1
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Alberti L, König P, Zeidler S, Poehlein A, Daniel R, Averhoff B, Müller V. Identification and characterization of a novel pathway for aldopentose degradation in Acinetobacter baumannii. Environ Microbiol 2023; 25:2416-2430. [PMID: 37522309 DOI: 10.1111/1462-2920.16471] [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: 03/24/2023] [Accepted: 07/14/2023] [Indexed: 08/01/2023]
Abstract
The nosocomial pathogen Acinetobacter baumannii is well known for its extraordinary metabolic diversity. Recently, we demonstrated growth on L-arabinose, but the pathway remained elusive. Transcriptome analyses revealed two upregulated gene clusters that code for isoenzymes catalysing oxidation of a pentonate to α-ketoglutarate. Molecular, genetic, and biochemical experiments revealed one branch to be specific for L-arabonate oxidation, and the other for D-xylonate and D-ribonate. Both clusters also encode an uptake system and a regulator that acts as activator (L-arabonate) or repressor (D-xylonate and D-ribonate). Genes encoding the initial oxidation of pentose to pentonate were not part of the clusters, but our data are consistent with the hypothesis of a promiscous, pyrroloquinoline quinone (PQQ)-dependent, periplasmic pentose dehydrogenase, followed by the uptake of the pentonates and their degradation by specific pathways. However, there is a cross-talk between the two different pathways since the isoenzymes can replace each other. Growth on pentoses was found only in pathogenic Acinetobacter species but not in non-pathogenic such as Acinetobacter baylyi. However, mutants impaired in growth on pentoses were not affected in traits important for infection, but growth on L-arabinose was beneficial for long-term survival and desiccation resistance in A. baumannii ATCC 19606.
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Affiliation(s)
- Lydia Alberti
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Patricia König
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Sabine Zeidler
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Beate Averhoff
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Volker Müller
- Department of Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe-University Frankfurt am Main, Frankfurt, Germany
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2
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Shrestha S, Awasthi D, Chen Y, Gin J, Petzold CJ, Adams PD, Simmons BA, Singer SW. Simultaneous carbon catabolite repression governs sugar and aromatic co-utilization in Pseudomonas putida M2. Appl Environ Microbiol 2023; 89:e0085223. [PMID: 37724856 PMCID: PMC10617552 DOI: 10.1128/aem.00852-23] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
Pseudomonas putida have emerged as promising biocatalysts for the conversion of sugars and aromatic compounds obtained from lignocellulosic biomass. Understanding the role of carbon catabolite repression (CCR) in these strains is critical to optimize biomass conversion to fuels and chemicals. The CCR functioning in P. putida M2, a strain capable of consuming both hexose and pentose sugars as well as aromatic compounds, was investigated by cultivation experiments, proteomics, and CRISPRi-based gene repression. Strain M2 co-utilized sugars and aromatic compounds simultaneously; however, during cultivation with glucose and aromatic compounds (p-coumarate and ferulate) mixture, intermediates (4-hydroxybenzoate and vanillate) accumulated, and substrate consumption was incomplete. In contrast, xylose-aromatic consumption resulted in transient intermediate accumulation and complete aromatic consumption, while xylose was incompletely consumed. Proteomics analysis revealed that glucose exerted stronger repression than xylose on the aromatic catabolic proteins. Key glucose (Eda) and xylose (XylX) catabolic proteins were also identified at lower abundance during cultivation with aromatic compounds implying simultaneous catabolite repression by sugars and aromatic compounds. Reduction of crc expression via CRISPRi led to faster growth and glucose and p-coumarate uptake in the CRISPRi strains compared to the control, while no difference was observed on xylose+p-coumarate. The increased abundances of Eda and amino acid biosynthesis proteins in the CRISPRi strain further supported these observations. Lastly, small RNAs (sRNAs) sequencing results showed that CrcY and CrcZ homologues levels in M2, previously identified in P. putida strains, were lower under strong CCR (glucose+p-coumarate) condition compared to when repression was absent (p-coumarate or glucose only).IMPORTANCEA newly isolated Pseudomonas putida strain, P. putida M2, can utilize both hexose and pentose sugars as well as aromatic compounds making it a promising host for the valorization of lignocellulosic biomass. Pseudomonads have developed a regulatory strategy, carbon catabolite repression, to control the assimilation of carbon sources in the environment. Carbon catabolite repression may impede the simultaneous and complete metabolism of sugars and aromatic compounds present in lignocellulosic biomass and hinder the development of an efficient industrial biocatalyst. This study provides insight into the cellular physiology and proteome during mixed-substrate utilization in P. putida M2. The phenotypic and proteomics results demonstrated simultaneous catabolite repression in the sugar-aromatic mixtures, while the CRISPRi and sRNA sequencing demonstrated the potential role of the crc gene and small RNAs in carbon catabolite repression.
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Affiliation(s)
- Shilva Shrestha
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Deepika Awasthi
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jennifer Gin
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher J. Petzold
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Paul D. Adams
- Joint BioEnergy Institute, Emeryville, California, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A. Simmons
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W. Singer
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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3
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Trivedi VD, Sullivan SF, Choudhury D, Endalur Gopinarayanan V, Hart T, Nair NU. Integration of metabolism and regulation reveals rapid adaptability to growth on non-native substrates. Cell Chem Biol 2023; 30:1135-1143.e5. [PMID: 37421944 PMCID: PMC10529486 DOI: 10.1016/j.chembiol.2023.06.009] [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] [Received: 05/03/2023] [Revised: 05/18/2023] [Accepted: 06/08/2023] [Indexed: 07/10/2023]
Abstract
Engineering synthetic heterotrophy is a key to the efficient bio-based valorization of renewable and waste substrates. Among these, engineering hemicellulosic pentose utilization has been well-explored in Saccharomyces cerevisiae (yeast) over several decades-yet the answer to what makes their utilization inherently recalcitrant remains elusive. Through implementation of a semi-synthetic regulon, we find that harmonizing cellular and engineering objectives are a key to obtaining highest growth rates and yields with minimal metabolic engineering effort. Concurrently, results indicate that "extrinsic" factors-specifically, upstream genes that direct flux of pentoses into central carbon metabolism-are rate-limiting. We also reveal that yeast metabolism is innately highly adaptable to rapid growth on non-native substrates and that systems metabolic engineering (i.e., functional genomics, network modeling, etc.) is largely unnecessary. Overall, this work provides an alternate, novel, holistic (and yet minimalistic) approach based on integrating non-native metabolic genes with a native regulon system.
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Affiliation(s)
- Vikas D Trivedi
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Sean F Sullivan
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Debika Choudhury
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | | | - Taylor Hart
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA
| | - Nikhil U Nair
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, USA.
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4
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Adamczyk PA, Coradetti ST, Gladden JM. Non-canonical D-xylose and L-arabinose metabolism via D-arabitol in the oleaginous yeast Rhodosporidium toruloides. Microb Cell Fact 2023; 22:145. [PMID: 37537595 PMCID: PMC10398940 DOI: 10.1186/s12934-023-02126-x] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/17/2023] [Indexed: 08/05/2023] Open
Abstract
R. toruloides is an oleaginous yeast, with diverse metabolic capacities and high tolerance for inhibitory compounds abundant in plant biomass hydrolysates. While R. toruloides grows on several pentose sugars and alcohols, further engineering of the native pathway is required for efficient conversion of biomass-derived sugars to higher value bioproducts. A previous high-throughput study inferred that R. toruloides possesses a non-canonical L-arabinose and D-xylose metabolism proceeding through D-arabitol and D-ribulose. In this study, we present a combination of genetic and metabolite data that refine and extend that model. Chiral separations definitively illustrate that D-arabitol is the enantiomer that accumulates under pentose metabolism. Deletion of putative D-arabitol-2-dehydrogenase (RTO4_9990) results in > 75% conversion of D-xylose to D-arabitol, and is growth-complemented on pentoses by heterologous xylulose kinase expression. Deletion of putative D-ribulose kinase (RTO4_14368) arrests all growth on any pentose tested. Analysis of several pentose dehydrogenase mutants elucidates a complex pathway with multiple enzymes mediating multiple different reactions in differing combinations, from which we also inferred a putative L-ribulose utilization pathway. Our results suggest that we have identified enzymes responsible for the majority of pathway flux, with additional unknown enzymes providing accessory activity at multiple steps. Further biochemical characterization of the enzymes described here will enable a more complete and quantitative understanding of R. toruloides pentose metabolism. These findings add to a growing understanding of the diversity and complexity of microbial pentose metabolism.
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Affiliation(s)
- Paul A Adamczyk
- Agile Biofoundry, Emeryville, CA, USA
- Sandia National Laboratories, Livermore, CA, USA
| | - Samuel T Coradetti
- Agile Biofoundry, Emeryville, CA, USA
- Sandia National Laboratories, Livermore, CA, USA
- United States Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA
| | - John M Gladden
- Agile Biofoundry, Emeryville, CA, USA.
- Sandia National Laboratories, Livermore, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Sandia National Laboratories, DOE Agile Biofoundry, 5885 Hollis Street, Fourth Floor, Emeryville, CA, 94608, USA.
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da Silva RR, Zaiter MA, Boscolo M, da Silva R, Gomes E. Xylose consumption and ethanol production by Pichia guilliermondii and Candida oleophila in the presence of furans, phenolic compounds, and organic acids commonly produced during the pre-treatment of plant biomass. Braz J Microbiol 2023; 54:753-759. [PMID: 36826705 PMCID: PMC10234969 DOI: 10.1007/s42770-023-00937-z] [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: 07/13/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
For 2G ethanol production, pentose fermentation and yeast tolerance to lignocellulosic hydrolyzate components are essential to improve biorefinery yields. Generally, physicochemical pre-treatment methodologies are used to facilitate access to cellulose and hemicellulose in plant material, which consequently can generate microbial growth inhibitory compounds, such as furans, weak acids, and phenolic compounds. Because of the unsatisfactory yield of wild-type Saccharomyces cerevisiae during pentose fermentation, the search for xylose-fermenting yeasts tolerant to microbial growth inhibitors has gained attention. In this study, we investigated the ability of the yeasts Pichia guilliermondii G1.2 and Candida oleophila G10.1 to produce ethanol from xylose and tolerate the inhibitors furfural, 5-hydroxymethylfurfural (HMF), acetic acid, formic acid, ferulic acid, and vanillin. We demonstrated that both yeasts were able to grow and consume xylose in the presence of all single inhibitors, with greater growth limitation in media containing furfural, acetic acid, and vanillin. In saline medium containing a mixture of these inhibitors (2.5-3.5 mM furfural and HMF, 1 mM ferulic acid, 1-1.5 mM vanillin, 10-13 mM acetic acid, and 5-7 mM formic acid), both yeasts were able to produce ethanol from xylose, similar to that detected in the control medium (without inhibitors). In future studies, the proteins involved in the transport of pentose and tolerance to these inhibitors need to be investigated.
