: 04/24/2016] [Indexed: 12/25/2022]
Abstract
The genomes of hybrid organisms, such as lager yeast (Saccharomyces cerevisiae × Saccharomyces eubayanus), contain orthologous genes, the functionality and effect of which may differ depending on their origin and copy number. How the parental subgenomes in lager yeast contribute to important phenotypic traits such as fermentation performance, aroma production, and stress tolerance remains poorly understood. Here, three de novo lager yeast hybrids with different ploidy levels (allodiploid, allotriploid, and allotetraploid) were generated through hybridization techniques without genetic modification. The hybrids were characterized in fermentations of both high gravity wort (15 °P) and very high gravity wort (25 °P), which were monitored for aroma compound and sugar concentrations. The hybrid strains with higher DNA content performed better during fermentation and produced higher concentrations of flavor-active esters in both worts. The hybrid strains also outperformed both the parent strains. Genome sequencing revealed that several genes related to the formation of flavor-active esters (ATF1, ATF2¸ EHT1, EEB1, and BAT1) were present in higher copy numbers in the higher ploidy hybrid strains. A direct relationship between gene copy number and transcript level was also observed. The measured ester concentrations and transcript levels also suggest that the functionality of the S. cerevisiae- and S. eubayanus-derived gene products differs. The results contribute to our understanding of the complex molecular mechanisms that determine phenotypes in lager yeast hybrids and are expected to facilitate targeted strain development through interspecific hybridization.
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Affiliation(s)
- Kristoffer Krogerus
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland.
- Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, P.O. Box 16100, FI-00076, Espoo, Finland.
| | - Mikko Arvas
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Matteo De Chiara
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, 06107, Nice, France
| | - Frederico Magalhães
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
- Department of Biotechnology and Chemical Technology, Aalto University, School of Chemical Technology, Kemistintie 1, Aalto, P.O. Box 16100, FI-00076, Espoo, Finland
| | - Laura Mattinen
- ValiRx Finland Oy, Kiviharjuntie 8, FI-90220, Oulu, Finland
| | - Merja Oja
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Virve Vidgren
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
| | - Jia-Xing Yue
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, 06107, Nice, France
| | - Gianni Liti
- Institute for Research on Cancer and Ageing of Nice (IRCAN), CNRS UMR 7284, INSERM U1081, University of Nice Sophia Antipolis, 06107, Nice, France
| | - Brian Gibson
- VTT Technical Research Centre of Finland, Tietotie 2, P.O. Box 1000, FI-02044, Espoo, Finland
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Papapetridis I, van Dijk M, Dobbe APA, Metz B, Pronk JT, van Maris AJA. Improving ethanol yield in acetate-reducing Saccharomyces cerevisiae by cofactor engineering of 6-phosphogluconate dehydrogenase and deletion of ALD6. Microb Cell Fact 2016; 15:67. [PMID: 27118055 PMCID: PMC5574463 DOI: 10.1186/s12934-016-0465-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/13/2016] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Acetic acid, an inhibitor of sugar fermentation by yeast, is invariably present in lignocellulosic hydrolysates which are used or considered as feedstocks for yeast-based bioethanol production. Saccharomyces cerevisiae strains have been constructed, in which anaerobic reduction of acetic acid to ethanol replaces glycerol formation as a mechanism for reoxidizing NADH formed in biosynthesis. An increase in the amount of acetate that can be reduced to ethanol should further decrease acetic acid concentrations and enable higher ethanol yields in industrial processes based on lignocellulosic feedstocks. The stoichiometric requirement of acetate reduction for NADH implies that increased generation of NADH in cytosolic biosynthetic reactions should enhance acetate consumption. RESULTS Replacement of the native NADP(+)-dependent 6-phosphogluconate dehydrogenase in S. cerevisiae by a prokaryotic NAD(+)-dependent enzyme resulted in increased cytosolic NADH formation, as demonstrated by a ca. 15% increase in the glycerol yield on glucose in anaerobic cultures. Additional deletion of ALD6, which encodes an NADP(+)-dependent acetaldehyde dehydrogenase, led to a 39% increase in the glycerol yield compared to a non-engineered strain. Subsequent replacement of glycerol formation by an acetate reduction pathway resulted in a 44% increase of acetate consumption per amount of biomass formed, as compared to an engineered, acetate-reducing strain that expressed the native 6-phosphogluconate dehydrogenase and ALD6. Compared to a non-acetate reducing reference strain under the same conditions, this resulted in a ca. 13% increase in the ethanol yield on glucose. CONCLUSIONS The combination of NAD(+)-dependent 6-phosphogluconate dehydrogenase expression and deletion of ALD6 resulted in a marked increase in the amount of acetate that was consumed in these proof-of-principle experiments, and this concept is ready for further testing in industrial strains as well as in hydrolysates. Altering the cofactor specificity of the oxidative branch of the pentose-phosphate pathway in S. cerevisiae can also be used to increase glycerol production in wine fermentation and to improve NADH generation and/or generation of precursors derived from the pentose-phosphate pathway in other industrial applications of this yeast.
