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du Preez LL, van der Walt E, Valverde A, Rothmann C, Neser FWC, Cason ED. A metagenomic survey of the fecal microbiome of the African savanna elephant (Loxodonta africana). Anim Genet 2024; 55:621-643. [PMID: 38923598 DOI: 10.1111/age.13458] [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: 03/08/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
The African savanna elephant (Loxodonta africana) is the largest terrestrial animal on Earth and is found primarily in Southern and Eastern Africa. It is a hindgut, colonic fermenter and subsists on a diet of raw plant materials found in its grazing area. In this study the bacterial, archaeal and fungal populations of seven African savanna elephant fecal metagenomes were first characterized using amplicon sequencing. On the genus level it was observed that the p-1088-a5 gut group in the bacteriome, Methanocorpusulum and Methanobrevibacter in the archaeome and Alternaria, Aurobasidium, Didymella and Preussia in the mycome, predominated. Subsequently, metagenomic shotgun sequencing was employed to identify possible functional pathways and carbohydrate-active enzymes (CAZymes). Carbohydrate catabolic pathways represented the main degradation pathways, and the fecal metagenome was enriched in the glycohydroside (GH) class of CAZymes. Additionally, the top GH families identified - GH43, GH2, GH13 and GH3 - are known to be associated with cellulytic, hemicellulytic and pectolytic activities. Finally, the CAZymes families identified in the African savanna elephant were compared with those found in the Asian elephant and it was demonstrated that there is a unique repository of CAZymes that could be leveraged in the biotechnological context such as the degradation of lignocellulose for the production of second-generation biofuels and energy.
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Affiliation(s)
- Louis Lategan du Preez
- Department of Animal Science, University of the Free State, Bloemfontein, Free State, South Africa
| | - Elzette van der Walt
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Free State, South Africa
| | - Angel Valverde
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Free State, South Africa
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Consejo Superior de Investigaciones Científicas, Salamanca, Spain
| | - Christopher Rothmann
- Department of Animal Science, University of the Free State, Bloemfontein, Free State, South Africa
- Department of Microbiology and Biochemistry, University of the Free State, Bloemfontein, Free State, South Africa
| | | | - Errol Duncan Cason
- Department of Animal Science, University of the Free State, Bloemfontein, Free State, South Africa
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Li J, Peng C, Mao A, Zhong M, Hu Z. An overview of microbial enzymatic approaches for pectin degradation. Int J Biol Macromol 2024; 254:127804. [PMID: 37913880 DOI: 10.1016/j.ijbiomac.2023.127804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/21/2023] [Accepted: 10/29/2023] [Indexed: 11/03/2023]
Abstract
Pectin, a complex natural macromolecule present in primary cell walls, exhibits high structural diversity. Pectin is composed of a main chain, which contains a high amount of partly methyl-esterified galacturonic acid (GalA), and numerous types of side chains that contain almost 17 different monosaccharides and over 20 different linkages. Due to this peculiar structure, pectin exhibits special physicochemical properties and a variety of bioactivities. For example, pectin exhibits strong bioactivity only in a low molecular weight range. Many different degrading enzymes, including hydrolases, lyases and esterases, are needed to depolymerize pectin due to its structural complexity. Pectin degradation involves polygalacturonases/rhamnogalacturonases and pectate/pectin lyases, which attack the linkages in the backbone via hydrolytic and β-elimination modes, respectively. Pectin methyl/acetyl esterases involved in the de-esterification of pectin also play crucial roles. Many α-L-rhamnohydrolases, unsaturated rhamnogalacturonyl hydrolases, arabinanases and galactanases also contribute to heterogeneous pectin degradation. Although numerous microbial pectin-degrading enzymes have been described, the mechanisms involved in the coordinated degradation of pectin through these enzymes remain unclear. In recent years, the degradation of pectin by Bacteroides has received increasing attention, as Bacteroides species contain a unique genetic structure, polysaccharide utilization loci (PULs). The specific PULs of pectin degradation in Bacteroides species are a new field to study pectin metabolism in gut microbiota. This paper reviews the scientific information available on pectin structural characteristics, pectin-degrading enzymes, and PULs for the specific degradation of pectin.
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Affiliation(s)
- Jin Li
- College of Life Sciences, China West Normal University, Nanchong 637002, China; Department of Biology, College of Science, Shantou University, Shantou 515063, China.
| | - Chao Peng
- College of Life Sciences, China West Normal University, Nanchong 637002, China
| | - Aihua Mao
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Mingqi Zhong
- Department of Biology, College of Science, Shantou University, Shantou 515063, China
| | - Zhong Hu
- Department of Biology, College of Science, Shantou University, Shantou 515063, China.