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Affiliation(s)
- Ronivaldo Rodrigues da Silva
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil.
| | - Mohammed Anas Zaiter
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Maurício Boscolo
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Roberto da Silva
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Eleni Gomes
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
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6
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Park MR, Gauttam R, Fong B, Chen Y, Lim HG, Feist AM, Mukhopadhyay A, Petzold CJ, Simmons BA, Singer SW. Revealing oxidative pentose metabolism in new Pseudomonas putida isolates. Environ Microbiol 2023; 25:493-504. [PMID: 36465038 PMCID: PMC10107873 DOI: 10.1111/1462-2920.16296] [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: 10/04/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well-characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth-promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism (xylDXA) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism (araDXA). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.
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Affiliation(s)
- Mee-Rye Park
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rahul Gauttam
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Bonnie Fong
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hyun Gyu Lim
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Adam M Feist
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Salazar JA, Ruiz D, Zapata P, Martínez-García PJ, Martínez-Gómez P. Whole Transcriptome Analyses of Apricots and Japanese Plum Fruits after 1-MCP (Ethylene-Inhibitor) and Ethrel (Ethylene-Precursor) Treatments Reveal New Insights into the Physiology of the Ripening Process. Int J Mol Sci 2022; 23:ijms231911045. [PMID: 36232348 PMCID: PMC9569840 DOI: 10.3390/ijms231911045] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after different ethylene regulator treatments, including 1-MCP (ethylene-inhibitor) and Ethrel (ethylene-precursor) in two contrasting selected apricot (Prunus armeniaca L.) and Japanese plum (P. salicina L.) cultivars, ‘Goldrich’ and ‘Santa Rosa’. KEEG and protein–protein interaction network analysis unveiled that the most significant metabolic pathways involved in the ripening process were photosynthesis and plant hormone signal transduction. In addition, previously discovered genes linked to fruit ripening, such as pectinesterase or auxin-responsive protein, have been confirmed as the main genes involved in this process. Genes encoding pectinesterase in the pentose and glucuronate interconversions pathway were the most overexpressed in both species, being upregulated by Ethrel. On the other hand, auxin-responsive protein IAA and aquaporin PIP were both upregulated by 1-MCP in ‘Goldrich’ and ‘Santa Rosa’, respectively. Results also showed the upregulation of chitinase and glutaredoxin 3 after Ethrel treatment in ‘Goldrich’ and ‘Santa Rosa’, respectively, while photosystem I subunit V psaG (photosynthesis) was upregulated after 1-MCP in both species. Furthermore, the overexpression of genes encoding GDP-L-galactose and ferredoxin in the ascorbate and aldarate metabolism and photosynthesis pathways caused by 1-MCP favored antioxidant activity and therefore slowed down the fruit senescence process.
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Affiliation(s)
- Juan A Salazar
- Department of Plant Breeding, CEBAS-CSIC, Espinardo, 30100 Murcia, Spain
| | - David Ruiz
- Department of Plant Breeding, CEBAS-CSIC, Espinardo, 30100 Murcia, Spain
| | - Patricio Zapata
- Facultad de Medicina Y Ciencia, Universidad San Sebastián, Santiago 7510157, Chile
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Xie D, Sun Y, Lei Y. Effect of glucose levels on carbon flow rate, antioxidant status, and enzyme activity of yeast during fermentation. J Sci Food Agric 2022; 102:5333-5347. [PMID: 35318660 DOI: 10.1002/jsfa.11887] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The physiological metabolism of yeast has a significant impact on the quality of fermentation products. The present study aimed to investigate yeast metabolism in response to a changing glucose content environment, especially in fermentation products, as well as the change of carbon flow rate, antioxidant status, and yeast enzyme activity. RESULTS Yeast in a 0 g L-1 glucose level was subjected to carbon starvation stress, cell growth retardation and cell proliferation was significantly inadequate; in the logarithmic growth stage of yeast, at a 30 g L-1 glucose level, the carbon source mainly flowed to tricarboxylic acid cycle and pentose phosphate metabolism, cell division, proliferation, and increased cell growth. In later logarithmic growth period and stable period, carbon flowed into glycerol and trehalose metabolism, to cope with the environmental stress; yeast in 60 and 150 g L-1 glucose levels faced high glucose stress at the beginning, the content of reactive oxygen increased, malondialdehyde content increased, cell damage was reduced through the regulation of superoxide dismutase and catalase enzyme activities, and most of the carbon flowed into the metabolic pathway of ethanol, glycerol, and trehalose to cope with high glucose stress, the pentose phosphate pathway showed a large late influx, and NADPH also started to increase rapidly after 24 h. CONCLUSION Yeast was stressed in a high-sugar environment and ensured the activity of yeast by preferentially increasing the metabolic intensity of trehalose, glycerol, and glycolytic metabolism, weakening tricarboxylic acid metabolism, and first weakening and then increasing pentose phosphate metabolism. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Dongdong Xie
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Yingqi Sun
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
| | - Yanan Lei
- National Engineering Laboratory/Key Laboratory of Henan Province, School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
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Hatano J, Kusama S, Tanaka K, Kohara A, Miyake C, Nakanishi S, Shimakawa G. NADPH production in dark stages is critical for cyanobacterial photocurrent generation: a study using mutants deficient in oxidative pentose phosphate pathway. Photosynth Res 2022; 153:113-120. [PMID: 35182311 DOI: 10.1007/s11120-022-00903-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/22/2021] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Live cyanobacteria and algae integrated onto an extracellular electrode can generate a light-induced current (i.e., a photocurrent). Although the photocurrent is expected to be correlated with the redox environment of the photosynthetic cells, the relationship between the photocurrent and the cellular redox state is poorly understood. Here, we investigated the effect of the reduced nicotinamide adenine dinucleotide phosphate [NADP(H)] redox level of cyanobacterial cells (before light exposure) on the photocurrent using several mutants (Δzwf, Δgnd, and ΔglgP) deficient in the oxidative pentose phosphate (OPP) pathway, which is the metabolic pathway that produces NADPH in darkness. The NAD(P)H redox level and photocurrent in the cyanobacterium Synechocystis sp. PCC 6803 were measured noninvasively. Dysfunction of the OPP pathway led to oxidation of the photosynthetic NADPH pool in darkness. In addition, photocurrent induction was retarded and the current density was lower in Δzwf, Δgnd, and ΔglgP than in wild-type cells. Exogenously added glucose compensated the phenotype of ΔglgP and drove the OPP pathway in the mutant, resulting in an increase in the photocurrent. The results indicated that NADPH accumulated by the OPP pathway before illumination is a key factor for the generation of a photocurrent. In addition, measuring the photocurrent can be a non-invasive approach to estimate the cellular redox level related to NADP(H) pool in cyanobacteria.
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Affiliation(s)
- Jiro Hatano
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan
| | - Shoko Kusama
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan
| | - Kenya Tanaka
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan
- Engineering Biology Research Center, Kobe University, Kobe, Japan
| | - Ayaka Kohara
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Chikahiro Miyake
- Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Shuji Nakanishi
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan.
- Innovative Catalysis Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, 565-0871, Japan.
| | - Ginga Shimakawa
- Research Center for Solar Energy Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8631, Japan.
- Department of Bioscience, School of Biological and Environmental Sciences, Kwansei-Gakuin University, 2-1 Gakuen, Sanda, Hyogo, 669-1337, Japan.
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10
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Abstract
C-Analogues of the canonical N-nucleosides have considerable importance in medicinal chemistry and are promising building blocks of xenobiotic nucleic acids (XNA) in synthetic biology. Although well established for synthesis of N-nucleosides, biocatalytic methods are lacking in C-nucleoside synthetic chemistry. Here, we identify pseudouridine monophosphate C-glycosidase for selective 5-β-C-glycosylation of uracil and derivatives thereof from pentose 5-phosphate (D-ribose, 2-deoxy-D-ribose, D-arabinose, D-xylose) substrates. Substrate requirements of the enzymatic reaction are consistent with a Mannich-like addition between the pyrimidine nucleobase and the iminium intermediate of enzyme (Lys166) and open-chain pentose 5-phosphate. β-Elimination of the lysine and stereoselective ring closure give the product. We demonstrate phosphorylation-glycosylation cascade reactions for efficient, one-pot synthesis of C-nucleoside phosphates (yield: 33 - 94%) from unprotected sugar and nucleobase. We show incorporation of the enzymatically synthesized C-nucleotide triphosphates into nucleic acids by RNA polymerase. Collectively, these findings implement biocatalytic methodology for C-nucleotide synthesis which can facilitate XNA engineering for synthetic biology applications.
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Affiliation(s)
- Martin Pfeiffer
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, 8010, Graz, Austria.
- Austrian Centre of Industrial Biotechnology (acib), Petersgasse 14, 8010, Graz, Austria.
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11
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Koendjbiharie JG, Hon S, Pabst M, Hooftman R, Stevenson DM, Cui J, Amador-Noguez D, Lynd LR, Olson DG, van Kranenburg R. The pentose phosphate pathway of cellulolytic clostridia relies on 6-phosphofructokinase instead of transaldolase. J Biol Chem 2020; 295:1867-1878. [PMID: 31871051 PMCID: PMC7029132 DOI: 10.1074/jbc.ra119.011239] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/16/2019] [Indexed: 01/24/2023] Open
Abstract
The genomes of most cellulolytic clostridia do not contain genes annotated as transaldolase. Therefore, for assimilating pentose sugars or for generating C5 precursors (such as ribose) during growth on other (non-C5) substrates, they must possess a pathway that connects pentose metabolism with the rest of metabolism. Here we provide evidence that for this connection cellulolytic clostridia rely on the sedoheptulose 1,7-bisphosphate (SBP) pathway, using pyrophosphate-dependent phosphofructokinase (PPi-PFK) instead of transaldolase. In this reversible pathway, PFK converts sedoheptulose 7-phosphate (S7P) to SBP, after which fructose-bisphosphate aldolase cleaves SBP into dihydroxyacetone phosphate and erythrose 4-phosphate. We show that PPi-PFKs of Clostridium thermosuccinogenes and Clostridium thermocellum indeed can convert S7P to SBP, and have similar affinities for S7P and the canonical substrate fructose 6-phosphate (F6P). By contrast, (ATP-dependent) PfkA of Escherichia coli, which does rely on transaldolase, had a very poor affinity for S7P. This indicates that the PPi-PFK of cellulolytic clostridia has evolved the use of S7P. We further show that C. thermosuccinogenes contains a significant SBP pool, an unusual metabolite that is elevated during growth on xylose, demonstrating its relevance for pentose assimilation. Last, we demonstrate that a second PFK of C. thermosuccinogenes that operates with ATP and GTP exhibits unusual kinetics toward F6P, as it appears to have an extremely high degree of cooperative binding, resulting in a virtual on/off switch for substrate concentrations near its K½ value. In summary, our results confirm the existence of an SBP pathway for pentose assimilation in cellulolytic clostridia.
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Affiliation(s)
| | - Shuen Hon
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755; Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830
| | - Martin Pabst
- Cell Systems Engineering, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Robert Hooftman
- Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands
| | - David M Stevenson
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jingxuan Cui
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830; Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, 03755
| | - Daniel Amador-Noguez
- Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830; Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Lee R Lynd
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755; Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830; Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire, 03755
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755; Center for Bioenergy Innovation, Oak Ridge National Laboratories, Oak Ridge, Tennessee 37830
| | - Richard van Kranenburg
- Corbion, 4206 AC Gorinchem, The Netherlands; Laboratory of Microbiology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands.
