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Li Z, Tian SY. A new alkaline pectin lyase with novel thermal and pH stability from Bacilus velezensis. Protein Expr Purif 2024; 224:106564. [PMID: 39111349 DOI: 10.1016/j.pep.2024.106564] [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: 06/28/2024] [Revised: 07/30/2024] [Accepted: 08/04/2024] [Indexed: 08/18/2024]
Abstract
Pectin lyases are important in various industries, including tobacco leaves processing. In this paper, a novel pectin lyase Pel04 from Bacillus velezensis was characterized. Pel04 molecular weight (Mw) and isoelectric point (pI) of the protein sequence after removing the signal peptide are 43.0 kDa. The optimal temperature and pH of Pel04 is 50 °C and 9.0, respectively. Pel04 was stable in the range of 30-50 °C, and pH 9.5-11. Ca2+ can significantly stimulate the enzyme activity, while Cu2+, Co2+, Fe3+, and Mn2+ have inhibitory effects on Pel04. By Pel04 treatment, the overall content of acids, alcohols, esters and other aromas in tobacco leaves increased, while the contents of phenolic and heterocyclic substances decreased. Pel04 has important potential for industrial application particularly in improving quality of tobacco leaves.
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Affiliation(s)
- Ze Li
- College of Ecological and Environmental Protection, Linyi Vocational University of Science and Technology, Linyi, China.
| | - Su-Yan Tian
- College of Ecological and Environmental Protection, Linyi Vocational University of Science and Technology, Linyi, China.
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2
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Pavlović M, Šokarda Slavić M, Kojić M, Margetić A, Ristović M, Drulović N, Vujčić Z. Unveiling novel insights into Bacillus velezensis 16B pectin lyase for improved fruit juice processing. Food Chem 2024; 456:140030. [PMID: 38909459 DOI: 10.1016/j.foodchem.2024.140030] [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: 03/31/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024]
Abstract
Microbial pectinolytic enzymes are important in various industries, particularly food processing. This study focuses on uncovering insights into a novel pectin lyase, BvPelB, from Bacillus velezensis 16B, with the aim of enhancing fruit juice processing. The study examines the structural and functional characteristics of pectinolytic enzyme, underscoring the critical nature of substrate specificity and enzymatic reaction mechanisms. BvPelB was successfully expressed and purified, exhibiting robust activity under alkaline conditions and thermal stability. Structural analysis revealed similarities with other pectin lyases, despite limited sequence identity. Biochemical characterization showed BvPelB's preference for highly methylated pectins and its endo-acting mode of cleavage. Treatment with BvPelB significantly increased juice yield and clarity without generating excessive methanol, making it a promising candidate for fruit juice processing. Overall, this study provides valuable insights into the enzymatic properties of BvPelB and its potential industrial applications in improving fruit juice processing efficiency and quality.
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Affiliation(s)
- Marija Pavlović
- University of Belgrade - Institute of Chemistry, Technology and Metallurgy - National Institute of the Republic of Serbia, Department of Chemistry, Belgrade, Serbia.
| | - Marinela Šokarda Slavić
- University of Belgrade - Institute of Chemistry, Technology and Metallurgy - National Institute of the Republic of Serbia, Department of Chemistry, Belgrade, Serbia
| | - Milan Kojić
- Institute of Virology, Vaccines and Sera "Torlak", Belgrade, Serbia
| | - Aleksandra Margetić
- University of Belgrade - Institute of Chemistry, Technology and Metallurgy - National Institute of the Republic of Serbia, Department of Chemistry, Belgrade, Serbia
| | - Marina Ristović
- University of Belgrade - Institute of Chemistry, Technology and Metallurgy - National Institute of the Republic of Serbia, Department of Chemistry, Belgrade, Serbia
| | - Nenad Drulović
- University of Belgrade - Institute of Chemistry, Technology and Metallurgy - National Institute of the Republic of Serbia, Department of Chemistry, Belgrade, Serbia; University of Belgrade -Faculty of Chemistry, Department of Biochemistry, Belgrade, Serbia
| | - Zoran Vujčić
- University of Belgrade -Faculty of Chemistry, Department of Biochemistry, Belgrade, Serbia
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3
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Saberi Riseh R, Gholizadeh Vazvani M, Taheri A, Kennedy JF. Pectin-associated immune responses in plant-microbe interactions: A review. Int J Biol Macromol 2024; 273:132790. [PMID: 38823736 DOI: 10.1016/j.ijbiomac.2024.132790] [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: 12/30/2023] [Revised: 05/04/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
This review explores the role of pectin, a complex polysaccharide found in the plant cell wall, in mediating immune responses during interactions between plants and microbes. The objectives of this study were to investigate the molecular mechanisms underlying pectin-mediated immune responses and to understand how these interactions shape plant-microbe communication. Pectin acts as a signaling molecule, triggering immune responses such as the production of antimicrobial compounds, reinforcement of the cell wall, and activation of defense-related genes. Pectin functions as a target for pathogen-derived enzymes, enabling successful colonization by certain microbial species. The document discusses the complexity of pectin-based immune signaling networks and their modulation by various factors, including pathogen effectors and host proteins. It also emphasizes the importance of understanding the crosstalk between pectin-mediated immunity and other defense pathways to develop strategies for enhancing plant resistance against diseases. The insights gained from this study have implications for the development of innovative approaches to enhance crop protection and disease management in agriculture. Further investigations into the components and mechanisms involved in pectin-mediated immunity will pave the way for future advancements in plant-microbe interaction research.
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Affiliation(s)
- Roohallah Saberi Riseh
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran.
| | - Mozhgan Gholizadeh Vazvani
- Department of Plant Protection, Faculty of Agriculture, Vali-e-Asr University of Rafsanjan, 7718897111 Rafsanjan, Iran
| | - Abdolhossein Taheri
- Department of Plant Protection, Faculty of Plant Production, University of agricultural Sciences and natural resources of Gorgan, Iran.
| | - John F Kennedy
- Chembiotech Laboratories Ltd, WR15 8FF Tenbury Wells, United Kingdom.
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4
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Berndsen ZT, Akhtar M, Thapa M, Vickers T, Schmitz A, Torres JL, Baboo S, Kumar P, Khatoom N, Sheikh A, Hamrick M, Diedrich JK, Martinez-Bartolome S, Garrett PT, Yates JR, Turner JS, Laird RM, Poly F, Porter CK, Copps J, Ellebedy AH, Ward AB, Fleckenstein JM. Repeat modules and N-linked glycans define structure and antigenicity of a critical enterotoxigenic E. coli adhesin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593125. [PMID: 38766097 PMCID: PMC11100705 DOI: 10.1101/2024.05.08.593125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Enterotoxigenic Escherichia coli (ETEC) cause hundreds of millions of cases of infectious diarrhea annually, predominantly in children from low-middle income regions. Notably, in children, as well as human volunteers challenged with ETEC, diarrheal severity is significantly increased severity in blood group A (bgA) individuals. EtpA, is a secreted glycoprotein adhesin that functions as a blood group A lectin to promote critical interactions between ETEC and blood group A glycans on intestinal epithelia for effective bacterial adhesion and toxin delivery. EtpA is highly immunogenic resulting in robust antibody responses following natural infection and experimental challenge of human volunteers with ETEC. To understand how EtpA directs ETEC-blood group A interactions and stimulates adaptive immunity, we mutated EtpA, mapped its glycosylation by mass-spectrometry (MS), isolated polyclonal (pAbs) and monoclonal antibodies (mAbs) from vaccinated mice and ETEC-infected human volunteers, and determined structures of antibody-EtpA complexes by cryo-electron microscopy. Both bgA and mAbs that inhibited EtpA-bgA interactions and ETEC adhesion, bound to the C-terminal repeat domain highlighting this region as crucial for ETEC pathogen-host interaction. MS analysis uncovered extensive and heterogeneous N-linked glycosylation of EtpA and cryo-EM structures revealed that mAbs directly engage these unique glycan containing epitopes. Finally, electron microscopy-based polyclonal epitope mapping revealed antibodies targeting numerous distinct epitopes on N and C-terminal domains, suggesting that EtpA vaccination generates responses against neutralizing and decoy regions of the molecule. Collectively, we anticipate that these data will inform our general understanding of pathogen-host glycan interactions and adaptive immunity relevant to rational vaccine subunit design.
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Affiliation(s)
- Zachary T Berndsen
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Marjahan Akhtar
- Department of Medicine, Division of Infectious Diseases, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA
| | - Mahima Thapa
- Department of Pathology and Immunology, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA. Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA and The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Tim Vickers
- Department of Medicine, Division of Infectious Diseases, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA
| | - Aaron Schmitz
- Department of Pathology and Immunology, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA. Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA and The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Jonathan L Torres
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Sabyasachi Baboo
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Pardeep Kumar
- Department of Medicine, Division of Infectious Diseases, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA
| | - Nazia Khatoom
- Department of Medicine, Division of Infectious Diseases, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA
| | - Alaullah Sheikh
- Department of Medicine, Division of Infectious Diseases, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA
| | - Melissa Hamrick
- Department of Medicine, Division of Infectious Diseases, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Patrick T Garrett
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jackson S Turner
- Department of Pathology and Immunology, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA. Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA and The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Renee M Laird
- Operationally Relevant Infections Department, Naval Medical Research Command (NMRC), Silver Spring, Maryland, USA
| | - Frédéric Poly
- Operationally Relevant Infections Department, Naval Medical Research Command (NMRC), Silver Spring, Maryland, USA
| | - Chad K Porter
- Naval Medical Research Command (NMRC), Silver Spring, Maryland, USA
- Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Jeffrey Copps
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA. Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA and The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - James M Fleckenstein
- Department of Medicine, Division of Infectious Diseases, Washington University in Saint Louis, School of Medicine. Saint Louis, Missouri, USA
- Medicine Service, Infectious Diseases, Veterans Affairs Health Care System, Saint Louis Missouri, USA
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Yang S, Yang S, Li Q, Lu Y, Huang X, Chen C, Xu C, Xie H. Pectate lyase genes from Radopholus similis and their application in pathotype identification. Appl Microbiol Biotechnol 2024; 108:298. [PMID: 38607493 PMCID: PMC11009743 DOI: 10.1007/s00253-024-13124-3] [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: 11/21/2023] [Revised: 03/06/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024]
Abstract
Radopholus similis is a destructive, migratory, and endophytoparasitic nematode. It has two morphologically indistinguishable pathotypes (or physiological races): banana and citrus pathotypes. At present, the only reliable method to differentiate the two pathotypes is testing the infestation and parasitism of nematodes on Citrus spp. via inoculation. However, differences in inoculation methods and conditions adopted by different researchers complicate obtaining consistent results. In this study, the parasitism and pathogenicity of 10 R. similis populations on rough lemon (Citrus limon) seedlings and the tropism and invasion of rough lemon roots were tested. It revealed that populations SWK, GJ, FZ, GZ, DBSR, and YJ were citrus pathotypes, which showed parasitism and pathogenicity on rough lemon and could invade rough lemon roots, whereas populations XIN, ML, HN6, and HL were banana pathotypes, having no parasitism and pathogenicity on rough lemon and they did not invade the rough lemon roots. Four pectate lyase genes (Rs-pel-2, Rs-pel-3, Rs-pel-4, and Rs-pel-5) belonging to the Class III family from these populations were amplified and analysed. The gene Rs-pel-3 could be amplified from six citrus pathotype populations and was stably expressed in the four developmental stages of the nematode, whereas it could not be amplified from the four banana pathotypes. Rs-pel-3 expression may be related to the parasitism and pathogenicity of R. similis on rough lemon. Hence, it can be used as a molecular marker to distinguish between banana and citrus pathotypes and as a target gene for the molecular identification of these two pathotypes. KEY POINTS: • Four pectate lyase genes (Rs-pels) from Radopholus similis were cloned and analysed. • The expression of Rs-pels is different in two pathotypes of Radopholus similis. • A molecular identification method for two pathotypes of Radopholus similis using pectate lyase gene Rs-pel-3 as the target gene was established.