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Ahmed J, Kumar K, Goyal A. A thermotolerant and pH stable rhamnogalacturonan acetylesterase (CtPae12B), a family 12 carbohydrate esterase from Clostridium thermocellum with broad substrate specificity. Int J Biol Macromol 2023; 226:1560-1569. [PMID: 36455821 DOI: 10.1016/j.ijbiomac.2022.11.267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/14/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022]
Abstract
The gene encoding rhamnogalacturonan acetylesterase, CtPae12B from Clostridium thermocellum was cloned, expressed, purified and biochemically characterized. Purified CtPae12B was soluble and exhibited homogenous single band. Phylogenetically it was most closely related to an RGAE, YesT from B. subtilis. CtPae12B production was maximum with LB medium. CtPae12B showed optimal temperature, 65 °C and thermostability with half-life, 5.1 h at 80 °C. CtPae12B was alkaliphilic with optimal pH, 8.0, while it displayed stability at both acidic and alkaline pH ranges. Inhibition of CtPae12B activity by PMSF showed the importance of nucleophilic serine in the catalytic triad. The metal ions, chemical or chelating agents used, did not enhance CtPae12B activity, which was also corroborated by protein melting study. The enzymatic activity of CtPae12B remained unaffected by 5 M urea. CtPae12B showed broad substrate specificity as it displayed activity against a range of synthetic substrates showing highest Vmax, 770 U/mg and Km, 1.2 mM with β-D-gluco pentaacetate. CtPae12B could deacetylate both pectic and xylan substrates showing highest Vmax, 770 U/mg and Km, 13.4 mg/mL with potato rhamnogalacturonan and Vmax, 105 U/mg and Km, 7.1 mg/mL with acetylated birchwood xylan. The thermostability, pH stability and broad substrate specificity of CtPae12B makes it a versatile enzyme for industrial applications.
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Affiliation(s)
- Jebin Ahmed
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Krishan Kumar
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arun Goyal
- Carbohydrate Enzyme Biotechnology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Influence of Human Age on the Prebiotic Effect of Pectin-Derived Oligosaccharides Obtained from Apple Pomace. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The aim of this study was to evaluate the prebiotic effect of pectin-derived oligosaccharides (POS) obtained from apple pomace on the growth and metabolism of microbiota from the human gastrointestinal tract as a function of the age of the host. The counts of major bacterial groups Bifidobacterium sp., lactobacilli, Clostridium sp., Bacteroides sp., Enterococcus sp. and Enterobacteria were assessed during long-term in vitro fermentation of mixed cultures in a prebiotic medium. Comparative assessment of bacterial diversity in the human fecal microbiota was performed relative to the age of the host, from childhood to old age, through younger years and middle age. The age group of the host was found to be an important factor that determined the prebiotic effect of POS, which was related to both the qualitative and quantitative composition of fecal microbiota and its metabolism. In contrast to the microbiota of elderly subjects, the child-derived intestinal microbiota underwent significantly different alterations in terms of the proportion and composition of lactic acid bacteria, leading to a more favorable pattern of short-chain fatty acids (SCFA) and lactic acid levels.
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Xu C, Zhang S, Suo J, Chang R, Xu X, Xu Z, Yang C, Qu C, Liu G. Bioinformatics analysis of PAE family in Populus trichocarpa and responsiveness to carbon and nitrogen treatment. 3 Biotech 2021; 11:370. [PMID: 34295610 DOI: 10.1007/s13205-021-02918-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022] Open
Abstract
Plant Pectin acetylesterase (PAE) belongs to family CE13 of carbohydrate esterases in the CAZy database. The ability of PAE to regulate the degree of acetylation of pectin, an important polysaccharide in the cell wall, affects the structure of plant cell wall. In this study, ten PtPAE genes were identified and characterized in Populus trichocarpa genome using bioinformatics methods, and the physiochemical properties such as molecular weight, isoelectric points, and hydrophilicity, as well as the secondary and tertiary structure of the protein were predicted. According to phylogenetic analysis, ten PtPAEs can be divided into three evolutionary clades, each of which had similar gene structure and motifs. Tissue-specific expression profiles indicated that the PtPAEs had different expression patterns. Real-time quantitative PCR (RT-qPCR) analysis showed that transcription level of PtPAEs was regulated by different CO2 and nitrogen concentrations. These results provide important information for the study of the phylogenetic relationship and function of PtPAEs in Populus trichocarpa. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02918-1.
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Wilkowska A, Berlowska J, Nowak A, Motyl I, Antczak-Chrobot A, Wojtczak M, Kunicka-Styczyńska A, Binczarski M, Dziugan P. Combined Yeast Cultivation and Pectin Hydrolysis as an Effective Method of Producing Prebiotic Animal Feed from Sugar Beet Pulp. Biomolecules 2020; 10:biom10050724. [PMID: 32384772 PMCID: PMC7277867 DOI: 10.3390/biom10050724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 05/03/2020] [Accepted: 05/04/2020] [Indexed: 11/24/2022] Open
Abstract
An effective and ecological method for liberation of pectin-derived oligosaccharides (POS) from sugar beet pulp (SBP) was developed using enzymatic and microorganism-mediated biomass conversion. The POS may be applied in the production of prebiotic feed additives. Various yeast strains were screened for their capacity for protein synthesis and monosaccharide assimilation. Combined yeast cultivation and pectin hydrolysis were found to be an effective method of producing prebiotics. Separate enzymatic hydrolysis and fermentation of SBP resulted in the release of 3.6 g of POS per 100 g d.w., whereas the yield of POS acquired after the combined process was 17.9% higher, giving 4.2 g of POS per 100 g d.w. Introducing the yeast into the process improved hydrolysis performance due to lower enzyme inhibition by mono- and disaccharides. The prebiotic effect of the POS was assessed by in vitro fermentation using individual cultures of gastrointestinal bacteria. The POS in the SBP hydrolysate effectively promoted the growth of lactobacilli and bifidobacteria. A large increase in adherence to Caco-2 cells in the presence of POS was noted for beneficial Lactobacillus brevis strains, whereas pathogenic bacteria and yeast (C. albicans, C. lusitanie, C. pelliculosa), responsible for infections in breeding animals, showed much weaker adhesion.