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12
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Dai Z, Guo F, Ma J, Dong W, Zhou J, Jiang M, Zhang W, Xin F. The Draft Genome Sequence of Methylophilus sp. D22, Capable of Growing Under High Concentration of Methanol. Curr Microbiol 2019; 76:1520-1524. [PMID: 31515628 DOI: 10.1007/s00284-019-01765-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 11/28/2018] [Accepted: 09/04/2019] [Indexed: 11/26/2022]
Abstract
In this study, a wild type Methylophilus sp. strain D22 belonging to the family Methylophilus was isolated and characterized, which shows high tolerance towards methanol, as it can grow under 50 g/L of methanol. Methylophilus sp. strain D22 was isolated from the lake sludge in Nanjing Tech University, China. The assembled draft genome contains one circular chromosome with 3,004,398 bp, 49.7% of GC content, and 2107 predicted encoding proteins. Sequence-based genomic analysis demonstrates that the assimilation pathway of ribulose monophosphate (RuMP) pathway and dissimilation pathway of tetrahydromethanopterin (H4MPT) pathway are co-existing and contribute to the high methanol utilization efficiency.
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Affiliation(s)
- Zhongxue Dai
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Jiangfeng Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Jie Zhou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
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da Silva RR, Prista C, Loureiro Dias MC, Boscolo M, da Silva R, Gomes E. Improved Utility of Pentoses from Lignocellulolytic Hydrolysate: Challenges and Perspectives for Enabling Saccharomyces cerevisiae. J Agric Food Chem 2019; 67:5919-5921. [PMID: 31099567 DOI: 10.1021/acs.jafc.9b02809] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Ronivaldo Rodrigues da Silva
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) , Universidade Estadual Paulista (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| | - Catarina Prista
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia , Universidade de Lisboa , Tapada da Ajuda, 1349-017 Lisboa , Portugal
| | - Maria Conceição Loureiro Dias
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia , Universidade de Lisboa , Tapada da Ajuda, 1349-017 Lisboa , Portugal
| | - Mauricio Boscolo
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) , Universidade Estadual Paulista (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| | - Roberto da Silva
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) , Universidade Estadual Paulista (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
| | - Eleni Gomes
- Instituto de Biociências, Letras e Ciências Exatas (IBILCE) , Universidade Estadual Paulista (UNESP) , São José do Rio Preto , São Paulo 15054-000 , Brazil
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14
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Liu X, Li Z, Chen Z, Wang N, Gao Y, Nakanishi H, Gao XD. Production of l-Ribulose Using an Encapsulated l-Arabinose Isomerase in Yeast Spores. J Agric Food Chem 2019; 67:4868-4875. [PMID: 30995033 DOI: 10.1021/acs.jafc.9b00640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The rare sugar l-ribulose is produced from the abundant sugar l-arabinose by enzymatic conversion. An l-arabinose isomerase (AI) from Geobacillus thermodenitrificans was efficiently expressed and encapsulated in Saccharomyces cerevisiae spores. Deletion of the yeast OSW2 gene, which causes a mild defect in the integrity of the spore wall, substantially improved the activity of encapsulated AI, without damaging its superior enzymatic properties of thermostability, pH tolerance,and resistance toward SDS and proteinase treatments. In a 10 mL reaction, 100 mg of dry AI encapsulated in spores produced 250 mg of l-ribulose from 1 g of l-arabinose, indicating a 25% conversion rate. Notably, the product of l-ribulose was directly purified from the reaction solution with an approximately 91% recovery using a Ca2+ ion exchange column. Our results describe not only a facile approach for the production of l-ribulose but also a useful strategy for the enzymatic conversion of rare sugars in "Izumoring".
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Affiliation(s)
- Xiaoxiao Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu 214122 , People's Republic of China
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu 214122 , People's Republic of China
| | - Zhou Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu 214122 , People's Republic of China
| | - Ning Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu 214122 , People's Republic of China
| | - Yahui Gao
- School of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , People's Republic of China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu 214122 , People's Republic of China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology , Jiangnan University , Wuxi , Jiangsu 214122 , People's Republic of China
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Borah AJ, Agarwal M, Goyal A, Moholkar VS. Physical insights of ultrasound-assisted ethanol production from composite feedstock of invasive weeds. Ultrason Sonochem 2019; 51:378-385. [PMID: 30097257 DOI: 10.1016/j.ultsonch.2018.07.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 06/06/2018] [Revised: 07/29/2018] [Accepted: 07/31/2018] [Indexed: 06/08/2023]
Abstract
Invasive weeds ubiquitously found in terrestrial and aquatic ecosystems form potential feedstock for lignocellulosic ethanol production. The present study has reported a bioprocess for production of ethanol using mixed feedstock of 8 invasive weeds found in India. The feedstock was subjected to pretreatment comprising dilute acid hydrolysis (for hydrolysis of hemicellulosic fraction), alkaline delignification and enzymatic hydrolysis of cellulosic fraction. Pentose-rich and hexose-rich hydrolyzates obtained from pretreatment were fermented separately using microbial cultures of S. cerevisiae and C. shehatae. Fermentation mixture was sonicated at 35 kHz at 10% duty cycle. The time profiles of total reducing sugars, ethanol and biomass was fitted to a kinetic model using Genetic Algorithm. Sonication boosted the kinetics of fermentation 2-fold. The net bioethanol yield of the process was ∼220 g/kg raw biomass (with contributions of 86.8 and 133 g/kg raw biomass from pentose and hexose fermentations, respectively). Comparative evaluation of parameters of kinetic model under control and test conditions revealed several beneficial influences of sonication on both pentose and hexose fermentation systems such as faster transport of nutrients, substrate and products across cell membrane, rise in Monod saturation constant for substrate with concurrent reduction in substrate inhibition, and reduction of energy requirements for cell maintenance. Flow cytometry analysis of native and ultrasound-treated cells revealed no adverse influence of sonication on cell viability.
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Affiliation(s)
- Arup Jyoti Borah
- Center for Energy, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Mayank Agarwal
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Arun Goyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Vijayanand S Moholkar
- Center for Energy, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India.
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16
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Borah AJ, Roy K, Goyal A, Moholkar VS. Mechanistic investigations in biobutanol synthesis via ultrasound-assisted ABE fermentation using mixed feedstock of invasive weeds. Bioresour Technol 2019; 272:389-397. [PMID: 30388576 DOI: 10.1016/j.biortech.2018.10.063] [Citation(s) in RCA: 5] [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: 08/31/2018] [Revised: 10/20/2018] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
This study reports an ultrasound-assisted Acetone-Butanol-Ethanol (ABE) fermentation process using Clostridium acetobutylicum MTCC 11,274 and mixed feedstock consisting of eight highly invasive weeds. Composite (pentose + hexose) hydrolyzate was fermented with sonication at 35 kHz and 10% duty cycle (test) and mechanical agitation at 150 rpm (control). Net solvent yield with sonication was 0.288 g/g raw biomass in 92 h against yield of 0.168 g/g raw biomass in 120 h with mechanical agitation. Butanol yield in test and control fermentation was 0.233 and 0.149 g/g total fermentable sugar, respectively. Substrate and metabolites profiles in test and control fermentation were analyzed using biokinetic model. Sonication enhanced kinetics of metabolic reactions with rise in substrate affinity of enzymes (reduced saturation constants) and greater resistance to substrate inhibition. Flow cytometry analysis of cells exposed to sonication revealed high cell viability with no adverse effect on physiology.
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Affiliation(s)
- Arup Jyoti Borah
- Center for Energy, Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Kuldeep Roy
- Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Arun Goyal
- Center for Energy, Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India
| | - Vijayanand S Moholkar
- Center for Energy, Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India; Department of Chemical Engineering, Indian Institute of Technology Guwahati, Guwahati 781 039, Assam, India.
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17
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Abstract
The rare branched-chain sugar apiose, once thought to only be present in the plant kingdom, was found in two bacterial species: Geminicoccus roseus and Xanthomonas pisi. Glycans with apiose residues were detected in aqueous methanol-soluble fractions as well as in the insoluble pellet fraction of X. pisi. Genes encoding bacterial uridine diphosphate apiose (UDP-apiose) synthases (bUASs) were characterized in these bacterial species, but the enzyme(s) involved in the incorporation of the apiose into glycans remained unknown. In the X. pisi genome two genes flanking the XpUAS were annotated as hypothetical glycosyltransferase (GT) proteins. The first GT (here on named XpApiT) belongs to GT family 90 and has a Leloir type B fold and a putative lipopolysaccharide-modifying (LPS) domain. The second GT (here on XpXylT) belongs to GT family 2 and has a type A fold. The XpXylT and XpApiT genes were cloned and heterologously expressed in E. coli. Analysis of nucleotide sugar extracts from E. coli expressing XpXylT or XpApiT with UAS showed that recombinant XpApiT utilized UDP-apiose and XpXylT utilized UDP-xylose as substrate. Indirect activity assay (UDP-Glo) revealed that XpApiT is an apiosyltransferase (ApiT) able to specifically use UDP-apiose. Further support for the apiosyltransferase activity was demonstrated by in microbe co-expression of UAS and XpApiT in E. coli showing the utilization of UDP-apiose to generate an apioside detectable in the pellet fraction. This work provides evidence that X. pisi developed the ability to synthesize an apioside of indeterminate function; however, the evolution of the bacterial ApiT remains to be determined. From genetic and evolutionary perspectives, the apiose operon may provide a unique opportunity to examine how genomic changes reflect ecological adaptation during the divergence of a bacterial group.
