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Meng J, Németh Z, Peng M, Fekete E, Garrigues S, Lipzen A, Ng V, Savage E, Zhang Y, Grigoriev IV, Mäkelä MR, Karaffa L, de Vries RP. GalR, GalX and AraR co-regulate d-galactose and l-arabinose utilization in Aspergillus nidulans. Microb Biotechnol 2022; 15:1839-1851. [PMID: 35213794 PMCID: PMC9151342 DOI: 10.1111/1751-7915.14025] [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: 11/25/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 11/27/2022] Open
Abstract
Filamentous fungi produce a wide variety of enzymes in order to efficiently degrade plant cell wall polysaccharides. The production of these enzymes is controlled by transcriptional regulators, which also control the catabolic pathways that convert the released monosaccharides. Two transcriptional regulators, GalX and GalR, control d-galactose utilization in the model filamentous fungus Aspergillus nidulans, while the arabinanolytic regulator AraR regulates l-arabinose catabolism. d-Galactose and l-arabinose are commonly found together in polysaccharides, such as arabinogalactan, xylan and rhamnogalacturonan I. Therefore, the catabolic pathways that convert d-galactose and l-arabinose are often also likely to be active simultaneously. In this study, we investigated the interaction between GalX, GalR and AraR in d-galactose and l-arabinose catabolism. For this, we generated single, double and triple mutants of the three regulators, and analysed their growth and enzyme and gene expression profiles. Our results clearly demonstrated that GalX, GalR and AraR co-regulate d-galactose catabolism in A. nidulans. GalX has a prominent role on the regulation of genes of d-galactose oxido-reductive pathway, while AraR can compensate for the absence of GalR and/or GalX.
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Affiliation(s)
- Jiali Meng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Zoltán Németh
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary
| | - Mao Peng
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary
| | - Sandra Garrigues
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
| | - Anna Lipzen
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Vivian Ng
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Emily Savage
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Yu Zhang
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Igor V Grigoriev
- Lawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Miia R Mäkelä
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, 00790, Finland
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary.,Institute of Metagenomics, University of Debrecen, Egyetem tér 1., Debrecen, H-4032, Hungary
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute & Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, Utrecht, 3584 CT, The Netherlands
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Orellana E, Guerrero LD, Davies-Sala C, Altina M, Pontiggia RM, Erijman L. Extracellular hydrolytic potential drives microbiome shifts during anaerobic co-digestion of sewage sludge and food waste. BIORESOURCE TECHNOLOGY 2022; 343:126102. [PMID: 34634462 DOI: 10.1016/j.biortech.2021.126102] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/03/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
Bacterial community structure and dynamics in anaerobic digesters are primarily influenced by feedstock composition. It is therefore important to unveil microbial traits that explain microbiome variations in response to substrate changes. Here, gene and genome-centric metagenomics were used to examine microbiome dynamics in four laboratory-scale reactors, in which sewage sludge was co-digested with increasing amounts of food waste. A co-occurrence network revealed microbiome shifts in response to changes in substrate composition and concentration. Food waste concentration correlated with extracellular enzymes and metagenome-assembled genomes (MAGs) involved in the degradation of complex carbohydrates commonly found in fruits and plant cell walls as well as with the abundance of hydrolytic MAGs. A key role was attributed to Proteiniphillum for being the only bacteria that encoded the complete pectin degradation pathway. These results suggest that changes of feedstock composition establish new microbial niches for bacteria with the capacity to degrade newly added substrates.
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Affiliation(s)
- Esteban Orellana
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET) Vuelta de Obligado, 2490 - C1428ADN, Buenos Aires, Argentina
| | - Leandro D Guerrero
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET) Vuelta de Obligado, 2490 - C1428ADN, Buenos Aires, Argentina
| | - Carol Davies-Sala
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET) Vuelta de Obligado, 2490 - C1428ADN, Buenos Aires, Argentina
| | - Melisa Altina
- Investigación, Desarrollo e Innovación, Benito Roggio Ambiental, Buenos Aires, Argentina
| | - Rodrigo M Pontiggia
- Investigación, Desarrollo e Innovación, Benito Roggio Ambiental, Buenos Aires, Argentina
| | - Leonardo Erijman
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr Héctor N. Torres" (INGEBI-CONICET) Vuelta de Obligado, 2490 - C1428ADN, Buenos Aires, Argentina; Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Intendente Güiraldes, 2160 - C1428EGA, Buenos Aires, Argentina.
