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Lin D, Ning H, Liu Y, Qin W, Liu J, Loy DA. Mechanism of promoting okara insoluble to soluble dietary fiber by high-pressure homogenization-microbial fermentation. BIORESOURCE TECHNOLOGY 2025; 416:131774. [PMID: 39521189 DOI: 10.1016/j.biortech.2024.131774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/08/2024] [Accepted: 11/06/2024] [Indexed: 11/16/2024]
Abstract
This study investigated the conversion of okara insoluble dietary fiber (IDF) to soluble dietary fiber (SDF) using high-pressure homogenization (HPH) combined with microbial fermentation. The conversion mechanism was analyzed from four aspects: correlation, proteomics, component and structure under. Results indicated a negative correlation between pH and SDF yield (r = -0.9885, p < 0.05), while cellulase and xylanase showed a positive correlation with SDF yield (p < 0.05). Proteomic analysis identified 22 key enzymes involved in IDF degradation. According to the composition and structure, the combined treatment effectively reduced the aggregation of IDF, promoting its transformation into SDF. HPH treatment primarily acted on the hemicellulose fractions in the amorphous region, while microbial fermentation broke hydrogen bonds between hydroxyl groups in the crystalline regions of cellulose, enhancing the conversion of more exposed cellulose. This study provided theoretical support for the development and utilization of okara IDF.
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Affiliation(s)
- Derong Lin
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China.
| | - Hongjin Ning
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Ya Liu
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Wen Qin
- College of Food Science, Sichuan Agricultural University, Ya'an 625014, China
| | - Jianhua Liu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Douglas A Loy
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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2
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Wu J, Wang P, Wang W, Hu H, Wei Q, Bao C, Yan Y. Comprehensive Genomic and Proteomic Analysis Identifies Effectors of Fusarium oxysporum f. sp. melongenae. J Fungi (Basel) 2024; 10:828. [PMID: 39728324 DOI: 10.3390/jof10120828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 11/08/2024] [Accepted: 11/10/2024] [Indexed: 12/28/2024] Open
Abstract
Fusarium wilt in eggplant caused by F. oxysporum f. sp. melongenae is a major devastating soil-borne disease on a worldwide scale. Effectors play important roles in the interactions in pathogen-plant interactions. Identifying effectors is essential for elucidating the pathogenic mechanisms of phytopathogenic fungi. In this study, bioinformatic prediction approaches, including SignalP v5.0, TMHMM v2.0, WoLF PSORT, PredGPI, and EffectorP, were employed to screen for candidate secreted effector proteins (CSEPs) in F. oxysporum f. sp. melongenae. A total of 1019 proteins exhibiting characteristics typical of classical secretory proteins were identified, 301 of which demonstrated carbohydrate activity, and 194 CSEPs were identified. Furthermore, a total of 563 proteins from F. oxysporum f. sp. melongenae under induced conditions were identified using mass spectrometry-based label-free quantitative proteomics. These findings suggest a potential role of these CSEPs in the interaction between F. oxysporum f. sp. melongenae and eggplant, thereby contributing to a deeper understanding of the pathogenic mechanisms of F. oxysporum f. sp. melongenae and strategies for disease management.
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Affiliation(s)
- Jiayelu Wu
- Institute of Vegetable, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Pengfei Wang
- Zhejiang Normal University, Jinhua 321004, China
| | - Wuhong Wang
- Institute of Vegetable, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Haijiao Hu
- Institute of Vegetable, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Qingzhen Wei
- Institute of Vegetable, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Chonglai Bao
- Institute of Vegetable, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Yaqin Yan
- Institute of Vegetable, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
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3
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Alves GS, de Andrades D, Salgado JCS, Mariano CB, Berto GL, Segato F, Ayub MAZ, Ward RJ, Alnoch RC, Polizeli MDLTM. Homologous expression, purification, and characterization of a recombinant acetylxylan esterase from Aspergillus nidulans. Int J Biol Macromol 2024; 280:135816. [PMID: 39306183 DOI: 10.1016/j.ijbiomac.2024.135816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 09/17/2024] [Accepted: 09/18/2024] [Indexed: 10/14/2024]
Abstract
Acetylxylan esterases (AXEs) are essential enzymes that break down the acetyl groups in acetylated xylan found in plant cell walls polysaccharides. They work synergistically with backbone-depolymerizing xylanolytic enzymes to accelerate the degradation of complex polysaccharides. In this study, we cloned the gene axeA, which encodes the acetylxylan esterase from Aspergillus nidulans FGSC A4 (AxeAN), into the pEXPYR expression vector and introduced it into the high protein-producing strain A. nidulans A773. The purified AxeAN, with a molecular weight of 33.5 kDa as confirmed by SDS-PAGE, was found to be active on ρ-nitrophenyl acetate (ρNPA), exhibiting a remarkably high specific activity (170 U mg-1) at pH 7.0 and 55 °C. AxeAN demonstrated stability over a wide pH range (5.5-9.0), retaining >80% of its initial activity after 24 h. The KM and Vmax were 0.098 mmol L-1 and 320 U mg-1, respectively, using ρNPA as a substrate. We also evaluated the synergistic effect of AxeAN with an endo-1,4-β-xylanase from Malbranchea pulchella (MpXyn10) in the hydrolysis of four different xylans (Birchwood, Beechwood, Oat spelt, and Arabinoxylan) to produce xylooligosaccharides (XOS). The best results were obtained using Birchwood xylan as substrate and MpXyn10-AxeAN as biocatalysts after 24 h of reaction (50 °C), with a XOS-yield of 91%, value 41% higher when compared to MpXyn10 (XOS-yield of 63%). These findings showed the potential of the application of AxeAN, together with other xylanases, to produce xylooligosaccharides with high purity and other products with high added value in the field of lignocellulosic biorefinery.
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Affiliation(s)
- Gabriela S Alves
- Department of Biochemistry and Immunology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil
| | - Diandra de Andrades
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil
| | - Jose C S Salgado
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil; Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-900, SP, Brazil
| | - Clara B Mariano
- Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil
| | - Gabriela Leila Berto
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena 12602-810, SP, Brazil
| | - Fernando Segato
- Department of Biotechnology, Lorena School of Engineering, University of São Paulo, Lorena 12602-810, SP, Brazil
| | - Marco Antônio Záchia Ayub
- Laboratory of Biotechnology and Biochemical Engineering (BiotecLab), Institute of Food Science and Technology, Federal University of Rio Grande do Sul, Porto Alegre 91501-970, RS, Brazil
| | - Richard J Ward
- Department of Chemistry, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-900, SP, Brazil
| | - Robson C Alnoch
- Department of Biochemistry and Immunology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil.
| | - Maria de Lourdes T M Polizeli
- Department of Biochemistry and Immunology, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil; Department of Biology, Faculty of Philosophy, Sciences and Letters of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-901, SP, Brazil.
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4
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He H, Fang C, Liu L, Li M, Liu W. Environmental Driving of Adaptation Mechanism on Rumen Microorganisms of Sheep Based on Metagenomics and Metabolomics Data Analysis. Int J Mol Sci 2024; 25:10957. [PMID: 39456741 PMCID: PMC11508146 DOI: 10.3390/ijms252010957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Revised: 10/04/2024] [Accepted: 10/05/2024] [Indexed: 10/28/2024] Open
Abstract
Natural or artificial selection causes animals to adapt to their environment. The adaptive changes generated by the rumen population and metabolism form the basis of ruminant evolution. In particular, the adaptive drive for environmental adaptation reflects the high-quality traits of sheep that have migrated from other places or have been distant from their origins for a long time. The Hu sheep is the most representative sheep breed in the humid and low-altitude environments (Tai Lake region) in East Asia and has been widely introduced into the arid and high-altitude environments (Tibetan Plateau and Hotan region), resulting in environmental adaptive changes in the Hu sheep. In this study, a joint analysis of the rumen microbial metagenome and metabolome was conducted on Hu sheep from different regions (area of origin and area of introduction) with the objective of investigating the quality traits of Hu sheep and identifying microorganisms that influence the adaptive drive of ruminants. The results demonstrated that the growth performance of Hu sheep was altered due to changes in rumen tissue and metabolism following their introduction to the arid area at relatively high altitude. Metagenomic and metabolomic analyses (five ramsper area) revealed that 3580 different microorganisms and 732 different metabolites were identified in the rumen fluid of arid sheep. Among these, the representative upregulated metabolites were 4,6-isocanedione, methanesulfonic acid and N2-succinyl-L-arginine, while the dominant microorganism was Prevotella ruminicola. The downregulated metabolites were identified as campesterol, teprenone and dihydroclavaminic acid, while the disadvantaged microorganisms were Dialister_succinatiphilus, Prevotella_sp._AGR2160, Prevotella_multisaccharivorax and Selenomonas_bovis. The results of the Pearson analysis indicated that the rumen microbiota and metabolite content of sheep were significantly altered and highly correlated following their relocation from a humid lowland to an arid upland. In particular, the observed changes in rumen microorganisms led to an acceleration of body metabolism, rendering sheep highly adaptable to environmental stress. Prevotella_ruminicola was identified as playing an important role in this process. These findings provide insights into the environmental adaptation mechanisms of sheep.
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Affiliation(s)
- Haiying He
- Department of Animal Science and Biotechnology, Xinjiang Agricultural University, Urumqi 830052, China; (H.H.); (L.L.); (M.L.)
| | - Chao Fang
- Faculte de Medecine Veterinaire, Universite de Liege, Quartier Vallee 2, Avenue de Cureghem 6 (B43), 4000 Liege, Belgium;
| | - Lingling Liu
- Department of Animal Science and Biotechnology, Xinjiang Agricultural University, Urumqi 830052, China; (H.H.); (L.L.); (M.L.)
| | - Mingming Li
- Department of Animal Science and Biotechnology, Xinjiang Agricultural University, Urumqi 830052, China; (H.H.); (L.L.); (M.L.)
| | - Wujun Liu
- Department of Animal Science and Biotechnology, Xinjiang Agricultural University, Urumqi 830052, China; (H.H.); (L.L.); (M.L.)
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5
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Khan FZ, Palmer KL, Guan Z. Biosynthesis of glucosaminyl phosphatidylglycerol in Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.10.617631. [PMID: 39415997 PMCID: PMC11483062 DOI: 10.1101/2024.10.10.617631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Glucosaminyl phosphatidylglycerol (GlcN-PG) was first identified in bacteria in the 1960s and was recently reported in Pseudomonas aeruginosa. Despite the important implications in altering membrane charge (by the modification of anionic PG with cationic glucosamine), the biosynthesis and functions of GlcN-PG have remained uncharacterized. Using bioinformatic and lipidomic analysis, we identified a 3-gene operon, renamed as gpgSDF, that is responsible for the biosynthesis and potential transport of GlcN-PG in P. aeruginosa: gpgS encodes a novel glycotransferase that is responsible for the modification of phosphatidylglycerol (PG) with N-acetylglucosamine (GlcNAc) to produce GlcNAc-PG, and gpgD encodes a novel deacetylase that removes the acetyl group from GlcNAc-PG to produce GlcN-PG. The third gene in the operon, gpgF, is predicated to encode a flippase whose activity remains to be experimentally verified. As expected, the heterologous expression of the gpgSDF operon in Escherichia coli resulted in production of both GlcNAc-PG and GlcN-PG. The identification of the biosynthetic genes of GlcN-PG paves the way for the investigation of its biological and pathological functions, which has significant implications in our understanding of the unique membrane physiology, pathogenesis and antimicrobial resistance of P. aeruginosa.
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Affiliation(s)
- Fabiha Zaheen Khan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, Texas, USA
| | - Ziqiang Guan
- Department of Biochemistry, Duke University Medical Center, Durham, North Carolina, USA
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Wang X, Han J, Zeng M, Chen Y, Jiang F, Zhang L, Zhou Y. Total ammonia nitrogen inhibits medium-chain fatty acid biosynthesis by disrupting hydrolysis, acidification, chain elongation, substrate transmembrane transport and ATP synthesis processes. BIORESOURCE TECHNOLOGY 2024; 409:131236. [PMID: 39122132 DOI: 10.1016/j.biortech.2024.131236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Revised: 07/22/2024] [Accepted: 08/06/2024] [Indexed: 08/12/2024]
Abstract
This study used 16S rRNA gene sequencing and metatranscriptomic analysis to comprehensively illustrate how ammonia stress influenced medium-chain fatty acids (MCFA) biosynthesis. MCFA synthesis was inhibited at total ammonia nitrogen (TAN) concentrations above 1000 mg N/L. TAN stress hindered organic hydrolysis, acidification, and volatile fatty acids elongation. Chain-elongating bacteria (e.g., Clostridium_sensu_stricto_12, Clostridium_sensu_stricto_1, Caproiciproducens) abundance remained unchanged, but their activity decreased, partially due to the increased reactive oxygen species. Metatranscriptomic analysis revealed reduced activity of enzymes critical for MCFA production under TAN stress. Fatty acid biosynthesis pathway rather than reverse β-oxidation pathway primarily contributed to MCFA production, and was inhibited under TAN stress. Functional populations likely survived TAN stress through osmoprotectant generation and potassium uptake regulation to maintain osmotic pressure, with NADH-ubiquinone oxidoreductase potentially compensating for ATP loss. This study enhances understanding of MCFA biosynthesis under TAN stress, aiding MCFA production system stability and efficiency improvement.