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Affiliation(s)
- James Amor Smith
- Complex Carbohydrate Research Center (CCRC), University of Georgia, Athens, GA, United States of America
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States of America
| | - Maor Bar-Peled
- Complex Carbohydrate Research Center (CCRC), University of Georgia, Athens, GA, United States of America
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States of America
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
- * E-mail:
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18
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Huang J, Yu L, Zhang W, Zhang T, Guang C, Mu W. Production of d-mannose from d-glucose by co-expression of d-glucose isomerase and d-lyxose isomerase in Escherichia coli. J Sci Food Agric 2018; 98:4895-4902. [PMID: 29569257 DOI: 10.1002/jsfa.9021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 01/20/2018] [Revised: 03/15/2018] [Accepted: 03/18/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND d-Mannose is not only the epimer of d-glucose at the C-2 position, but also the aldose isomer of d-fructose. Because of its physiological properties and health benefits, d-mannose has attracted public interest. It has been confirmed that d-mannose has broad applications in food, cosmetics, and pharmaceutical industries. According to the Izumoring strategy, d-glucose isomerase (d-GI) and d-lyxose isomerase (d-LI) play important roles in the conversions of d-fructose from d-glucose and of d-mannose from d-fructose respectively. In this study, a one-step enzyme process of d-mannose production from d-glucose has been constructed by co-expression of the d-GI from Acidothermus cellulolyticus and d-LI from Thermosediminibacter oceani in Escherichia coli BL21(DE3) cells. RESULTS The co-expression system exhibits maximum activity at pH 6.5 and 65 °C with Co2+ supplement. It is relatively thermostable at less than 65 °C. When the reaction reaches equilibrium, the ratio of d-glucose, d-fructose, and d-mannose is approximately 34 : 49.6 : 16.4. By using this co-expression system, about 60.0 g L-1 d-mannose is obtained from 400 g L-1 d-glucose in 8 h. CONCLUSION This co-expression of d-GI and d-LI system provides a novel and efficient approach for d-mannose production. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Jiawei Huang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Lina Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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Yoshida H, Yoshihara A, Gullapalli PK, Ohtani K, Akimitsu K, Izumori K, Kamitori S. X-ray structure of Arthrobacter globiformis M30 ketose 3-epimerase for the production of D-allulose from D-fructose. Acta Crystallogr F Struct Biol Commun 2018; 74:669-676. [PMID: 30279320 PMCID: PMC6168773 DOI: 10.1107/s2053230x18011706] [Citation(s) in RCA: 15] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/19/2018] [Indexed: 12/18/2022] Open
Abstract
The X-ray structure of ketose 3-epimerase from Arthrobacter globiformis M30, which was previously reported to be a D-allulose 3-epimerase (AgD-AE), was determined at 1.96 Å resolution. The crystal belonged to the hexagonal space group P6522, with unit-cell parameters a = b = 103.98, c = 256.53 Å. The structure was solved by molecular replacement using the structure of Mesorhizobium loti L-ribulose 3-epimerase (MlL-RE), which has 41% sequence identity, as a search model. A hexagonal crystal contained two molecules in the asymmetric unit, and AgD-AE formed a homotetramer with twofold symmetry. The overall structure of AgD-AE was more similar to that of MlL-RE than to the known structures of D-psicose (alternative name D-allulose) 3-epimerases (D-PEs or D-AEs), although AgD-AE and MlL-RE have different substrate specificities. Both AgD-AE and MlL-RE have long helices in the C-terminal region that would contribute to the stability of the homotetramer. AgD-AE showed higher enzymatic activity for L-ribulose than D-allulose; however, AgD-AE is stable and is a unique useful enzyme for the production of D-allulose from D-fructose.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
- International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan
| | - Akihide Yoshihara
- International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | | | - Kouhei Ohtani
- Matsutani Chemical Industry Co. Ltd, 5-3 Kita-Itami, Itami, Hyogo 664-8508, Japan
| | - Kazuya Akimitsu
- International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Ken Izumori
- International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
- International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan
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20
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Cassuriaga APA, Freitas BCB, Morais MG, Costa JAV. Innovative polyhydroxybutyrate production by Chlorella fusca grown with pentoses. Bioresour Technol 2018; 265:456-463. [PMID: 29935455 DOI: 10.1016/j.biortech.2018.06.026] [Citation(s) in RCA: 18] [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] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/08/2018] [Accepted: 06/10/2018] [Indexed: 06/08/2023]
Abstract
The current study aimed to evaluate if the addition of pentoses along with variations in light intensity and photoperiod can stimulate the production of polyhydroxybutyrate (PHB) and other biomolecules by Chlorella fusca LEB 111. The variables evaluated were the addition of xylose and arabinose as sources of organic carbon, different photoperiods (18 h, 12 h and 6 h light) and variations in light intensities (58, 28 and 9 μmolphotons m-2 s-1). The highest PHB accumulation (17.4% w w-1) and protein production (53.2% ww-1) were observed in assays with xylose addition and a photoperiod of 6 h of light provided at 28 and 58 μmolphotons m-2 s-1, respectively. The highest lipid content (24.7% w w-1) was obtained with 18 h of light. The current study contributes to the development of sustainable alternatives for the use of wastes and the production of biomolecules from algae.
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Affiliation(s)
- A P A Cassuriaga
- College of Chemistry and Food Engineering, Federal University of Rio Grande, Laboratory of Biochemical Engineering, Rio Grande, RS, Brazil
| | - B C B Freitas
- College of Chemistry and Food Engineering, Federal University of Rio Grande, Laboratory of Biochemical Engineering, Rio Grande, RS, Brazil
| | - M G Morais
- College of Chemistry and Food Engineering, Federal University of Rio Grande, Laboratory of Microbiology and Biochemistry, Rio Grande, RS, Brazil
| | - J A V Costa
- College of Chemistry and Food Engineering, Federal University of Rio Grande, Laboratory of Biochemical Engineering, Rio Grande, RS, Brazil.
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21
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Loman AA, Islam SMM, Ju LK. Production of arabitol from enzymatic hydrolysate of soybean flour by Debaryomyces hansenii fermentation. Appl Microbiol Biotechnol 2018; 102:641-653. [PMID: 29150708 DOI: 10.1007/s00253-017-8626-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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] [Received: 09/17/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 11/26/2022]
Abstract
Arabitol is a low-calorie sugar alcohol with anti-cariogenic properties. Enzymatic hydrolysate of soybean flour is a new renewable biorefinery feedstock containing hexose, pentose, and organic nitrogen sources. Arabitol production by Debaryomyces hansenii using soybean flour hydrolysate was investigated. Effects of medium composition, operating conditions, and culture stage (growing or stationary phase) were studied. Production was also compared at different culture volumes to understand the effect of dissolved oxygen concentration (DO). Main factors examined for medium composition effects were the carbon to nitrogen concentration ratio (C/N), inorganic (ammonium) to organic nitrogen ratio (I/O-N), and sugar composition. Arabitol yield increased with increasing C/N ratio and a high I/O-N (0.8-1.0), suggesting higher yield at stationary phase of low pH (3.5-4.5). Catabolite repression was observed, with the following order of consumption: glucose > fructose > galactose > xylose > arabinose. Arabitol production also favored hexoses and, among hexoses, glucose. DO condition was of critical importance to arabitol production and cell metabolism. The yeast consumed pentoses (xylose and arabinose) only at more favorable DO conditions. Finally, arabitol was produced in fermentors using mixed hydrolysates of soy flour and hulls. The process gave an arabitol yield of 54%, volumetric productivity of 0.90 g/L-h, and specific productivity of 0.031 g/g-h.
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Affiliation(s)
- Abdullah A Loman
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - S M M Islam
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA
| | - Lu-Kwang Ju
- Department of Chemical and Biomolecular Engineering, The University of Akron, Akron, OH, 44325, USA.
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Martins GM, Bocchini-Martins DA, Bezzerra-Bussoli C, Pagnocca FC, Boscolo M, Monteiro DA, Silva RD, Gomes E. The isolation of pentose-assimilating yeasts and their xylose fermentation potential. Braz J Microbiol 2017; 49:162-168. [PMID: 28888830 PMCID: PMC5790582 DOI: 10.1016/j.bjm.2016.11.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [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: 05/05/2016] [Revised: 07/05/2016] [Accepted: 11/13/2016] [Indexed: 11/19/2022] Open
Abstract
For the implementation of cellulosic ethanol technology, the maximum use of lignocellulosic materials is important to increase efficiency and to reduce costs. In this context, appropriate use of the pentose released by hemicellulose hydrolysis could improve de economic viability of this process. Since the Saccharomyces cerevisiae is unable to ferment the pentose, the search for pentose-fermenting microorganisms could be an alternative. In this work, the isolation of yeast strains from decaying vegetal materials, flowers, fruits and insects and their application for assimilation and alcoholic fermentation of xylose were carried out. From a total of 30 isolated strains, 12 were able to assimilate 30 g L−1 of xylose in 120 h. The strain Candida tropicalis S4 produced 6 g L−1 of ethanol from 56 g L−1 of xylose, while the strain C. tropicalis E2 produced 22 g L−1 of xylitol. The strains Candida oleophila G10.1 and Metschnikowia koreensis G18 consumed significant amount of xylose in aerobic cultivation releasing non-identified metabolites. The different materials in environment were source for pentose-assimilating yeast with variable metabolic profile.
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Affiliation(s)
- Gisele Marta Martins
- Universidade Estadual Paulista(UNESP), Instituto de Pesquisa em Bioenergia-IPBen, Laboratório de Microbiologia aplicada, São José do Rio Preto, SP, Brazil
| | | | - Carolina Bezzerra-Bussoli
- Universidade Estadual Paulista(UNESP), Instituto de Pesquisa em Bioenergia-IPBen, Laboratório de Microbiologia aplicada, São José do Rio Preto, SP, Brazil
| | - Fernando Carlos Pagnocca
- Universidade Estadual Paulista-UNESP, Centro de Estudos de Insetos Sociais-Ceis, Campus of Rio Claro, SP, Brazil
| | - Maurício Boscolo
- Universidade Estadual Paulista(UNESP), Instituto de Pesquisa em Bioenergia-IPBen, Laboratório de Microbiologia aplicada, São José do Rio Preto, SP, Brazil
| | - Diego Alves Monteiro
- Universidade Estadual Paulista(UNESP), Instituto de Pesquisa em Bioenergia-IPBen, Laboratório de Microbiologia aplicada, São José do Rio Preto, SP, Brazil
| | - Roberto da Silva
- Universidade Estadual Paulista(UNESP), Instituto de Pesquisa em Bioenergia-IPBen, Laboratório de Microbiologia aplicada, São José do Rio Preto, SP, Brazil
| | - Eleni Gomes
- Universidade Estadual Paulista(UNESP), Instituto de Pesquisa em Bioenergia-IPBen, Laboratório de Microbiologia aplicada, São José do Rio Preto, SP, Brazil.
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Yang W, Jiang Z, Liu L, Lin Y, Wang L, Zhou S. The effect of pentosanase on the solubilisation and degradation of arabinoxylan extracted from whole and refined wheat flour. J Sci Food Agric 2017; 97:1034-1041. [PMID: 27271725 DOI: 10.1002/jsfa.7833] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 04/21/2016] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND The quality improvement capability of pentosanase (Pn) for whole-wheat Chinese steamed bread (CSB) is not as efficient as that for refined CSB. However, the underlying mechanism remains to be elucidated. In this work, water-extractable arabinoxylan (WEAX) and water-unextractable solids (WUS) were extracted from whole and refined wheat flour, and then treated with Pn under the conditions similar to CSB-making. Solubilisation and degradation of arabinoxylan (AX) caused by Pn treatment were determined. RESULTS WEAX from whole flour exhibited higher molecular weight than that from refined flour before and after the treatment with equivalent Pn. Compared with WUS from refined flour, WUS from whole flour had a much lower dissolution degree but the degradation of AX released from the WUS was more efficiently. Moreover, AX released from WUS for refined flour showed a higher Ara/Xyl ratio and the percentage of residual ferulic acid in WUS decreased more significantly. CONCLUSION The difference in quality improvement degree for Pn in whole-wheat and refined CSB might be mainly explained by its effect on WUS. That is, Pn contributed much more to the solubilisation of WUS from refined flour but provoked degradation predominantly on AX solubilised from WUS isolated from whole flour. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Wei Yang
- School of Food Science and Technology in Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhijian Jiang
- School of Food Science and Technology in Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Liya Liu
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yanjun Lin
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Li Wang
- School of Food Science and Technology in Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Sumei Zhou
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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Chatellard L, Trably E, Carrère H. The type of carbohydrates specifically selects microbial community structures and fermentation patterns. Bioresour Technol 2016; 221:541-549. [PMID: 27686722 DOI: 10.1016/j.biortech.2016.09.084] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 07/20/2016] [Revised: 09/16/2016] [Accepted: 09/17/2016] [Indexed: 05/24/2023]
Abstract
The impact on dark fermentation of seven carbohydrates as model substrates of lignocellulosic fractions (glucose, cellobiose, microcrystalline cellulose, arabinose, xylose, xylan and wheat straw) was investigated. Metabolic patterns and bacterial communities were characterized at the end of batch tests inoculated with manure digestate. It was found that hydrogen production was linked to the sugar type (pentose or hexose) and the degree of polymerisation. Hexoses produced less hydrogen, with a specific selection of lactate-producing bacterial community structures. Maximal hydrogen production was five times higher on pentose-based substrates, with specific bacterial community structures producing acetate and butyrate as main metabolites. Low hydrogen amounts accumulated from complex sugars (cellulose, xylan and wheat straw). A relatively high proportion of the reads was affiliated to Ruminococcaceae suggesting an efficient hydrolytic activity. Knowing that the bacterial community structure is very specific to a particular substrate offers new possibilities to design more efficient H2-producing biological systems.