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Affiliation(s)
- Sihua Yang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Shuai Yang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Qianying Li
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Yang Lu
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Xin Huang
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Chun Chen
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Chunling Xu
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Hui Xie
- Laboratory of Plant Nematology and Research Center of Nematodes of Plant Quarantine, Department of Plant Pathology, College of Plant Protection, South China Agricultural University, Guangzhou, 510642, People's Republic of China.
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6
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Chebli Y, Geitmann A. Pectate lyase-like lubricates the male gametophyte's path toward its mating partner. PLANT PHYSIOLOGY 2023; 194:124-136. [PMID: 37658849 DOI: 10.1093/plphys/kiad481] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/10/2023] [Accepted: 08/12/2023] [Indexed: 09/05/2023]
Abstract
The pollen tube is an extension of the male gametophyte in plants and mediates sexual reproduction by delivering the sperm cells to the female gametophyte. To accomplish this task, the elongating pollen tube must break through the thick wall of the pollen grain and penetrate multiple pistillar tissues. Both processes require the loosening of cell wall material-that of the pollen intine and that of the apoplast of the transmitting tract. The enzymatic toolbox for these cell wall modifying processes employed by the invading male gametophyte is elusive. We investigated the role of the pectin-digesting pectate lyase-like (PLL) by combining mutant analysis with microscopy observations, fluorescence recovery after photo-bleaching experiments, and immuno-detection. We show that in Arabidopsis (Arabidopsis thaliana), PLLs are required for intine loosening during the first steps of pollen tube germination. We provide evidence that during pollen tube elongation, PLLs are released by the pollen tube into the extracellular space, suggesting that they may be employed to soften the apoplast of the transmitting tissue. The synergistic enzymatic action of PLLs in the pollen grain, the pollen tube, and the transmitting track contribute to an effective fertilization process.
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Affiliation(s)
- Youssef Chebli
- Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada
- ECP3-Multi-Scale Imaging Facility, McGill University, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada
| | - Anja Geitmann
- Department of Plant Science, McGill University, Ste-Anne-de-Bellevue, Québec H9X 3V9, Canada
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Banerjee B, Yuan X, Yang CH. Dissecting the molecular dance: c-di-GMP, cAMP-CRP, and VfmH collaboration in pectate lyase regulation for Dickeya dadantii-unveiling the soft rot pathogen's strategy. Microbiol Spectr 2023; 11:e0153723. [PMID: 37811940 PMCID: PMC10714721 DOI: 10.1128/spectrum.01537-23] [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: 04/17/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023] Open
Abstract
IMPORTANCE Bacteria respond to environmental changes and adapt to host systems. The response regulator VfmH of the Vfm quorum sensing system regulates a crucial virulence factor, pectate lyase (Pel), in Dickeya dadantii. At high c-di-GMP concentrations, VfmH binds c-di-GMP, resulting in the loss of its activation property in the Pel and virulence regulation in D. dadantii. VfmH binds to c-di-GMP via three conserved arginine residues, and mutations of these residues eliminate the c-di-GMP-related phenotypes of VfmH in Pel synthesis. Our data also show that VfmH interacts with CRP to regulate pelD transcription, thus integrating cyclic AMP and c-di-GMP signaling pathways to control virulence in D. dadantii. We propose that VfmH is an important intermediate factor incorporating quorum sensing and nucleotide signaling pathways for the collective regulation of D. dadantii pathogenesis.
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Affiliation(s)
- Biswarup Banerjee
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Xiaochen Yuan
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Ching-Hong Yang
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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8
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Huang X, Sun G, Wu Z, Jiang Y, Li Q, Yi Y, Yan H. Genome-wide identification and expression analyses of the pectate lyase (PL) gene family in Fragaria vesca. BMC Genomics 2023; 24:435. [PMID: 37537572 PMCID: PMC10401794 DOI: 10.1186/s12864-023-09533-9] [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: 04/15/2023] [Accepted: 07/26/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Pectate lyase (PL, EC 4.2.2.2), as an endo-acting depolymerizing enzyme, cleaves α-1,4-glycosidic linkages in esterified pectin and involves a broad range of cell wall modifications. However, the knowledge concerning the genome-wide analysis of the PL gene family in Fragaria vesca has not been thoroughly elucidated. RESULTS In this study, sixteen PLs members in F. vesca were identified based on a genome-wide investigation. Substantial divergences existed among FvePLs in gene duplication, cis-acting elements, and tissue expression patterns. Four clusters were classified according to phylogenetic analysis. FvePL6, 8 and 13 in cluster II significantly contributed to the significant expansions during evolution by comparing orthologous PL genes from Malus domestica, Solanum lycopersicum, Arabidopsis thaliana, and Fragaria×ananassa. The cis-acting elements implicated in the abscisic acid signaling pathway were abundant in the regions of FvePLs promoters. The RNA-seq data and in situ hybridization revealed that FvePL1, 4, and 7 exhibited maximum expression in fruits at twenty days after pollination, whereas FvePL8 and FvePL13 were preferentially and prominently expressed in mature anthers and pollens. Additionally, the co-expression networks displayed that FvePLs had tight correlations with transcription factors and genes implicated in plant development, abiotic/biotic stresses, ions/Ca2+, and hormones, suggesting the potential roles of FvePLs during strawberry development. Besides, histological observations suggested that FvePL1, 4 and 7 enhanced cell division and expansion of the cortex, thus negatively influencing fruit firmness. Finally, FvePL1-RNAi reduced leaf size, altered petal architectures, disrupted normal pollen development, and rendered partial male sterility. CONCLUSION These results provide valuable information for characterizing the evolution, expansion, expression patterns and functional analysis, which help to understand the molecular mechanisms of the FvePLs in the development of strawberries.
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Affiliation(s)
- Xiaolong Huang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
| | - Guilian Sun
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
| | - Zongmin Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
| | - Yu Jiang
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
| | - Qiaohong Li
- Kiwifruit Breeding and Utilization Key Laboratory of Sichuan Province, Sichuan Provincial Academy of Natural Resource Science, Chengdu, 610015, China
| | - Yin Yi
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of Plant Physiology and Development Regulation, Guizhou Normal University, Guiyang, 550001, China
- Key Laboratory of National Forestry and Grassland Administration on Biodiversity Conservation in Karst Mountainous Areas of Southwestern China, Guizhou Normal University, Guiyang, 550001, China
| | - Huiqing Yan
- School of Life Sciences, Guizhou Normal University, Guiyang, 550001, China.
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9
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Gogoi A, Rossmann SL, Lysøe E, Stensvand A, Brurberg MB. Genome analysis of Phytophthora cactorum strains associated with crown- and leather-rot in strawberry. Front Microbiol 2023; 14:1214924. [PMID: 37465018 PMCID: PMC10351607 DOI: 10.3389/fmicb.2023.1214924] [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: 04/30/2023] [Accepted: 06/12/2023] [Indexed: 07/20/2023] Open
Abstract
Phytophthora cactorum has two distinct pathotypes that cause crown rot and leather rot in strawberry (Fragaria × ananassa). Strains of the crown rot pathotype can infect both the rhizome (crown) and fruit tissues, while strains of the leather rot pathotype can only infect the fruits of strawberry. The genome of a highly virulent crown rot strain, a low virulent crown rot strain, and three leather rot strains were sequenced using PacBio high fidelity (HiFi) long read sequencing. The reads were de novo assembled to 66.4-67.6 megabases genomes in 178-204 contigs, with N50 values ranging from 892 to 1,036 kilobases. The total number of predicted complete genes in the five P. cactorum genomes ranged from 17,286 to 17,398. Orthology analysis identified a core secretome of 8,238 genes. Comparative genomic analysis revealed differences in the composition of potential virulence effectors, such as putative RxLR and Crinklers, between the crown rot and the leather rot pathotypes. Insertions, deletions, and amino acid substitutions were detected in genes encoding putative elicitors such as beta elicitin and cellulose-binding domain proteins from the leather rot strains compared to the highly virulent crown rot strain, suggesting a potential mechanism for the crown rot strain to escape host recognition during compatible interaction with strawberry. The results presented here highlight several effectors that may facilitate the tissue-specific colonization of P. cactorum in strawberry.