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Affiliation(s)
- Agnieszka Wilkowska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Łódź University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland;
- Correspondence: ; Tel.: +48-42-631-3490
| | - Joanna Berlowska
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland; (J.B.); (A.N.); (I.M.); (P.D.)
| | - Adriana Nowak
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland; (J.B.); (A.N.); (I.M.); (P.D.)
| | - Ilona Motyl
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland; (J.B.); (A.N.); (I.M.); (P.D.)
| | - Aneta Antczak-Chrobot
- Institute of Technology and Analysis of Food, Faculty of Biotechnology and Food Science, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland; (A.A.-C.); (M.W.)
| | - Maciej Wojtczak
- Institute of Technology and Analysis of Food, Faculty of Biotechnology and Food Science, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland; (A.A.-C.); (M.W.)
| | - Alina Kunicka-Styczyńska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Łódź University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland;
| | - Michał Binczarski
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Łódź, Poland;
| | - Piotr Dziugan
- Department of Environmental Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland; (J.B.); (A.N.); (I.M.); (P.D.)
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Polysaccharides from sunflower stalk pith: Chemical, structural and functional characterization. Food Hydrocoll 2020. [DOI: 10.1016/j.foodhyd.2019.04.053] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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8
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Wilkowska A, Nowak A, Antczak-Chrobot A, Motyl I, Czyżowska A, Paliwoda A. Structurally Different Pectic Oligosaccharides Produced from Apple Pomace and Their Biological Activity In Vitro. Foods 2019; 8:foods8090365. [PMID: 31454989 PMCID: PMC6769907 DOI: 10.3390/foods8090365] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/17/2019] [Accepted: 08/19/2019] [Indexed: 12/04/2022] Open
Abstract
This study set out to identify the composition and the biological activity of pectin-derived oligosaccharides (POS) generated from mild acid or enzymatic hydrolysis of apple pomace (AP). The effect of the polymerization of the structural units of POS contained in the AP hydrolysate on the growth and metabolism of microbiota from the human gastrointestinal tract and the adhesion of lactic acid bacteria (LAB) or pathogens to human gut epithelial cells was investigated in vitro. Mild acid hydrolysis followed by pectinolysis with Rohapect MaPlusT yielded the highest concentration of POS. In contrast, pure enzymatic processing of the AP performed with a mixed preparation of cellulase and Rohapect MaPlusT resulted in 1.8-fold lower overall POS. The concentration of higher-order oligosaccharides (degree of polymerization (DP) 7–10), however, was 1.7-fold higher. The increased ratio of higher-order oligosaccharides caused an increase in the bifidogenic effect, as well as affecting the amount and nature of short-chain fatty acid produced. Inhibition of Enterobacteriaceae was also observed. The strongest stimulation of LAB adhesion to the human epithelial cells occurred in the presence of the preparation containing the highest concentration of higher-order oligosaccharides. The fecal bacteria and pathogens showed much weaker adhesion to intestinal cells in the presence of all the tested AP hydrolysates. Both of the tested POS preparations, containing structurally different oligosaccharides (DPs 2–10 with different ratios of higher-order oligosaccharides), have the potential to be used as prebiotics for humans and animals. They stimulate bowel colonization with lactic acid bacteria and inhibit the development of infections caused by pathogens.
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Affiliation(s)
- Agnieszka Wilkowska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Łódź University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland.
| | - Adriana Nowak
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Łódź University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland
| | - Aneta Antczak-Chrobot
- Institute of Technology and Analysis of Food, Faculty of Biotechnology and Food Science, Łódź University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland
| | - Ilona Motyl
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Łódź University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland
| | - Agata Czyżowska
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Łódź University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland
| | - Anna Paliwoda
- Institute of Fermentation Technology and Microbiology, Faculty of Biotechnology and Food Science, Łódź University of Technology, Wólczańska 171/173, 90-924 Łódź, Poland
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Shakhmatov EG, Makarova EN, Belyy VA. Structural studies of biologically active pectin-containing polysaccharides of pomegranate Punica granatum. Int J Biol Macromol 2019; 122:29-36. [DOI: 10.1016/j.ijbiomac.2018.10.146] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 10/21/2018] [Indexed: 11/29/2022]
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Stranne M, Ren Y, Fimognari L, Birdseye D, Yan J, Bardor M, Mollet JC, Komatsu T, Kikuchi J, Scheller HV, Sakuragi Y. TBL10 is required for O-acetylation of pectic rhamnogalacturonan-I in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:772-785. [PMID: 30118566 DOI: 10.1111/tpj.14067] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/06/2018] [Indexed: 05/12/2023]
Abstract
O-Acetylated pectins are abundant in the primary cell wall of plants and growing evidence suggests they have important roles in plant cell growth and interaction with the environment. Despite their importance, genes required for O-acetylation of pectins are still largely unknown. In this study, we showed that TRICHOME BIREFRINGENCE LIKE 10 (AT3G06080) is involved in O-acetylation of pectins in Arabidopsis (Arabidopsis thaliana). The activity of the TBL10 promoter was strong in tissues where pectins are highly abundant (e.g. leaves). Two homozygous knock-out mutants of Arabidopsis, tbl10-1 and tbl10-2, were isolated and shown to exhibit reduced levels of wall-bound acetyl esters, equivalent of ~50% of the wild-type level in pectin-enriched fractions derived from leaves. Further fractionation revealed that the degree of acetylation of the pectin rhamnogalacturonan-I (RG-I) was reduced in the tbl10 mutant compared to the wild type, whereas the pectin homogalacturonan (HG) was unaffected. The degrees of acetylation in hemicelluloses (i.e. xyloglucan, xylan and mannan) were indistinguishable between the tbl10 mutants and the wild type. The mutant plants contained normal trichomes in leaves and exhibited a similar level of susceptibility to the phytopathogenic microorganisms Pseudomonas syringae pv. tomato DC3000 and Botrytis cinerea; while they displayed enhanced tolerance to drought. These results indicate that TBL10 is required for O-acetylation of RG-I, possibly as an acetyltransferase, and suggest that O-acetylated RG-I plays a role in abiotic stress responses in Arabidopsis.