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Affiliation(s)
| | - Eric Trably
- LBE, INRA, 102 avenue des Etangs, 11100 Narbonne, France.
| | - Hélène Carrère
- LBE, INRA, 102 avenue des Etangs, 11100 Narbonne, France
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Chomvong K, Bauer S, Benjamin DI, Li X, Nomura DK, Cate JHD. Bypassing the Pentose Phosphate Pathway: Towards Modular Utilization of Xylose. PLoS One 2016; 11:e0158111. [PMID: 27336308 PMCID: PMC4918971 DOI: 10.1371/journal.pone.0158111] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [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: 03/11/2016] [Accepted: 06/12/2016] [Indexed: 12/22/2022] Open
Abstract
The efficient use of hemicellulose in the plant cell wall is critical for the economic conversion of plant biomass to renewable fuels and chemicals. Previously, the yeast Saccharomyces cerevisiae has been engineered to convert the hemicellulose-derived pentose sugars xylose and arabinose to d-xylulose-5-phosphate for conversion via the pentose phosphate pathway (PPP). However, efficient pentose utilization requires PPP optimization and may interfere with its roles in NADPH and pentose production. Here, we developed an alternative xylose utilization pathway that largely bypasses the PPP. In the new pathway, d-xylulose is converted to d-xylulose-1-phosphate, a novel metabolite to S. cerevisiae, which is then cleaved to glycolaldehyde and dihydroxyacetone phosphate. This synthetic pathway served as a platform for the biosynthesis of ethanol and ethylene glycol. The use of d-xylulose-1-phosphate as an entry point for xylose metabolism opens the way for optimizing chemical conversion of pentose sugars in S. cerevisiae in a modular fashion.
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Affiliation(s)
- Kulika Chomvong
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Stefan Bauer
- Energy Biosciences Institute, Berkeley, CA, United States of America
| | - Daniel I. Benjamin
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, United States of America
| | - Xin Li
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
| | - Daniel K. Nomura
- Program in Metabolic Biology, Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA, United States of America
| | - Jamie H. D. Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
- Department of Chemistry, University of California, Berkeley, CA, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
- * E-mail:
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Vargas-Tah A, Moss-Acosta CL, Trujillo-Martinez B, Tiessen A, Lozoya-Gloria E, Orencio-Trejo M, Gosset G, Martinez A. Non-severe thermochemical hydrolysis of stover from white corn and sequential enzymatic saccharification and fermentation to ethanol. Bioresour Technol 2015; 198:611-618. [PMID: 26433785 DOI: 10.1016/j.biortech.2015.09.036] [Citation(s) in RCA: 9] [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: 07/22/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 06/05/2023]
Abstract
A parametric study, with an initial load of 15%w/w of dry stover from white corn, was conducted to evaluate the sequential thermochemical hydrolysis (TH), enzymatic saccharification (ES) and fermentation of the whole slurry with ethanologenic Escherichia coli. The TH was designed to release the maximum amount of xylose with a concomitant formation of minimal amounts of furans. It was found that 29.0% or 93.2% of the xylan was recovered as free xylose at 130°C after 8 min in the presence of 1% or 2%w/w H2SO4 and produced only 0.06 or 0.44 g/L of total furans, respectively. After 24h of ES, 76.14-77.18 g/L of monosaccharides (pentoses and hexoses) were obtained. These slurries, which contained 0.03-0.26 g/L of total furans and 5.14-5.91 g/L of acetate, were fermented with 3.7 g/L of ethanologenic E. coli to produce 24.5-23.5 g/L of ethanol.
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Affiliation(s)
- Alejandra Vargas-Tah
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos 62250, Mexico
| | - Cessna L Moss-Acosta
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos 62250, Mexico
| | - Berenice Trujillo-Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos 62250, Mexico
| | - Axel Tiessen
- Departamento de Ingeniería Genética, CINVESTAV IPN Unidad Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato Gto., Mexico
| | - Edmundo Lozoya-Gloria
- Departamento de Ingeniería Genética, CINVESTAV IPN Unidad Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato Gto., Mexico
| | - Montserrat Orencio-Trejo
- Departamento de Ingeniería Genética, CINVESTAV IPN Unidad Irapuato, Km 9.6 Libramiento Norte Carretera Irapuato-León, C.P. 36821 Irapuato Gto., Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos 62250, Mexico
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca, Morelos 62250, Mexico.
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Yang M, Kuittinen S, Zhang J, Vepsäläinen J, Keinänen M, Pappinen A. Co-fermentation of hemicellulose and starch from barley straw and grain for efficient pentoses utilization in acetone-butanol-ethanol production. Bioresour Technol 2015; 179:128-135. [PMID: 25536510 DOI: 10.1016/j.biortech.2014.12.005] [Citation(s) in RCA: 16] [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] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/01/2014] [Accepted: 12/03/2014] [Indexed: 06/04/2023]
Abstract
This study aims to efficiently use hemicellulose-based biomass for ABE (acetone-butanol-ethanol) production by co-fermentation with starch-based biomass. Two processes were investigated: (I) co-fermentation of sugars derived from hemicellulose and starch in a mixture of barley straw and grain that was pretreated with dilute acid; (II) co-fermentation of straw hemicellulosic hydrolysate and gelatinized grain slurry in which the straw was pretreated with dilute acid. The two processes produced 11.3 and 13.5 g/L ABE that contains 7.4 and 7.8 g/L butanol, respectively. In process I, pretreatment with 1.0% H2SO4 resulted in better ABE fermentability than with 1.5% H2SO4, but only 19% of pentoses were consumed. In process II, 95% of pentoses were utilized even in the hemicellulosic hydrolysate pretreated with more severe condition (1.5% H2SO4). The results suggest that process II is more favorable for hemicellulosic biomass utilization, and it is also attractive for sustainable biofuel production due to great biomass availability.
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Affiliation(s)
- Ming Yang
- School of Forest Sciences, University of Eastern Finland, P.O. Box 111, FI80101 Joensuu, Finland.
| | - Suvi Kuittinen
- School of Forest Sciences, University of Eastern Finland, P.O. Box 111, FI80101 Joensuu, Finland
| | - Junhua Zhang
- College of Forestry, Northwest A&F University, 3 Taicheng Road, 712100 Yangling, China
| | - Jouko Vepsäläinen
- School of Pharmacy, University of Eastern Finland, P.O. Box 1627, FI70211 Kuopio, Finland
| | - Markku Keinänen
- Department of Biology, University of Eastern Finland, P.O. Box 111, FI80101 Joensuu, Finland
| | - Ari Pappinen
- School of Forest Sciences, University of Eastern Finland, P.O. Box 111, FI80101 Joensuu, Finland
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Lennartsson PR, Erlandsson P, Taherzadeh MJ. Integration of the first and second generation bioethanol processes and the importance of by-products. Bioresour Technol 2014; 165:3-8. [PMID: 24582951 DOI: 10.1016/j.biortech.2014.01.127] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [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: 12/14/2013] [Revised: 01/28/2014] [Accepted: 01/30/2014] [Indexed: 05/25/2023]
Abstract
Lignocellulosic ethanol has obstacles in the investment costs and uncertainties in the process. One solution is to integrate it with the running dry mills of ethanol from grains. However, the economy of these mills, which dominate the world market, are dependent on their by-products DDGS (Distiller's Dried Grains and Solubles), sold as animal feed. The quality of DDGS therefore must not be negatively influenced by the integration. This puts restraints on the choice of pretreatment of lignocelluloses and utilizing the pentose sugars by food-grade microorganisms. The proposed solution is to use food related filamentous Zygomycetes and Ascomycetes fungi, and to produce fungal biomass as a high-grade animal feed from the residues after the distillation (stillage). This also has the potential to improve the first generation process by increasing the amount of the thin stillage directly sent back into the process, and by decreasing the evaporator based problems.
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Affiliation(s)
- Patrik R Lennartsson
- Swedish Centre for Resource Recovery, University of Borås, SE 501 90 Borås, Sweden
| | - Per Erlandsson
- Lantmännen Energi, S:t Göransgatan 160A, Stockholm, Sweden
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Jung WS, Singh RK, Lee JK, Pan CH. Crystal structure and substrate specificity of D-galactose-6-phosphate isomerase complexed with substrates. PLoS One 2013; 8:e72902. [PMID: 24015281 PMCID: PMC3755991 DOI: 10.1371/journal.pone.0072902] [Citation(s) in RCA: 2] [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: 04/11/2013] [Accepted: 07/14/2013] [Indexed: 11/29/2022] Open
Abstract
D-Galactose-6-phosphate isomerase from Lactobacillus rhamnosus (LacAB; EC 5.3.1.26), which is encoded by the tagatose-6-phosphate pathway gene cluster (lacABCD), catalyzes the isomerization of D-galactose-6-phosphate to D-tagatose-6-phosphate during lactose catabolism and is used to produce rare sugars as low-calorie natural sweeteners. The crystal structures of LacAB and its complex with D-tagatose-6-phosphate revealed that LacAB is a homotetramer of LacA and LacB subunits, with a structure similar to that of ribose-5-phosphate isomerase (Rpi). Structurally, LacAB belongs to the RpiB/LacAB superfamily, having a Rossmann-like αβα sandwich fold as has been identified in pentose phosphate isomerase and hexose phosphate isomerase. In contrast to other family members, the LacB subunit also has a unique α7 helix in its C-terminus. One active site is distinctly located at the interface between LacA and LacB, whereas two active sites are present in RpiB. In the structure of the product complex, the phosphate group of D-tagatose-6-phosphate is bound to three arginine residues, including Arg-39, producing a different substrate orientation than that in RpiB, where the substrate binds at Asp-43. Due to the proximity of the Arg-134 residue and backbone Cα of the α6 helix in LacA to the last Asp-172 residue of LacB with a hydrogen bond, a six-carbon sugar-phosphate can bind in the larger pocket of LacAB, compared with RpiB. His-96 in the active site is important for ring opening and substrate orientation, and Cys-65 is essential for the isomerization activity of the enzyme. Two rare sugar substrates, D-psicose and D-ribulose, show optimal binding in the LacAB-substrate complex. These findings were supported by the results of LacA activity assays.