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Affiliation(s)
- Xiuping Wang
- School of Environmental Science & Engineering, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
| | - Junjie Han
- School of Environmental Science & Engineering, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
| | - Meihui Zeng
- School of Environmental Science & Engineering, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China
| | - Yun Chen
- School of Environment, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Feng Jiang
- School of Environmental Science & Engineering, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China; Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology
| | - Liang Zhang
- School of Environmental Science & Engineering, Sun Yat-sen University, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Guangzhou, China; Guangdong Provincial Key Lab of Environmental Pollution Control and Remediation Technology.
| | - Yan Zhou
- School of Civil and Environmental Engineering, Nanyang Technological University, Singapore, Singapore.
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Paściak M, Pawlik KJ, Martynowski D, Łaczmański Ł, Ciekot J, Szponar B, Wójcik‐Fatla A, Mackiewicz B, Farian E, Cholewa G, Cholewa A, Dutkiewicz J. Discovery of a new bacterium, Microbacterium betulae sp. nov., in birch wood associated with hypersensitivity pneumonitis in woodworkers. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13311. [PMID: 39135302 PMCID: PMC11319209 DOI: 10.1111/1758-2229.13311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/26/2024] [Indexed: 08/16/2024]
Abstract
A Gram-positive, aerobic, rod-shaped mesophilic bacterium was isolated from birch wood, referred to as the AB strain. Allergological tests suggest that this strain may cause allergic alveolitis in sawmill workers. Employing a polyphasic taxonomic approach, the AB strain's 16S rRNA gene sequence showed high similarity to Microbacterium barkeri and M. oryzae, with 97.25% and 96.91%, respectively, a finding supported by rpoB and gyrB sequence analysis. Further genome sequence comparison with the closely related M. barkeri type strain indicated a digital DNA-DNA hybridization value of 25.5% and an average nucleotide identity of 82.52%. The AB strain's cell wall peptidoglycan contains ornithine, and its polar lipids comprise diphosphatidylglycerol, phosphatidylglycerol, and unidentified glycolipids. Its major fatty acids include anteiso C15:0, anteiso C17:0, and iso C16:0, while MK-10 is its predominant respiratory quinone. Comprehensive analysis through 16S rRNA, whole-genome sequencing, phenotyping, chemotaxonomy, and MALDI-TOF MS profiling indicates that the AB strain represents a new species within the Microbacterium genus. It has been proposed to name this species Microbacterium betulae sp. nov., with ABT (PCM 3040T = CEST 30706T) designated as the type strain.
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Affiliation(s)
- Mariola Paściak
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Krzysztof J. Pawlik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Dariusz Martynowski
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Łukasz Łaczmański
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Jarosław Ciekot
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Bogumiła Szponar
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocławPoland
| | - Angelina Wójcik‐Fatla
- Department of Health Biohazards and ParasitologyInstitute of Rural HealthLublinPoland
| | - Barbara Mackiewicz
- Department of Pneumonology, Oncology and AllergologyMedical UniversityLublinPoland
| | - Ewelina Farian
- Department of Health Biohazards and ParasitologyInstitute of Rural HealthLublinPoland
| | - Grażyna Cholewa
- Department of Health Biohazards and ParasitologyInstitute of Rural HealthLublinPoland
| | - Alicja Cholewa
- Department of Health Biohazards and ParasitologyInstitute of Rural HealthLublinPoland
| | - Jacek Dutkiewicz
- Department of Health Biohazards and ParasitologyInstitute of Rural HealthLublinPoland
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da Silva AS, Adriani PP, de Oliveira GS, Rocha ARL, Perpétuo EA, Dias MVB, Chambergo FS. Biochemical characterization of an esterase from Thermobifida fusca YX with acetyl xylan esterase activity. Mol Biol Rep 2024; 51:767. [PMID: 38878205 DOI: 10.1007/s11033-024-09601-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 05/01/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Esterases (EC 3.1.1.X) are enzymes that catalyze the hydrolysis ester bonds. These enzymes have large potential for diverse applications in fine industries, particularly in pharmaceuticals, cosmetics, and bioethanol production. METHODS AND RESULTS In this study, a gene encoding an esterase from Thermobifida fusca YX (TfEst) was successfully cloned, and its product was overexpressed in Escherichia coli and purified using affinity chromatography. The TfEst kinetic assay revealed catalytic efficiencies of 0.58 s-1 mM-1, 1.09 s-1 mM-1, and 0.062 s-1 mM-1 against p-Nitrophenyl acetate, p-Nitrophenyl butyrate, and 1-naphthyl acetate substrates, respectively. Furthermore, TfEst also exhibited activity in a pH range from 6.0 to 10.0, with maximum activity at pH 8.0. The enzyme demonstrated a half-life of 20 min at 70 °C. Notably, TfEst displayed acetyl xylan esterase activity as evidenced by the acetylated xylan assay. The structural prediction of TfEst using AlphaFold indicated that has an α/β-hydrolase fold, which is consistent with other esterases. CONCLUSIONS The enzyme stability over a broad pH range and its activity at elevated temperatures make it an appealing candidate for industrial processes. Overall, TfEst emerges as a promising enzymatic tool with significant implications for the advancement of biotechnology and biofuels industries.
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Affiliation(s)
- Adriana S da Silva
- Escola de Artes, Ciências e HumanidadesErmelino Matarazzo, Universidade de São Paulo, 1000 Av. Arlindo Bettio, São Paulo, CEP: 3828-000, Brazil
| | - Patricia P Adriani
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel S de Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Elen A Perpétuo
- Bio4Tec, Centro de Capacitação e Pesquisa em Meio Ambiente, CEPEMA-POLI-USP, Universidade de São Paulo, Cubatão, Brazil
- Institute of Marine Sciences (IMar), Federal University of Sao Paulo, Santos, Brazil
| | - Marcio V B Dias
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Felipe S Chambergo
- Escola de Artes, Ciências e HumanidadesErmelino Matarazzo, Universidade de São Paulo, 1000 Av. Arlindo Bettio, São Paulo, CEP: 3828-000, Brazil.
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9
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Wang Q, Zhan PC, Han XL, Lu T. Metagenomic and culture-dependent analysis of Rhinopithecius bieti gut microbiota and characterization of a novel genus of Sphingobacteriaceae. Sci Rep 2024; 14:13819. [PMID: 38879636 PMCID: PMC11180105 DOI: 10.1038/s41598-024-64727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 06/12/2024] [Indexed: 06/19/2024] Open
Abstract
Culture-dependent and metagenomic binning techniques were employed to gain an insight into the diversification of gut bacteria in Rhinopithecius bieti, a highly endangered primate endemic to China. Our analyses revealed that Bacillota_A and Bacteroidota were the dominant phyla. These two phyla species are rich in carbohydrate active enzymes, which could provide nutrients and energy for their own or hosts' survival under different circumstances. Among the culturable bacteria, one novel bacterium, designated as WQ 2009T, formed a distinct branch that had a low similarity to the known species in the family Sphingobacteriaceae, based on the phylogenetic analysis of its 16S rRNA gene sequence or phylogenomic analysis. The ANI, dDDH and AAI values between WQ 2009T and its most closely related strains S. kitahiroshimense 10CT, S. pakistanense NCCP-246T and S. faecium DSM 11690T were significantly lower than the accepted cut-off values for microbial species delineation. All results demonstrated that WQ 2009T represent a novel genus, for which names Rhinopithecimicrobium gen. nov. and Rhinopithecimicrobium faecis sp. nov. (Type strain WQ 2009T = CCTCC AA 2021153T = KCTC 82941T) are proposed.
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Affiliation(s)
- Qiong Wang
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China
- Center for Pharmaceutical Sciences, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, PR China
| | - Peng-Chao Zhan
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China
| | - Xiu-Lin Han
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China.
| | - Tao Lu
- Yunnan Institute of Microbiology, Key Laboratory for Southwest Microbial Diversity of the Ministry of Education, School of Life Sciences, Yunnan University, Kunming, Yunnan, 650500, PR China.
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10
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Liu Y, Angelov A, Übelacker M, Baudrexl M, Ludwig C, Rühmann B, Sieber V, Liebl W. Proteomic analysis of Viscozyme L and its major enzyme components for pectic substrate degradation. Int J Biol Macromol 2024; 266:131309. [PMID: 38580019 DOI: 10.1016/j.ijbiomac.2024.131309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/14/2024] [Accepted: 03/30/2024] [Indexed: 04/07/2024]
Abstract
Enzymatic degradation of plant biomass requires the coordinated action of various enzymes. In this study, the production of reducing sugars from pectic substrates and sugar beet pulp (SBP) was investigated and compared using commercial enzyme preparations, including M2, pectinase (E1), Viscozyme L (V-L) and L-40. V-L, a cellulolytic enzyme mix produced by Aspergillus sp. was further evaluated as the most robust enzyme cocktail with the strongest SBP degradation ability in terms of the release of monosaccharides, methanol, and acetate from SBP. Mass-spectrometry-based proteomics analysis of V-L revealed 156 individual proteins. Of these, 101 proteins were annotated as containing a carbohydrate-active enzyme module. Notably, of the 50 most abundant proteins, ca. 44 % were predicted to be involved in pectin degradation. To reveal the role of individual putative key enzymes in pectic substrate decomposition, two abundant galacturonases (PglA and PglB), were heterologously expressed in Pichia pastoris and further characterized. PglA and PglB demonstrated maximum activity at 57 °C and 68 °C, respectively, and exhibited endo-type cleavage patterns towards polygalacturonic acid. Further studies along this line may lead to a better understanding of efficient SBP degradation and may help to design improved artificial enzyme mixtures with lower complexity for future application in biotechnology.
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Affiliation(s)
- Yajing Liu
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany; Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Angel Angelov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany; NGS Competence Center Tübingen, Universitätsklinikum Tübingen, Calwerstraße 7, 72076 Tübingen, Germany
| | - Maria Übelacker
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich, Gregor-Mendel-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Broder Rühmann
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Volker Sieber
- Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany.
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11
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Liu Y, Li T, Zhu H, Cao L, Liang L, Liu D, Shen Q. Methionine inducing carbohydrate esterase secretion of Trichoderma harzianum enhances the accessibility of substrate glycosidic bonds. Microb Cell Fact 2024; 23:120. [PMID: 38664812 PMCID: PMC11046756 DOI: 10.1186/s12934-024-02394-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND The conversion of plant biomass into biochemicals is a promising way to alleviate energy shortage, which depends on efficient microbial saccharification and cellular metabolism. Trichoderma spp. have plentiful CAZymes systems that can utilize all-components of lignocellulose. Acetylation of polysaccharides causes nanostructure densification and hydrophobicity enhancement, which is an obstacle for glycoside hydrolases to hydrolyze glycosidic bonds. The improvement of deacetylation ability can effectively release the potential for polysaccharide degradation. RESULTS Ammonium sulfate addition facilitated the deacetylation of xylan by inducing the up-regulation of multiple carbohydrate esterases (CE3/CE4/CE15/CE16) of Trichoderma harzianum. Mainly, the pathway of ammonium-sulfate's cellular assimilates inducing up-regulation of the deacetylase gene (Thce3) was revealed. The intracellular metabolite changes were revealed through metabonomic analysis. Whole genome bisulfite sequencing identified a novel differentially methylated region (DMR) that existed in the ThgsfR2 promoter, and the DMR was closely related to lignocellulolytic response. ThGsfR2 was identified as a negative regulatory factor of Thce3, and methylation in ThgsfR2 promoter released the expression of Thce3. The up-regulation of CEs facilitated the substrate deacetylation. CONCLUSION Ammonium sulfate increased the polysaccharide deacetylation capacity by inducing the up-regulation of multiple carbohydrate esterases of T. harzianum, which removed the spatial barrier of the glycosidic bond and improved hydrophilicity, and ultimately increased the accessibility of glycosidic bond to glycoside hydrolases.
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Affiliation(s)
- Yang Liu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Tuo Li
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Han Zhu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Linhua Cao
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Lebin Liang
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Dongyang Liu
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Qirong Shen
- Key Lab of Organic-Based Fertilizers of China and Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- College of Resource and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
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12
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You X, Wang S, Du L, Chen Y, Wang T, Bo X. Metagenomics reveals the variations in functional metabolism associated with greenhouse gas emissions during legume-vegetable rotation process. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 275:116268. [PMID: 38569319 DOI: 10.1016/j.ecoenv.2024.116268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024]
Abstract
Legume-based rotation is commonly recognized for its mitigation efficiency of greenhouse gas (GHG) emissions. However, variations in GHG emission-associated metabolic functions during the legume-vegetable rotation process remain largely uncharacterized. Accordingly, a soybean-radish rotation field experiment was designed to clarify the responses of microbial communities and their GHG emission-associated functional metabolism through metagenomics. The results showed that the contents of soil organic carbon and total phosphorus significantly decreased during the soybean-radish process (P < 0.05), while soil total potassium content and bacterial richness and diversity significantly increased (P < 0.05). Moreover, the predominant bacterial phyla varied, with a decrease in the relative abundance of Proteobacteria and an increase in the relative abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi. Metagenomics clarified that bacterial carbohydrate metabolism substantially increased during the rotation process, whereas formaldehyde assimilation, methanogenesis, nitrification, and dissimilatory nitrate reduction decreased (P < 0.05). Specifically, the expression of phosphate acetyltransferase (functional methanogenesis gene, pta) and nitrate reductase gamma subunit (functional dissimilatory nitrate reduction gene, narI) was inhibited, indicating of low methane production and nitrogen metabolism. Additionally, the partial least squares path model revealed that the Shannon diversity index was negatively correlated with methane and nitrogen metabolism (P < 0.01), further demonstrating that the response of the soil bacterial microbiome responses are closely linked with GHG-associated metabolism during the soybean-radish rotation process. Collectively, our findings shed light on the responses of soil microbial communities to functional metabolism associated with GHG emissions and provide important insights to mitigate GHG emissions during the rotational cropping of legumes and vegetables.