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Affiliation(s)
- Maria Stranne
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, DK-1871, Denmark
| | - Yanfang Ren
- Feedstocks Division, Joint Bioenergy Institute, Emeryville, CA, 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Lorenzo Fimognari
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, DK-1871, Denmark
| | - Devon Birdseye
- Feedstocks Division, Joint Bioenergy Institute, Emeryville, CA, 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jingwei Yan
- Feedstocks Division, Joint Bioenergy Institute, Emeryville, CA, 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Muriel Bardor
- Normandie Univ, UNIROUEN, Laboratoire Glyco-MEV, 76000, Rouen, France
| | | | - Takanori Komatsu
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jun Kikuchi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Henrik V Scheller
- Feedstocks Division, Joint Bioenergy Institute, Emeryville, CA, 94608, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Yumiko Sakuragi
- Copenhagen Plant Science Center, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, DK-1871, Denmark
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Philippe F, Pelloux J, Rayon C. Plant pectin acetylesterase structure and function: new insights from bioinformatic analysis. BMC Genomics 2017; 18:456. [PMID: 28595570 PMCID: PMC5465549 DOI: 10.1186/s12864-017-3833-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 05/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background Pectins are plant cell wall polysaccharides that can be acetylated on C2 and/or C3 of galacturonic acid residues. The degree of acetylation of pectin can be modulated by pectin acetylesterase (EC 3.1.1.6, PAE). The function and structure of plant PAEs remain poorly understood and the role of the fine-tuning of pectin acetylation on cell wall properties has not yet been elucidated. Results In the present study, a bioinformatic approach was used on 72 plant PAEs from 16 species among 611 plant PAEs available in plant genomic databases. An overview of plant PAE proteins, particularly Arabidopsis thaliana PAEs, based on phylogeny analysis, protein motif identification and modeled 3D structure is presented. A phylogenetic tree analysis using protein sequences clustered the plant PAEs into five clades. AtPAEs clustered in four clades in the plant kingdom PAE tree while they formed three clades when a phylogenetic tree was performed only on Arabidopsis proteins, due to isoform AtPAE9. Primitive plants that display a smaller number of PAEs clustered into two clades, while in higher plants, the presence of multiple members of PAE genes indicated a diversification of AtPAEs. 3D homology modeling of AtPAE8 from clade 2 with a human Notum protein showed an α/β hydrolase structure with the hallmark Ser-His-Asp of the active site. A 3D model of AtPAE4 from clade 1 and AtPAE10 from clade 3 showed a similar shape suggesting that the diversification of AtPAEs is unlikely to arise from the shape of the protein. Primary structure prediction analysis of AtPAEs showed a specific motif characteristic of each clade and identified one major group of AtPAEs with a signal peptide and one group without a signal peptide. A multiple sequence alignment of the putative plant PAEs revealed consensus sequences with important putative catalytic residues: Ser, Asp, His and a pectin binding site. Data mining of gene expression profiles of AtPAE revealed that genes from clade 2 including AtPAE7, AtPAE8 and AtPAE11, which are duplicated genes, are highly expressed during plant growth and development while AtPAEs without a signal peptide, including AtPAE2 and AtPAE4, are more regulated in response to plant environmental conditions. Conclusion Bioinformatic analysis of plant, and particularly Arabidopsis, AtPAEs provides novel insights, including new motifs that could play a role in pectin binding and catalytic sites. The diversification of AtPAEs is likely to be related to neofunctionalization of some AtPAE genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3833-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florian Philippe
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039, Amiens, France
| | - Jérôme Pelloux
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039, Amiens, France
| | - Catherine Rayon
- EA3900-BIOPI, Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 80039, Amiens, France.
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12
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Oleas G, Callegari E, Sepúlveda R, Eyzaguirre J. Heterologous expression, purification and characterization of three novel esterases secreted by the lignocellulolytic fungus Penicillium purpurogenum when grown on sugar beet pulp. Carbohydr Res 2017; 443-444:42-48. [PMID: 28342968 PMCID: PMC5560272 DOI: 10.1016/j.carres.2017.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/13/2017] [Accepted: 03/16/2017] [Indexed: 11/24/2022]
Abstract
The lignocellulolytic fungus, Penicillium purpurogenum, grows on a variety of natural carbon sources, among them sugar beet pulp. Culture supernatants of P. purpurogenum grown on sugar beet pulp were partially purified and the fractions obtained analyzed for esterase activity by zymograms. The bands with activity on methyl umbelliferyl acetate were subjected to mass spectrometry to identify peptides. The peptides obtained were probed against the proteins deduced from the genome sequence of P. purpurogenum. Eight putative esterases thus identified were chosen for future work. Their cDNAs were expressed in Pichia pastoris. The supernatants of the recombinant clones were assayed for esterase activity, and five of the proteins were active against one or more substrates: methyl umbelliferyl acetate, indoxyl acetate, methyl esterified pectin and fluorescein diacetate. Three of those enzymes were purified, further characterized and subjected to a BLAST search. Based on their amino acid sequence and properties, they were identified as follows: RAE1, pectin acetyl esterase (CAZy family CE 12); FAEA, feruloyl esterase (could not be assigned to a CAZy family) and EAN, acetyl esterase (former CAZy family CE 10).