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Affiliation(s)
- Woo-Suk Jung
- Functional Food Center, Korea Institute of Science and Technology Gangneung Institute, Gangneung, Korea
| | - Raushan Kumar Singh
- Department of Chemical Engineering, Konkuk University, Gwangjin-Gu, Seoul, Korea
| | - Jung-Kul Lee
- Department of Chemical Engineering, Konkuk University, Gwangjin-Gu, Seoul, Korea
| | - Cheol-Ho Pan
- Functional Food Center, Korea Institute of Science and Technology Gangneung Institute, Gangneung, Korea
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Mariano AP, Dias MOS, Junqueira TL, Cunha MP, Bonomi A, Filho RM. Utilization of pentoses from sugarcane biomass: techno-economics of biogas vs. butanol production. Bioresour Technol 2013; 142:390-399. [PMID: 23748087 DOI: 10.1016/j.biortech.2013.05.052] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [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: 04/09/2013] [Revised: 05/14/2013] [Accepted: 05/15/2013] [Indexed: 06/02/2023]
Abstract
This paper presents the techno-economics of greenfield projects of an integrated first and second-generation sugarcane biorefinery in which pentose sugars obtained from sugarcane biomass are used either for biogas (consumed internally in the power boiler) or n-butanol production via the ABE batch fermentation process. The complete sugarcane biorefinery was simulated using Aspen Plus®. Although the pentoses stream available in the sugarcane biorefinery gives room for a relatively small biobutanol plant (7.1-12 thousand tonnes per year), the introduction of butanol and acetone to the product portfolio of the biorefinery increased and diversified its revenues. Whereas the IRR of the investment on a biorefinery with biogas production is 11.3%, IRR varied between 13.1% and 15.2% in the butanol production option, depending on technology (regular or engineered microorganism with improved butanol yield and pentoses conversion) and target market (chemicals or automotive fuels). Additional discussions include the effects of energy-efficient technologies for butanol processing on the profitability of the biorefinery.
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Affiliation(s)
- Adriano Pinto Mariano
- Laboratory of Optimization, Design and Advanced Control (LOPCA), School of Chemical Engineering - University of Campinas (UNICAMP), Av. Albert Einstein 500, CEP 13083-852 Campinas, SP, Brazil.
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Kawata Y, Jin YX, Nojiri M. Efficient secretion of (R)-3-hydroxybutyric acid from Halomonas sp. KM-1 cultured with saccharified Japanese cedar under microaerobic conditions. Bioresour Technol 2013; 140:443-445. [PMID: 23719194 DOI: 10.1016/j.biortech.2013.05.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 05/01/2013] [Accepted: 05/04/2013] [Indexed: 06/02/2023]
Abstract
In the presence of d-glucose, consumption of pentoses such as d-xylose is somewhat repressed by most bacteria. However, in Halomonas sp. KM-1, simultaneous utilization of a pure hexose and pentose for growth and PHB production has been observed. Moreover, this strain has been shown to preferentially utilize d-xylose from a mixture of hexose and pentose. In addition, the KM-1 strain produced (R)-3-hydroxybutyric acid ((R)-3-HB) by using saccharified Japanese cedar (Cryptomeria japonica) wood. The concentration of intracellular PHB after aerobic cultivation for 24h was 8.4 g/L, and after shifting to microaerobic conditions and further cultivation for 18 h, the concentration of (R)-3-HB in the medium reached 8.0 g/L. These results show that the KM-1 strain can efficiently utilize saccharified Japanese cedar and secreted (R)-3-HB under microaerobic conditions.
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Affiliation(s)
- Yoshikazu Kawata
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Midorigaoka, Ikeda, Osaka 563-8577, Japan.
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Napora K, Wrodnigg TM, Kosmus P, Thonhofer M, Robins K, Winkler M. Yarrowia lipolytica dehydrogenase/reductase: an enzyme tolerant for lipophilic compounds and carbohydrate substrates. Bioorg Med Chem Lett 2013; 23:3393-5. [PMID: 23608762 DOI: 10.1016/j.bmcl.2013.03.064] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 02/09/2013] [Revised: 03/15/2013] [Accepted: 03/20/2013] [Indexed: 11/18/2022]
Abstract
Yarrowia lipolytica short chain dehydrogenase/reductase (YlSDR) was expressed in Escherichia coli, purified and characterized in vitro. The substrate scope for YlSDR mediated oxidation was investigated with alcohols and unprotected carbohydrates spectrophotometrically, revealing a preference for secondary compared to primary alcohols. In reduction direction, YlSDR was highly active on ribulose and fructose, suggesting that the enzyme is a mannitol-2-dehydrogenase. In order to explore substrate tolerance especially for space-demanding, lipophilic protecting groups, 5-O-trityl-D-ribitol and 5-O-trityl-α,β-D-ribose were investigated as substrates: YlSDR oxidized 5-O-trityl-D-ribitol and 5-O-trityl-α,β-D-ribose and reduced the latter at the expense of NADP(H).
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Zhao J, Xu L, Wang Y, Zhao X, Wang J. [Production of L-lactic acid from pentose by a genetically engineered Escherichia coli]. Wei Sheng Wu Xue Bao 2013; 53:328-337. [PMID: 23858707] [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] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
OBJECTIVE In this study, we constructed a recombinant Escherichia coli strain for the production of high-purity L-lactic acid, using a homoethanol fermenting mutant E. coli SZ470 (deltafrdBC deltaldhA deltaackA deltafocA-pflB deltapdhR: :pflBp6-pflBrbs-aceEF-lpd) as the starting strain. METHODS By using homologous recombination, we deleted the adhE gene from SZ470 to obtain a mutant Escherichia coli JH01, which could not grow under anaerobic conditions. Then we cloned the L-lactate dehydrogenase gene (ldhL) of Pediococcus acidilactici and inserted it into the chromosome of JH01 via electroporation to obtain a recombinant strain Escherichia coli JH12. We evaluated the L-lactic acid production of the recombinant strain in a 15 L fermenter. RESULTS In 10 L LB medium supplemented with 6% glucose, JH12 maintained maximal cell growth and an efficient L-lactic acid production rate for 36 h. Glucose consumption rate achieved was 1.46 g/(L x h) and L-lactic acid production rate was 1.14 g/(L x h). The results also show that 41.13 g/L lactic acid was produced, achieving a purity of 95.69% (based on total fermentation products). Xylose consumption rate was 0.88 g/(L x h) and L-lactic acid production rate was 0.60 g/(L x h). The production of lactic acid was 34.73 g/L, achieving a purity of 98%. There were no succinic acid and formic acid detected and only little amount of acetic acid generated during the fermentation. CONCLUSION We constructed a homolactic acid fermentation strain E. coli JH12, which could efficiently convert glucose and xylose into high-purity L-lactic acid. JH12 could have great potential in industrial fermentation for L-lactic acid production.
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Affiliation(s)
- Jinfang Zhao
- Key Laboratory of Fermentation Engineering of Ministry of Education, Hubei University of Technology, Wuhan 430068, China.
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Avci A, Saha BC, Dien BS, Kennedy GJ, Cotta MA. Response surface optimization of corn stover pretreatment using dilute phosphoric acid for enzymatic hydrolysis and ethanol production. Bioresour Technol 2013; 130:603-12. [PMID: 23334017 DOI: 10.1016/j.biortech.2012.12.104] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 10/02/2012] [Accepted: 12/14/2012] [Indexed: 05/02/2023]
Abstract
Dilute H(3)PO(4) (0.0-2.0%, v/v) was used to pretreat corn stover (10%, w/w) for conversion to ethanol. Pretreatment conditions were optimized for temperature, acid loading, and time using central composite design. Optimal pretreatment conditions were chosen to promote sugar yields following enzymatic digestion while minimizing formation of furans, which are potent inhibitors of fermentation. The maximum glucose yield (85%) was obtained after enzymatic hydrolysis of corn stover pretreated with 0.5% (v/v) acid at 180°C for 15min while highest yield for xylose (91.4%) was observed from corn stover pretreated with 1% (v/v) acid at 160°C for 10min. About 26.4±0.1g ethanol was produced per L by recombinant Escherichia coli strain FBR5 from 55.1±1.0g sugars generated from enzymatically hydrolyzed corn stover (10%, w/w) pretreated under a balanced optimized condition (161.81°C, 0.78% acid, 9.78min) where only 0.4±0.0g furfural and 0.1±0.0 hydroxylmethyl furfural were produced.
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Affiliation(s)
- Ayse Avci
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture(1), 1815 N. University Street, Peoria, IL 61604, USA.
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Lertwattanasakul N, Murata M, Rodrussamee N, Limtong S, Kosaka T, Yamada M. Essentiality of respiratory activity for pentose utilization in thermotolerant yeast Kluyveromyces marxianus DMKU 3-1042. Antonie Van Leeuwenhoek 2013; 103:933-45. [PMID: 23338601 DOI: 10.1007/s10482-012-9874-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2012] [Accepted: 12/31/2012] [Indexed: 11/26/2022]
Abstract
By random integrative mutagenesis with a kanMX4 cassette in Kluyveromyces marxianus DMKU 3-1042, we obtained three mutants of COX15, ATP25 and CYC3 encoding a cytochrome oxidase assembly factor (singleton), a transcription factor required for assembly of the Atp9p subunit of mitochondrial ATP synthase and cytochrome c heme lyase, respectively, as mutants lacking growth capability on xylose and/or arabinose. They exhibited incapability of growth on non-fermentable carbon sources, such as acetate or glycerol, and thermosensitiveness. Their biomass formation in glucose medium was reduced, but ethanol yields were increased with a high ethanol level in the medium, compared to those of the parental strain. Experiments with respiratory inhibitors showed that cox15 and cyc3, but not atp25, were able to grow in glucose medium containing antimycin A and that the atp25 mutant was KCN-resistant. Activities of NADH and ubiquinol oxidases in membrane fractions of each mutant became a half of that of the parent and negligible, respectively, and their remaining NADH oxidase activities were found to be resistant to KCN. Absolute absorption spectral analysis revealed that the peak corresponding to a + a 3 was very small in atp25 and negligible in cox15 and cyc3. These findings suggest that the K. marxianus strain possesses an alternative KCN-resistant oxidase that is located between primary dehydrogenases and the ubiquinone pool and that the respiratory activity is essential for utilization of pentoses.
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Affiliation(s)
- Noppon Lertwattanasakul
- Applied Molecular Bioscience, Graduate School of Medicine, Yamaguchi University, Ube, 755-8505, Japan.