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Lannuzel C, Smith A, Mary A, Della Pia E, Kabel M, de Vries S. Improving fiber utilization from rapeseed and sunflower seed meals to substitute soybean meal in pig and chicken diets: A review. Anim Feed Sci Technol 2022. [DOI: 10.1016/j.anifeedsci.2022.115213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Complete genome sequence of Sphingobium sp. strain PAMC 28499 reveals a potential for degrading pectin with comparative genomics approach. Genes Genomics 2020; 42:1087-1096. [PMID: 32737807 DOI: 10.1007/s13258-020-00976-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 07/17/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Spingobium sp. PAMC 28499 is isolated from the glaciers of Uganda. Uganda is a unique region where hot areas and glaciers coexist, with a variety of living creatures surviving, but the survey on them is very poor. The genetic character and complete genome information of Sphingobium strains help with environmental studies and the development of better to enzyme industry. OBJECTIVE In this study, complete genome sequence of Spingobium sp. PAMC 28499 and comparative analysis of Spingobium species strains isolated from variety of the region. METHODS Genome sequencing was performed using PacBio sequel single-molecule real-time (SMRT) sequencing technology. The predicted gene sequences were functionally annotated and gene prediction was carried out using the program NCBI non-redundant database. And using dbCAN2 and KEGG data base were degradation pathway predicted and protein prediction about carbohydrate active enzymes (CAZymes). RESULTS The genome sequence has 64.5% GC content, 4432 coding protein coding genes, 61 tRNAs, and 12 rRNA operons. Its genome encodes a simple set of metabolic pathways relevant to pectin and its predicted degradation protein an unusual distribution of CAZymes with extracellular esterases and pectate lyases. CAZyme annotation analyses revealed 165 genes related to carbohydrate active, and especially we have found GH1, GH2, GH3, GH38, GH35, GH51, GH51, GH53, GH106, GH146, CE12, PL1 and PL11 such as known pectin degradation genes from Sphingobium yanoikuiae. These results confirmed that this Sphingobium sp. strain PAMC 28499 have similar patterns to RG I pectin-degrading pathway. CONCLUSION In this study, isolated and sequenced the complete genome of Spingobium sp. PAMC 28499. Also, this strain has comparative genome analysis. Through the complete genome we can predict how this strain can store and produce energy in extreme environment. It can also provide bioengineered data by finding new genes that degradation the pectin.
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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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do Prado SBR, Castro-Alves VC, Ferreira GF, Fabi JP. Ingestion of Non-digestible Carbohydrates From Plant-Source Foods and Decreased Risk of Colorectal Cancer: A Review on the Biological Effects and the Mechanisms of Action. Front Nutr 2019; 6:72. [PMID: 31157230 PMCID: PMC6529955 DOI: 10.3389/fnut.2019.00072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 04/30/2019] [Indexed: 12/13/2022] Open
Abstract
The hypothesis that links the increase in the intake of plant-source foods to a decrease in colorectal cancer (CRC) risk has almost 50 years. Nowadays, systematic reviews and meta-analysis of case-control and cohort studies confirmed the association between dietary patterns and CRC risk, in which the non-digestible carbohydrates (NDC) from plant-source foods are known to play beneficial effects. However, the mechanisms behind the physicochemical properties and biological effects induced by NDC on the decrease of CRC development and progression remain not fully understood. NDC from plant-source foods consist mainly of complex carbohydrates from plant cell wall including pectin and hemicellulose, which vary among foods in structure and in composition, therefore in both physicochemical properties and biological effects. In the present review, we highlighted the mechanisms and described the recent findings showing how these complex NDC from plant-source foods are related to a decrease in CRC risk through induction of both physicochemical effects in the gastrointestinal tract, fermentation-related effects, and direct effects resulting from the interaction between NDC and cellular components including toll-like receptors and galectin-3. Studies support that the definition of the structure-function relationship-especially regarding the fermentation-related effects of NDC, as well as the direct effects of these complex carbohydrates in cells-is crucial for understanding the possible NDC anticancer effects. The dietary recommendations for the intake of NDC are usually quantitative, describing a defined amount of intake per day. However, as NDC from plant-source foods can exert effects that vary widely according to the NDC structure, the dietary recommendations for the intake of NDC plant-source foods are expected to change from a quantitative to a qualitative perspective in the next few years, as occurred for lipid recommendations. Thus, further studies are necessary to define whether specific and well-characterized NDC from plant-source foods induce beneficial effects related to a decrease in CRC risk, thereby improving nutritional recommendations of healthy individuals and CRC patients.