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Affiliation(s)
- Anupam Gogoi
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Simeon L. Rossmann
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Erik Lysøe
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - Arne Stensvand
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
| | - May Bente Brurberg
- Department of Plant Sciences, Faculty of Biosciences (BIOVIT), Norwegian University of Life Sciences (NMBU), Ås, Norway
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research (NIBIO), Ås, Norway
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10
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Deng Q, Li SQ, Sun XB, Gao DY, Li N, Zhang HE, Wang ZG, Wang JK, Wang Q. Cloning, expression, and characterization of two pectate lyases isolated from the sheep rumen microbiome. Appl Microbiol Biotechnol 2023; 107:677-689. [PMID: 36572830 DOI: 10.1007/s00253-022-12344-9] [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: 09/27/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022]
Abstract
Pectate lyases (Pels) have a vital function in degradation of the primary plant cell wall and the middle lamella and have been widely used in the industry. In this study, two pectate lyase genes, IDSPel16 and IDSPel17, were cloned from a sheep rumen microbiome. The recombinant enzymes were expressed in Escherichia coli and functionally characterized. Both IDSPel16 and IDSPel17 proteins had an optimal temperature of 60 ℃, and an optimal pH of 10.0. IDSPel16 was relatively stable below 60 °C, maintaining 77.51% residual activity after preincubation at 60 °C for 1 h, whereas IDSPel17 denatured rapidly at 60 °C. IDSPel16 was relatively stable between pH 6.0 and 12.0, after pretreatment for 1 h, retaining over 60% residual activity. IDSPel16 had high activity towards polygalacturonic acid, with a Vmax of 942.90 ± 68.11, whereas IDSPel17 had a Vmax of only 28.19 ± 2.23 μmol/min/mg. Reaction product analyses revealed that IDSPel17 liberated unsaturated digalacturonate (uG2) and unsaturated trigalacturonate (uG3) from the substrate, indicating a typical endo-acting pectate lyase (EC 4.2.2.2). In contrast, IDSPel16 initially generated unsaturated oligogalacturonic acids, then converted these intermediates into uG2 and unsaturated galacturonic acid (uG1) as end products, a unique depolymerization profile among Pels. To the best of our knowledge, the IDSPel16 discovered with both endo-Pel (EC 4.2.2.2) and exo-Pel (EC 4.2.2.9) activities. These two pectate lyases, particularly the relatively thermo- and pH-stable IDSPel16, will be of interest for potential application in the textile, food, and feed industries. KEY POINTS: • Two novel pectate lyase genes, IDSPel16 and IDSPel17, were isolated and characterized from the sheep rumen microbiome. • Both IDSPel16 and IDSPel17 are alkaline pectate lyases, releasing unsaturated digalacturonate and unsaturated trigalacturonate from polygalacturonic acid. • IDSPel16, a bifunctional pectate lyase with endo-Pel (EC 4.2.2.2) and exo-Pel (EC 4.2.2.9) activities, could be a potential candidate for industrial application.
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Affiliation(s)
- Qian Deng
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shi-Qi Li
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiao-Bao Sun
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - De-Ying Gao
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Nuo Li
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Hui-En Zhang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, China
| | - Zheng-Guang Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jia-Kun Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, 310058, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qian Wang
- Key Laboratory of Molecular Animal Nutrition, Ministry of Education, Zhejiang University, Hangzhou, 310058, China.
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China.
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11
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Zhao H, Lv F, Liu G, Pang X, Han X, Wang X. Effects of starters with different NDF/starch ratio on rumen fermentation parameters and rumen microorganisms in lambs. Front Vet Sci 2023; 10:1064774. [PMID: 36777666 PMCID: PMC9911143 DOI: 10.3389/fvets.2023.1064774] [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: 10/08/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
Starch and NDF are the main components in the diets of ruminants worldwide and are the main energy source for rumen microorganisms and hosts. The purpose of this study was to investigate the effects of different NDF/starch ratios on rumen fermentation parameters, rumen development and rumen microbes in lambs and to predict the function of rumen microbes by metagenomic techniques. In this study, 30 lambs with birth weights of (3.0 ± 0.5) kg were selected. The lambs of Hu sheep were randomly divided into two groups, fed starter with an NDF/starch ratio of 0.5 (group A) or 1.0 (group C). Samples of the rumen tissue and contents were collected after slaughter. The results showed that the ADG and ADFI of group A were significantly higher than those of group C (P < 0.05), but there was no significant difference in the FCR (P > 0.05). Therefore, from the perspective of feed-related economic benefits, group C showed greater economic value; the A/P of group C was significantly lower than that of group A (0.05 < P < 0.1), and the TVFA showed no significant difference (P > 0.05); The lengths of the rumen papillae of group C was significantly higher than that of group A (0.05 < P < 0.1). There was no significant difference in the abundance of the top 10 species at the phylum level and genus level (P > 0.05). CAZymes gene enrichment was observed in the rumen microbial community of lambs in group C (P < 0.05). In conclusion, group C, fed with starter with a higher NDF/starch ratio, had a higher feeding value. This study provides comprehensive insights into the composition of NDF and starch in lamb starter.
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12
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Structure of an Alkaline Pectate Lyase and Rational Engineering with Improved Thermo-Alkaline Stability for Efficient Ramie Degumming. Int J Mol Sci 2022; 24:ijms24010538. [PMID: 36613981 PMCID: PMC9820310 DOI: 10.3390/ijms24010538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/31/2022] Open
Abstract
Alkaline pectate lyases have biotechnological applications in plant fiber processing, such as ramie degumming. Previously, we characterized an alkaline pectate lyase from Bacillus clausii S10, named BacPelA, which showed potential for enzymatic ramie degumming because of its high cleavage activity toward methylated pectins in alkaline conditions. However, BacPelA displayed poor thermo-alkaline stability. Here, we report the 1.78 Å resolution crystal structure of BacPelA in apo form. The enzyme has the characteristic right-handed β-helix fold of members of the polysaccharide lyase 1 family and shows overall structural similarity to them, but it displays some differences in the details of the secondary structure and Ca2+-binding site. On the basis of the structure, 10 sites located in flexible regions and showing high B-factor and positive ΔTm values were selected for mutation, aiming to improve the thermo-alkaline stability of the enzyme. Following site-directed saturation mutagenesis and screening, mutants A238C, R150G, and R216H showed an increase in the T5015 value at pH 10.0 of 3.0 °C, 6.5 °C, and 7.0 °C, respectively, compared with the wild-type enzyme, interestingly accompanied by a 24.5%, 46.6%, and 61.9% increase in activity. The combined mutant R150G/R216H/A238C showed an 8.5 °C increase in the T5015 value at pH 10.0, and an 86.1% increase in the specific activity at 60 °C, with approximately doubled catalytic efficiency, compared with the wild-type enzyme. Moreover, this mutant retained 86.2% activity after incubation in ramie degumming conditions (4 h, 60 °C, pH 10.0), compared with only 3.4% for wild-type BacPelA. The combined mutant increased the weight loss of ramie fibers in degumming by 30.2% compared with wild-type BacPelA. This work provides a thermo-alkaline stable, highly active pectate lyase with great potential for application in the textile industry, and also illustrates an effective strategy for rational design and improvement of pectate lyases.
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Transcriptomic Analysis to Unravel Potential Pathways and Genes Involved in Pecan ( Carya illinoinensis) Resistance to Pestalotiopsis microspora. Int J Mol Sci 2022; 23:ijms231911621. [PMID: 36232919 PMCID: PMC9570006 DOI: 10.3390/ijms231911621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
Fruit black spot (FBS), a fungal disease of pecan (Carya illinoinensis (Wangenh) K. Koch) caused by the pathogen Pestalotiopsis microspora, is a serious disease and poses a critical threat to pecan yield and quality. However, the details of pecan responses to FBS infection at the transcriptional level remain to be elucidated. In present study, we used RNA-Seq to analyze differential gene expression in three pecan cultivars with varied resistance to FBS infection: Xinxuan-4 (X4), Mahan (M), and Wichita (W), which were categorized as having low, mild, and high susceptibility to FBS, respectively. Nine RNA-Seq libraries were constructed, comprising a total of 58.56 Gb of high-quality bases, and 2420, 4380, and 8754 differentially expressed genes (DEGs) with |log2Fold change| ≥ 1 and p-value < 0.05 were identified between M vs. X4, W vs. M, and W vs. X4, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed to further annotate DEGs that were part of specific pathways, which revealed that out of 134 total pathways, MAPK signaling pathway, plant−pathogen interaction, and plant hormone signal transduction were highly enriched. Transcriptomic profiling analysis revealed that 1681 pathogen-related genes (PRGs), including 24 genes encoding WRKY transcription factors, potentially participate in the process of defense against Pestalotiopsis microspora infection in pecan. The correlation of WRKY TFs and PRGs was also performed to reveal the potential interaction networks among disease-resistance/pathogenesis-related genes and WRKY TFs. Expression profiling of nine genes annotated as TIFY, WRKY TF, and disease-resistance protein-related genes was performed using qRT-PCR, and the results were correlated with RNA-Seq data. This study provides valuable information on the molecular basis of pecan−Pestalotiopsis microspora interaction mechanisms and offers a repertoire of candidate genes related to pecan fruit response to FBS infection.
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Yadav K, Dwivedi S, Gupta S, Dubey AK, Singh VK, Tanveer A, Yadav S, Yadav D. Genome mining of Fusarium reveals structural and functional diversity of pectin lyases: a bioinformatics approach. 3 Biotech 2022; 12:261. [PMID: 36082361 PMCID: PMC9445148 DOI: 10.1007/s13205-022-03333-w] [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: 03/09/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Pectin lyase (PNL) is an important enzyme of the pectinases group which degrades pectin polymer to 4,5-unsaturated oligogalacturonides by a unique β-elimination mechanism and is used in several industries. The existence of multigene families of pectin lyases has been investigated by mining microbial genomes. In the present study, 52 pectin lyase genes were predicted from sequenced six species of Fusarium, namely F. fujikuroi, F. graminearum, F. proliferatum, F. oxysporum, F. verticillioides and F. virguliforme. These sequences were in silico characterized for several physico-chemical, structural and functional attributes. The translated PNL proteins showed variability with 344-1142 amino acid residues, 35.44-127.41 kDa molecular weight, and pI ranging from 4.63 to 9.28. The aliphatic index ranged from 75.33 to 84.75. Multiple sequence alignment analysis showed several conserved amino acid residues and five distinct groups marked as I, II, III, IV, and V were observed in the phylogenetic tree. The Three-dimensional Structure of five of these PNLs, each representing a distinct group of phylogenetic trees was predicted using I-TASSER Server and validated. The pectin lyase proteins of Fusarium species revealed close similarity with pectin lyase of Aspergillus niger PelA(1IDJ) and PelB(1QCX). Diversity in the structural motifs was observed among Fusarium species with 2 β-sheets, 1 β-hairpin, 7-12 β bulges, 18-25 strands, 6 -11 helices, 1 helix-helix interaction, 32-49 β turns, 2-6 γ turns and 2- 3 disulfide bonds. The unique Pec_lyase domain was uniformly observed among all PNL proteins confirming its identity. The genome-wide mining of Fusarium species was attempted to provide the diversity of PNL genes, which could be explored for diverse applications after performing cloning and expression studies. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03333-w.