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Affiliation(s)
- Xinxin You
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China; Southern Zhejiang Key Laboratory of Crop Breeding, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China
| | - Sheng Wang
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China.
| | - Linna Du
- College of Advanced Materials Engineering, Jiaxing Nanhu University, Jiaxing 314001, PR China.
| | - Yurong Chen
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China
| | - Ting Wang
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China
| | - Xiaoxu Bo
- Institute of Eco-environmental Sciences, Wenzhou Academy of Agricultural Sciences, Wenzhou 325006, PR China
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13
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Li H, Wang G, Yan X, Hu X, Li J. Effects of acetyl groups on the prebiotic properties of glucomannan extracted from Artemisia sphaerocephala Krasch seeds. Carbohydr Polym 2024; 330:121805. [PMID: 38368082 DOI: 10.1016/j.carbpol.2024.121805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 02/19/2024]
Abstract
This study explores the structural modification of glucomannan extracted from Artemisia sphaerocephala Krasch seeds (60S) to assess the impact of acetyl groups on its prebiotic characteristics. The structural changes were examined, with a focus on the degree of acetyl group substitution (DS). Both deacetylation and acetylation had limited influence on the molecular properties of 60S. Despite these modifications, the apparent viscosity of all samples remained consistently low. In vitro fermentation experiments revealed that Escherichia-Shigella decreased as DS increased, while Bacteroides ovatus was enriched. Acetylation had no significant impact on the utilization rate of 60S but led to a reduction in the production of propionic acid. Furthermore, untargeted metabolomics analysis confirmed the changes in propionic acid levels. Notably, metabolites such as N-acetyl-L-tyrosine, γ-muricholic acid, and taurocholate were upregulated by acetylated derivatives. Overall, acetyl groups are speculated to play a pivotal role in the prebiotic properties of 60S.
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Affiliation(s)
- Haocheng Li
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Gongda Wang
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ximei Yan
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xinzhong Hu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, China.
| | - Junjun Li
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China.
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14
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Li S, Chen M, Wang Z, Abudourexiti W, Zhang L, Ding C, Ding L, Gong J. Ant may well destroy a whole dam: glycans of colonic mucus barrier disintegrated by gut bacteria. Microbiol Res 2024; 281:127599. [PMID: 38219635 DOI: 10.1016/j.micres.2023.127599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
The colonic mucus layer plays a critical role in maintaining the integrity of the colonic mucosal barrier, serving as the primary defense against colonic microorganisms. Predominantly composed of mucin 2 (MUC2), a glycosylation-rich protein, the mucus layer forms a gel-like coating that covers the colonic epithelium surface. This layer provides a habitat for intestinal microorganisms, which can utilize mucin glycans present in the mucus layer as a sustainable source of nutrients. Additionally, metabolites produced by the microbiota during the metabolism of mucus glycans have a profound impact on host health. Under normal conditions, the production and consumption of mucus maintain a dynamic balance. However, several studies have demonstrated that certain factors, such as dietary fiber deficiency, can enhance the metabolism of mucus glycans by gut bacteria, thereby disturbing this balance and weakening the mucus barrier function of the mucus layer. To better understand the occurrence and development of colon-related diseases, it is crucial to investigate the complex metabolic patterns of mucus glycosylation by intestinal microorganisms. Our objective was to comprehensively review these patterns in order to clarify the effects of mucus layer glycan metabolism by intestinal microorganisms on the host.
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Affiliation(s)
- Song Li
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Mingfei Chen
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Zhongyuan Wang
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Waresi Abudourexiti
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Liang Zhang
- Department of Gastrointestinal Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, Jiangsu, China
| | - Chao Ding
- Department of General Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China.
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Jianfeng Gong
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China.
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15
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Contato AG, Borelli TC, Buckeridge MS, Rogers J, Hartson S, Prade RA, Polizeli MDLTDM. Secretome Analysis of Thermothelomyces thermophilus LMBC 162 Cultivated with Tamarindus indica Seeds Reveals CAZymes for Degradation of Lignocellulosic Biomass. J Fungi (Basel) 2024; 10:121. [PMID: 38392793 PMCID: PMC10890306 DOI: 10.3390/jof10020121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 02/24/2024] Open
Abstract
The analysis of the secretome allows us to identify the proteins, especially carbohydrate-active enzymes (CAZymes), secreted by different microorganisms cultivated under different conditions. The CAZymes are divided into five classes containing different protein families. Thermothelomyces thermophilus is a thermophilic ascomycete, a source of many glycoside hydrolases and oxidative enzymes that aid in the breakdown of lignocellulosic materials. The secretome analysis of T. thermophilus LMBC 162 cultivated with submerged fermentation using tamarind seeds as a carbon source revealed 79 proteins distributed between the five diverse classes of CAZymes: 5.55% auxiliary activity (AAs); 2.58% carbohydrate esterases (CEs); 20.58% polysaccharide lyases (PLs); and 71.29% glycoside hydrolases (GHs). In the identified GH families, 54.97% are cellulolytic, 16.27% are hemicellulolytic, and 0.05 are classified as other. Furthermore, 48.74% of CAZymes have carbohydrate-binding modules (CBMs). Observing the relative abundance, it is possible to state that only thirteen proteins comprise 92.19% of the identified proteins secreted and are probably the main proteins responsible for the efficient degradation of the bulk of the biomass: cellulose, hemicellulose, and pectin.
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Affiliation(s)
- Alex Graça Contato
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, SP, Brazil
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Tiago Cabral Borelli
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-901, SP, Brazil
| | - Marcos Silveira Buckeridge
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo 05508-090, SP, Brazil
| | - Janet Rogers
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Steven Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Rolf Alexander Prade
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA
| | - Maria de Lourdes Teixeira de Moraes Polizeli
- Departamento de Bioquímica e Imunologia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14049-900, SP, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, SP, Brazil
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16
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Denagbe W, Covis R, Guegan JP, Robinson JC, Bereau D, Benvegnu T. Structure and emulsifying properties of unprecedent glucomannan oligo- and polysaccharides from Amazonia Acrocomia aculeata palm fruit. Carbohydr Polym 2024; 324:121510. [PMID: 37985095 DOI: 10.1016/j.carbpol.2023.121510] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/01/2023] [Accepted: 10/17/2023] [Indexed: 11/22/2023]
Abstract
Acrocomia aculeata fruit pulp contains oil (4.1-82.8 % fresh matter) and carbohydrates (6.6-98.0 % fresh matter). To date, only the oil fraction is valorized because very little is known about the nature of carbohydrates. This study explores new ways of adding value to this pulp by developing simple and efficient extraction processes for its carbohydrate components and characterizing their structure and physicochemical properties over two harvest periods. A water-soluble monosaccharide fraction F1 (solubility limit (SL): 98.5-99.3 g/L) (yield: 21 % dry pulp (DP)), a water-soluble polysaccharide fraction F2 (SL: 93.3-95.3 g/L) (yield: 26 % DP) and two additional water-insoluble polysaccharide fractions F3 and F4 (SL: <8 g/L) (yields: 10 and 19 % DP, respectively) were isolated. NMR structural characterizations of fraction F2 revealed it to be a linear glucomannan with β-(1 → 4) osidic linkages between d-Manp and d-Glcp residues. F2 is unique for its d-Manp/d-Glcp ratio of 3:1 and the position of its acetyl group (13-14 %, C-2 d-Manp). Finally, the polysaccharide showed a molecular weight (Mw) variation ranging from 8.2 × 104 to 1.1 × 103 Da over the two harvest periods, with remarkable emulsifying properties associated with a low Mw of F2 (stability >6 months, 1 % w/v in a water-in-oil emulsion).
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Affiliation(s)
- Wilfried Denagbe
- Université de Guyane, Laboratoire COVAPAM, UMR QualiSud, Campus universitaire de Troubiran, BP 792, 97337 Cayenne cedex, Guyane, France; CNRS, ISCR-UMR 6226, Ecole Nationale Supérieure de Chimie de Rennes, Université de Rennes, F-35000 Rennes, France
| | - Rudy Covis
- Université de Guyane, Laboratoire COVAPAM, UMR QualiSud, Campus universitaire de Troubiran, BP 792, 97337 Cayenne cedex, Guyane, France
| | - Jean-Paul Guegan
- CNRS, ISCR-UMR 6226, Ecole Nationale Supérieure de Chimie de Rennes, Université de Rennes, F-35000 Rennes, France
| | - Jean-Charles Robinson
- Université de Guyane, Laboratoire COVAPAM, UMR QualiSud, Campus universitaire de Troubiran, BP 792, 97337 Cayenne cedex, Guyane, France
| | - Didier Bereau
- Université de Guyane, Laboratoire COVAPAM, UMR QualiSud, Campus universitaire de Troubiran, BP 792, 97337 Cayenne cedex, Guyane, France
| | - Thierry Benvegnu
- CNRS, ISCR-UMR 6226, Ecole Nationale Supérieure de Chimie de Rennes, Université de Rennes, F-35000 Rennes, France.
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17
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Ma X, La Y, Yang G, Dai R, Zhang J, Zhang Y, Jin J, Ma X, Guo X, Chu M, Yan P, Zhang Q, Liang C. Multi-omics revealed the effects of dietary energy levels on the rumen microbiota and metabolites in yaks under house-feeding conditions. Front Microbiol 2024; 14:1309535. [PMID: 38264487 PMCID: PMC10803511 DOI: 10.3389/fmicb.2023.1309535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024] Open
Abstract
Yak (Bos grunniens) is a unique large ruminant species in the Qinghai-Tibetan Plateau (QTP). Changing the energy levels of their rations can significantly improve their growth performance. Therefore, studying the effects of dietary energy levels on the rumen microflora and metabolites of yak is crucial for enhancing the development of the yak industry. Currently, there is a lack of understanding regarding the impact of feeding energy diets on rumen fermentation parameters, microbial functions, and metabolites. This study was designed to determine the appropriate energy level for feeding yak. Three test diets with metabolizable energy levels of 7.57 MJ/kg, 9.44 MJ/kg, and 11.9 MJ/kg were used and the concentration of volatile fatty acids (VFA) in rumen fluid was measured. The microbial communities, functions, and metabolites in yaks were studied by 16S rRNA sequencing, metagenome, and LC-MS non-targeted metabolomics to investigate the relationships among rumen fermentation parameters, microbial diversity, and metabolites. Ration energy levels significantly affect total VFA, acetate, propionate, butyrate, iso-valerate, valerate, and acetate/propionate (p < 0.05). At the phylum level, the dominant phyla in all three treatment groups were Bacteroidota, Firmicutes, and Actinobacteriota. At the genus level, the abundance of the unclassified_o__Bacteroidales, norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, and Family _XIII_AD3011_group showed significant differences (p < 0.05) and were significantly correlated with differential metabolites screened for phosphatidylcholine [PC(16:0/0:0), PC(18:3/0:0)], uridine 3'-monophosphate, and adenosine monophosphate, etc. CAZymes family analysis showed that GHs and CEs differed significantly among the three groups. In addition, differential metabolites were mainly enriched in the pathways of lipid metabolism, nucleotide metabolism, and biosynthesis of other secondary metabolites, and the concentrations of differential metabolites were correlated with microbial abundance. In summary, this study analyzed the effects of ration energy levels on rumen microorganisms and metabolites of yaks and their relationships. The results provided a scientific basis for the selection of dietary energy for yaks in the house feeding period in the future.
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Affiliation(s)
- Xiaoyong Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Yongfu La
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Guowu Yang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Rongfeng Dai
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Juanxiang Zhang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Yonghui Zhang
- Gansu Grassland Technical Extension Station, Lanzhou, China
| | - Jiaming Jin
- Gansu Grassland Technical Extension Station, Lanzhou, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Qiang Zhang
- Institute of Animal Husbandry and Veterinary, Tibet Autonomous Regional Academy of Agricultural Sciences, Lhasa, China
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
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18
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Hu X, Bi J, Yu Q, Li H. Metagenomics reveals the divergence of gut microbiome composition and function in two common pika species (Ochotona curzoniae and Ochotona daurica) in China. FEMS Microbiol Lett 2024; 371:fnae092. [PMID: 39500545 DOI: 10.1093/femsle/fnae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Revised: 10/05/2024] [Accepted: 10/31/2024] [Indexed: 11/24/2024] Open
Abstract
Gut microbiome plays crucial roles in animal adaptation and evolution. However, research on adaptation and evolution of small wild high-altitude mammals from the perspective of gut microbiome is still limited. In this study, we compared differences in intestinal microbiota composition and function in Plateau pikas (Ochotona curzoniae) and Daurian pikas (O. daurica) using metagenomic sequencing. Our results showed that microbial community structure had distinct differences in different pika species. Prevotella, Methanosarcina, Rhizophagus, and Podoviridae were abundant bacteria, archaea, eukaryotes, and viruses in Plateau pikas, respectively. However, Prevotella, Methanosarcina, Ustilago, and Retroviridae were dominated in Daurian pikas. Functional pathways related to carbohydrate metabolism that refer to the utilization of pectin, hemicellulose, and debranching enzymes were abundant in Plateau pikas, while the function for degradation of chitin, lignin, and cellulose was more concentrated in Daurian pikas. Pika gut had abundant multidrug resistance genes, followed by glycopeptide and beta-lactamase resistance genes, as well as high-risk antibiotic resistance genes, such as mepA, tetM, and bacA. Escherichia coli and Klebsiella pneumoniae may be potential hosts of mepA. This research provided new insights for adaptation and evolution of wild animals from perspective of gut microbiome and broadened our understanding of high-risk antibiotic resistance genes and potential pathogens of wild animals.