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Affiliation(s)
- Samira Bernardino Ramos do Prado
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, Brazil
| | - Victor Costa Castro-Alves
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, Brazil
| | - Gabrielle Fernandez Ferreira
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - João Paulo Fabi
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, Brazil
- Food and Nutrition Research Center (NAPAN), University of São Paulo, São Paulo, Brazil
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Fabi JP, do Prado SBR. Fast and Furious: Ethylene-Triggered Changes in the Metabolism of Papaya Fruit During Ripening. FRONTIERS IN PLANT SCIENCE 2019; 10:535. [PMID: 31105730 PMCID: PMC6497978 DOI: 10.3389/fpls.2019.00535] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/08/2019] [Indexed: 06/09/2023]
Abstract
Papaya is a climacteric fleshy fruit characterized by fast ripening after harvest. During the relatively short postharvest period, papaya fruit undergoes several changes in metabolism that result in pulp softening and sweetening, as well as the development of a characteristic aroma. Since papaya is one of the most cultivated and appreciated tropical fruit crops worldwide, extensive research has been conducted to not only understand the formation of the quality and nutritional attributes of ripe fruit but also to develop methods for controlling the ripening process. However, most strategies to postpone papaya ripening, and therefore to increase shelf life, have failed to maintain fruit quality. Ethylene blockage precludes carotenoid biosynthesis, while cold storage can induce chilling injury and negatively affect the volatile profile of papaya. As a climacteric fruit, the fast ripening of papaya is triggered by ethylene biosynthesis. The generation of the climacteric ethylene positive feedback loop is elicited by the expression of a specific transcription factor that leads to an up-regulation of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase (ACS) and ACC-oxidase (ACO) expression, triggering the system II ethylene biosynthesis. The ethylene burst occurs about 3 to 4 days after harvest and induces pectinase expression. The disassembling of the papaya cell wall appears to help in fruit sweetness, while glucose and fructose are also produced by acidic invertases. The increase in ethylene production also results in carotenoid accumulation due to the induction of cyclases and hydroxylases, leading to yellow and red/orange-colored pulp phenotypes. Moreover, the production of volatile terpene linalool, an important biological marker for papaya's sensorial quality, is also induced by ethylene. All these mentioned processes are related to papaya's sensorial and nutritional quality. We describe the understanding of ethylene-triggered events that influence papaya quality and nutritional traits, as these characteristics are a consequence of an accelerated metabolism during fruit ripening.