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Affiliation(s)
- Kanchan Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Shruti Dwivedi
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Supriya Gupta
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Amit K. Dubey
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Vinay K. Singh
- Centre for Bioinformatics, School of Biotechnology, Banaras Hindu University, Varanasi, Uttar Pradesh 221005 India
| | - Aiman Tanveer
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Sangeeta Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
| | - Dinesh Yadav
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh 273009 India
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Sharma N, Sahoo D, Rai AK, Singh SP. A highly alkaline pectate lyase from the Himalayan hot spring metagenome and its bioscouring applications. Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Liu N, Wang P, Li X, Pei Y, Sun Y, Ma X, Ge X, Zhu Y, Li F, Hou Y. Long Non-Coding RNAs profiling in pathogenesis of Verticillium dahliae: New insights in the host-pathogen interaction. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 314:111098. [PMID: 34895536 DOI: 10.1016/j.plantsci.2021.111098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 09/29/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
Verticillium dahliae causes vascular wilt disease on cotton (Gossypium hirsutum), resulting in devastating yield loss worldwide. While little is known about the mechanism of long non-coding RNAs (lncRNAs), several lncRNAs have been implicated in numerous physiological processes and diseases. To better understand V. dahliae pathogenesis, lncRNA was conducted in a V. dahliae virulence model. Potential target genes of significantly regulated lncRNAs were predicted using cis/trans-regulatory algorithms. This study provides evidence for lncRNAs' regulatory role in pathogenesis-related genes. Interestingly, lncRNAs were identified and varying in terms of RNA length and nutrient starvation treatments. Efficient pathogen nutrition during the interaction with the host is a requisite factor during infection. Our observations directly link to mutated V. dahliae invasion, explaining infected cotton have lower pathogenicity and lethality compared to V. dahliae. Remarkably, lncRNAs XLOC_006536 and XLOC_000836 involved in the complex regulation of pathogenesis-related genes in V. dahliae were identified. For the first time the regulatory role of lncRNAs in filamentous fungi was uncovered, and it is our contention that elucidation of lncRNAs will advance our understanding in the development and pathogenesis of V. dahliae and offer alternatives in the control of the diseases caused by fungus V. dahliae attack.
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Affiliation(s)
- Nana Liu
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Ping Wang
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Xiancai Li
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Yakun Pei
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Yun Sun
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Xiaowen Ma
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, People's Republic of China
| | - Yutao Zhu
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, People's Republic of China.
| | - Yuxia Hou
- College of Science, China Agricultural University, No. 2 Yuanmingyuan West Road, Beijing, 100193, People's Republic of China.
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Anand G, Rajeshkumar KC. Challenges and Threats Posed by Plant Pathogenic Fungi on Agricultural Productivity and Economy. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Gene deletion and constitutive expression of the pectate lyase gene 1 (MoPL1) lead to diminished virulence of Magnaporthe oryzae. J Microbiol 2021; 60:79-88. [DOI: 10.1007/s12275-022-1074-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 08/20/2021] [Accepted: 09/27/2021] [Indexed: 01/06/2023]
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Amplification, sequencing and characterization of pectin methyl esterase inhibitor 51 gene in Tectona grandis L.f. Saudi J Biol Sci 2021; 28:5451-5460. [PMID: 34588855 PMCID: PMC8459126 DOI: 10.1016/j.sjbs.2021.07.015] [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: 04/09/2021] [Revised: 06/25/2021] [Accepted: 07/04/2021] [Indexed: 11/25/2022] Open
Abstract
Tectona grandis L.f. (Teak), a very important source of incomparable timber, withstands a wide range of tropical deciduous conditions. We achieved partial amplification of pectin methylesterase inhibitor 51 (PMEI) gene in teak by E. pilularis cinnamoyl Co-A reductase (CCR) gene specific primer. The amplified teak gene was of 750 bp, 79% identity and 97% query cover with PMEI of Sesamum indicum. The phylogenetic tree clustered the amplified gene with PMEI of database plant species, Erythranthe guttata and Sesamum indicum (87% bootstrap value). On conversion to amino acid sequence, the obtained protein comprised 237 amino acids. However, PMEI region spanned from 24 to 171 amino acids, 15.94 kDa molecular weight, 8.97 pI value and C697H1117N199O211S9 molecular formula with four conserved cysteine residues as disulfide bridges. 25.9 % protein residues were hydrophilic, 42.7% hydrophobic and 31.2% neutral. Teak 3D PMEI protein structure corresponded well with Arabidopsis thaliana and Actinidia deliciosa PMEIs. The gene maintains integrity of pectin component of middle lamella of primary cell wall and confers tolerance against various kinds of stresses. Teak conferred with overexpression of PMEI may secure a wide adaptability as well as luxuriant timber productivity and quality in adverse/ fluctuating/ scarce climatic and environmental conditions of tropical forests.
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20
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Rice RBH1 Encoding A Pectate Lyase is Critical for Apical Panicle Development. PLANTS 2021; 10:plants10020271. [PMID: 33573206 PMCID: PMC7912155 DOI: 10.3390/plants10020271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/09/2021] [Accepted: 01/11/2021] [Indexed: 12/12/2022]
Abstract
Panicle morphology is one of the main determinants of the rice yield. Panicle abortion, a typical panicle morphological defect results in yield reduction due to defective spikelet development. To further elucidate the molecular mechanism of panicle abortion in rice, a rice panicle bald head 1 (rbh1) mutant with transfer DNA (T-DNA) insertion showing severely aborted apical spikelets during panicle development was identified and characterized. The rbh1-1 mutant showed obviously altered cell morphology and structure in the degenerated spikelet. Molecular genetic studies revealed that RBH1 encodes a pectate lyase protein. Pectate lyase-specific activity of Rice panicle Bald Head 1 (RBH1) protein assay using polygalacturonic acid (PGA) as substrates illustrated that the enzyme retained a significant capacity to degrade PGA. In addition, immunohistochemical analysis showed that the degradation of pectin is inhibited in the rbh1-1 mutant. Further analysis revealed that a significant increase in reactive oxygen species (ROS) level was found in degenerated rbh1-1 spikelets. Taken together, our findings suggest that RBH1 is required for the formation of panicle and for preventing panicle abortion.
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21
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Ma ST, Lee CW, Liu WM. Synthesis of 4-thiol-furanosidic uronate via hydrothiolation reaction. RSC Adv 2021; 11:18409-18416. [PMID: 35480947 PMCID: PMC9033442 DOI: 10.1039/d1ra02110a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/05/2021] [Indexed: 11/25/2022] Open
Abstract
Uronic acids are not only important building blocks of polysaccharides and oligosaccharides but also are widely used in the food and pharmaceutical industries. Inspired by the structure of natural products, here, we disclosed base-mediated and radical-mediated hydrothiolation reactions for the preparation of thiol-contained uronates. In comparison with base-mediated reaction, radical-mediated hydrothiolation is inefficient due to the electron-withdrawing group on the ethylene group; nevertheless, the adduct had excellent stereoselectivity at both C-4 and C-5 positions. For the alkaline approach, thiols as nucleophiles can regioselectively and stereoselectively attach to the C-4 position of Δ-4,5-unsaturated uronate with moderate to good yields. However, poor stereoselectivity at the C-5 position was observed due to retro thiol-Michael addition. After removing the protecting group of the thiol, the thiol adduct was isomerized to the furanosidic form and the 4-thiol-furanosidic uronate derivative was synthesized for the first time. Uronic acids are not only important building blocks of bioactive molecules but also are widely used in the food and pharmaceutical industries. Its derivative, 4-thiol-furanosidic uronate was successfully synthesized and firstly reported here.![]()
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Affiliation(s)
- Shih-Ting Ma
- Department of Chemistry
- Fu Jen Catholic University
- New Taipei City 24205
- Republic of China
| | - Chia-Wei Lee
- Department of Chemistry
- Fu Jen Catholic University
- New Taipei City 24205
- Republic of China
| | - Wei-Min Liu
- Department of Chemistry
- Fu Jen Catholic University
- New Taipei City 24205
- Republic of China
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22
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23
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Thilini Chethana KW, Peng J, Li X, Xing Q, Liu M, Zhang W, Hyde KD, Zhao W, Yan J. LtEPG1, a Secretory Endopolygalacturonase Protein, Regulates the Virulence of Lasiodiplodia theobromae in Vitis vinifera and Is Recognized as a Microbe-Associated Molecular Patterns. PHYTOPATHOLOGY 2020; 110:1727-1736. [PMID: 32460690 DOI: 10.1094/phyto-04-20-0118-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Lasiodiplodia theobromae genome encodes numerous glycoside hydrolases involved in organic matter degradation and conducive to pathogen infection, whereas their molecular mechanisms are still largely unknown. Here, we identified the glycoside hydrolase family 28 endopolygalacturonase LtEPG1 in L. theobromae and characterized its function in detail. LtEPG1 acts as a virulence factor during L. theobromae infection. Overexpression and silencing of LtEPG1 in L. theobromae led to significantly increased and decreased lesion areas, respectively. Further, the high transcript level of LtEPG1 during the infection process supported its virulence function. Polygalacturonase activity of LtEPG1 was substantiated by detecting its ability to degrade pectin. Furthermore, LtEPG1 functioned as microbe-associated molecular patterns during the infection process. Both transient expression of LtEPG1 in planta and infiltration of purified LtEPG1 triggered cell death in Nicotiana benthamiana. Site-directed mutation of LtEPG1 indicated that the enzymatic activity of LtEPG1 is independent from its elicitor activity. A protein kinase, KINβ1, was shown to interact in the yeast two-hybrid system with LtEPG1. This interaction was further confirmed in vitro using a pull-down assay. Our data indicate that LtEPG1 functions as a polygalacturonase and also serves as an elicitor with two independent mechanisms. Moreover, LtEPG1 may be able to manipulate host immune responses by regulating the KINβ1-mediated signal pathway and consequently promote its own successful infection and symptom development.