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Affiliation(s)
- Xueqian Hu
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jie Bi
- School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qiaoling Yu
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiota, College of pastoral agriculture science and technology, Lanzhou University, Lanzhou 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou 730000, China
- State Key Laboratory of Grassland Agro-ecosystems, Center for Grassland Microbiota, College of pastoral agriculture science and technology, Lanzhou University, Lanzhou 730000, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810008, China
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19
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Feng M, Varliero G, Qi W, Stierli B, Edwards A, Robinson S, van der Heijden MGA, Frey B. Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential. Environ Microbiol 2023; 25:3116-3138. [PMID: 37688461 DOI: 10.1111/1462-2920.16497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.
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Affiliation(s)
- Maomao Feng
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gilda Varliero
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics SIB, Geneva, Switzerland
| | - Beat Stierli
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
| | - Arwyn Edwards
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, UK
| | - Serina Robinson
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Dübendorf, Switzerland
| | - Marcel G A van der Heijden
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Plant-Soil Interactions, Agroscope, Zurich, Switzerland
| | - Beat Frey
- Rhizosphere Processes Group, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL), Birmensdorf, Switzerland
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20
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Low KE, Tingley JP, Klassen L, King ML, Xing X, Watt C, Hoover SER, Gorzelak M, Abbott DW. Carbohydrate flow through agricultural ecosystems: Implications for synthesis and microbial conversion of carbohydrates. Biotechnol Adv 2023; 69:108245. [PMID: 37652144 DOI: 10.1016/j.biotechadv.2023.108245] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/10/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
Carbohydrates are chemically and structurally diverse biomolecules, serving numerous and varied roles in agricultural ecosystems. Crops and horticulture products are inherent sources of carbohydrates that are consumed by humans and non-human animals alike; however carbohydrates are also present in other agricultural materials, such as soil and compost, human and animal tissues, milk and dairy products, and honey. The biosynthesis, modification, and flow of carbohydrates within and between agricultural ecosystems is intimately related with microbial communities that colonize and thrive within these environments. Recent advances in -omics techniques have ushered in a new era for microbial ecology by illuminating the functional potential for carbohydrate metabolism encoded within microbial genomes, while agricultural glycomics is providing fresh perspective on carbohydrate-microbe interactions and how they influence the flow of functionalized carbon. Indeed, carbohydrates and carbohydrate-active enzymes are interventions with unrealized potential for improving carbon sequestration, soil fertility and stability, developing alternatives to antimicrobials, and circular production systems. In this manner, glycomics represents a new frontier for carbohydrate-based biotechnological solutions for agricultural systems facing escalating challenges, such as the changing climate.
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Affiliation(s)
- Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Leeann Klassen
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Marissa L King
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Caitlin Watt
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - Shelley E R Hoover
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Monika Gorzelak
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
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21
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Wang S, Chen D, Liu Q, Zang L, Zhang G, Sui M, Dai Y, Zhou C, Li Y, Yang Y, Ding F. Dominant influence of plants on soil microbial carbon cycling functions during natural restoration of degraded karst vegetation. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 345:118889. [PMID: 37666128 DOI: 10.1016/j.jenvman.2023.118889] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/16/2023] [Accepted: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The impacts of natural restoration projects on soil microbial carbon (C) cycling functions have not been well recognized despite their wide implementation in the degraded karst areas of southwest China. In this study, metagenomic sequencing assays were conducted on functional genes and microorganisms related to soil C-cycling at three natural restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) in the southeast of Guizhou Province, China. The aims were to investigate the changes in microbial potentials responsible for soil C cycling and the underlying driving forces. The natural restoration resulted in vegetation establishment at all three restoration stages, rendering alterations of soil microbial C cycle functions as indicated by metagenomic gene assays. When TG was restored into OG, the number and diversity of genes and microorganisms involved in soil C cycling remained unchanged, but their composition underwent significant shifts. Specifically, microbial potentials for soil C decomposition exhibited an increase driven by the collaborative efforts of plants and soils, while microbial potentials for soil C biosynthesis displayed an initial upswing followed by a subsequent decline which was primarily influenced by plants alone. In comparison to soil nutrients, it was determined that plant diversities served as the primary driving factor for the alterations in microbial carbon cycle potentials. Soil microbial communities involved in C cycling were predominantly attributed to Proteobacteria (31.87%-40.25%) and Actinobacteria (11.29%-26.07%), although their contributions varied across the three restoration stages. The natural restoration of degraded karst vegetation thus influences soil microbial C cycle functions by enhancing C decomposition potentials and displaying a nuanced pattern of biosynthesis potentials, primarily influenced by above-ground plants. These results provide valuable new insights into the regulation of soil C cycling during the restoration of degraded karst vegetation from genetic and microbial perspectives.
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Affiliation(s)
- Shasha Wang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Danmei Chen
- College of Forestry, Guizhou University, Guiyang, 550025, China.
| | - Qingfu Liu
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Lipeng Zang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Guangqi Zhang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Mingzhen Sui
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yu Dai
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Chunjie Zhou
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yujuan Li
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Yousu Yang
- College of Forestry, Guizhou University, Guiyang, 550025, China
| | - Fangjun Ding
- Guizhou Libo Observation and Research Station for Karst Forest Ecosystem, National Forestry and Grassland Administration, Libo, 558400, China
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22
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Fujii S, Yamamoto E, Ito S, Tangpranomkorn S, Kimura Y, Miura H, Yamaguchi N, Kato Y, Niidome M, Yoshida A, Shimosato-Asano H, Wada Y, Ito T, Takayama S. SHI family transcription factors regulate an interspecific barrier. NATURE PLANTS 2023; 9:1862-1873. [PMID: 37798337 DOI: 10.1038/s41477-023-01535-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 09/05/2023] [Indexed: 10/07/2023]
Abstract
Pre-zygotic interspecies incompatibility in angiosperms is an important mechanism to prevent unfavourable hybrids between species. Here we report our identification of STIGMATIC PRIVACY 2 (SPRI2), a transcription factor that has a zinc-finger domain and regulates interspecies barriers in Arabidopsis thaliana, via genome-wide association study. Knockout analysis of SPRI2/SRS7 and its paralogue SPRI2-like/SRS5 demonstrated their necessity in rejecting male pollen from other species within female pistils. Additionally, they govern mRNA transcription of xylan O-acetyltransferases (TBL45 and TBL40) related to cell wall modification, alongside SPRI1, a pivotal transmembrane protein for interspecific pollen rejection. SPRI2/SRS7 is localized as condensed structures in the nucleus formed via liquid-liquid phase separation (LLPS), and a prion-like sequence in its amino-terminal region was found to be responsible for the formation of the condensates. The LLPS-regulated SPRI2/SRS7 discovered in this study may contribute to the establishment of interspecific reproductive barriers through the transcriptional regulation of cell wall modification genes and SPRI1.
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Affiliation(s)
- Sota Fujii
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.
- Suntory Rising Stars Encouragement Program in Life Sciences Fellow, Tokyo, Japan.
| | - Eri Yamamoto
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Seitaro Ito
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Surachat Tangpranomkorn
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- GRA&GREEN Inc., Nagoya, Japan
| | - Yuka Kimura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroki Miura
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Nobutoshi Yamaguchi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Yoshinobu Kato
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
- Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Saitama, Japan
| | - Maki Niidome
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Aya Yoshida
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Hiroko Shimosato-Asano
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Yuko Wada
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Toshiro Ito
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Seiji Takayama
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.
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23
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Yu C, Dong Q, Chen M, Zhao R, Zha L, Zhao Y, Zhang M, Zhang B, Ma A. The Effect of Mushroom Dietary Fiber on the Gut Microbiota and Related Health Benefits: A Review. J Fungi (Basel) 2023; 9:1028. [PMID: 37888284 PMCID: PMC10608147 DOI: 10.3390/jof9101028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Mushroom dietary fiber is a type of bioactive macromolecule derived from the mycelia, fruiting bodies, or sclerotia of edible or medicinal fungi. The use of mushroom dietary fiber as a prebiotic has recently gained significant attention for providing health benefits to the host by promoting the growth of beneficial microorganisms; therefore, mushroom dietary fiber has promising prospects for application in the functional food industry and in drug development. This review summarizes methods for the preparation and modification of mushroom dietary fiber, its degradation and metabolism in the intestine, its impact on the gut microbiota community, and the generation of short-chain fatty acids (SCFAs); this review also systematically summarizes the beneficial effects of mushroom dietary fiber on host health. Overall, this review aims to provide theoretical guidance and a fresh perspective for the prebiotic application of mushroom dietary fiber in the development of new functional foods and drugs.
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Affiliation(s)
- Changxia Yu
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Qin Dong
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Mingjie Chen
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Ruihua Zhao
- School of Life Sciences, Yan’an University, Yan’an 716000, China;
| | - Lei Zha
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Yan Zhao
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Mengke Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Baosheng Zhang
- Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China; (C.Y.); (Q.D.); (M.C.); (L.Z.); (M.Z.); (B.Z.)
| | - Aimin Ma
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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24
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Mafa MS, Malgas S. Towards an understanding of the enzymatic degradation of complex plant mannan structures. World J Microbiol Biotechnol 2023; 39:302. [PMID: 37688610 PMCID: PMC10492685 DOI: 10.1007/s11274-023-03753-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/04/2023] [Indexed: 09/11/2023]
Abstract
Plant cell walls are composed of a heterogeneous mixture of polysaccharides that require several different enzymes to degrade. These enzymes are important for a variety of biotechnological processes, from biofuel production to food processing. Several classical mannanolytic enzyme functions of glycoside hydrolases (GH), such as β-mannanase, β-mannosidase and α-galactosidase activities, are helpful for efficient mannan hydrolysis. In this light, we bring three enzymes into the model of mannan degradation that have received little or no attention. By linking their three-dimensional structures and substrate specificities, we have predicted the interactions and cooperativity of these novel enzymes with classical mannanolytic enzymes for efficient mannan hydrolysis. The novel exo-β-1,4-mannobiohydrolases are indispensable for the production of mannobiose from the terminal ends of mannans, this product being the preferred product for short-chain mannooligosaccharides (MOS)-specific β-mannosidases. Second, the side-chain cleaving enzymes, acetyl mannan esterases (AcME), remove acetyl decorations on mannan that would have hindered backbone cleaving enzymes, while the backbone cleaving enzymes liberate MOS, which are preferred substrates of the debranching and sidechain cleaving enzymes. The nonhydrolytic expansins and swollenins disrupt the crystalline regions of the biomass, improving their accessibility for AcME and GH activities. Finally, lytic polysaccharide monooxygenases have also been implicated in promoting the degradation of lignocellulosic biomass or mannan degradation by classical mannanolytic enzymes, possibly by disrupting adsorbed mannan residues. Modelling effective enzymatic mannan degradation has implications for improving the saccharification of biomass for the synthesis of value-added and upcycling of lignocellulosic wastes.
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Affiliation(s)
- Mpho Stephen Mafa
- Carbohydrates and Enzymology Laboratory (CHEM-LAB), Department of Plant Sciences, University of the Free State, Bloemfontein, 9300 South Africa
| | - Samkelo Malgas
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, 0028 South Africa
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25
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Yao L, Zhang J, Lu J, Chen D, Song S, Wang H, Sun M, Feng T. Revealing the influence of microbiota on the flavor of kombucha during natural fermentation process by metagenomic and GC-MS analysis. Food Res Int 2023; 169:112909. [PMID: 37254344 DOI: 10.1016/j.foodres.2023.112909] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/23/2023] [Accepted: 04/25/2023] [Indexed: 06/01/2023]
Abstract
In this work, raw Pu-erh tea (RAPT) was employed for kombucha preparation, and the microbial composition and volatile flavor compounds of the fermented tea had been investigated during natural fermentation process. The head space-solid phase microextraction-gas chromatograph mass spectrometry (HS-SPME-GC-MS) was performed for volatiles analysis of unfermented tea and kombucha fermented for 3 days (KF-3) and 6 days (KF-6). Meanwhile, the microbial community of KF-3 and KF-6 were evaluated by metagenomic analysis. A total of 72 volatile compounds were identified and obvious changes in volatiles were observed during the fermentation process based on the results of GC-MS and principal component analysis (PCA). Metagenomic sequencing analysis demonstrated that bacterium Komagataeibacter saccharivorans and unclassified-g-komagataeibacter and yeast Saccharomyces cerevisiae and Brettanomyces bruxellensis were the most common microbes contained in the sampled kombucha communities. Furthermore, the relevance among microbial community and volatile compounds was evaluated through correlation heatmap analysis. The results suggested that the main flavor volatiles of kombucha (i.e., acids, esters and terpenes) were closely related to species of genus Komagataeibacter, Gluconacetobacter, Saccharomyces, Brettanomyces, Acetobacter, Novacetimonas and Pichia microorganisms. The obtained results would help to better understand microbial communities and volatile compounds of kombucha, which could provide useful information for enhancing the flavor quality of kombucha products.