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Wang F, Zhao Y, Niu Y, Wang C, Wang M, Li Y, Sun C. Activated glucose-6-phosphate dehydrogenase is associated with insulin resistance by upregulating pentose and pentosidine in diet-induced obesity of rats. Horm Metab Res 2012; 44:938-42. [PMID: 23015612 DOI: 10.1055/s-0032-1323727] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Recent studies have shown that glucose-6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme for the pentose phosphate pathway, was involved in insulin resistance via reduced nicotinamide adenine dinucleotide phosphate, while the roles of pentose were not examined. In the present study, the association of G6PD, pentose, and pentosidine with insulin resistance was investigated in diet-induced obesity of rats. Male Wistar rats were fed a high-fat diet for 6 weeks to generate obesity-prone (OP, n=14) and obesity-resistant (OR, n=14) rats. The levels of G6PD, pentose, and pentosidine, and oxidative stress were analyzed in serum and tissues. The OP rats, compared to the OR and control rats, had a significant increase in body weight (16.2% and 12.8%), serum triglyceride (43.4% and 12.3), and free fatty acids (49.5% and 23.6%), and developed marked insulin resistance. G6PD activities were increased in the pancreas and liver with upregulated pentose levels in serum, pancreas, and liver of OP rats. Pentosidine levels were increased only under the condition of high pentose levels and oxidative stress status in serum and pancreas of OP rats. G6PD activities in pancreas and liver, pentose levels in serum, pancreas, and liver, and pentosidine levels in serum and pancreas were positively correlated with homeostasis model of assessment-insulin resistance. Our results suggest that the upregulation of G6PD causes an increase in the accumulation of pentose and pentosidine, which might be associated with insulin resistance in the condition of obesity.
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Affiliation(s)
- F Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, China
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Zhang Y, Zagnitko O, Rodionova I, Osterman A, Godzik A. The FGGY carbohydrate kinase family: insights into the evolution of functional specificities. PLoS Comput Biol 2011; 7:e1002318. [PMID: 22215998 PMCID: PMC3245297 DOI: 10.1371/journal.pcbi.1002318] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [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: 07/13/2011] [Accepted: 11/06/2011] [Indexed: 12/29/2022] Open
Abstract
Function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. However, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. Here, using the FGGY carbohydrate kinase family as an example, we built a confidently annotated reference set (CARS) of proteins by propagating experimentally verified functional assignments to a limited number of homologous proteins that are supported by their genomic and functional contexts. Then, we analyzed, on both the phylogenetic and the molecular levels, the evolution of different functional specificities in this family. The results show that the different functions (substrate specificities) encoded by FGGY kinases have emerged only once in the evolutionary history following an apparently simple divergent evolutionary model. At the same time, on the molecular level, one isofunctional group (L-ribulokinase, AraB) evolved at least two independent solutions that employed distinct specificity-determining residues for the recognition of a same substrate (L-ribulose). Our analysis provides a detailed model of the evolution of the FGGY kinase family. It also shows that only combined molecular and phylogenetic approaches can help reconstruct a full picture of functional diversifications in such diverse families. The protein universe is under constant expansion and is reshaping through multiple duplication, gene losses, lateral gene transfers, and speciation events. Large and functionally heterogeneous protein families that evolve through these processes contain conserved motifs and structural scaffolds, yet their individual members often perform diverse functions. For this reason, the exact functional annotation for their individual members is difficult without detailed analysis of the family. In our study, we performed such a detailed analysis of a particularly heterogeneous FGGY kinase family through the integration of several computational approaches. The combination of phylogenetic and molecular approaches allowed us to precisely assign function to hundreds of proteins, thus reconstructing carbohydrate utilization pathways in almost 200 bacterial species. This analysis also showed that different molecular mechanisms could evolve within a group of isofunctional proteins. Moreover, based on our experience with this specific protein family of FGGY kinases, we believe that our approach can be generally adapted for the analyses of other protein families and that the accumulation of evolutionary models for various families would lead to a better understanding of the protein universe.
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Affiliation(s)
- Ying Zhang
- Graduate School of Biomedical Sciences, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Olga Zagnitko
- Fellowship for Interpretation of Genomes, Burr Ridge, Illinois, United States of America
| | - Irina Rodionova
- Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Andrei Osterman
- Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- * E-mail: (AO); (AG)
| | - Adam Godzik
- Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- * E-mail: (AO); (AG)
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Ghosh A, Zhao H, Price ND. Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae. PLoS One 2011; 6:e27316. [PMID: 22076150 PMCID: PMC3208632 DOI: 10.1371/journal.pone.0027316] [Citation(s) in RCA: 49] [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: 04/14/2011] [Accepted: 10/14/2011] [Indexed: 11/18/2022] Open
Abstract
Biofuels derived from lignocellulosic biomass offer promising alternative renewable energy sources for transportation fuels. Significant effort has been made to engineer Saccharomyces cerevisiae to efficiently ferment pentose sugars such as D-xylose and L-arabinose into biofuels such as ethanol through heterologous expression of the fungal D-xylose and L-arabinose pathways. However, one of the major bottlenecks in these fungal pathways is that the cofactors are not balanced, which contributes to inefficient utilization of pentose sugars. We utilized a genome-scale model of S. cerevisiae to predict the maximal achievable growth rate for cofactor balanced and imbalanced D-xylose and L-arabinose utilization pathways. Dynamic flux balance analysis (DFBA) was used to simulate batch fermentation of glucose, D-xylose, and L-arabinose. The dynamic models and experimental results are in good agreement for the wild type and for the engineered D-xylose utilization pathway. Cofactor balancing the engineered D-xylose and L-arabinose utilization pathways simulated an increase in ethanol batch production of 24.7% while simultaneously reducing the predicted substrate utilization time by 70%. Furthermore, the effects of cofactor balancing the engineered pentose utilization pathways were evaluated throughout the genome-scale metabolic network. This work not only provides new insights to the global network effects of cofactor balancing but also provides useful guidelines for engineering a recombinant yeast strain with cofactor balanced engineered pathways that efficiently co-utilizes pentose and hexose sugars for biofuels production. Experimental switching of cofactor usage in enzymes has been demonstrated, but is a time-consuming effort. Therefore, systems biology models that can predict the likely outcome of such strain engineering efforts are highly useful for motivating which efforts are likely to be worth the significant time investment.
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Affiliation(s)
- Amit Ghosh
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (HZ); (NDP)
| | - Nathan D. Price
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (HZ); (NDP)
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Lin L, Song H, Tu Q, Qin Y, Zhou A, Liu W, He Z, Zhou J, Xu J. The Thermoanaerobacter glycobiome reveals mechanisms of pentose and hexose co-utilization in bacteria. PLoS Genet 2011; 7:e1002318. [PMID: 22022280 PMCID: PMC3192829 DOI: 10.1371/journal.pgen.1002318] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [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: 03/12/2011] [Accepted: 08/07/2011] [Indexed: 11/18/2022] Open
Abstract
Thermoanaerobic bacteria are of interest in cellulosic-biofuel production, due to their simultaneous pentose and hexose utilization (co-utilization) and thermophilic nature. In this study, we experimentally reconstructed the structure and dynamics of the first genome-wide carbon utilization network of thermoanaerobes. The network uncovers numerous novel pathways and identifies previously unrecognized but crucial pathway interactions and the associated key junctions. First, glucose, xylose, fructose, and cellobiose catabolism are each featured in distinct functional modules; the transport systems of hexose and pentose are apparently both regulated by transcriptional antiterminators of the BglG family, which is consistent with pentose and hexose co-utilization. Second, glucose and xylose modules cooperate in that the activity of the former promotes the activity of the latter via activating xylose transport and catabolism, while xylose delays cell lysis by sustaining coenzyme and ion metabolism. Third, the vitamin B12 pathway appears to promote ethanologenesis through ethanolamine and 1, 2-propanediol, while the arginine deiminase pathway probably contributes to cell survival in stationary phase. Moreover, by experimentally validating the distinct yet collaborative nature of glucose and xylose catabolism, we demonstrated that these novel network-derived features can be rationally exploited for product-yield enhancement via optimized timing and balanced loading of the carbon supply in a substrate-specific manner. Thus, this thermoanaerobic glycobiome reveals novel genetic features in carbon catabolism that may have immediate industrial implications and provides novel strategies and targets for fermentation and genome engineering. Renewable liquid fuels derived from lignocellulosic biomass could alleviate global energy shortage and climate change. Cellulose and hemicellulose are the main components of lignocellulosic biomass. Therefore, the ability to simultaneously utilize pentose and hexose (i.e., co-utilization) has been a crucial challenge for industrial microbes producing lignocellulosic biofuels. Certain thermoanaerobic bacteria demonstrate this unusual talent, but the genetic foundation and molecular mechanism of this process remain unknown. In this study, we reconstructed the structure and dynamics of the first genome-wide carbon utilization network of thermoanaerobes. This transcriptome-based co-expression network reveals that glucose, xylose, fructose, and cellobiose catabolism are each featured on distinct functional modules. Furthermore, the dynamics of the network suggests a distinct yet collaborative nature between glucose and xylose catabolism. In addition, we experimentally demonstrated that these novel network-derived features can be rationally exploited for product-yield enhancement via optimized timing and balanced loading of the carbon supply in a substrate-specific manner. Thus, the newly discovered modular and precisely regulated network elucidates unique features of thermoanaerobic glycobiomes and reveals novel perturbation strategies and targets for the enhanced thermophilic production of lignocellulosic biofuels.
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Affiliation(s)
- Lu Lin
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, China
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Houhui Song
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Qichao Tu
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Yujia Qin
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Aifen Zhou
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Wenbin Liu
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Zhili He
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Jizhong Zhou
- Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States of America
- * E-mail: (JZ); (JX)
| | - Jian Xu
- CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics and BioEnergy Genome Center, Qingdao Institute of BioEnergy and BioProcess Technology, Chinese Academy of Sciences, Qingdao, China
- * E-mail: (JZ); (JX)
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Patel DH, Wi SG, Lee SG, Lee DS, Song YH, Bae HJ. Substrate specificity of the Bacillus licheniformis lyxose isomerase YdaE and its application in in vitro catalysis for bioproduction of lyxose and glucose by two-step isomerization. Appl Environ Microbiol 2011; 77:3343-50. [PMID: 21421786 PMCID: PMC3126444 DOI: 10.1128/aem.02693-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [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: 11/17/2010] [Accepted: 03/10/2011] [Indexed: 12/25/2022] Open
Abstract
Enzymatic processes are useful for industrially important sugar production, and in vitro two-step isomerization has proven to be an efficient process in utilizing readily available sugar sources. A hypothetical uncharacterized protein encoded by ydaE of Bacillus licheniformis was found to have broad substrate specificities and has shown high catalytic efficiency on D-lyxose, suggesting that the enzyme is D-lyxose isomerase. Escherichia coli BL21 expressing the recombinant protein, of 19.5 kDa, showed higher activity at 40 to 45°C and pH 7.5 to 8.0 in the presence of 1.0 mM Mn²+. The apparent K(m) values for D-lyxose and D-mannose were 30.4 ± 0.7 mM and 26 ± 0.8 mM, respectively. The catalytic efficiency (k(cat)/K(m)) for lyxose (3.2 ± 0.1 mM⁻¹ s⁻¹) was higher than that for D-mannose (1.6 mM⁻¹ s⁻¹). The purified protein was applied to the bioproduction of D-lyxose and D-glucose from d-xylose and D-mannose, respectively, along with the thermostable xylose isomerase of Thermus thermophilus HB08. From an initial concentration of 10 mM D-lyxose and D-mannose, 3.7 mM and 3.8 mM D-lyxose and D-glucose, respectively, were produced by two-step isomerization. This two-step isomerization is an easy method for in vitro catalysis and can be applied to industrial production.