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Affiliation(s)
- Ioannis Papapetridis
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Marlous van Dijk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Arthur PA Dobbe
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Benjamin Metz
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Jack T. Pronk
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
| | - Antonius J. A. van Maris
- Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The Netherlands
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Olson AC, Carter CJ. The Involvement of hybrid cluster protein 4, HCP4, in Anaerobic Metabolism in Chlamydomonas reinhardtii. PLoS One 2016; 11:e0149816. [PMID: 26930496 PMCID: PMC4773151 DOI: 10.1371/journal.pone.0149816] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 02/04/2016] [Indexed: 12/28/2022] Open
Abstract
The unicellular green algae Chlamydomonas reinhardtii has long been studied for its unique fermentation pathways and has been evaluated as a candidate organism for biofuel production. Fermentation in C. reinhardtii is facilitated by a network of three predominant pathways producing four major byproducts: formate, ethanol, acetate and hydrogen. Previous microarray studies identified many genes as being highly up-regulated during anaerobiosis. For example, hybrid cluster protein 4 (HCP4) was found to be one of the most highly up-regulated genes under anoxic conditions. Hybrid cluster proteins have long been studied for their unique spectroscopic properties, yet their biological functions remain largely unclear. To probe its role during anaerobiosis, HCP4 was silenced using artificial microRNAs (ami-hcp4) followed by extensive phenotypic analyses of cells grown under anoxic conditions. Both the expression of key fermentative enzymes and their respective metabolites were significantly altered in ami-hcp4, with nitrogen uptake from the media also being significantly different than wild-type cells. The results strongly suggest a role for HCP4 in regulating key fermentative and nitrogen utilization pathways.
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Affiliation(s)
- Adam C. Olson
- Integrated Biosciences Graduate Program, University of Minnesota, Duluth, MN, 55812, United States of America
| | - Clay J. Carter
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, United States of America
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Wang H, Yang L, Ping Y, Bai Y, Luo H, Huang H, Yao B. Engineering of a Bacillus amyloliquefaciens Strain with High Neutral Protease Producing Capacity and Optimization of Its Fermentation Conditions. PLoS One 2016; 11:e0146373. [PMID: 26752595 PMCID: PMC4708984 DOI: 10.1371/journal.pone.0146373] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/16/2015] [Indexed: 01/03/2023] Open
Abstract
The neutral protease has high potential for industrial applications, and attempts to improve enzyme expression level have important application values. In the present study, a neutral protease-encoding gene, Banpr, was cloned from Bacillus amyloliquefaciens strain K11, and a genetic manipulation method specific for this difficult-to-transform strain was developed for the high-level expression of neutral protease. The recombinant plasmid pUB110-Banpr was constructed in Bacillus subtilis strain WB600 and then transformed into strain K11 under optimized conditions. A positive transformant 110N-6 with the highest protease secreting capacity on skim milk plates and great genetic stability for more than 100 generations was selected for further study. Optimization of the fermentation conditions increased the enzyme activity of strain 110N-6 to 8995 ± 250 U/ml in flask culture and 28084 ± 1282 U/ml in 15-l fermentor, which are significantly higher than that of the native strain K11 and industrial strain B. subtilis AS.1398, respectively. The high expression level and extreme genetic stability make B. amyloliquefaciens strain 110N-6 more favorable for mass production of neutral protease for industrial uses.
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Affiliation(s)
- Hui Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Lian Yang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yanhai Ping
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Huoqing Huang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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Perpetuini G, Pham-Hoang BN, Scornec H, Tofalo R, Schirone M, Suzzi G, Cavin JF, Waché Y, Corsetti A, Licandro-Seraut H. In Lactobacillus pentosus, the olive brine adaptation genes are required for biofilm formation. Int J Food Microbiol 2015; 216:104-9. [PMID: 26447789 DOI: 10.1016/j.ijfoodmicro.2015.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/09/2015] [Accepted: 10/01/2015] [Indexed: 11/13/2022]
Abstract
Lactobacillus pentosus is one of the few lactic acid bacteria (LAB) species capable of surviving in olive brine, and thus desirable during table olive fermentation. We have recently generated mutants of the efficient strain L. pentosus C11 by transposon mutagenesis and identified five mutants unable to survive and adapt to olive brine conditions. Since biofilm formation represents one of the main bacterial strategy to survive in stressful environments, in this study, the capacity of adhesion and formation of biofilm on olive skin was investigated for this strain and five derivative mutants which are interrupted in metabolic genes (enoA1 and gpi), and in genes of unknown function ("oba" genes). Confocal microscopy together with bacteria count revealed that the sessile state represented the prevailing L. pentosus C11 life-style during table olive fermentation. The characterization of cell surface properties showed that mutants present less hydrophobic and basic properties than the wild type (WT). In fact, their ability to adhere to both abiotic (polystyrene plates) and biotic (olive skin) surfaces was lower than that of the WT. Confocal microscopy revealed that mutants adhered sparsely to the olive skin instead of building a thin, multilayer biofilm. Moreover, RT-qPCR showed that the three genes enoA1, gpi and obaC were upregulated in the olive biofilm compared to the planktonic state. Thus enoA1, gpi and "oba" genes are necessary in L. pentosus to form an organized biofilm on the olive skin.
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Affiliation(s)
- G Perpetuini
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Italy; UMR PAM, Univ. Bourgogne Franche-Comté, AgroSup Dijon, Dijon, France
| | - B N Pham-Hoang
- UMR PAM, Univ. Bourgogne Franche-Comté, AgroSup Dijon, Dijon, France
| | - H Scornec
- UMR PAM, Univ. Bourgogne Franche-Comté, AgroSup Dijon, Dijon, France
| | - R Tofalo
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | - M Schirone
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | - G Suzzi
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | - J F Cavin
- UMR PAM, Univ. Bourgogne Franche-Comté, AgroSup Dijon, Dijon, France
| | - Y Waché
- UMR PAM, Univ. Bourgogne Franche-Comté, AgroSup Dijon, Dijon, France
| | - A Corsetti
- Faculty of BioScience and Technology for Food, Agriculture and Environment, University of Teramo, Italy
| | - H Licandro-Seraut
- UMR PAM, Univ. Bourgogne Franche-Comté, AgroSup Dijon, Dijon, France.
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