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Affiliation(s)
- Lingyun Yao
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Jing Zhang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Jun Lu
- Auckland Bioengineering Institute, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Da Chen
- Department of Animal, Veterinary and Food Sciences, University of Idaho, 875 Perimeter Drive, Moscow, ID 83844, USA
| | - Shiqing Song
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Huatian Wang
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Min Sun
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China
| | - Tao Feng
- School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, China.
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26
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Chen Z, Song B, Guo H, Xia D, Cai Y, Wang Y, Zhao W. Metagenomic characterization of biomethane transformation by lipid-catalyzed anaerobic fermentation of lignite. ENVIRONMENTAL RESEARCH 2023; 227:115777. [PMID: 36966989 DOI: 10.1016/j.envres.2023.115777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/02/2023] [Accepted: 03/24/2023] [Indexed: 05/08/2023]
Abstract
The present study aims at using lipid in a novel way to improve the efficiency of methane production from lignite anaerobic digestion. The obtained results showed an increase by 3.13 times of the cumulative biomethane content of lignite anaerobic fermentation, when 1.8 g lipid was added. The gene expression of functional metabolic enzymes was also found to be enhanced during the anaerobic fermentation. Moreover, the enzymes related to fatty acid degradation such as long-chain Acyl-CoA synthetase and Acyl-CoA dehydrogenase were increased by 1.72 and 10.48 times, respectively, which consequently, accelerated the conversion of fatty acid. Furthermore, the addition of lipid enhanced the carbon dioxide trophic and acetic acid trophic metabolic pathways. Hence, the addition of lipids was argued to promote the production of methane from lignite anaerobic fermentation, which provided a new insight for the conversion and utilization of lipid waste.
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Affiliation(s)
- Zhenhong Chen
- Research Institute of Petroleum Exploration & Development, Beijing, 100083, China.
| | - Bo Song
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo, 454000, China.
| | - Hongyu Guo
- School of Energy Science and Engineering, Henan Polytechnic University, Jiaozuo, 454000, China; Collaborative Innovation Center of Coal Work Safety and Clean High Efficiency Utilization, Henan Polytechnic University, Jiaozuo, 454000, China.
| | - Dapin Xia
- Mining Research Institute of Henan Polytechnic University, Jiaozuo, 454000, China.
| | - Yidong Cai
- School of Energy Resources, China University of Geosciences, Beijing, 100083, China.
| | - Yongjun Wang
- College of Computer Science and Technology, Henan Polytechnic University, Jiaozuo, 454000, China.
| | - Weizhong Zhao
- Department of Environmental Engineering, Technical University of Denmark, DK-2800, Lyngby, Denmark.
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27
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Yang WT, Yi YJ, Xia B. Unveiling the duality of Pantoea dispersa: A mini review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 873:162320. [PMID: 36801414 DOI: 10.1016/j.scitotenv.2023.162320] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Pantoea dispersa is a Gram-negative bacterium that exists in a variety of environments and has potential in many commercial and agricultural applications, such as biotechnology, environmental protection, soil bioremediation, and plant growth stimulation. However, P. dispersa is also a harmful pathogen to both humans and plants. This "double-edged sword" phenomenon is not uncommon in nature. To ensure survival, microorganisms respond to both environmental and biological stimuli, which could be beneficial or detrimental to other species. Therefore, to harness the full potential of P. dispersa, while minimizing potential harm, it is imperative to unravel its genetic makeup, understand its ecological interactions and underlying mechanisms. This review aims to provide a comprehensive and up-to-date overview of the genetic and biological characteristics of P. dispersa, in addition to potential impacts on plants and humans, as well as to provide insights into potential applications.
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Affiliation(s)
- Wen-Tao Yang
- College of Food Science and Technology, Hunan Agricultural University, East Renmin Road, Changsha 410128, Hunan, China
| | - You-Jin Yi
- College of Food Science and Technology, Hunan Agricultural University, East Renmin Road, Changsha 410128, Hunan, China
| | - Bo Xia
- College of Food Science and Technology, Hunan Agricultural University, East Renmin Road, Changsha 410128, Hunan, China.
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28
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Parra M, Libkind D, Hittinger CT, Álvarez L, Bellora N. Assembly and comparative genome analysis of a Patagonian Aureobasidium pullulans isolate reveals unexpected intraspecific variation. Yeast 2023. [PMID: 37114349 DOI: 10.1002/yea.3853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 03/27/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Aureobasidium pullulans is a yeast-like fungus with remarkable phenotypic plasticity widely studied for its importance for the pharmaceutical and food industries. So far, genomic studies with strains from all over the world suggest they constitute a genetically unstructured population, with no association by habitat. However, the mechanisms by which this genome supports so many phenotypic permutations are still poorly understood. Recent works have shown the importance of sequencing yeast genomes from extreme environments to increase the repertoire of phenotypic diversity of unconventional yeasts. In this study, we present the genomic draft of A. pullulans strain from a Patagonian yeast diversity hotspot, re-evaluate its taxonomic classification based on taxogenomic approaches, and annotate its genome with high-depth transcriptomic data. Our analysis suggests this isolate could be considered a novel variant at an early stage of the speciation process. The discovery of divergent strains in a genomically homogeneous group, such as A. pullulans, can be valuable in understanding the evolution of the species. The identification and characterization of new variants will not only allow finding unique traits of biotechnological importance, but also optimize the choice of strains whose phenotypes will be characterized, providing new elements to explore questions about plasticity and adaptation.
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Affiliation(s)
- Micaela Parra
- Laboratorio de Genómica Computacional, Instituto de Tecnologías Nucleares para la Salud (INTECNUS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Carlos de Bariloche, Argentina
| | - Diego Libkind
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Comahue, San Carlos de Bariloche, Argentina
| | - Chris Todd Hittinger
- Laboratory of Genetics, Center for Genomic Science Innovation, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lucía Álvarez
- Centro de Referencia en Levaduras y Tecnología Cervecera (CRELTEC), Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales (IPATEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Comahue, San Carlos de Bariloche, Argentina
| | - Nicolás Bellora
- Laboratorio de Genómica Computacional, Instituto de Tecnologías Nucleares para la Salud (INTECNUS), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), San Carlos de Bariloche, Argentina
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29
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Khamassi A, Dumon C. Enzyme synergy for plant cell wall polysaccharide degradation. Essays Biochem 2023; 67:521-531. [PMID: 37067158 DOI: 10.1042/ebc20220166] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/17/2023] [Accepted: 03/07/2023] [Indexed: 04/18/2023]
Abstract
Valorizing plant cell wall, marine and algal polysaccharides is of utmost importance for the development of the circular bioeconomy. This is because polysaccharides are by far the most abundant organic molecules found in nature with complex chemical structures that require a large set of enzymes for their degradation. Microorganisms produce polysaccharide-specific enzymes that act in synergy when performing hydrolysis. Although discovered since decades enzyme synergy is still poorly understood at the molecular level and thus it is difficult to harness and optimize. In the last few years, more attention has been given to improve and characterize enzyme synergy for polysaccharide valorization. In this review, we summarize literature to provide an overview of the different type of synergy involving carbohydrate modifying enzymes and the recent advances in the field exemplified by plant cell-wall degradation.
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Affiliation(s)
- Ahmed Khamassi
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Claire Dumon
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
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Novak JK, Gardner JG. Galactomannan utilization by Cellvibrio japonicus relies on a single essential α-galactosidase encoded by the aga27A gene. Mol Microbiol 2023; 119:312-325. [PMID: 36604822 DOI: 10.1111/mmi.15024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/30/2022] [Indexed: 01/07/2023]
Abstract
Plant mannans are a component of lignocellulose that can have diverse compositions in terms of its backbone and side-chain substitutions. Consequently, the degradation of mannan substrates requires a cadre of enzymes for complete reduction to substituent monosaccharides that can include mannose, galactose, and/or glucose. One bacterium that possesses this suite of enzymes is the Gram-negative saprophyte Cellvibrio japonicus, which has 10 predicted mannanases from the Glycoside Hydrolase (GH) families 5, 26, and 27. Here we describe a systems biology approach to identify and characterize the essential mannan-degrading components in this bacterium. The transcriptomic analysis uncovered significant changes in gene expression for most mannanases, as well as many genes that encode carbohydrate active enzymes (CAZymes) when mannan was actively being degraded. A comprehensive mutational analysis characterized 54 CAZyme-encoding genes in the context of mannan utilization. Growth analysis of the mutant strains found that the man26C, aga27A, and man5D genes, which encode a mannobiohydrolase, α-galactosidase, and mannosidase, respectively, were important for the deconstruction of galactomannan, with Aga27A being essential. Our updated model of mannan degradation in C. japonicus proposes that the removal of galactose sidechains from substituted mannans constitutes a crucial step for the complete degradation of this hemicellulose.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, Maryland, USA
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Wang J, Zhuang Y, Song X, Lin X, Wang X, Yang F, Chen X. Differential transcriptome analysis of Sporocytophaga sp. CX11 and identification of candidate genes involved in lignocellulose degradation. BIORESOUR BIOPROCESS 2023; 10:8. [PMID: 38647554 PMCID: PMC10992098 DOI: 10.1186/s40643-023-00629-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/12/2023] [Indexed: 01/31/2023] Open
Abstract
Cellulose is the most abundant renewable bioresources on earth, and the biodegradation and utilization of cellulose would contribute to the sustainable development of global environment. Sporocytophaga species are common aerobic cellulose-degrading bacteria in soil, which can adhere to the surface of cellulose matrix and motile by gliding. In this study, a differential transcriptome analysis of Sporocytophaga sp. CX11 was performed and a total of 4,217 differentially expressed genes (DEGs) were identified. Gene Ontology enrichment results showed that there are three GO categories related to cellulose degradation function among the annotated DEGs. A total of 177 DEGs were identified as genes encoding carbohydrate-active enzymes (CAZymes), among which 54 significantly upregulated CAZymes were mainly cellulases, hemicellulases, pectinases, etc. 39 DEGs were screened to associate with gliding function. In order to explore unannotated genes potentially related to cellulose metabolism, cluster analysis was performed using the Short-Time Series Expression Miner algorithm (STEM). 281 unannotated genes were predicted to be associated with the initial-middle stage of cellulose degradation and 289 unannotated genes might function in the middle-last stage of cellulose degradation. Sporocytophaga sp. CX11 could produce extracellular endo-xylanase, endo-glucanase, FPase and β-glucosidase, respectively, according to different carbon source conditions. Altogether, this study provides valuable insights into the transcriptome information of Sporocytophaga sp. CX11, which would be useful to explore its application in biodegradation and utilization of cellulose resources.
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Affiliation(s)
- Jiwei Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Ying Zhuang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Xianghe Song
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Xu Lin
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Xiangyi Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China.
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian, 116034, People's Republic of China.
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Tabaght FE, Azzaoui K, Idrissi AE, Jodeh S, Khalaf B, Rhazi L, Bellaouchi R, Asehraou A, Hammouti B, Sabbahi R. Synthesis, characterization, and biodegradation studies of new cellulose-based polymers. Sci Rep 2023; 13:1673. [PMID: 36717660 PMCID: PMC9887067 DOI: 10.1038/s41598-023-28298-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/16/2023] [Indexed: 01/31/2023] Open
Abstract
New cellulose carbamates and cellulose acetate carbamates were prepared by classical addition reaction of isocyanates with alcohols. A Telomerization technique was used to make the grafted molecules strongly anchored and more hydrophobic. These molecules were grafted into cellulose and CA chains, respectively. The structures of the synthesized derivatives were confirmed using Nuclear Magnetic Resonance Spectroscopy, Fourier Transform Infrared and Thermogravimetric Analysis, and their solubility phenomenon was also established, and the carbamate derivatives showed better solubility compared to cellulose. Their ability to biodegrade was investigated, and it was concluded that Cell-P1 and CA-P1 derivatives are more biodegradable than the other samples. These results suggest that the resulting compounds can be used effectively in many useful industrial fields, for instance, eco-friendly food packaging, domains that use materials that are environmentally friendly and sustainable and the development of green chemistry.