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Affiliation(s)
- João Paulo Fabi
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, Brazil
- Food and Nutrition Research Center (NAPAN), University of São Paulo, São Paulo, Brazil
| | - Samira Bernardino Ramos do Prado
- Department of Food Science and Experimental Nutrition, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
- Food Research Center (FoRC), CEPID-FAPESP (Research, Innovation and Dissemination Centers, São Paulo Research Foundation), São Paulo, Brazil
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Li Y, Wang Y, Tu T, Zhang D, Ma R, You S, Wang X, Yao B, Luo H, Xu B. Two acidic, thermophilic GH28 polygalacturonases from Talaromyces leycettanus JCM 12802 with application potentials for grape juice clarification. Food Chem 2017; 237:997-1003. [DOI: 10.1016/j.foodchem.2017.06.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/01/2017] [Accepted: 06/06/2017] [Indexed: 11/29/2022]
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Wagschal KC, Rose Stoller J, Chan VJ, Jordan DB. Expression and Characterization of Hyperthermostable Exopolygalacturonase RmGH28 from Rhodothermus marinus. Appl Biochem Biotechnol 2017; 183:1503-1515. [DOI: 10.1007/s12010-017-2518-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 05/19/2017] [Indexed: 11/28/2022]
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Matsumoto S, Yamada H, Kunishige Y, Takenaka S, Nakazawa M, Ueda M, Sakamoto T. Identification of a novel Penicillium chrysogenum rhamnogalacturonan rhamnohydrolase and the first report of a rhamnogalacturonan rhamnohydrolase gene. Enzyme Microb Technol 2017; 98:76-85. [DOI: 10.1016/j.enzmictec.2016.12.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 11/04/2016] [Accepted: 12/26/2016] [Indexed: 01/29/2023]
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Brahem M, Renard CM, Gouble B, Bureau S, Le Bourvellec C. Characterization of tissue specific differences in cell wall polysaccharides of ripe and overripe pear fruit. Carbohydr Polym 2017; 156:152-164. [DOI: 10.1016/j.carbpol.2016.09.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/05/2016] [Accepted: 09/06/2016] [Indexed: 10/21/2022]
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Lee Y, Ayeh KO, Ambrose M, Hvoslef-Eide AK. Immunolocalization of pectic polysaccharides during abscission in pea seeds (Pisum sativum L.) and in abscission less def pea mutant seeds. BMC Res Notes 2016; 9:427. [PMID: 27581466 PMCID: PMC5007855 DOI: 10.1186/s13104-016-2231-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/19/2016] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND In pea seeds (Pisum sativum L.), the presence of the Def locus determines abscission event between its funicle and the seed coat. Cell wall remodeling is a necessary condition for abscission of pea seed. The changes in cell wall components in wild type (WT) pea seed with Def loci showing seed abscission and in abscission less def mutant peas were studied to identify the factors determining abscission and non-abscission event. METHODS Changes in pectic polysaccharides components were investigated in WT and def mutant pea seeds using immunolabeling techniques. Pectic monoclonal antibodies (1 → 4)-β-D-galactan (LM5), (1 → 5)-α-L-arabinan(LM6), partially de-methyl esterified homogalacturonan (HG) (JIM5) and methyl esterified HG (JIM7) were used for this study. RESULTS Prior to abscission zone (AZ) development, galactan and arabinan reduced in the predestined AZ of the pea seed and disappeared during the abscission process. The AZ cells had partially de-methyl esterified HG while other areas had highly methyl esterified HG. A strong JIM5 labeling in the def mutant may be related to cell wall rigidity in the mature def mutants. In addition, the appearance of pectic epitopes in two F3 populations resulting from cross between WT and def mutant parents was studied. As a result, we identified that homozygous dominant lines (Def/Def) showing abscission and homozygous recessive lines (def/def) showing non-abscission had similar immunolabeling pattern to their parents. However, the heterogeneous lines (Def/def) showed various immunolabeling pattern and the segregation pattern of the Def locus. CONCLUSIONS Through the study of the complexity and variability of pectins in plant cell walls as well as understanding the segregation patterns of the Def locus using immunolabeling techniques, we conclude that cell wall remodeling occurs in the abscission process and de-methyl esterification may play a role in the non-abscission event in def mutant. Overall, this study contributes new insights into understanding the structural and architectural organization of the cell walls during abscission.