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Affiliation(s)
- Gabriela Oleas
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile.
| | - Eduardo Callegari
- BRIN-USDSSOM Proteomics Facility, University of South Dakota, Vermillion, SD, USA.
| | - Romina Sepúlveda
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile.
| | - Jaime Eyzaguirre
- Facultad de Ciencias Biológicas, Universidad Andrés Bello, Santiago, Chile.
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Verrijssen TA, Christiaens S, Verkempinck SH, Boeve J, Grauwet T, Van Loey AM, Salvia-Trujillo L, Hendrickx ME. In vitro
β-Carotene Bioaccessibility and Lipid Digestion in Emulsions: Influence of Pectin Type and Degree of Methyl-Esterification. J Food Sci 2016; 81:C2327-C2336. [DOI: 10.1111/1750-3841.13408] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 06/17/2016] [Accepted: 07/01/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Tina A.J. Verrijssen
- Laboratory of Food Technology and Leuven Food Science and Nutrition Research Centre (LFoRCe); Dept. of Microbial and Molecular Systems (M2S); KU Leuven, Kasteelpark Arenberg 22, PB 2457 3001 Leuven Belgium
| | - Stefanie Christiaens
- Laboratory of Food Technology and Leuven Food Science and Nutrition Research Centre (LFoRCe); Dept. of Microbial and Molecular Systems (M2S); KU Leuven, Kasteelpark Arenberg 22, PB 2457 3001 Leuven Belgium
| | - Sarah H.E. Verkempinck
- Laboratory of Food Technology and Leuven Food Science and Nutrition Research Centre (LFoRCe); Dept. of Microbial and Molecular Systems (M2S); KU Leuven, Kasteelpark Arenberg 22, PB 2457 3001 Leuven Belgium
| | - Jeroen Boeve
- Laboratory of Food Technology and Leuven Food Science and Nutrition Research Centre (LFoRCe); Dept. of Microbial and Molecular Systems (M2S); KU Leuven, Kasteelpark Arenberg 22, PB 2457 3001 Leuven Belgium
| | - Tara Grauwet
- Laboratory of Food Technology and Leuven Food Science and Nutrition Research Centre (LFoRCe); Dept. of Microbial and Molecular Systems (M2S); KU Leuven, Kasteelpark Arenberg 22, PB 2457 3001 Leuven Belgium
| | - Ann M. Van Loey
- Laboratory of Food Technology and Leuven Food Science and Nutrition Research Centre (LFoRCe); Dept. of Microbial and Molecular Systems (M2S); KU Leuven, Kasteelpark Arenberg 22, PB 2457 3001 Leuven Belgium
| | - Laura Salvia-Trujillo
- Laboratory of Food Technology and Leuven Food Science and Nutrition Research Centre (LFoRCe); Dept. of Microbial and Molecular Systems (M2S); KU Leuven, Kasteelpark Arenberg 22, PB 2457 3001 Leuven Belgium
| | - Marc E. Hendrickx
- Laboratory of Food Technology and Leuven Food Science and Nutrition Research Centre (LFoRCe); Dept. of Microbial and Molecular Systems (M2S); KU Leuven, Kasteelpark Arenberg 22, PB 2457 3001 Leuven Belgium
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Blackman LM, Cullerne DP, Torreña P, Taylor J, Hardham AR. RNA-Seq Analysis of the Expression of Genes Encoding Cell Wall Degrading Enzymes during Infection of Lupin (Lupinus angustifolius) by Phytophthora parasitica. PLoS One 2015; 10:e0136899. [PMID: 26332397 PMCID: PMC4558045 DOI: 10.1371/journal.pone.0136899] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/10/2015] [Indexed: 11/18/2022] Open
Abstract
RNA-Seq analysis has shown that over 60% (12,962) of the predicted transcripts in the Phytophthora parasitica genome are expressed during the first 60 h of lupin root infection. The infection transcriptomes included 278 of the 431 genes encoding P. parasitica cell wall degrading enzymes. The transcriptome data provide strong evidence of global transcriptional cascades of genes whose encoded proteins target the main categories of plant cell wall components. A major cohort of pectinases is predominantly expressed early but as infection progresses, the transcriptome becomes increasingly dominated by transcripts encoding cellulases, hemicellulases, β-1,3-glucanases and glycoproteins. The most highly expressed P. parasitica carbohydrate active enzyme gene contains two CBM1 cellulose binding modules and no catalytic domains. The top 200 differentially expressed genes include β-1,4-glucosidases, β-1,4-glucanases, β-1,4-galactanases, a β-1,3-glucanase, an α-1,4-polygalacturonase, a pectin deacetylase and a pectin methylesterase. Detailed analysis of gene expression profiles provides clues as to the order in which linkages within the complex carbohydrates may come under attack. The gene expression profiles suggest that (i) demethylation of pectic homogalacturonan occurs before its deacetylation; (ii) cleavage of the backbone of pectic rhamnogalacturonan I precedes digestion of its side chains; (iii) early attack on cellulose microfibrils by non-catalytic cellulose-binding proteins and enzymes with auxiliary activities may facilitate subsequent attack by glycosyl hydrolases and enzymes containing CBM1 cellulose-binding modules; (iv) terminal hemicellulose backbone residues are targeted after extensive internal backbone cleavage has occurred; and (v) the carbohydrate chains on glycoproteins are degraded late in infection. A notable feature of the P. parasitica infection transcriptome is the high level of transcription of genes encoding enzymes that degrade β-1,3-glucanases during middle and late stages of infection. The results suggest that high levels of β-1,3-glucanases may effectively degrade callose as it is produced by the plant during the defence response.