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Affiliation(s)
- F E Tabaght
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, 60000, Oujda, Morocco
| | - K Azzaoui
- Laboratory of Engineering, Electrochemistry, Modeling and Environment, Faculty of Sciences, Sidi Mohamed Ben Abdellah University, 30000, Fez, Morocco.
| | - A El Idrissi
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, 60000, Oujda, Morocco
| | - S Jodeh
- Department of Chemistry, An-Najah National University, P.O. Box 7, Nablus, Palestine.
| | - B Khalaf
- Department of Chemistry, Arab American University, Jenin, Palestine
| | - L Rhazi
- Institut Polytechnique UniLaSalle Transformations & Agro-Resources Research Unit (ULR7519), 19 Rue Pierre Waguet, BP 30313, 60026, Beauvais, France
| | - R Bellaouchi
- Laboratory of Biochemistry and Biotechnology, Mohammed First University, Faculty of Sciences, 60000, Oujda, Morocco
| | - A Asehraou
- Laboratory of Biochemistry and Biotechnology, Mohammed First University, Faculty of Sciences, 60000, Oujda, Morocco
| | - B Hammouti
- Laboratory of Applied Chemistry and Environment, Faculty of Sciences, Mohammed First University, 60000, Oujda, Morocco
| | - R Sabbahi
- Laboratory of Development and Valorization of Resources in Desert Zones, Higher School of Technology, Ibn Zohr University, Quartier 25 Mars, P.O. Box 3007, Laayoune, Morocco
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Chen L, Qu Z, Yu W, Zheng L, Qiao H, Wang D, Wei B, Zhao Z. Comparative genomic and transcriptome analysis of Bacillus velezensis CL-4 fermented corn germ meal. AMB Express 2023; 13:10. [PMID: 36683079 PMCID: PMC9868226 DOI: 10.1186/s13568-023-01510-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/08/2023] [Indexed: 01/24/2023] Open
Abstract
Bacillus, an excellent organic-degrading agent, can degrade lignocellulose. Notably, some B. velezensis strains encode lignocellulases. However, their ability to degrade lignocellulose in fermented feed is not much appreciated. This study performed a comparative genomic analysis of twenty-three B. velezensis strains to find common carbohydrate-active enzymes (CAZymes) encoding genes and evaluated their potential to degrade lignocellulose. The comparative genomic and CAZyme database-based analyses identified several potential CAZymes genes that degrade cellulose (GH1, GH4, GH5, GH13, GH16, GH32, PL1, and PL9), hemicellulose (GH11, GH26, GH43, GH51, and CE3) and lignin (AA4, AA6, AA7, and AA10). Furthermore, Illumina RNA-seq transcriptome analysis revealed the expression of more than 1794 genes in B. velezensis CL-4 fermented corn germ meal at 48 h (FCGM 48 h). Gene ontology analysis of expressed genes revealed their enrichment in hydrolase activity (breaking the glycosyl bonds during carbohydrate metabolism), indicating the upregulation of CAZymes. In total, 58 differentially upregulated CAZymes-encoding genes were identified in FCGM 48 h compared to FCGM 0 h. The upregulated CAZymes-encoding genes were related to cellulose (6-phospho-β-galactosidase and 6-phospho-α-glucosidase), starch (α-glucosidase and α-amylase), pectin (pectin lyase), and hemicellulose (arabinan endo-1,5-α-L-arabinosidase, xylan 1,4-beta-xylosidase, α-N-arabinofuranosidase, and acetyl xylan esterase). Importantly, arabinoxylan degradation mainly occurred in FCGM 48 h, followed by partial degradation of cellulose, pectin, and starch. This study can support the development of enzymatic cocktails for the solid-state fermented feed (SFF).
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Affiliation(s)
- Long Chen
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Zihui Qu
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Wei Yu
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Lin Zheng
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Haixin Qiao
- Information Application Department, Jilin Intellectual Property Protection Center, Changchun, 130000 China
| | - Dan Wang
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Bingdong Wei
- grid.464388.50000 0004 1756 0215Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, 136100 Jilin China
| | - Zijian Zhao
- grid.464388.50000 0004 1756 0215Institute of Agro-Food Technology, Jilin Academy of Agricultural Sciences, No. 1366 Cai Yu Street, Changchun, 130033 Jilin Province China
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Zhao J, Hu Y, Qian C, Hussain M, Liu S, Zhang A, He R, Sun P. The Interaction between Mushroom Polysaccharides and Gut Microbiota and Their Effect on Human Health: A Review. BIOLOGY 2023; 12:biology12010122. [PMID: 36671814 PMCID: PMC9856211 DOI: 10.3390/biology12010122] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 01/13/2023]
Abstract
Mushroom polysaccharides are a kind of biological macromolecule extracted from the fruiting body, mycelium or fermentation liquid of edible fungi. In recent years, the research on mushroom polysaccharides for alleviating metabolic diseases, inflammatory bowel diseases, cancers and other symptoms by changing the intestinal microenvironment has been increasing. Mushroom polysaccharides could promote human health by regulating gut microbiota, increasing the production of short-chain fatty acids, improving intestinal mucosal barrier, regulating lipid metabolism and activating specific signaling pathways. Notably, these biological activities are closely related to the molecular weight, monosaccharide composition and type of the glycosidic bond of mushroom polysaccharide. This review aims to summarize the latest studies: (1) Regulatory effects of mushroom polysaccharides on gut microbiota; (2) The effect of mushroom polysaccharide structure on gut microbiota; (3) Metabolism of mushroom polysaccharides by gut microbiota; and (4) Effects of mushroom polysaccharides on gut microbe-mediated diseases. It provides a theoretical basis for further exploring the mechanism of mushroom polysaccharides for regulating gut microbiota and gives a reference for developing and utilizing mushroom polysaccharides as promising prebiotics in the future.
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Affiliation(s)
- Jiahui Zhao
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yixin Hu
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chao Qian
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Muhammad Hussain
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shizhu Liu
- Zhejiang Fangge Pharmaceutical Co., Ltd., Qingyuan 323800, China
| | - Anqiang Zhang
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
| | - Rongjun He
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
- Zhejiang Fangge Pharmaceutical Co., Ltd., Qingyuan 323800, China
- Bioactives and Functional Foods Research Center, China National Light Industry, Hangzhou 310014, China
- Correspondence: (R.H.); (P.S.)
| | - Peilong Sun
- College of Food Science and Technology, Zhejiang University of Technology, Hangzhou 310014, China
- Zhejiang Fangge Pharmaceutical Co., Ltd., Qingyuan 323800, China
- Key Laboratory of Food Macromolecular Resources Processing Technology Research, China National Light Industry, Hangzhou 310014, China
- Correspondence: (R.H.); (P.S.)
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Chen C, Chen S, Wang B. A glance at the gut microbiota and the functional roles of the microbes based on marmot fecal samples. Front Microbiol 2023; 14:1035944. [PMID: 37125200 PMCID: PMC10140447 DOI: 10.3389/fmicb.2023.1035944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/13/2023] [Indexed: 05/02/2023] Open
Abstract
Research on the gut microbiota, which involves a large and complex microbial community, is an important part of infectious disease control. In China, few studies have been reported on the diversity of the gut microbiota of wild marmots. To obtain full details of the gut microbiota, including bacteria, fungi, viruses and archaea, in wild marmots, we have sequenced metagenomes from five sample-sites feces on the Hulun Buir Grassland in Inner Mongolia, China. We have created a comprehensive database of bacterial, fungal, viral, and archaeal genomes and aligned metagenomic sequences (determined based on marmot fecal samples) against the database. We delineated the detailed and distinct gut microbiota structures of marmots. A total of 5,891 bacteria, 233 viruses, 236 fungi, and 217 archaea were found. The dominant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinomycetes. The viral families were Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae and Podoviridae. The dominant fungi phyla were Ascomycota, Basidiomycota, and Blastocladiomycota. The dominant archaea were Biobacteria, Omoarchaea, Nanoarchaea, and Microbacteria. Furthermore, the gut microbiota was affected by host species and environment, and environment was the most important factor. There were 36,989 glycoside hydrolase genes in the microbiota, with 365 genes homologous to genes encoding β-glucosidase, cellulase, and cellulose β-1,4-cellobiosidase. Additionally, antibiotic resistance genes such as macB, bcrA, and msbA were abundant. To sum up, the gut microbiota of marmot had population diversity and functional diversity, which provides a basis for further research on the regulatory effects of the gut microbiota on the host. In addition, metagenomics revealed that the gut microbiota of marmots can degrade cellulose and hemicellulose.
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Affiliation(s)
- Chuizhe Chen
- Department of Pathology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Shu Chen
- Medical Laboratory Center, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Bo Wang
- Department of Pathology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
- *Correspondence: Bo Wang,
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Cheng Z, Lv X, Duan C, Zhu H, Wang J, Xu Z, Yin H, Zhou X, Li M, Hao Z, Li F, Li X, Weng J. Pathogenicity Variation in Two Genomes of Cercospora Species Causing Gray Leaf Spot in Maize. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:14-25. [PMID: 36251001 DOI: 10.1094/mpmi-06-22-0138-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The gray leaf spots caused by Cercospora spp. severely affect the yield and quality of maize. However, the evolutionary relation and pathogenicity variation between species of the Cercospora genus is largely unknown. In this study, we constructed high-quality reference genomes by nanopore sequencing two Cercospora species, namely, C. zeae-maydis and C. zeina, with differing pathogenicity, collected from northeast (Liaoning [LN]) and southeast (Yunnan [YN]) China, respectively. The genome size of C. zeae-maydis-LN is 45.08 Mb, containing 10,839 annotated genes, whereas that of Cercospora zeina-YN is 42.18 Mb, containing 10,867 annotated genes, of which approximately 86.58% are common in the two species. The difference in their genome size is largely attributed to increased long terminal repeat retrotransposons of 3.8 Mb in total length in C. zeae-maydis-LN. There are 41 and 30 carbohydrate-binding gene subfamilies identified in C. zeae-maydis-LN and C. zeina-YN, respectively. A higher number of carbohydrate-binding families found in C. zeae-maydis-LN, and its unique CBM4, CBM37, and CBM66, in particular, may contribute to variation in pathogenicity between the two species, as the carbohydrate-binding genes are known to encode cell wall-degrading enzymes. Moreover, there are 114 and 107 effectors predicted, with 47 and 46 having unique potential pathogenicity in C. zeae-maydis-LN and C. zeina-YN, respectively. Of eight effectors randomly selected for pathogenic testing, five were found to inhibit cell apoptosis induced by Bcl-2-associated X. Taken together, our results provide genomic insights into variation in pathogenicity between C. zeae-maydis and C. zeina. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Zixiang Cheng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiangling Lv
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, 110161, China
| | - Canxing Duan
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hanyong Zhu
- Wenshan Academy of Agricultural Sciences, Wenshan, Yunnan, 663000, China
| | - Jianjun Wang
- Corn Research Institute, Shanxi Agricultural University, Xinzhou, Shanxi, 030600, China
| | - Zhennan Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huifei Yin
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, 110161, China
| | - Xiaohang Zhou
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, 110161, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhuafang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Fenghai Li
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning, 110161, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Dai R, Ma X, Dingkao R, Huang C, La Y, Li X, Ma X, Wu X, Chu M, Guo X, Pei J, Yan P, Liang C. Effects of dietary crude protein levels in the concentrate supplement after grazing on rumen microbiota and metabolites by using metagenomics and metabolomics in Jersey-yak. Front Microbiol 2023; 14:1124917. [PMID: 37200912 PMCID: PMC10185794 DOI: 10.3389/fmicb.2023.1124917] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/13/2023] [Indexed: 05/20/2023] Open
Abstract
Introduction The crude protein level in the diet will affect the fermentation parameters, microflora, and metabolites in the rumen of ruminants. It is of great significance to study the effect of crude protein levels in supplementary diet on microbial community and metabolites for improving animal growth performance. At present, the effects of crude protein level in supplementary diet on rumen fermentation parameters, microbial community, and metabolites of Jersey-Yak (JY) are still unclear. Methods The purpose of this experiment was to study the appropriate crude protein level in the diet of JY. The rumen fermentation indexes (volatile fatty acids and pH) were determined by supplementary diets with crude protein levels of 15.16 and 17.90%, respectively, and the microbial community and metabolites of JYs were analyzed by non-target metabonomics and metagenome sequencing technology, and the changes of rumen fermentation parameters, microbial flora, and metabolites in the three groups and their interactions were studied. Results and Discussion The crude protein level in the supplementary diet had significant effects on pH, valeric acid, and the ratio of acetic acid to propionic acid (p < 0.05). The protein level had no significant effect on the dominant microflora at the phylum level (p > 0.05), and all three groups were Bacteroides and Firmicutes. The results of metabolite analysis showed that the crude protein level of supplementary diet significantly affected the metabolic pathways such as Bile secretion and styrene degradation (p < 0.05), and there were different metabolites between the LP group and HP group, and these different metabolites were related to the dominant microbial to some extent. To sum up, in this experiment, the effects of crude protein level in supplementary diet on rumen microorganisms and metabolites of JY and their relationship were studied, which provided the theoretical basis for formulating a more scientific and reasonable supplementary diet in the future.
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Affiliation(s)
- Rongfeng Dai
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoming Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Renqing Dingkao
- Animal Husbandry Station, Gannan Tibetan Autonomous Prefecture, Gannan, Gansu, China
| | - Chun Huang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Yongfu La
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xinyi Li
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoyong Ma
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xiaoyun Wu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Min Chu
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Xian Guo
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Jie Pei
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- Ping Yan,
| | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou, China
- *Correspondence: Chunnian Liang,
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Microbial xylanolytic carbohydrate esterases. Essays Biochem 2022; 67:479-491. [PMID: 36468678 DOI: 10.1042/ebc20220129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/04/2022] [Accepted: 11/17/2022] [Indexed: 12/12/2022]
Abstract
Abstract
This article reviews microbial esterases participating in the degradation of the major plant hemicellulose, xylan. The main chain of this polysaccharide built of β-1,4-glycosidically linked xylopyranosyl residues is substituted by other sugars and also partially acetylated. Besides esters of acetic acid, there are two other types of ester linkages in plant xylans. L-Arabinofuranosyl side chains form esters with phenolic acids, predominantly with ferulic acid. The dimerization of ferulic acid residues leads to cross-links connecting the hemicellulose molecules. Ferulic acid cross-links were shown to serve as covalent linkage between lignin and hemicellulose. Another cross-linking between lignin and hemicellulose is provided by esters between the xylan side residues of glucuronic or 4-O-methyl-D-glucurononic acid and lignin alcohols. Regardless of the cross-linking, the side residues prevent xylan main chains from association that leads to crystallization similar to that of cellulose. Simultaneously, xylan decorations hamper the action of enzymes acting on the main chain. The enzymatic breakdown of plant xylan, therefore, requires a concerted action of glycanases attacking the main chain and enzymes catalyzing debranching, called accessory xylanolytic enzymes including xylanolytic esterases. While acetylxylan esterases and feruloyl esterases participate directly in xylan degradation, glucuronoyl esterases catalyze its separation from lignin. The current state of knowledge of diversity, classification and structure–function relationship of these three types of xylanolytic carbohydrate esterases is discussed with emphasis on important aspects of their future research relevant to their industrial applications.