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Affiliation(s)
- K W Thilini Chethana
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- College of Plant Protection, China Agricultural University, Beijing 100097, China
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Junbo Peng
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xinghong Li
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Qikai Xing
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Mei Liu
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Wei Zhang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Kevin D Hyde
- Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Wensheng Zhao
- College of Plant Protection, China Agricultural University, Beijing 100097, China
| | - Jiye Yan
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Zeuner B, Thomsen TB, Stringer MA, Krogh KBRM, Meyer AS, Holck J. Comparative Characterization of Aspergillus Pectin Lyases by Discriminative Substrate Degradation Profiling. Front Bioeng Biotechnol 2020; 8:873. [PMID: 32850731 PMCID: PMC7406575 DOI: 10.3389/fbioe.2020.00873] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 07/07/2020] [Indexed: 11/13/2022] Open
Abstract
Fungal genomes often contain several copies of genes that encode carbohydrate active enzymes having similar activity. The copies usually have slight sequence variability, and it has been suggested that the multigenecity represents distinct reaction optima versions of the enzyme. Whether the copies represent differences in substrate attack proficiencies of the enzyme have rarely been considered. The genomes of Aspergillus species encode several pectin lyases (EC 4.2.2.10), which all belong to polysaccharide lyase subfamily PL1_4 in the CAZy database. The enzymes differ in terms of sequence identity and phylogeny, and exhibit structural differences near the active site in their homology models. These enzymes catalyze pectin degradation via eliminative cleavage of the α-(1,4) glycosidic linkages in homogalacturonan with a preference for linkages between methyl-esterified galacturonate residues. This study examines four different pectin lyases (PelB, PelC, PelD, and PelF) encoded by the same Aspergillus sp. (namely A. luchuensis), and further compares two PelA pectin lyases from two related Aspergillus spp. (A. aculeatus and A. tubingensis). We report the phylogeny, enzyme kinetics, and enzymatic degradation profiles of the enzymes' action on apple pectin, citrus pectin, and sugar beet pectin. All the pectin lyases exerted highest reaction rate on apple pectin [degree of methoxylation (DM) 69%, degree of acetylation (DAc) 2%] and lowest reaction rate on sugar beet pectin (DM 56%, DAc 19%). Activity comparison at pH 5-5.5 produced the following ranking: PelB > PelA > PelD > PelF > PelC. The evolution of homogalacturonan-oligomer product profiles during reaction was analyzed by liquid chromatography with mass spectrometry (LC-MS) detection. This analyses revealed subtle differences in the product profiles indicating distinct substrate degradation preferences amongst the enzymes, notably with regard to acetyl substitutions. The LC-MS product profiling analysis thus disclosed that the multigenecity appears to provide the fungus with additional substrate degradation versatility. This product profiling furthermore represents a novel approach to functionally compare pectin-degrading enzymes, which can help explain structure-function relations and reaction properties of disparate copies of carbohydrate active enzymes. A better understanding of the product profiles generated by pectin modifying enzymes has significant implications for targeted pectin modification in food and biorefinery processes.
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Affiliation(s)
- Birgitte Zeuner
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Thore Bach Thomsen
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | | | - Anne S Meyer
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Jesper Holck
- Protein Chemistry and Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
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Roy A, Jayaprakash A, Rajeswary T R, Annamalai A, Lakshmi PTV. Genome-wide annotation, comparison and functional genomics of carbohydrate-active enzymes in legumes infecting Fusarium oxysporum formae speciales. Mycology 2020; 11:56-70. [PMID: 32128282 PMCID: PMC7033727 DOI: 10.1080/21501203.2019.1706656] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 11/25/2019] [Indexed: 11/01/2022] Open
Abstract
Fusarium wilt caused by soil borne ascomycetes fungi Fusarium oxysporum which has host-specific forms known as formae speciales (ff. spp.), apparently requires plant cell wall degrading enzymes (PCWDE) for successful invasion. In this study, 12 F. oxysporum ff. spp. were taken for genome-wide annotation and comparative analysis of CAZymes, with an assessment of secretory PCWDE and orthologues identification in the three legumes infecting ff. spp. Further, transcriptomic analysis in two legumes infecting ff. spp. using publically available data was also done. The comparative studies showed Glycoside hydrolase (GH) families to be abundant and Principle Component Analysis (PCA) formed two distinct clusters of ff. spp. based on the CAZymes modules and families. Nearly half of the CAZymes in the legumes infecting ff. spp. coded for signal peptides. The orthologue clusters of secretory CAZymes common in all the three legume infecting ff. spp. mostly belonged to families of AA9, GH28, CE5 and PL1 and the expression analysis revealed the abundant PCWDE were differentially expressed in these legumes infecting ff. spp. Therefore, this study gave an insight into the distribution of CAZymes especially extracellular PCWDE in legumes infecting ff. spp. with further shedding light onto some of the key PCWDE families through differential expression analysis.
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Affiliation(s)
- Abhijeet Roy
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Aiswarya Jayaprakash
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - Raja Rajeswary T
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
| | - A. Annamalai
- PG and Research Department of Botany, Arignar Anna Government Arts College, Villupuram, India
| | - PTV Lakshmi
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Puducherry, India
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Knollenberg BJ, Li GX, Lambert JD, Maximova SN, Guiltinan MJ. Clovamide, a Hydroxycinnamic Acid Amide, Is a Resistance Factor Against Phytophthora spp. in Theobroma cacao. FRONTIERS IN PLANT SCIENCE 2020; 11:617520. [PMID: 33424909 PMCID: PMC7786005 DOI: 10.3389/fpls.2020.617520] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/04/2020] [Indexed: 05/13/2023]
Abstract
The hydroxycinnamic acid amides (HCAAs) are a diverse group of plant-specialized phenylpropanoid metabolites distributed widely in the plant kingdom and are known to be involved in tolerance to abiotic and biotic stress. The HCAA clovamide is reported in a small number of distantly related species. To explore the contribution of specialized metabolites to disease resistance in cacao (Theobroma cacao L., chocolate tree), we performed untargeted metabolomics using liquid chromatography - tandem mass spectrometry (LC-MS/MS) and compared the basal metabolite profiles in leaves of two cacao genotypes with contrasting levels of susceptibility to Phytophthora spp. Leaves of the tolerant genotype 'Scavina 6' ('Sca6') were found to accumulate dramatically higher levels of clovamide and several other HCAAs compared to the susceptible 'Imperial College Selection 1' ('ICS1'). Clovamide was the most abundant metabolite in 'Sca6' leaf extracts based on MS signal, and was up to 58-fold higher in 'Sca6' than in 'ICS1'. In vitro assays demonstrated that clovamide inhibits growth of three pathogens of cacao in the genus Phytophthora, is a substrate for cacao polyphenol oxidase, and is a contributor to enzymatic browning. Furthermore, clovamide inhibited proteinase and pectinase in vitro, activities associated with defense in plant-pathogen interactions. Fruit epidermal peels from both genotypes contained substantial amounts of clovamide, but two sulfated HCAAs were present at high abundance exclusively in 'Sca6' suggesting a potential functional role of these compounds. The potential to breed cacao with increased HCAAs for improved agricultural performance is discussed.
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Affiliation(s)
- Benjamin J. Knollenberg
- Plant Biology PhD Program ‐ Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
- Department of Plant Sciences, Pennsylvania State University, University Park, PA, United States
| | - Guo-Xing Li
- Department of Chemistry, Pennsylvania State University, University Park, PA, United States
| | - Joshua D. Lambert
- Department of Food Science, Pennsylvania State University, University Park, PA, United States
| | - Siela N. Maximova
- Department of Plant Sciences, Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Mark J. Guiltinan
- Department of Plant Sciences, Pennsylvania State University, University Park, PA, United States
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
- *Correspondence: Mark J. Guiltinan,
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27
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Kanungo A, Bag BP. Structural insights into the molecular mechanisms of pectinolytic enzymes. ACTA ACUST UNITED AC 2019. [DOI: 10.1007/s42485-019-00027-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Uluisik S, Seymour GB. Pectate lyases: Their role in plants and importance in fruit ripening. Food Chem 2019; 309:125559. [PMID: 31679850 DOI: 10.1016/j.foodchem.2019.125559] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 09/12/2019] [Accepted: 09/16/2019] [Indexed: 11/25/2022]
Abstract
Plant cell walls are complex structures that are modified throughout development. They are a major contributor to the properties of plant structure and act as barriers against pathogens. The primary cell walls of plants are composed of polysaccharides and proteins. The polysaccharide fraction is divided into components cellulose, hemicelluloses and pectin, are all modified during fruit ripening. Pectin plays an important role in intercellular adhesion and controlling the porosity of the wall. A large number of pectin degrading enzymes have been characterised from plants and they are involved in numerous aspects of plant development. The role of pectate lyases in plant development has received little attention, probably because they are normally associated with the action of plant pathogenic organisms. However their importance in plant development and ripening is now becoming well established and new information about the role of pectate lyases in plant development forms the focus of this review.
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Affiliation(s)
- Selman Uluisik
- Burdur Mehmet Akif Ersoy University, Burdur Food Agriculture and Livestock Vocational School, 15030 Burdur, Turkey.
| | - Graham B Seymour
- Nottinham University, Division of Plant and Crop Sciences, University of Nottingham, Sutton Bonington, Loughborough LE12, UK.
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Wang Z, Xu B, Luo H, Meng K, Wang Y, Liu M, Bai Y, Yao B, Tu T. Production pectin oligosaccharides using Humicola insolens Y1-derived unusual pectate lyase. J Biosci Bioeng 2019; 129:16-22. [PMID: 31400994 DOI: 10.1016/j.jbiosc.2019.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/01/2019] [Accepted: 07/22/2019] [Indexed: 12/27/2022]
Abstract
The economical production of pectin oligosaccharides with a specific degree of polymerization and structure from agro-food waste is an industrially important process. This study identified a novel pectate lyase gene (plhy1) from the thermophilic cellulolytic fungus H. insolens Y1 and tested its ability to produce pectin oligosaccharides. The recombinant PLHY1 produced in Pichia pastoris was superior to other similar enzymes due to its high thermal and pH stability. PLHY1 demonstrated optimal enzymatic activity at 55°C and pH 10.0 in the presence of 0.4 mM Ca2+, and preferred methyl esterified substrates for digestion. High performance anion exchange chromatography-pulsed amperometric detector and ultra high performance liquid chromatography in combination with electrospray ionization tandem mass spectrometry analysis showed that galacturonic acid-oligosaccharides with a small degree of polymerization (4-6) were the major hydrolysates produced by the degradation of apple peel pectin by PLHY1. The properties of PLHY1 make it valuable for application in the agro-food industry for the production of pectin oligosaccharides.
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Affiliation(s)
- Zhiyun Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China; College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang 330100, PR China
| | - Bo Xu
- College of Biological Sciences and Engineering, Jiangxi Agricultural University, Nanchang 330100, PR China
| | - Huiying Luo
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Kun Meng
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yuan Wang
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Mengting Liu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Yingguo Bai
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Bin Yao
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China
| | - Tao Tu
- Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, PR China.