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Affiliation(s)
- Darshan H. Patel
- Bio-energy Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Seung Gon Wi
- Bio-energy Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Seong-Gene Lee
- Department of Biotechnology, Bio-energy Research Center, Biotechnology Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Dae-Seok Lee
- Bio-energy Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Youn-ho Song
- Department of Biotechnology, Bio-energy Research Center, Biotechnology Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hyeun-Jong Bae
- Bio-energy Research Institute, Chonnam National University, Gwangju 500-757, Republic of Korea
- Department of Forest Products and Technology (BK21 Program), Chonnam National University, Gwangju 500-757, Republic of Korea
- Department of Bioenergy Science and Technology, Chonnam National University, Gwangju 500-757, Republic of Korea
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Kim YA, Yoon KH. Characterization of a Paenibacillus woosongensis beta-Xylosidase/alpha-Arabinofuranosidase produced by recombinant Escherichia coli. J Microbiol Biotechnol 2010; 20:1711-1716. [PMID: 21193828] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A gene encoding the beta-xylosidase/alpha-arabinofuranosidase (XylC) of Paenibacillus woosongensis was cloned into Escherichia coli. This xylC gene consisted of 1,425 nucleotides, encoding a polypeptide of 474 amino acid residues. The deduced amino acid sequence exhibited an 80% similarity with those of both Clostridium stercorarium beta-xylosidase/alpha-N-arabinosidase and Bacillus cellulosilyticus alpha-arabinofuranosidase, belonging to the glycosyl hydrolase family 43. The structural gene was subcloned with a Cterminal His-tag into a pET23a(+) expression vector. The His-tagged XylC, purified from a cell-free extract of a recombinant E. coli BL21(DE3) Codon Plus carrying a xylC gene by affinity chromatography, was active on paranitrophenyl- alpha-arabinofuranoside (pNPA) as well as paranitrophenyl- beta-xylopyranoside (pNPX). However, the enzymatic activities for the substrates were somewhat incongruously influenced by reaction pHs and temperatures. The enzyme was also affected by various chemicals at different levels. SDS (5 mM) inhibited the enzymatic activity for pNPX, while enhancing the enzymatic activity for pNPA. Enzyme activity was also found to be inhibited by addition of pentose or hexose. The Michaelis constant and maximum velocity of the purified enzyme were determined for hydrolysis of pNPX and pNPA, respectively.
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Affiliation(s)
- Yeon A Kim
- Department of Food Science and Biotechnology, Woosong University, Daejeon 300-718, Korea
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43
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Kim JH, Block DE, Mills DA. Simultaneous consumption of pentose and hexose sugars: an optimal microbial phenotype for efficient fermentation of lignocellulosic biomass. Appl Microbiol Biotechnol 2010; 88:1077-85. [PMID: 20838789 PMCID: PMC2956055 DOI: 10.1007/s00253-010-2839-1] [Citation(s) in RCA: 201] [Impact Index Per Article: 14.4] [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: 07/09/2010] [Revised: 08/09/2010] [Accepted: 08/11/2010] [Indexed: 11/25/2022]
Abstract
Lignocellulosic biomass is an attractive carbon source for bio-based fuel and chemical production; however, its compositional heterogeneity hinders its commercial use. Since most microbes possess carbon catabolite repression (CCR), mixed sugars derived from the lignocellulose are consumed sequentially, reducing the efficacy of the overall process. To overcome this barrier, microbes that exhibit the simultaneous consumption of mixed sugars have been isolated and/or developed and evaluated for the lignocellulosic biomass utilization. Specific strains of Escherichia coli, Saccharomyces cerevisiae, and Zymomonas mobilis have been engineered for simultaneous glucose and xylose utilization via mutagenesis or introduction of a xylose metabolic pathway. Other microbes, such as Lactobacillus brevis, Lactobacillus buchneri, and Candida shehatae possess a relaxed CCR mechanism, showing simultaneous consumption of glucose and xylose. By exploiting CCR-negative phenotypes, various integrated processes have been developed that incorporate both enzyme hydrolysis of lignocellulosic material and mixed sugar fermentation, thereby enabling greater productivity and fermentation efficacy.
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Affiliation(s)
- Jae-Han Kim
- Robert Mondavi Institute for Wine and Food Science, Department of Viticulture and Enology, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - David E. Block
- Robert Mondavi Institute for Wine and Food Science, Department of Viticulture and Enology, University of California, One Shields Avenue, Davis, CA 95616 USA
- Department of Chemical Engineering and Materials Science, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - David A. Mills
- Robert Mondavi Institute for Wine and Food Science, Department of Viticulture and Enology, University of California, One Shields Avenue, Davis, CA 95616 USA
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Horler RSP, Müller A, Williamson DC, Potts JR, Wilson KS, Thomas GH. Furanose-specific sugar transport: characterization of a bacterial galactofuranose-binding protein. J Biol Chem 2009; 284:31156-63. [PMID: 19744923 PMCID: PMC2781514 DOI: 10.1074/jbc.m109.054296] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [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: 08/10/2009] [Revised: 09/06/2009] [Indexed: 12/31/2022] Open
Abstract
The widespread utilization of sugars by microbes is reflected in the diversity and multiplicity of cellular transporters used to acquire these compounds from the environment. The model bacterium Escherichia coli has numerous transporters that allow it to take up hexoses and pentoses, which recognize the more abundant pyranose forms of these sugars. Here we report the biochemical and structural characterization of a transporter protein YtfQ from E. coli that forms part of an uncharacterized ABC transporter system. Remarkably the crystal structure of this protein, solved to 1.2 A using x-ray crystallography, revealed that YtfQ binds a single molecule of galactofuranose in its ligand binding pocket. Selective binding of galactofuranose over galactopyranose was also observed using NMR methods that determined the form of the sugar released from the protein. The pattern of expression of the ytfQRTyjfF operon encoding this transporter mirrors that of the high affinity galactopyranose transporter of E. coli, suggesting that this bacterium has evolved complementary transporters that enable it to use all the available galactose present during carbon limiting conditions.
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Affiliation(s)
| | - Axel Müller
- From the Department of Biology
- York Structural Biology Laboratory,and
| | | | - Jennifer R. Potts
- From the Department of Biology
- Department of Chemistry, University of York, York YO10 5YW, United Kingdom
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Lelevich SV. [Functional state of glucose metabolism in rat liver under chronic alcohol intoxication]. Biomed Khim 2009; 55:727-733. [PMID: 20469720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Chronic alcohol intoxication caused inhibition of some glycolytic enzymes observed after the 29 days alcohol intoxication. Ethanol administration increased liver glucose and lactate contents, and decreased the glycogen level. The 29 day alcohol intoxication also caused to the inhibition of the transketolase activity and decreased liver pentoses and serum insulin.
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HENRIKSEN SD, ERIKSEN J. IMMUNOCHEMICAL STUDIES ON SOME SEROLOGICAL CROSS-REACTIONS IN THE KLEBSIELLA GROUP. Acta Pathologica Microbiologica Scandinavica 2009; 54:382-6. [PMID: 13906522 DOI: 10.1111/j.1699-0463.1962.tb05078.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Takeda K, Yoshida H, Takada G, Izumori K, Kamitori S. Overexpression, purification, crystallization and preliminary X-ray crystal analysis of Bacillus pallidusD-arabinose isomerase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:945-8. [PMID: 18931442 PMCID: PMC2564884 DOI: 10.1107/s1744309108028352] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 09/04/2008] [Indexed: 11/10/2022]
Abstract
D-Arabinose isomerase catalyzes the isomerization of D-arabinose to D-ribulose. Bacillus pallidus D-arabinose isomerase has broad substrate specificity and can catalyze the isomerization of D-arabinose, L-fucose, L-xylose, L-galactose and D-altrose. Recombinant B. pallidus D-arabinose isomerase was overexpressed, purified and crystallized. A crystal of the enzyme was obtained by the sitting-drop method at room temperature and belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 144.9, b = 127.9, c = 109.5 A. Diffraction data were collected to 2.3 A resolution.
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Affiliation(s)
- Kosei Takeda
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
- Department of Biochemistry and Food Science, Faculty of Agriculture and Rare Sugar Research Center, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Hiromi Yoshida
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Goro Takada
- Department of Biochemistry and Food Science, Faculty of Agriculture and Rare Sugar Research Center, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Ken Izumori
- Department of Biochemistry and Food Science, Faculty of Agriculture and Rare Sugar Research Center, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Shigehiro Kamitori
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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Portis AR, Parry MAJ. Discoveries in Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase): a historical perspective. Photosynth Res 2007; 94:121-43. [PMID: 17665149 DOI: 10.1007/s11120-007-9225-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Accepted: 07/04/2007] [Indexed: 05/16/2023]
Abstract
Historic discoveries and key observations related to Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase), from 1947 to 2006, are presented. Currently, around 200 papers describing Rubisco research are published each year and the literature contains more than 5000 manuscripts on the subject. While trying to ensure that all the major events over this period are recorded, this analysis will inevitably be incomplete and will reflect the areas of particular interest to the authors.
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Affiliation(s)
- Archie R Portis
- Photosynthesis Research Unit, Agricultural Research Service, U.S. Department of Agriculture, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA.
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Toivari MH, Ruohonen L, Miasnikov AN, Richard P, Penttilä M. Metabolic engineering of Saccharomyces cerevisiae for conversion of D-glucose to xylitol and other five-carbon sugars and sugar alcohols. Appl Environ Microbiol 2007; 73:5471-6. [PMID: 17630301 PMCID: PMC2042063 DOI: 10.1128/aem.02707-06] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recombinant Saccharomyces cerevisiae strains that produce the sugar alcohols xylitol and ribitol and the pentose sugar D-ribose from D-glucose in a single fermentation step are described. A transketolase-deficient S. cerevisiae strain accumulated D-xylulose 5-phosphate intracellularly and released ribitol and pentose sugars (D-ribose, D-ribulose, and D-xylulose) into the growth medium. Expression of the xylitol dehydrogenase-encoding gene XYL2 of Pichia stipitis in the transketolase-deficient strain resulted in an 8.5-fold enhancement of the total amount of the excreted sugar alcohols ribitol and xylitol. The additional introduction of the 2-deoxy-glucose 6-phosphate phosphatase-encoding gene DOG1 into the transketolase-deficient strain expressing the XYL2 gene resulted in a further 1.6-fold increase in ribitol production. Finally, deletion of the endogenous xylulokinase-encoding gene XKS1 was necessary to increase the amount of xylitol to 50% of the 5-carbon sugar alcohols excreted.
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Affiliation(s)
- Mervi H Toivari
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Espoo, Finland.
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