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Jardine KJ, Dewhirst RA, Som S, Lei J, Tucker E, Young RP, Portillo‐Estrada M, Gao Y, Su L, Fares S, Castanha C, Scheller HV, Mortimer JC. Cell wall ester modifications and volatile emission signatures of plant response to abiotic stress. PLANT, CELL & ENVIRONMENT 2022; 45:3429-3444. [PMID: 36222152 PMCID: PMC9828120 DOI: 10.1111/pce.14464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/29/2022] [Accepted: 10/08/2022] [Indexed: 06/16/2023]
Abstract
Growth suppression and defence signalling are simultaneous strategies that plants invoke to respond to abiotic stress. Here, we show that the drought stress response of poplar trees (Populus trichocarpa) is initiated by a suppression in cell wall derived methanol (MeOH) emissions and activation of acetic acid (AA) fermentation defences. Temperature sensitive emissions dominated by MeOH (AA/MeOH <30%) were observed from physiologically active leaves, branches, detached stems, leaf cell wall isolations and whole ecosystems. In contrast, drought treatment resulted in a suppression of MeOH emissions and strong enhancement in AA emissions together with volatiles acetaldehyde, ethanol, and acetone. These drought-induced changes coincided with a reduction in stomatal conductance, photosynthesis, transpiration, and leaf water potential. The strong enhancement in AA/MeOH emission ratios during drought (400%-3500%) was associated with an increase in acetate content of whole leaf cell walls, which became significantly 13 C2 -labelled following the delivery of 13 C2 -acetate via the transpiration stream. The results are consistent with both enzymatic and nonenzymatic MeOH and AA production at high temperature in hydrated tissues associated with accelerated primary cell wall growth processes, which are downregulated during drought. While the metabolic source(s) require further investigation, the observations are consistent with drought-induced activation of aerobic fermentation driving high rates of foliar AA emissions and enhancements in leaf cell wall O-acetylation. We suggest that atmospheric AA/MeOH emission ratios could be useful as a highly sensitive signal in studies investigating environmental and biological factors influencing growth-defence trade-offs in plants and ecosystems.
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Affiliation(s)
- Kolby J. Jardine
- Lawrence Berkeley National LabClimate and Ecosystem Science DivisionBerkeleyCaliforniaUSA
| | - Rebecca A. Dewhirst
- Lawrence Berkeley National LabClimate and Ecosystem Science DivisionBerkeleyCaliforniaUSA
| | - Suman Som
- Lawrence Berkeley National LabClimate and Ecosystem Science DivisionBerkeleyCaliforniaUSA
| | - Joseph Lei
- Lawrence Berkeley National LabClimate and Ecosystem Science DivisionBerkeleyCaliforniaUSA
| | - Eliana Tucker
- Lawrence Berkeley National LabClimate and Ecosystem Science DivisionBerkeleyCaliforniaUSA
| | - Robert P. Young
- Environmental Molecular Sciences LaboratoryPacific Northwest National LabRichlandWashingtonUSA
| | - Miguel Portillo‐Estrada
- Department of Biology, Research group PLECO (Plants and Ecosystems)University of AntwerpWilrijkBelgium
| | - Yu Gao
- Lawrence Berkeley National LabJoint BioEnergy InstituteEmeryvilleCaliforniaUSA
| | | | - Silvano Fares
- Institute of BioEconomyNational Research CouncilRomeItaly
- Department of Environmental Science, Policy, and ManagementUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Cristina Castanha
- Lawrence Berkeley National LabClimate and Ecosystem Science DivisionBerkeleyCaliforniaUSA
| | - Henrik V. Scheller
- Lawrence Berkeley National LabJoint BioEnergy InstituteEmeryvilleCaliforniaUSA
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Jenny C. Mortimer
- Lawrence Berkeley National LabJoint BioEnergy InstituteEmeryvilleCaliforniaUSA
- School of Agriculture, Food, and WineUniversity of AdelaideGlen OsmondSouth AustraliaAustralia
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Liu S, Lu SY, Qureshi N, Enshasy HAE, Skory CD. Antibacterial Property and Metagenomic Analysis of Milk Kefir. Probiotics Antimicrob Proteins 2022; 14:1170-1183. [PMID: 35995909 DOI: 10.1007/s12602-022-09976-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 12/25/2022]
Abstract
Milk kefir fermentation has been used in households for generations. Consumption of milk kefir has been associated with various health benefits, presumably from the probiotics of yeast and bacteria that make up the kefir grains. In addition, many of the microbes are known to produce novel antimicrobial compounds that can be used for other applications. The microbes living inside kefir grains differ significantly depending on geographical location and production methods. In this study, we aimed to use metagenomic analysis of fermented milk by using three different kefir grains (kefir 1, kefir 2, and kefir 3) from different US sources. We analyzed the microbial compositions of the three milk fermentation samples. This study revealed that each sample contains unique and distinct groups of microbes, kefir 1 showed the least diversity, and kefir 3 showed the highest diversity. Kefir 3 is rich in Proteobacteria while kefir 2 is dominated by the Firmicutes. Using bacterial indicator growth analyses carried out by continuous readings from microplate-based bioreactor assays suggested that kefir 2 fermentation filtrate has higher antibacterial property. We have screened 30 purified cultures of kefir 2 sample and isolated two lactic acid bacteria strains with higher antibacterial activities; the two strains were identified as Leuconostoc mesenteroides 28-1 and Lentilactobacillus kefiri 25-2 by 16S genomic PCR with confirmed antibacterial activities of fermentation filtrate after growing under both aerobic and anaerobic conditions.
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Affiliation(s)
- Siqing Liu
- Agricultural Research Service, Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, 1815 N University St, Peoria, IL, 61604, USA.
| | - Shao-Yeh Lu
- Agricultural Research Service, Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, 1815 N University St, Peoria, IL, 61604, USA
| | - Nasib Qureshi
- Bioenergy Research Unit, Agricultural Research Service, National Center for Agricultural Utilization Research, USDA, 1815 N University St, Peoria, IL, 61604, USA
| | - Hesham A El Enshasy
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Johor Bahru, Malaysia.,City of Scientific Research and Technology Applications (SRTA), New Burge Al Arab, Alexandria, 21934, Egypt
| | - Chris D Skory
- Agricultural Research Service, Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, USDA, 1815 N University St, Peoria, IL, 61604, USA
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Embaby AM, Mahmoud HE. Recombinant acetylxylan esterase of Halalkalibacterium halodurans NAH-Egypt: molecular and biochemical study. AMB Express 2022; 12:135. [DOI: 10.1186/s13568-022-01476-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractAcetylxylan esterase plays a crucial role in xylan hydrolysis as the acetyl side-groups restrict endoxylanase action by stearic hindrance. In this study, an acetylxylan esterase (AXE-HAS10: 960 bp & 319 a.a) putative ORF from Halalkalibacterium halodurans NAH-Egypt was extensively studied through heterologous overexpression in Escherichia coli, biochemical characterization, and structural modeling. The AXE-HAS10 tertiary structure was predicted by the Local Meta Threading Server. AXE-HAS10 belongs to the carbohydrate esterase Family 7. Purified to homogeneity AXE-HAS10 showed specific activity (36.99 U/mg), fold purification (11.42), and molecular mass (41.39 kDa). AXE-HAS10 showed optimal pH (8.5) and temperature (40 oC). After 15 h of incubation at pH 7.0–9.0, AXE-HAS10 maintained 100% activity. After 120 min at 35 and 40 oC, the retained activity was 80 and 50%, respectively. At 10 mM Mn2+, Fe3+, K+, and Ca2+ after 30 min, retained activity was 329 ± 15, 212 ± 5.2, 123 ± 1.4, and 120 ± 3.0%, respectively. After 30 min of preincubation with triton x-100, SDS, and CTAB at 0.1% (v/v), the retained activity was 150 ± 19, 88 ± 4, and 82 ± 7%, respectively. At 6.0 M NaCl after 30 min, retained activity was 58%. A 1.44-fold enhancement of beechwood xylan hydrolysis was achieved by AXE-HAS10 and Penicillium chrysogenum DSM105774 β-xylanase concurrently. Present data underpins AXE-HAS10 as a promising AXE for industrial exploitation.
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da Costa RMF, Bosch M, Simister R, Gomez LD, Canhoto JM, Batista de Carvalho LAE. Valorisation Potential of Invasive Acacia dealbata, A. longifolia and A. melanoxylon from Land Clearings. Molecules 2022; 27:7006. [PMID: 36296599 PMCID: PMC9610895 DOI: 10.3390/molecules27207006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/04/2022] [Accepted: 10/14/2022] [Indexed: 08/02/2023] Open
Abstract
Acacia spp. are invasive in Southern Europe, and their high propagation rates produce excessive biomass, exacerbating wildfire risk. However, lignocellulosic biomass from Acacia spp. may be utilised for diverse biorefinery applications. In this study, attenuated total reflectance Fourier transform infrared spectroscopy (FTIR-ATR), high-performance anion-exchange chromatography pulsed amperometric detection (HPAEC-PAD) and lignin content determinations were used for a comparative compositional characterisation of A. dealbata, A. longifolia and A. melanoxylon. Additionally, biomass was treated with three white-rot fungi species (Ganoderma lucidum, Pleurotus ostreatus and Trametes versicolor), which preferentially degrade lignin. Our results showed that the pre-treatments do not significantly alter neutral sugar composition while reducing lignin content. Sugar release from enzymatic saccharification was enhanced, in some cases possibly due to a synergy between white-rot fungi and mild alkali pretreatments. For example, in A. dealbata stems treated with alkali and P. ostreatus, saccharification yield was 702.3 nmol mg-1, which is higher than the samples treated only with alkali (608.1 nmol mg-1), and 2.9-fold higher than the non-pretreated controls (243.9 nmol mg-1). By characterising biomass and pretreatments, generated data creates value for unused biomass resources, contributing to the implementation of sustainable biorefining systems. In due course, the generated value will lead to economic incentives for landowners to cut back invasive Acacia spp. more frequently, thus reducing excess biomass, which exacerbates wildfire risk.
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Affiliation(s)
- Ricardo M. F. da Costa
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion SY23 3EE, UK
| | - Rachael Simister
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Leonardo D. Gomez
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Jorge M. Canhoto
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Luís A. E. Batista de Carvalho
- Molecular Physical-Chemistry R&D Unit, Department of Chemistry, University of Coimbra, Rua Larga, 3004-535 Coimbra, Portugal
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Sasamoto K, Himiyama T, Moriyoshi K, Ohmoto T, Uegaki K, Nakamura T, Nishiya Y. Functional analysis of the N-terminal region of acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis. FEBS Open Bio 2022; 12:1875-1885. [PMID: 36054591 PMCID: PMC9527590 DOI: 10.1002/2211-5463.13476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 12/14/2022] Open
Abstract
Acetylxylan esterase from Caldanaerobacter subterraneus subsp. tengcongensis (TTE0866) has an N-terminal region (NTR; residues 23-135) between the signal sequence (residues 1-22) and the catalytic domain (residues 136-324), which is of unknown function. Our previous study revealed the crystal structure of the wild-type (WT) enzyme containing the NTR and the catalytic domain. Although the structure of the catalytic domain was successfully determined, that of the NTR was undetermined, as its electron density was unclear. In this study, we investigated the role of the NTR through functional and structural analyses of NTR truncation mutants. Based on sequence and secondary structure analyses, NTR was confirmed to be an intrinsically disordered region. The truncation of NTR significantly decreased the solubility of the proteins at low salt concentrations compared with that of the WT. The NTR-truncated mutant easily crystallized in a conventional buffer solution. The crystal exhibited crystallographic properties comparable with those of the WT crystals suitable for structural determination. These results suggest that NTR plays a role in maintaining the solubility and inhibiting the crystallization of the catalytic domain.