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Kumar V, Hainaut M, Delhomme N, Mannapperuma C, Immerzeel P, Street NR, Henrissat B, Mellerowicz EJ. Poplar carbohydrate-active enzymes: whole-genome annotation and functional analyses based on RNA expression data. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:589-609. [PMID: 31111606 PMCID: PMC6852159 DOI: 10.1111/tpj.14417] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/06/2019] [Accepted: 05/13/2019] [Indexed: 05/20/2023]
Abstract
Carbohydrate-active enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key enzymes for the biosynthesis of food and renewable biomass. Woody biomass is particularly important for long-term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents a re-annotation of CAZyme genes in the current Populus trichocarpa genome assembly and in silico functional characterization, based on high-resolution RNA-Seq data sets. Altogether, 1914 CAZyme and expansin genes were annotated in 101 families. About 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in the biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and Arabidopsis thaliana (with the exception of CBM13 found only in poplar), a few families had significantly different copy numbers between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co-expression network analysis of CAZymes in wood-forming tissues using the AspWood database (http://aspwood.popgenie.org/aspwood-v3.0/) for Populus tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and the clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue-specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for the modification of secondary cell wall biosynthesis and other developmental processes in woody plants.
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Affiliation(s)
- Vikash Kumar
- Umeå Plant Science CenterDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSweden
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Aix‐Marseille UniversityMarseilleFrance
- INRAUSC 1408 AFMBMarseilleFrance
| | - Nicolas Delhomme
- Umeå Plant Science CenterDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSweden
| | | | - Peter Immerzeel
- Umeå Plant Science CenterDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSweden
- Chemical EngineeringKarlstad UniversityKarlstad65188Sweden
| | - Nathaniel R. Street
- Umeå Plant Science CenterPlant Physiology DepartmentUmeå UniversityUmeåSweden
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules BiologiquesCentre National de la Recherche Scientifique (CNRS)Aix‐Marseille UniversityMarseilleFrance
- INRAUSC 1408 AFMBMarseilleFrance
| | - Ewa J. Mellerowicz
- Umeå Plant Science CenterDepartment of Forest Genetics and Plant PhysiologySwedish University of Agricultural SciencesUmeaSweden
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31
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Yuan Y, Zhang XY, Zhao Y, Zhang H, Zhou YF, Gao J. A Novel PL9 Pectate Lyase from Paenibacillus polymyxa KF-1: Cloning, Expression, and Its Application in Pectin Degradation. Int J Mol Sci 2019; 20:E3060. [PMID: 31234557 PMCID: PMC6627557 DOI: 10.3390/ijms20123060] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 12/27/2022] Open
Abstract
Pectate lyases play an important role in pectin degradation, and therefore are highly useful in the food and textile industries. Here, we report on the cloning of an alkaline pectate lyase gene (pppel9a) from Paenibacillus polymyxa KF-1. The full-length gene (1350 bp) encodes for a 449-residue protein that belongs to the polysaccharide lyase family 9 (PL9). Recombinant PpPel9a produced in Escherichia coli was purified to electrophoretic homogeneity in a single step using Ni2+-NTA affinity chromatography. The enzyme activity of PpPel9a (apparent molecular weight of 45.3 kDa) was found to be optimal at pH 10.0 and 40 °C, with substrate preference for homogalacturonan type (HG) pectins vis-à-vis rhamnogalacturonan-I (RG-I) type pectins. Using HG-type pectins as substrate, PpPel9a showed greater activity with de-esterified HGs. In addition, PpPel9a was active against water-soluble pectins isolated from different plants. Using this lyase, we degraded citrus pectin, purified fractions using Diethylaminoethyl (DEAE)-sepharose column chromatography, and characterized the main fraction MCP-0.3. High-performance gel permeation chromatography (HPGPC) analysis showed that the molecular mass of citrus pectin (~230.2 kDa) was reduced to ~24 kDa upon degradation. Ultra-performance liquid chromatography - tandem mass spectrometer (UPLC-MS) and monosaccharide composition analyses demonstrated that PpPel9a worked as an endo-pectate lyase, which acted primarily on the HG domain of citrus pectin. In vitro testing showed that the degradation product MCP-0.3 significantly promotes the growth of Lactobacillus plantarum and L. rhamnosus. In this regard, the enzyme has potential in the preparation of pharmacologically active pectin products.
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Affiliation(s)
- Ye Yuan
- School of Life Sciences, Northeast Normal University, Changchun 130024, China.
| | - Xin-Yu Zhang
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China.
| | - Yan Zhao
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China.
| | - Han Zhang
- School of Life Sciences, Northeast Normal University, Changchun 130024, China.
| | - Yi-Fa Zhou
- School of Life Sciences, Northeast Normal University, Changchun 130024, China.
| | - Juan Gao
- School of Life Sciences, Northeast Normal University, Changchun 130024, China.
- School of Biological Science and Technology, University of Jinan, Jinan 250022, China.
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32
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Comparative study of Fourier transform infrared spectroscopy (FTIR) analysis of natural fibres treated with chemical, physical and biological methods. Polym Bull (Berl) 2019. [DOI: 10.1007/s00289-019-02824-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Tang Y, Wu P, Jiang S, Selvaraj JN, Yang S, Zhang G. A new cold-active and alkaline pectate lyase from Antarctic bacterium with high catalytic efficiency. Appl Microbiol Biotechnol 2019; 103:5231-5241. [PMID: 31028436 DOI: 10.1007/s00253-019-09803-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 10/26/2022]
Abstract
Cold-active enzymes have become attractive biocatalysts in biotechnological applications for their ability to retain high catalytic activity below 30 °C, which allows energy reduction and cost saving. Here, a 1041 bp gene pel1 encoding a 34.7 KDa pectate lyase was cloned from a facultatively psychrophilic Antarctic bacterium Massilia eurypsychrophila and heterologously expressed in Escherichia coli. PEL1 presented the highest 66% identity to the reported mesophilic pectate lyase PLXc. The purified PEL1 exhibits the optimum temperature and pH of 30 °C and 10 toward polygalacturonic acid, respectively. PEL1 is a cold-active enzyme that can retain 60% and 25% relative activity at 10 °C and 0 °C, respectively, while it loses most of activity at 40 °C for 10 min. PEL1 has the highest specific activity (78.75 U mg-1) than all other reported cold-active pectinase, making it a better choice for use in industry. Based on the detailed sequence and structure comparison between PEL1 and PLXc and mutation analysis, more flexible structure and some loop regions may contribute to the cold activity and thermal instability of PEL1. Our investigations of the cold-active mechanism of PEL1 might guide the rational design of PEL1 and other related enzymes.
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Affiliation(s)
- Yumeng Tang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Pan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Sijing Jiang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jonathan Nimal Selvaraj
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Guimin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China.
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Herburger K, Xin A, Holzinger A. Homogalacturonan Accumulation in Cell Walls of the Green Alga Zygnema sp. (Charophyta) Increases Desiccation Resistance. FRONTIERS IN PLANT SCIENCE 2019; 10:540. [PMID: 31105732 PMCID: PMC6494968 DOI: 10.3389/fpls.2019.00540] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 04/09/2019] [Indexed: 05/13/2023]
Abstract
Land plants inherited several traits from their green algal ancestors (Zygnematophyceae), including a polysaccharide-rich cell wall, which is a prerequisite for terrestrial survival. A major component of both land plant and Zygnematophyceaen cell walls is the pectin homogalacturonan (HG), and its high water holding capacity may have helped algae to colonize terrestrial habitats, characterized by water scarcity. To test this, HG was removed from the cell walls of Zygnema filaments by pectate lyase (PL), and their effective quantum yield of photosystem II (YII) as a proxy for photosynthetic performance was measured in response to desiccation stress by pulse amplitude modulation (PAM). Old filaments were found to contain more HG and are more resistant against desiccation stress but relatively lose more desiccation resistance after HG removal than young filaments. After rehydration, the photosynthetic performance recovered less efficiently in filaments with a HG content reduced by PL, independently of filament age. Immunolabeling showed that partial or un-methylesterified HG occurs throughout the longitudinal cell walls of both young and old filaments, while no labeling signal occurred when filaments were treated with PL prior labeling. This confirmed that most HG can be removed from the cell walls by PL. The initial labeling pattern was restored after ~3 days. A different form of methylesterified HG was restricted to cell poles and cross cell walls. In conclusion, it was shown that the accumulation of HG in Zygnema filaments increases their resistance against desiccation stress. This trait might have played an important role during the colonization of land by Zygnematophyceae, which founded the evolution of all land plants.
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Affiliation(s)
- Klaus Herburger
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- Functional Plant Biology, Department of Botany, University of Innsbruck, Innsbruck, Austria
| | - Anzhou Xin
- The Edinburgh Cell Wall Group, Institute of Molecular Plant Sciences, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
| | - Andreas Holzinger
- Functional Plant Biology, Department of Botany, University of Innsbruck, Innsbruck, Austria
- *Correspondence: Andreas Holzinger,
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35
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Yu S, Shen H, Cheng Y, Zhu Y, Li X, Mu W. Structural and Functional Basis of Difructose Anhydride III Hydrolase, Which Sequentially Converts Inulin Using the Same Catalytic Residue. ACS Catal 2018. [DOI: 10.1021/acscatal.8b02424] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shuhuai Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Hui Shen
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yuanyuan Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
| | - Xu Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi, Jiangsu 214122, China
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36
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SAXS and homology modelling based structure characterization of pectin methylesterase a family 8 carbohydrate esterase from Clostridium thermocellum ATCC 27405. Arch Biochem Biophys 2018; 641:39-49. [DOI: 10.1016/j.abb.2018.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/12/2018] [Accepted: 01/23/2018] [Indexed: 11/17/2022]
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37
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Liu MQ, Huo WK, Dai X, Dang YH. Preparation of low-molecular-weight citrus pectin by recombinant Bacillus subtilis pectate lyase and promotion of growth of Bifidobacterium longum. CATAL COMMUN 2018. [DOI: 10.1016/j.catcom.2018.01.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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Yang Y, Yu Y, Liang Y, Anderson CT, Cao J. A Profusion of Molecular Scissors for Pectins: Classification, Expression, and Functions of Plant Polygalacturonases. FRONTIERS IN PLANT SCIENCE 2018; 9:1208. [PMID: 30154820 PMCID: PMC6102391 DOI: 10.3389/fpls.2018.01208] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 07/27/2018] [Indexed: 05/21/2023]
Abstract
In plants, the construction, differentiation, maturation, and degradation of the cell wall are essential for development. Pectins, which are major constituents of primary cell walls in eudicots, function in multiple developmental processes through their synthesis, modification, and degradation. Several pectin modifying enzymes regulate pectin degradation via different modes of action. Polygalacturonases (PGs), which function in the last step of pectin degradation, are a crucial class of pectin-modifying enzymes. Based on differences in their hydrolyzing activities, PGs can be divided into three main types: exo-PGs, endo-PGs, and rhamno-PGs. Their functions were initially investigated based on the expression patterns of PG genes and measurements of total PG activity in organs. In most plant species, PGs are encoded by a large, multigene family. However, due to the lack of genome sequencing data in early studies, the number of identified PG genes was initially limited. Little was initially known about the evolution and expression patterns of PG family members in different species. Furthermore, the functions of PGs in cell dynamics and developmental processes, as well as the regulatory pathways that govern these functions, are far from fully understood. In this review, we focus on how recent studies have begun to fill in these blanks. On the basis of identified PG family members in multiple species, we review their structural characteristics, classification, and molecular evolution in terms of plant phylogenetics. We also highlight the diverse expression patterns and biological functions of PGs during various developmental processes, as well as their mechanisms of action in cell dynamic processes. How PG functions are potentially regulated by hormones, transcription factors, environmental factors, pH and Ca2+ is discussed, indicating directions for future research into PG function and regulation.