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Affiliation(s)
- Leila M. Blackman
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
- * E-mail:
| | - Darren P. Cullerne
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
- Agriculture Flagship, CSIRO, Canberra ACT, Australia
| | - Pernelyn Torreña
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
| | - Jen Taylor
- Agriculture Flagship, CSIRO, Canberra ACT, Australia
| | - Adrienne R. Hardham
- Plant Science Division, Research School of Biology, College of Medicine, Biology and Environment, The Australian National University, Canberra ACT, Australia
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Extraction and structural characteristics of pectic polysaccharides from Abies sibirica L. Carbohydr Polym 2015; 123:228-36. [DOI: 10.1016/j.carbpol.2015.01.041] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/22/2015] [Accepted: 01/23/2015] [Indexed: 11/20/2022]
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Sénéchal F, Wattier C, Rustérucci C, Pelloux J. Homogalacturonan-modifying enzymes: structure, expression, and roles in plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:5125-60. [PMID: 25056773 PMCID: PMC4400535 DOI: 10.1093/jxb/eru272] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 05/20/2014] [Accepted: 05/22/2014] [Indexed: 05/18/2023]
Abstract
Understanding the changes affecting the plant cell wall is a key element in addressing its functional role in plant growth and in the response to stress. Pectins, which are the main constituents of the primary cell wall in dicot species, play a central role in the control of cellular adhesion and thereby of the rheological properties of the wall. This is likely to be a major determinant of plant growth. How the discrete changes in pectin structure are mediated is thus a key issue in our understanding of plant development and plant responses to changes in the environment. In particular, understanding the remodelling of homogalacturonan (HG), the most abundant pectic polymer, by specific enzymes is a current challenge in addressing its fundamental role. HG, a polymer that can be methylesterified or acetylated, can be modified by HGMEs (HG-modifying enzymes) which all belong to large multigenic families in all species sequenced to date. In particular, both the degrees of substitution (methylesterification and/or acetylation) and polymerization can be controlled by specific enzymes such as pectin methylesterases (PMEs), pectin acetylesterases (PAEs), polygalacturonases (PGs), or pectate lyases-like (PLLs). Major advances in the biochemical and functional characterization of these enzymes have been made over the last 10 years. This review aims to provide a comprehensive, up to date summary of the recent data concerning the structure, regulation, and function of these fascinating enzymes in plant development and in response to biotic stresses.
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Affiliation(s)
- Fabien Sénéchal
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Christopher Wattier
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Christine Rustérucci
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
| | - Jérôme Pelloux
- EA3900 BIOPI Biologie des Plantes et Innovation, Université de Picardie Jules Verne, 33 Rue St Leu, F-80039 Amiens, France
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Kwak MJ, Jeong H, Madhaiyan M, Lee Y, Sa TM, Oh TK, Kim JF. Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere. PLoS One 2014; 9:e106704. [PMID: 25211235 PMCID: PMC4161386 DOI: 10.1371/journal.pone.0106704] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 07/31/2014] [Indexed: 11/19/2022] Open
Abstract
Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the environment, and many Methylobacterium species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. M. oryzae is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of M. oryzae, we provide information on the full gene complement of M. oryzae that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated.
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Affiliation(s)
- Min-Jung Kwak
- Department of Systems Biology, and Division of Life Sciences, Yonsei University, Seodaemun-gu, Seoul, Republic of Korea
- Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Yuseong-gu, Daejeon, Republic of Korea
| | - Haeyoung Jeong
- Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
| | - Munusamy Madhaiyan
- Department of Agricultural Chemistry, Chungbuk National University, Heungdeok-gu, Cheongju, Republic of Korea
- Biomaterials and Biocatalysts Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Heungdeok-gu, Cheongju, Republic of Korea
| | - Tong-Min Sa
- Department of Agricultural Chemistry, Chungbuk National University, Heungdeok-gu, Cheongju, Republic of Korea
| | - Tae Kwang Oh
- Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
- 21C Frontier Microbial Genomics and Applications Center, Yuseong-gu, Daejeon, Republic of Korea
| | - Jihyun F. Kim
- Department of Systems Biology, and Division of Life Sciences, Yonsei University, Seodaemun-gu, Seoul, Republic of Korea
- Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Republic of Korea
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Remoroza C, Wagenknecht M, Gu F, Buchholt H, Moerschbacher B, Schols H, Gruppen H. A Bacillus licheniformis pectin acetylesterase is specific for homogalacturonans acetylated at O-3. Carbohydr Polym 2014; 107:85-93. [DOI: 10.1016/j.carbpol.2014.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 01/21/2014] [Accepted: 02/03/2014] [Indexed: 10/25/2022]
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Bonnin E, Garnier C, Ralet MC. Pectin-modifying enzymes and pectin-derived materials: applications and impacts. Appl Microbiol Biotechnol 2013; 98:519-32. [DOI: 10.1007/s00253-013-5388-6] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/05/2013] [Accepted: 11/05/2013] [Indexed: 11/30/2022]
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Characterization of sugar beet pectic-derived oligosaccharides obtained by enzymatic hydrolysis. Int J Biol Macromol 2012; 52:148-56. [PMID: 22986181 DOI: 10.1016/j.ijbiomac.2012.09.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 09/01/2012] [Accepted: 09/09/2012] [Indexed: 11/23/2022]
Abstract
Three pectic oligosaccharides (POS) obtained by enzymatic hydrolysis of sugar beet pectin by combining endopolygalacturonase and pectinmethylesterase, were characterized using high performance liquid chromatography, thermogravimetric analysis, Fourier transform infrared spectroscopy, differential scanning calorimetry and X-ray diffraction. According to chromatographic analyses, POS are composed of mixture of polymers with different molecular weights and different galacturonic acid contents. The thermal analysis showed no major variation in thermal behavior regarding POS composition but showed that POS were more sensitive to thermal degradation than the parent pectin as well as the deesterified pectin. No change in composition of the gaseous products was obtained through TGA-FTIR analysis. The X-ray pattern of POS clearly indicated a considerable decrease in crystallinity when compared to the native pectin. Thus, thermal characterization of POS may have practical repercussions if the formulation in which POS is incorporated is submitted to a high temperature treatment.