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Affiliation(s)
- YeonKyeong Lee
- Department of Plant Sciences, Norwegian University of Life Sciences (NMBU), P.O. BOX 5003, 1432 Ås, Norway
| | - Kwadwo Owusu Ayeh
- Department of Botany, School of Biological Sciences, College of Basic and Applied Sciences, University of Ghana, Legon-Accra, Ghana
| | - Mike Ambrose
- Department of Crops Genetics, John Innes Centre, Norwich Research Park, Colney Lane, NR4 7UH Norwich, UK
| | - Anne Kathrine Hvoslef-Eide
- Department of Plant Sciences, Norwegian University of Life Sciences (NMBU), P.O. BOX 5003, 1432 Ås, Norway
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Expression and Characterization of Hyperthermostable Exo-polygalacturonase TtGH28 from Thermotoga thermophilus. Mol Biotechnol 2016; 58:509-19. [DOI: 10.1007/s12033-016-9948-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Pérez R, Eyzaguirre J. Aspergillus fumigatus Produces Two Arabinofuranosidases From Glycosyl Hydrolase Family 62: Comparative Properties of the Recombinant Enzymes. Appl Biochem Biotechnol 2016; 179:143-54. [DOI: 10.1007/s12010-016-1984-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/07/2016] [Indexed: 10/22/2022]
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Ngouémazong ED, Christiaens S, Shpigelman A, Van Loey A, Hendrickx M. The Emulsifying and Emulsion-Stabilizing Properties of Pectin: A Review. Compr Rev Food Sci Food Saf 2015. [DOI: 10.1111/1541-4337.12160] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Eugénie D. Ngouémazong
- Dept. of Microbial and Molecular Systems (M²S), Laboratory of Food Technology; Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Univ. Leuven; Kasteelpark Arenberg 22, Box 2457 3001 Leuven Belgium
| | - Stefanie Christiaens
- Dept. of Microbial and Molecular Systems (M²S), Laboratory of Food Technology; Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Univ. Leuven; Kasteelpark Arenberg 22, Box 2457 3001 Leuven Belgium
| | - Avi Shpigelman
- Dept. of Microbial and Molecular Systems (M²S), Laboratory of Food Technology; Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Univ. Leuven; Kasteelpark Arenberg 22, Box 2457 3001 Leuven Belgium
| | - Ann Van Loey
- Dept. of Microbial and Molecular Systems (M²S), Laboratory of Food Technology; Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Univ. Leuven; Kasteelpark Arenberg 22, Box 2457 3001 Leuven Belgium
| | - Marc Hendrickx
- Dept. of Microbial and Molecular Systems (M²S), Laboratory of Food Technology; Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Univ. Leuven; Kasteelpark Arenberg 22, Box 2457 3001 Leuven Belgium
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Iwai M, Kawakami T, Ikemoto T, Fujiwara D, Takenaka S, Nakazawa M, Ueda M, Sakamoto T. Molecular characterization of a Penicillium chrysogenum exo-rhamnogalacturonan lyase that is structurally distinct from other polysaccharide lyase family proteins. Appl Microbiol Biotechnol 2015; 99:8515-25. [PMID: 25921806 DOI: 10.1007/s00253-015-6600-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/14/2015] [Accepted: 04/01/2015] [Indexed: 10/23/2022]
Abstract
We previously described an endo-acting rhamnogalacturonan (RG) lyase, termed PcRGL4A, of Penicillium chrysogenum 31B. Here, we describe a second RG lyase, called PcRGLX. We determined the cDNA sequence of the Pcrglx gene, which encodes PcRGLX. Based on analyses using a BLAST search and a conserved domain search, PcRGLX was found to be structurally distinct from known RG lyases and might belong to a new polysaccharide lyase family together with uncharacterized fungal proteins of Nectria haematococca, Aspergillus oryzae, and Fusarium oxysporum. The Pcrglx cDNA gene product (rPcRGLX) expressed in Escherichia coli demonstrated specific activity against RG but not against homogalacturonan. Divalent cations were not essential for the enzymatic activity of rPcRGLX. rPcRGLX mainly released unsaturated galacturonosyl rhamnose (ΔGR) from RG backbones used as the substrate from the initial stage of the reaction, indicating that the enzyme can be classified as an exo-acting RG lyase (EC 4.2.2.24). This is the first report of an RG lyase with this mode of action in Eukaryota. rPcRGLX acted synergistically with PcRGL4A to degrade soybean RG and released ΔGR. This ΔGR was partially decorated with galactose (Gal) residues, indicating that rPcRGLX preferred oligomeric RGs to polymeric RGs, that the enzyme did not require Gal decoration of RG backbones for degradation, and that the enzyme bypassed the Gal side chains of RG backbones. These characteristics of rPcRGLX might be useful in the determination of complex structures of pectins.