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Affiliation(s)
- Yang Yang
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture – Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Youjian Yu
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Department of Horticulture, College of Agriculture and Food Science, Zhejiang A & F University, Hangzhou, China
| | - Ying Liang
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture – Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
| | - Charles T. Anderson
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, PA, United States
- Center for Lignocellulose Structure and Formation, The Pennsylvania State University, University Park, Pennsylvania, PA, United States
| | - Jiashu Cao
- Laboratory of Cell and Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture – Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, China
- *Correspondence: Jiashu Cao,
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Shanmugam G, Jeon J. Computer-Aided Drug Discovery in Plant Pathology. THE PLANT PATHOLOGY JOURNAL 2017; 33:529-542. [PMID: 29238276 PMCID: PMC5720600 DOI: 10.5423/ppj.rw.04.2017.0084] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 05/31/2023]
Abstract
Control of plant diseases is largely dependent on use of agrochemicals. However, there are widening gaps between our knowledge on plant diseases gained from genetic/mechanistic studies and rapid translation of the knowledge into target-oriented development of effective agrochemicals. Here we propose that the time is ripe for computer-aided drug discovery/design (CADD) in molecular plant pathology. CADD has played a pivotal role in development of medically important molecules over the last three decades. Now, explosive increase in information on genome sequences and three dimensional structures of biological molecules, in combination with advances in computational and informational technologies, opens up exciting possibilities for application of CADD in discovery and development of agrochemicals. In this review, we outline two categories of the drug discovery strategies: structure- and ligand-based CADD, and relevant computational approaches that are being employed in modern drug discovery. In order to help readers to dive into CADD, we explain concepts of homology modelling, molecular docking, virtual screening, and de novo ligand design in structure-based CADD, and pharmacophore modelling, ligand-based virtual screening, quantitative structure activity relationship modelling and de novo ligand design for ligand-based CADD. We also provide the important resources available to carry out CADD. Finally, we present a case study showing how CADD approach can be implemented in reality for identification of potent chemical compounds against the important plant pathogens, Pseudomonas syringae and Colletotrichum gloeosporioides.
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Affiliation(s)
| | - Junhyun Jeon
- Corresponding author. Phone) +82-53-810-3030, FAX) +82-53-810-4769, E-mail)
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Lara-Márquez A, Oyama K, Zavala-Páramo MG, Villa-Rivera MG, Conejo-Saucedo U, Cano-Camacho H. Evolutionary Analysis of Pectin Lyases of the Genus Colletotrichum. J Mol Evol 2017; 85:120-136. [PMID: 29071357 DOI: 10.1007/s00239-017-9812-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/11/2017] [Indexed: 10/18/2022]
Abstract
Pectin lyases (PNLs) are important enzymes that are involved in plant cell wall degradation during the infection process. Colletotrichum is a diverse genus of fungi, which allows the study of the evolution of PNLs and their possible role in pathogen-host interactions and lifestyle adaptations. The phylogenetic reconstruction of PNLs from Colletotrichum and analysis of selection pressures showed the formation of protein lineages by groups of species with different selection pressures and specific patterns. The analysis of positive selection at individual sites using different methods allowed for the identification of three codons with evidence of positive selection in the oligosaccharide-binding region and two codons on the antiparallel sheet, which may influence the interaction with the substrate. Seven codons on the surface of the protein, mainly in the peripheral helices of the PNLs, could have an important function in evasion of plant defenses, as has been proposed in other enzymes. According to our results, it is possible that events of genetic duplication occurred in ancestral lines, followed by episodes of genetic diversification and gene loss, probably influenced by differences in the composition of the host cell wall. Additionally, different patterns of evolution in Colletotrichum appear to be molded by a strong purifying selection and positive selection episodes that forged the observed evolutionary patterns, possibly influenced by host interaction or substrate specificity. This work represents a starting point for the study of sites that may be important for evasion of plant defenses and biotechnological purposes.
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Affiliation(s)
- Alicia Lara-Márquez
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Morelia, Michoacán, México
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Morelia, Michoacán, México
| | - María G Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Maria G Villa-Rivera
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Ulises Conejo-Saucedo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México.
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Sarrocco S, Matarese F, Baroncelli R, Vannacci G, Seidl-Seiboth V, Kubicek CP, Vergara M. The Constitutive Endopolygalacturonase TvPG2 Regulates the Induction of Plant Systemic Resistance by Trichoderma virens. PHYTOPATHOLOGY 2017; 107:537-544. [PMID: 28095207 DOI: 10.1094/phyto-03-16-0139-r] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Trichoderma spp. are opportunistic fungi some of which are commonly present in the rhizosphere. Several species, such as T. virens, are also efficient biocontrol agents against phytopathogenic fungi and exert beneficial effects on plants. These effects are the consequence of interactions between Trichoderma and plant roots, which trigger enhanced plant growth and induce plant resistance. We have previously shown that T. virens I10 expresses two endopolygalacturonase genes, tvpg1 and tvpg2, during the interaction with plant roots; tvpg1 is inducible while tvpg2 is constitutively transcribed. Using the same system, the tomato polygalacturonase-inhibitor gene Lepgip1 was induced at the same time as tvpg1. Here we show by gene disruption that TvPG2 performs a regulatory role on the inducible tvpg1 gene and in triggering the plant immune response. A tvpg2-knockout strain fails to transcribe the inducible tvpg1 gene in neither in vitro in inducing media containing pectin or plant cell walls, nor during the in vivo interaction with tomato roots. Likewise, the in vivo induction of Lepgip1 does not occur, and its defense against the pathogen Botrytis cinerea is significantly reduced. Our data prove the importance of a T. virens constitutively produced endopolygalacturonase in eliciting plant induced systemic resistance against pathogenic fungi.
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Affiliation(s)
- Sabrina Sarrocco
- First, second, third, fourth, and seventh authors: Department of Agriculture, Food and Environment, University of Pisa, Italy, via del Borghetto 80, 56124 Pisa, Italy; fifth and sixth authors: Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria; and seventh author: Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Fabiola Matarese
- First, second, third, fourth, and seventh authors: Department of Agriculture, Food and Environment, University of Pisa, Italy, via del Borghetto 80, 56124 Pisa, Italy; fifth and sixth authors: Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria; and seventh author: Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Riccardo Baroncelli
- First, second, third, fourth, and seventh authors: Department of Agriculture, Food and Environment, University of Pisa, Italy, via del Borghetto 80, 56124 Pisa, Italy; fifth and sixth authors: Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria; and seventh author: Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Giovanni Vannacci
- First, second, third, fourth, and seventh authors: Department of Agriculture, Food and Environment, University of Pisa, Italy, via del Borghetto 80, 56124 Pisa, Italy; fifth and sixth authors: Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria; and seventh author: Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Verena Seidl-Seiboth
- First, second, third, fourth, and seventh authors: Department of Agriculture, Food and Environment, University of Pisa, Italy, via del Borghetto 80, 56124 Pisa, Italy; fifth and sixth authors: Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria; and seventh author: Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Christian Peter Kubicek
- First, second, third, fourth, and seventh authors: Department of Agriculture, Food and Environment, University of Pisa, Italy, via del Borghetto 80, 56124 Pisa, Italy; fifth and sixth authors: Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria; and seventh author: Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
| | - Mariarosaria Vergara
- First, second, third, fourth, and seventh authors: Department of Agriculture, Food and Environment, University of Pisa, Italy, via del Borghetto 80, 56124 Pisa, Italy; fifth and sixth authors: Research Area Biotechnology and Microbiology, Institute of Chemical Engineering, TU Wien, 1060 Vienna, Austria; and seventh author: Scuola Normale Superiore di Pisa, piazza dei Cavalieri 7, 56126 Pisa, Italy
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Protein homology modeling, docking, and phylogenetic analyses of an endo-1,4-β-xylanase GH11 of Colletotrichum lindemuthianum. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1291-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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44
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Liu CQ, Hu KD, Li TT, Yang Y, Yang F, Li YH, Liu HP, Chen XY, Zhang H. Polygalacturonase gene pgxB in Aspergillus niger is a virulence factor in apple fruit. PLoS One 2017; 12:e0173277. [PMID: 28257463 PMCID: PMC5336277 DOI: 10.1371/journal.pone.0173277] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/17/2017] [Indexed: 02/03/2023] Open
Abstract
Aspergillus niger, a saprophytic fungus, is widely distributed in soil, air and cereals, and can cause postharvest diseases in fruit. Polygalacturonase (PG) is one of the main enzymes in fungal pathogens to degrade plant cell wall. To evaluate whether the deletion of an exo-polygalacturonase gene pgxB would influence fungal pathogenicity to fruit, pgxB gene was deleted in Aspergillus niger MA 70.15 (wild type) via homologous recombination. The ΔpgxB mutant showed similar growth behavior compared with the wild type. Pectin medium induced significant higher expression of all pectinase genes in both wild type and ΔpgxB in comparison to potato dextrose agar medium. However, the ΔpgxB mutant was less virulent on apple fruits as the necrosis diameter caused by ΔpgxB mutant was significantly smaller than that of wild type. Results of quantitive-PCR showed that, in the process of infection in apple fruit, gene expressions of polygalacturonase genes pgaI, pgaII, pgaA, pgaC, pgaD and pgaE were enhanced in ΔpgxB mutant in comparison to wild type. These results prove that, despite the increased gene expression of other polygalacturonase genes in ΔpgxB mutant, the lack of pgxB gene significantly reduced the virulence of A. niger on apple fruit, suggesting that pgxB plays an important role in the infection process on the apple fruit.