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Orfila C, Dal Degan F, Jørgensen B, Scheller HV, Ray PM, Ulvskov P. Expression of mung bean pectin acetyl esterase in potato tubers: effect on acetylation of cell wall polymers and tuber mechanical properties. PLANTA 2012; 236:185-96. [PMID: 22293853 DOI: 10.1007/s00425-012-1596-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2011] [Accepted: 01/11/2012] [Indexed: 05/22/2023]
Abstract
A mung bean (Vigna radiata) pectin acetyl esterase (CAA67728) was heterologously expressed in tubers of potato (Solanum tuberosum) under the control of the granule-bound starch synthase promoter or the patatin promoter in order to probe the significance of O-acetylation on cell wall and tissue properties. The recombinant tubers showed no apparent macroscopic phenotype. The enzyme was recovered from transgenic tubers using a high ionic strength buffer and the extract was active against a range of pectic substrates. Partial in vivo de-acetylation of cell wall polysaccharides occurred in the transformants, as shown by a 39% decrease in the degree of acetylation (DA) of tuber cell wall material (CWM). Treatment of CWM using a combination of endo-polygalacturonase and pectin methyl esterase extracted more pectin polymers from the transformed tissue compared to wild type. The largest effect of the pectin acetyl esterase (68% decrease in DA) was seen in the residue from this extraction, suggesting that the enzyme is preferentially active on acetylated pectin that is tightly bound to the cell wall. The effects of acetylation on tuber mechanical properties were investigated by tests of failure under compression and by determination of viscoelastic relaxation spectra. These tests suggested that de-acetylation resulted in a stiffer tuber tissue and a stronger cell wall matrix, as a result of changes to a rapidly relaxing viscoelastic component. These results are discussed in relation to the role of pectin acetylation in primary cell walls and its implications for industrial uses of potato fibres.
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Affiliation(s)
- Caroline Orfila
- Department of Plant Biology and Biotechnology, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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Van Dyk JS, Pletschke BI. A review of lignocellulose bioconversion using enzymatic hydrolysis and synergistic cooperation between enzymes--factors affecting enzymes, conversion and synergy. Biotechnol Adv 2012; 30:1458-80. [PMID: 22445788 DOI: 10.1016/j.biotechadv.2012.03.002] [Citation(s) in RCA: 477] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 02/10/2012] [Accepted: 03/06/2012] [Indexed: 02/04/2023]
Abstract
Lignocellulose is a complex substrate which requires a variety of enzymes, acting in synergy, for its complete hydrolysis. These synergistic interactions between different enzymes have been investigated in order to design optimal combinations and ratios of enzymes for different lignocellulosic substrates that have been subjected to different pretreatments. This review examines the enzymes required to degrade various components of lignocellulose and the impact of pretreatments on the lignocellulose components and the enzymes required for degradation. Many factors affect the enzymes and the optimisation of the hydrolysis process, such as enzyme ratios, substrate loadings, enzyme loadings, inhibitors, adsorption and surfactants. Consideration is also given to the calculation of degrees of synergy and yield. A model is further proposed for the optimisation of enzyme combinations based on a selection of individual or commercial enzyme mixtures. The main area for further study is the effect of and interaction between different hemicellulases on complex substrates.
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Affiliation(s)
- J S Van Dyk
- Department of Biochemistry, Microbiology and Biotechnology, Rhodes University, PO Box 94, Grahamstown, 6140, South Africa
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Gou JY, Miller LM, Hou G, Yu XH, Chen XY, Liu CJ. Acetylesterase-mediated deacetylation of pectin impairs cell elongation, pollen germination, and plant reproduction. THE PLANT CELL 2012; 24:50-65. [PMID: 22247250 PMCID: PMC3289554 DOI: 10.1105/tpc.111.092411] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 12/02/2011] [Accepted: 12/22/2011] [Indexed: 05/17/2023]
Abstract
Pectin is a major component of the primary cell wall of higher plants. Some galacturonyl residues in the backbone of pectinaceous polysaccharides are often O-acetylated at the C-2 or C-3 position, and the resulting acetylesters change dynamically during the growth and development of plants. The processes involve both enzymatic acetylation and deacetylation. Through genomic sequence analysis, we identified a pectin acetylesterase (PAE1) from black cottonwood (Populus trichocarpa). Recombinant Pt PAE1 exhibited preferential activity in releasing the acetate moiety from sugar beet (Beta vulgaris) and potato (Solanum tuberosum) pectin in vitro. Overexpressing Pt PAE1 in tobacco (Nicotiana tabacum) decreased the level of acetyl esters of pectin but not of xylan. Deacetylation engendered differential changes in the composition and/or structure of cell wall polysaccharides that subsequently impaired the cellular elongation of floral styles and filaments, the germination of pollen grains, and the growth of pollen tubes. Consequently, plants overexpressing PAE1 exhibited severe male sterility. Furthermore, in contrast to the conventional view, PAE1-mediated deacetylation substantially lowered the digestibility of pectin. Our data suggest that pectin acetylesterase functions as an important structural regulator in planta by modulating the precise status of pectin acetylation to affect the remodeling and physiochemical properties of the cell wall's polysaccharides, thereby affecting cell extensibility.