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Affiliation(s)
- Marin Iwai
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Takuya Kawakami
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Takeshi Ikemoto
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Daisuke Fujiwara
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Shigeo Takenaka
- Division of Veterinary science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, 598-8531, Japan
| | - Masami Nakazawa
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Mitsuhiro Ueda
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan
| | - Tatsuji Sakamoto
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, 599-8531, Japan.
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Biochemical Characterization and Overexpression of an Endo-rhamnogalacturonan Lyase from Penicillium chrysogenum. Mol Biotechnol 2015; 57:539-48. [DOI: 10.1007/s12033-015-9847-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Babbar N, Dejonghe W, Gatti M, Sforza S, Elst K. Pectic oligosaccharides from agricultural by-products: production, characterization and health benefits. Crit Rev Biotechnol 2015; 36:594-606. [DOI: 10.3109/07388551.2014.996732] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Neha Babbar
- Separation & Conversion Technology, VITO-Flemish Institute for Technological Research, Boeretang, Mol, Belgium and
- Department of Food Science, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Winnie Dejonghe
- Separation & Conversion Technology, VITO-Flemish Institute for Technological Research, Boeretang, Mol, Belgium and
| | - Monica Gatti
- Department of Food Science, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Stefano Sforza
- Department of Food Science, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Kathy Elst
- Separation & Conversion Technology, VITO-Flemish Institute for Technological Research, Boeretang, Mol, Belgium and
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Biochemical characterization of uronate dehydrogenases from three Pseudomonads, Chromohalobacter salixigens, and Polaromonas naphthalenivorans. Enzyme Microb Technol 2014; 69:62-8. [PMID: 25640726 DOI: 10.1016/j.enzmictec.2014.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 11/20/2022]
Abstract
Enzyme catalysts will be vital in the development of synthetic biology approaches for converting pectinic monosaccharides from citrus and beet processing waste streams to value-added materials. We describe here the biophysical and mechanistic characterization of uronate dehydrogenases from a wide variety of bacterial sources that convert galacturonic acid, the predominate building block of pectin from these plant sources, and glucuronic acid to their corresponding dicarboxylic acids galactarate and glucarate, the latter being a DOE top value biochemical from biomass. The enzymes from Pseudomonas syringae and Polaromonas naphthalenivorans were found to have the highest reported kcat(glucuronic acid) values, on the order of 220-270 s(-1). The thermal stability of this enzyme type is described for the first time here, where it was found that the Kt((0.5)) value range was >20 °C, and the enzyme from Chromohalobacter was moderately thermostable with Kt((0.5))=62.2 °C. The binding mechanism for these bi-substrate enzymes was also investigated in initial rate experiments, where a predominately steady-state ordered binding pattern was indicated.
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Hugouvieux-Cotte-Pattat N, Condemine G, Shevchik VE. Bacterial pectate lyases, structural and functional diversity. ENVIRONMENTAL MICROBIOLOGY REPORTS 2014; 6:427-40. [PMID: 25646533 DOI: 10.1111/1758-2229.12166] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Pectate lyases are enzymes involved in plant cell wall degradation. They cleave pectin using a β-elimination mechanism, specific for acidic polysaccharides. They are mainly produced by plant pathogens and plant-associated organisms, and only rarely by animals. Pectate lyases are also commonly produced in the bacterial world, either by bacteria living in close proximity with plants or by gut bacteria that find plant material in the digestive tract of their hosts. The role of pectate lyases is essential for plant pathogens, such as Dickeya dadantii, that use a set of pectate lyases as their main virulence factor. Symbiotic bacteria produce their own pectate lyases, but they also induce plant pectate lyases to initiate the symbiosis. Pectin degradation products may act as signals affecting the plant–bacteria interactions. Bacterial pectate lyases are also essential for using the pectin of dead or living plants as a carbon source for growth. In the animal gut, Bacteroides pectate lyases degrade the pectin of ingested food, and this is particularly important for herbivores that depend on their microflora for the digestion of pectin. Some human pathogens, such as Yersinia enterocolitica, produce a few intracellular pectate lyases that can facilitate their growth in the presence of highly pectinolytic bacteria, at the plant surface, in the soil or in the animal gut.