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Affiliation(s)
- Kohei Sasamoto
- Division of Life Science, Graduate School of Science and EngineeringSetsunan UniversityOsakaJapan,Biomedical Research InstituteNational Institute of Advanced Industrial Science and TechnologyOsakaJapan
| | - Tomoki Himiyama
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and TechnologyOsakaJapan
| | | | - Takashi Ohmoto
- Osaka Research Institute of Industrial Science and TechnologyJapan
| | - Koichi Uegaki
- Department of Applied Biological Chemistry, Faculty of AgricultureKindai UniversityNaraJapan,Agricultural Technology and Innovation Research InstituteKindai UniversityNaraJapan
| | - Tsutomu Nakamura
- Biomedical Research InstituteNational Institute of Advanced Industrial Science and TechnologyOsakaJapan
| | - Yoshiaki Nishiya
- Division of Life Science, Graduate School of Science and EngineeringSetsunan UniversityOsakaJapan
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YÜCEL H, EKİNCİ K. Carbohydrate active enzyme system in rumen fungi: a review. INTERNATIONAL JOURNAL OF SECONDARY METABOLITE 2022. [DOI: 10.21448/ijsm.1075030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Hydrolysis and dehydration reactions of carbohydrates, which are used as energy raw materials by all living things in nature, are controlled by Carbohydrate Active Enzyme (CAZy) systems. These enzymes are also used in different industrial areas today. There are different types of microorganisms that have the CAZy system and are used in the industrial sector. Apart from current organisms, there are also rumen fungi within the group of candidate microorganisms with the CAZy system. It has been reported that xylanase (EC3.2.1.8 and EC3.2.1.37) enzyme, a member of the glycoside hydrolase enzyme family obtained from Trichoderma sp. and used especially in areas such as bread, paper, and feed industry, is more synthesized in rumen fungi such as Orpinomyces sp. and Neocallimastix sp. Therefore, this study reviews Neocallimastixsp., Orpinomyces sp., Caecomyces sp., Piromyces sp., and Anaeromyces sp., registered in the CAZy and Mycocosm database for rumen fungi to have both CAZy enzyme activity and to be an alternative microorganism in the industry. Furthermore the CAZy enzyme activities of the strains are investigated. The review shows thatNeocallimax sp. and Orpinomyces sp. areconsidered as candidate microorganisms.
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Affiliation(s)
- Halit YÜCEL
- KAHRAMANMARAŞ SÜTÇÜ İMAM ÜNİVERSİTESİ, ZİRAAT FAKÜLTESİ
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45
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Xie Y, Xu M, Han B, Chen T, Cai G, Lu J. Barley Husk Degraded by Fusarium graminearum MH1 Induced Premature Yeast Flocculation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:10296-10304. [PMID: 35947430 DOI: 10.1021/acs.jafc.2c03114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Premature yeast flocculation (PYF) is one of the pivotal problems affecting beer flavor and production. PYF is induced by certain non-starch polysaccharides produced by the degradation of malted barley husks upon the growth of contaminated microorganisms, such as Fusarium graminearum. In this research, the formation mechanism of PYF was uncovered by investigating the secretome of F. graminearum MH1 inoculated to the barley husk. The polysaccharide extract of degraded husk was ultrafiltrated into four fractions and characterized by the minimum PYF concentration, molecular mass distribution, monosaccharide composition, and zeta potential. Among the four fractions, the high-molecular-weight polysaccharide fraction had the highest content of uronic acid and the most negative zeta potential, which contributed to the most severe PYF phenomenon. In addition, the PYF yeast showed a more negative zeta potential than the control yeast during the small-scale brewing process. This is aligned to the negatively charged polysaccharides potentially bonded to the surface of yeast cells through the calcium cation in the same fermentation system, which results in rapid flocculation and precipitation. Approximately 12% of the 214 proteins identified in the Fusarium graminearum MH1 secretome were hemicellulases, which substantially interpreted the mechanism of polysaccharides inducing PYF yeast during beer brewing.
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Affiliation(s)
- Ying Xie
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- College of Biology and Food Engineering, Jilin Institute of Chemical Technology, Jilin 132022, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Minwei Xu
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Bingxin Han
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Tianming Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
| | - Guolin Cai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
| | - Jian Lu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi 214122, China
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Chen L, Chen W, Zheng B, Yu W, Zheng L, Qu Z, Yan X, Wei B, Zhao Z. Fermentation of NaHCO 3-treated corn germ meal by Bacillus velezensis CL-4 promotes lignocellulose degradation and nutrient utilization. Appl Microbiol Biotechnol 2022; 106:6077-6094. [PMID: 35976426 DOI: 10.1007/s00253-022-12130-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/30/2022] [Accepted: 08/02/2022] [Indexed: 11/25/2022]
Abstract
Sodium bicarbonate pretreatment and solid-state fermentation (SSF) were used to maximize the nutritional value of corn germ meal (CGM) by inoculating it with Bacillus velezensis CL-4 (isolated from chicken cecal contents and capable of degrading lignocellulose). Based on genome sequencing, B. velezensis CL-4 has a 4,063,558 bp ring chromosome and 46.27% GC content. Furthermore, genes associated with degradation of lignocellulose degradation were detected. Pretreatment of CGM (PCGM) with sodium bicarbonate (optimized to 0.06 g/mL) neutralized low pH. Fermented and pretreated CGM (FPCGM) contained more crude protein (CP), soluble protein of trichloroacetic acid (TCA-SP), and total amino acids (aa) than CGM and PCGM. Degradation rates of cellulose and hemicellulose were reduced by 21.33 and 71.35%, respectively, after 48 h fermentation. Based on electron microscopy, FPCGM destroys the surface structure and adds small debris of the CGM substrate, due to lignocellulose breakdown. Furthermore, 2-oxoadipic acid and dimethyl sulfone were the most important metabolites during pretreatment. Concentrations of adenosine, cytidine, guanosine, S-methyl-5'-thioadenosine, and adenine decreased significantly after 48 h fermentation, whereas concentrations of probiotics, enzymes, and fatty acids (including palmitic, 16-hydroxypalmitic, and linoleic acids) were significantly improved after fermentation. In conclusion, the novel pretreatment of CGM provided a proof of concept for using B. velezensis CL-4 to degrade lignocellulose components, improve nutritional characteristics of CGM, and expand CGM lignocellulosic biological feed production. KEY POINTS: • Sodium bicarbonate (baking soda) can be used as an economical and green additive to pretreat corn germ meal; • Fermentation with B. velezensis degrades the cellulose and hemicellulose component of corn germ meal and improves its feed quality; • As a novel qualified presumption of safety (QPS) strain, B. velezensis should have broad potential applications in food and feed industries.
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Affiliation(s)
- Long Chen
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Wanying Chen
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Boyu Zheng
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Wei Yu
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Lin Zheng
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Zihui Qu
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Xiaogang Yan
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China
| | - Bingdong Wei
- Institute of Animal Nutrition and Feed, Jilin Academy of Agricultural Sciences, No. 186 Dong Xinghua Street, Gongzhuling, Jilin Province, 136100, People's Republic of China.
| | - Zijian Zhao
- Institute of Agro-Food Technology, Jilin Academy of Agricultural Sciences, No. 1366 Cai Yu Street, Changchun, Jilin Province, 130033, People's Republic of China.
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Staudt A, Brack Y, Jr II, Leal ICR. Biocatalytic synthesis of monoterpene esters – A review study on the phylogenetic evolution of biocatalysts. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Genome analysis uncovers the prolific antagonistic and plant growth-promoting potential of endophyte Bacillus velezensis K1. Gene 2022; 836:146671. [PMID: 35714801 DOI: 10.1016/j.gene.2022.146671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/23/2022] [Accepted: 06/10/2022] [Indexed: 11/24/2022]
Abstract
Insights into the application of endophytic bacilli in sustainable agricultural practices have opened up new avenues for the inhibition of soil-borne pathogens and the improvement of plant health. Bacillus subtilis K1, an endophytic bacterium originally isolated from aerial roots of Ficus benghalensis is a potential biocontrol agent secreting a mixture of surfactins, iturins and fengycins. The current study extends the characterization of this bacterium through genomic and comparative genomics approaches. The sequencing of the bacterial genome at Illumina MiSeq platform revealed that it possessed a 4,103,502-bp circular chromosome with 45.98% GC content and 4325 predicted protein-coding sequences. Based on phylogenomics and whole-genome average nucleotide identity, the B. subtilis K1 was taxonomically classified as Bacillus velezensis. The formerly evaluated phenotypic traits viz. C-source utilization and lipopeptide-mediated fungal antagonism were correlated to their molecular determinants. The genome also harbored several genes associated with induced systemic resistance and plant growth promotion i.e, phytohormone production, nitrogen assimilation and reduction, siderophore production, phosphate solubilization, biofilm formation, swarming motility, acetoin and butanediol synthesis. The production of antifungal volatile organic compounds and plant growth promotion was experimentally demonstrated by volatile compound assay and seed germination assay on cumin and groundnut. The isolate also holds great prospects for application as a soil inoculant as indicated by enhancement in the growth of groundnut via in planta pot studies. Bacterial pan-genome analysis based on a comparison of whole genomes with eighteen other Bacillus strains was also conducted. Comparative examination of biosynthetic gene clusters across all genomes indicated that the largest number of gene clusters were harbored by the K1 genome. Based on the findings, we propose K1 as a model for scrutinizing non-ribosomally synthesized peptide synthetase and polyketide synthetase derived molecules.
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The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China. Nutrients 2022; 14:nu14112347. [PMID: 35684146 PMCID: PMC9183100 DOI: 10.3390/nu14112347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 02/06/2023] Open
Abstract
Eighty-eight Bifidobacterium pseudocatenulatum strains, which were isolated from human, chicken and cow fecal samples from different niches of China, were compared genomically in this study to evaluate their diversity. It was found that B. pseudocatenulatum displayed a closed pan-genome, including abundant glycoside hydrolase families of the carbohydrate active enzyme (CAZy). A total of 30 kinds of glycoside hydrolases (GHs), 14 kinds of glycosyl transferases (GTs), 13 kinds of carbohydrate-binding modules (CBMs), 6 kinds of carbohydrate-esterases (CEs), and 2 kinds of auxiliary activities (AAs) gene families were identified across the genomes of the 88 B. pseudocatenulatum strains. Specifically, this showed that significant differences were also present in the number of 10 carbohydrate-active enzyme gene families (GT51, GH13_32, GH26, GH42, GH121, GH3, AA3, CBM46, CE2, and CE6) among the strains derived from the hosts of different age groups, particularly between strains from infants and those from other human age groups. Twelve different individuals of B. pseudocatenulatum from four main clusters were selected for further study to reveal the genetic diversity of carbohydrate metabolism-related genes within the same phylogenetics. The animal experiment showed that 3 weeks of oral administration and 1 week after cessation of administration of these strains did not markedly alter the serum routine inflammatory indicators in mice. Furthermore, the administration of these strains did not significantly cause adverse changes in the gut microbiota, as indicated by the α- and β-diversity indexes, relative to the control group (normal diet). Beyond that, FAHBZ9L5 significantly increased the abundance of B. pseudocatenulatum after 3 weeks and significantly increased the abundance of acetic acid and butyric acid in the host’s intestinal tract 3 and 4 weeks after the first administration, respectively, compared with the control group. Corresponding to this, comparative genomic analyses of 12 B. pseudocatenulatum suggest that FAHBZ9L5-specific genes were rich in ABC transporters and carbohydrate esterase. Combining the results of comparative genomics analyses and animal experiment, it is suggested that the strains containing certain gene clusters contribute to another competitive growth advantage of B. pseudocatenulatum, which facilitates its intestinal carbohydrate metabolism in a host.
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Comparative analysis of genome-based CAZyme cassette in Antarctic Microbacterium sp. PAMC28756 with 31 other Microbacterium species. Genes Genomics 2022; 44:733-746. [PMID: 35486322 DOI: 10.1007/s13258-022-01254-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/31/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND The genus Microbacterium belongs to the family Microbacteriaceae and phylum Actinobacteria. A detailed study on the complete genome and systematic comparative analysis of carbohydrate-active enzyme (CAZyme) among the Microbacterium species would add knowledge on metabolic and environmental adaptation. Here we present the comparative genomic analysis of CAZyme using the complete genome of Antarctic Microbacterium sp. PAMC28756 with other complete genomes of 31 Microbacterium species available. OBJECTIVE The genomic and CAZyme comparison of Microbacterium species and to rule out the specific features of CAZyme for the environmental and metabolic adaptation. METHODS Bacterial source were collected from NCBI database, CAZyme annotation of Microbacterium species was analyzed using dbCAN2 Meta server. Cluster of orthologous groups (COGs) analysis was performed using the eggNOG4.5 database. Whereas, KEGG database was used to compare and obtained the functional genome annotation information in carbohydrate metabolism and glyoxylate cycle. RESULTS Out of 32 complete genomes of Microbacterium species, strain No. 7 isolated from Activated Sludge showed the largest genomic size at 4.83 Mb. The genomic size of PAMC28756 isolated from Antarctic lichen species Stereocaulons was 3.54 Mb, the G + C content was 70.4% with 3,407 predicted genes, of which 3.36% were predicted CAZyme. In addition, while comparing the Glyoxylate cycle among 32 bacteria, except 10 strains, all other, including our strain have Glyoxylate pathway. PAMC28756 contained the genes that degrade cellulose, hemicellulose, amylase, pectinase, chitins and other exo-and endo glycosidases. Utilizing these polysaccharides can provides source of energy in an extreme environment. In addition, PAMC28756 assigned the (10.15%) genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. CONCLUSIONS The genomic content and CAZymes distribution was varied in Microbacterium species. There was the presence of more than 10% genes in the carbohydrate transport and metabolism functional group closely related to the CAZyme for polysaccharides degradation. In addition, occurrence of glyoxylate cycle for alternative utilization of carbon sources suggest the adaptation of PAMC28756 in the harsh microenvironment.
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