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Affiliation(s)
- Jin-Ying Gou
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Lisa M. Miller
- National Synchrotron Light Source, Brookhaven National Laboratory, Upton, New York 11973
| | - Guichuan Hou
- Appalachian State University, Boone, North Carolina 28608-2027
| | - Xiao-Hong Yu
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Xiao-Ya Chen
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Shanghai 200032, China
| | - Chang-Jun Liu
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
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Normand J, Bonnin E, Delavault P. Cloning and expression in Pichia pastoris of an Irpex lacteus rhamnogalacturonan hydrolase tolerant to acetylated rhamnogalacturonan. Appl Microbiol Biotechnol 2011; 94:1543-52. [PMID: 22101785 DOI: 10.1007/s00253-011-3705-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 10/19/2011] [Accepted: 11/02/2011] [Indexed: 12/01/2022]
Abstract
In order to produce a recombinant rhamnogalacturonase from the basidiomycete Irpex lacteus using a molecular approach, PCR primers were designed based on a sequence alignment of four known ascomycete rhamnogalacturonases. Using 5' and 3' rapid amplification of cDNA ends (RACE) experiments, a 1,437-bp full-length cDNA containing an open reading frame of 1,329 bp was isolated. The corresponding putative protein sequence is of 443 amino acids and contains a secretion signal sequence of 22 amino acids. The theoretical mass of this protein is 44.6 kDa with a theoretical isoelectric point of 6.2. The amino acid sequence shared not only significant identities with ascomycete and basidiomycete putative rhamnogalacturonases but also complete similarity with peptides obtained from a recently purified rhamnogalacturonase from I. lacteus. The recombinant protein was successfully expressed in active form in Pichia pastoris. SDS-PAGE assay demonstrated that the recombinant enzyme was secreted in the culture medium and had a molar mass of 56 kDa. This recombinant rhamnogalacturonan hydrolase exhibited a pH optimum between 4.5 and 5 and a temperature optimum between 40°C and 50°C, which correspond to that of the native rhamnogalacturonase from I. lacteus. The study of its specificity through reaction products analysis showed that it was highly tolerant to the presence of acetyl groups on its substrate, even more than the native enzyme.
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Affiliation(s)
- J Normand
- INRA, Unité de Recherche Biopolymères, Interactions, Assemblages, BP 71627, 44316 Nantes Cedex 03, France
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Alimardani-Theuil P, Gainvors-Claisse A, Duchiron F. Yeasts: An attractive source of pectinases—From gene expression to potential applications: A review. Process Biochem 2011. [DOI: 10.1016/j.procbio.2011.05.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Optimization of nitric acid-mediated extraction of pectin from cacao pod husks (Theobroma cacao L.) using response surface methodology. Carbohydr Polym 2011. [DOI: 10.1016/j.carbpol.2011.01.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Normand J, Ralet MC, Thibault JF, Rogniaux H, Delavault P, Bonnin E. Purification, characterization, and mode of action of a rhamnogalacturonan hydrolase from Irpex lacteus, tolerant to an acetylated substrate. Appl Microbiol Biotechnol 2009; 86:577-88. [PMID: 19862512 DOI: 10.1007/s00253-009-2310-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 10/13/2009] [Accepted: 10/13/2009] [Indexed: 11/29/2022]
Abstract
A novel rhamnogalacturonase (RGase) acting on an acetylated substrate was detected in the commercial preparation Driselase, an enzymatic mixture derived from the basidiomycete Irpex lacteus. The activity was isolated by hydrophobic interaction chromatography, gel filtration, and preparative isoelectric focusing, resulting in the isolation of five different rhamnogalacturonan hydrolases exhibiting various isoelectric points from 6.2 to 7.7. Sodium dodecyl sulfate polyacrylamide gel electrophoresis and mass spectrometry analyses after trypsin cleavage of the five fractions revealed that the five rhamnogalacturonases have a molar mass of 55 kDa without any divergences in the identified peptides. The RGase with a pI of 7.2 exhibited a pH optimum between 4.5 and 5 and a temperature optimum between 40 degrees C and 50 degrees C. Its mode of action was analyzed by mass spectrometry of the oligosaccharides produced after hydrolysis of acetylated and nonacetylated rhamnogalacturonan. Oligomers esterified by an acetyl group on the reducing galacturonic acid residue or fully acetylated were detected in the hydrolysate showing that the novel enzyme is able to bind acetylated galacturonic acid in its active site.
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Affiliation(s)
- Jessica Normand
- INRA, Unité de Recherche Biopolymères, Interactions, Assemblages, BP 71627, 44316, Nantes, Cedex 03, France
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