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Affiliation(s)
- Cheng-Qian Liu
- School of Food Science and Engineering, Hefei University of Technology, Hefei, China
| | - Kang-Di Hu
- School of Food Science and Engineering, Hefei University of Technology, Hefei, China
| | - Ting-Ting Li
- School of Food Science and Engineering, Hefei University of Technology, Hefei, China
| | - Ying Yang
- College of Environment and Energy Engineering, Anhui Jianzhu University, Hefei, China
| | - Feng Yang
- Xuzhou Institute of Agricultural Sciences of the Xuhuai District of Jiangsu Province, Xuzhou, China
| | - Yan-Hong Li
- School of Food Science and Engineering, Hefei University of Technology, Hefei, China
- Anhui Siping Food Development Co. Ltd., Tongling, China
| | - He-Ping Liu
- Anhui Siping Food Development Co. Ltd., Tongling, China
| | - Xiao-Yan Chen
- School of Food Science and Engineering, Hefei University of Technology, Hefei, China
| | - Hua Zhang
- School of Food Science and Engineering, Hefei University of Technology, Hefei, China
- * E-mail:
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45
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Zhou C, Xue Y, Ma Y. Characterization and overproduction of a thermo-alkaline pectate lyase from alkaliphilic Bacillus licheniformis with potential in ramie degumming. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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46
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Lionetti V, Fabri E, De Caroli M, Hansen AR, Willats WGT, Piro G, Bellincampi D. Three Pectin Methylesterase Inhibitors Protect Cell Wall Integrity for Arabidopsis Immunity to Botrytis. PLANT PHYSIOLOGY 2017; 173:1844-1863. [PMID: 28082716 PMCID: PMC5338656 DOI: 10.1104/pp.16.01185] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 01/11/2017] [Indexed: 05/18/2023]
Abstract
Infection by necrotrophs is a complex process that starts with the breakdown of the cell wall (CW) matrix initiated by CW-degrading enzymes and results in an extensive tissue maceration. Plants exploit induced defense mechanisms based on biochemical modification of the CW components to protect themselves from enzymatic degradation. The pectin matrix is the main CW target of Botrytis cinerea, and pectin methylesterification status is strongly altered in response to infection. The methylesterification of pectin is controlled mainly by pectin methylesterases (PMEs), whose activity is posttranscriptionally regulated by endogenous protein inhibitors (PMEIs). Here, AtPMEI10, AtPMEI11, and AtPMEI12 are identified as functional PMEIs induced in Arabidopsis (Arabidopsis thaliana) during B. cinerea infection. AtPMEI expression is strictly regulated by jasmonic acid and ethylene signaling, while only AtPMEI11 expression is controlled by PME-related damage-associated molecular patterns, such as oligogalacturonides and methanol. The decrease of pectin methylesterification during infection is higher and the immunity to B. cinerea is compromised in pmei10, pmei11, and pmei12 mutants with respect to the control plants. A higher stimulation of the fungal oxalic acid biosynthetic pathway also can contribute to the higher susceptibility of pmei mutants. The lack of PMEI expression does not affect hemicellulose strengthening, callose deposition, and the synthesis of structural defense proteins, proposed as CW-remodeling mechanisms exploited by Arabidopsis to resist CW degradation upon B. cinerea infection. We show that PME activity and pectin methylesterification are dynamically modulated by PMEIs during B. cinerea infection. Our findings point to AtPMEI10, AtPMEI11, and AtPMEI12 as mediators of CW integrity maintenance in plant immunity.
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Affiliation(s)
- Vincenzo Lionetti
- Dipartimento di Biologia e Biotecnologie, Charles Darwin, Sapienza Università di Roma, 00185 Rome, Italy (V.L., E.F., D.B.);
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy (M.D.C., G.P.); and
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Copenhagen, Denmark (A.R.H., W.G.T.W.)
| | - Eleonora Fabri
- Dipartimento di Biologia e Biotecnologie, Charles Darwin, Sapienza Università di Roma, 00185 Rome, Italy (V.L., E.F., D.B.)
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy (M.D.C., G.P.); and
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Copenhagen, Denmark (A.R.H., W.G.T.W.)
| | - Monica De Caroli
- Dipartimento di Biologia e Biotecnologie, Charles Darwin, Sapienza Università di Roma, 00185 Rome, Italy (V.L., E.F., D.B.)
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy (M.D.C., G.P.); and
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Copenhagen, Denmark (A.R.H., W.G.T.W.)
| | - Aleksander R Hansen
- Dipartimento di Biologia e Biotecnologie, Charles Darwin, Sapienza Università di Roma, 00185 Rome, Italy (V.L., E.F., D.B.)
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy (M.D.C., G.P.); and
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Copenhagen, Denmark (A.R.H., W.G.T.W.)
| | - William G T Willats
- Dipartimento di Biologia e Biotecnologie, Charles Darwin, Sapienza Università di Roma, 00185 Rome, Italy (V.L., E.F., D.B.)
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy (M.D.C., G.P.); and
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Copenhagen, Denmark (A.R.H., W.G.T.W.)
| | - Gabriella Piro
- Dipartimento di Biologia e Biotecnologie, Charles Darwin, Sapienza Università di Roma, 00185 Rome, Italy (V.L., E.F., D.B.)
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy (M.D.C., G.P.); and
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Copenhagen, Denmark (A.R.H., W.G.T.W.)
| | - Daniela Bellincampi
- Dipartimento di Biologia e Biotecnologie, Charles Darwin, Sapienza Università di Roma, 00185 Rome, Italy (V.L., E.F., D.B.)
- Dipartimento di Scienze e Tecnologie Biologiche ed Ambientali, Università del Salento, 73100 Lecce, Italy (M.D.C., G.P.); and
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, 1871 Copenhagen, Denmark (A.R.H., W.G.T.W.)
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Zhou C, Xue Y, Ma Y. Cloning, evaluation, and high-level expression of a thermo-alkaline pectate lyase from alkaliphilic Bacillus clausii with potential in ramie degumming. Appl Microbiol Biotechnol 2017; 101:3663-3676. [DOI: 10.1007/s00253-017-8110-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/28/2016] [Accepted: 12/31/2016] [Indexed: 10/20/2022]
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48
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Peng H, Cui J, Long H, Huang W, Kong L, Liu S, He W, Hu X, Peng D. Novel Pectate Lyase Genes of Heterodera glycines Play Key Roles in the Early Stage of Parasitism. PLoS One 2016; 11:e0149959. [PMID: 26930215 PMCID: PMC4773153 DOI: 10.1371/journal.pone.0149959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 02/08/2016] [Indexed: 11/19/2022] Open
Abstract
Pectate lyases are known to play a key role in pectin degradation by catalyzing the random cleavage of internal polymer linkages (endo-pectinases). In this paper, four novel cDNAs, designated Hg-pel-3, Hg-pel-4, Hg-pel-6 and Hg-pel-7, that encode pectate lyases were cloned and characterized from the soybean cyst nematode, Heterodera glycines. The predicted protein sequences of HG-PEL-3, HG-PEL-4 and HG-PEL-6 differed significantly in both their amino acid sequences and their genomic structures from other pectate lyases of H. glycines (HG-PEL-1, HG-PEL-2 and HG-PEL-7). A phylogenetic study revealed that the pectate lyase proteins of H. glycines are clustered into distinct clades and have distinct numbers and positioning of introns, which suggests that the pectate lyase genes of H. glycines may have evolved from at least two ancestral genes. A Southern blot analysis revealed that multiple Hg-pel-6-like genes were present in the H. glycines genome. In situ hybridization showed that four novel pectate lyases (Hg-pel-3, Hg-pel-4, Hg-pel-6 and Hg-pel-7) were actively transcribed in the subventral esophageal gland cells. A semi-quantitative RT-PCR assay supported the finding that the expression of these genes was strong in the egg, pre-parasitic second-stage juvenile (J2) and early parasitic J2 stages and that it declined in further developmental stages of the nematode. This expression pattern suggests that these proteins play a role in the migratory phase of the nematode life cycle. Knocking down Hg-pel-6 using in vitro RNA interference resulted in a 46.9% reduction of the number of nematodes that invaded the plants and a 61.5% suppression of the development of H. glycines females within roots compared to the GFP-dsRNA control. Plant host-derived RNAi induced the silencing of the Hg-pel-6gene, which significantly reduced the nematode infection levels at 7 Days post inoculation (dpi). Similarly, this procedure reduced the number of female adults at 40 dpi, which suggests the important roles of this gene in the early stages of parasitism. Our combined data suggest that two types of pectate lyases are present in the H. glycines genome and may have different roles during infection.
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Affiliation(s)
- Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiangkuan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Haibo Long
- Key Laboratory of Pests Comprehensive Governance for Tropical crops, Ministry of Agriculture, P. R. China, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Science, Danzhou, China
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lingan Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wenting He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianqi Hu
- The National Engineering Research Center of Agri-biodiversity Applied Technologies, Yunnan Agricultural University, Kunming, China
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Gacura MD, Sprockett DD, Heidenreich B, Blackwood CB. Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi. J Microbiol Methods 2016; 123:108-13. [PMID: 26899925 DOI: 10.1016/j.mimet.2016.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/15/2016] [Accepted: 02/16/2016] [Indexed: 01/22/2023]
Abstract
Fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this study we developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from 40 fungal genomes. The primers were used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senesced tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communities were up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystem type were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes.
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Affiliation(s)
- Matthew D Gacura
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States.
| | - Daniel D Sprockett
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States
| | - Bess Heidenreich
- Department of Biological Sciences, Kent State University, Kent, OH 44242, United States
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Poturcu K, Ozmen I, Biyik HH. Characterization of an Alkaline Thermostable Pectin Lyase from Newly Isolated Aspergillus niger _WHAK1 and Its Application on Fruit Juice Clarification. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2016. [DOI: 10.1007/s13369-016-2041-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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