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21
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Hamaker BR, Tuncil YE. A perspective on the complexity of dietary fiber structures and their potential effect on the gut microbiota. J Mol Biol 2014; 426:3838-50. [PMID: 25088686 DOI: 10.1016/j.jmb.2014.07.028] [Citation(s) in RCA: 343] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/30/2014] [Accepted: 07/23/2014] [Indexed: 12/22/2022]
Abstract
Even though there are many factors that determine the human colon microbiota composition, diet is an important one because most microorganisms in the colon obtain energy for their growth by degrading complex dietary compounds, particularly dietary fibers. While fiber carbohydrates that escape digestion in the upper gastrointestinal tract are recognized to have a range of structures, the vastness in number of chemical structures from the perspective of the bacteria is not well appreciated. In this article, we introduce the concept of "discrete structure" that is defined as a unique chemical structure, often within a fiber molecule, which aligns with encoded gene clusters in bacterial genomes. The multitude of discrete structures originates from the array of different fiber types coupled with structural variations within types due to genotype and growing environment, anatomical parts of the grain or plant, discrete regions within polymers, and size of oligosaccharides and small polysaccharides. These thousands of discrete structures conceivably could be used to favor bacteria in the competitive colon environment. A global framework needs to be developed to better understand how dietary fibers can be used to obtain predicted changes in microbiota composition for improved health. This will require a multi-disciplinary effort that includes biological scientists, clinicians, and carbohydrate specialists.
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Affiliation(s)
- Bruce R Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907-2009, USA.
| | - Yunus E Tuncil
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, 745 Agriculture Mall Drive, West Lafayette, IN 47907-2009, USA
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22
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Santos CR, Polo CC, Costa MCMF, Nascimento AFZ, Meza AN, Cota J, Hoffmam ZB, Honorato RV, Oliveira PSL, Goldman GH, Gilbert HJ, Prade RA, Ruller R, Squina FM, Wong DWS, Murakami MT. Mechanistic strategies for catalysis adopted by evolutionary distinct family 43 arabinanases. J Biol Chem 2014; 289:7362-73. [PMID: 24469445 DOI: 10.1074/jbc.m113.537167] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Arabinanases (ABNs, EC 3.2.1.99) are promising catalysts for environmentally friendly biomass conversion into energy and chemicals. These enzymes catalyze the hydrolysis of the α-1,5-linked L-arabinofuranoside backbone of plant cell wall arabinans releasing arabino-oligosaccharides and arabinose, the second most abundant pentose in nature. In this work, new findings about the molecular mechanisms governing activation, functional differentiation, and catalysis of GH43 ABNs are presented. Biophysical, mutational, and biochemical studies with the hyperthermostable two-domain endo-acting ABN from Thermotoga petrophila (TpABN) revealed how some GH43 ABNs are activated by calcium ions via hyperpolarization of the catalytically relevant histidine and the importance of the ancillary domain for catalysis and conformational stability. On the other hand, the two GH43 ABNs from rumen metagenome, ARN2 and ARN3, presented a calcium-independent mechanism in which sodium is the most likely substituent for calcium ions. The crystal structure of the two-domain endo-acting ARN2 showed that its ability to efficiently degrade branched substrates is due to a larger catalytic interface with higher accessibility than that observed in other ABNs with preference for linear arabinan. Moreover, crystallographic characterization of the single-domain exo-acting ARN3 indicated that its cleavage pattern producing arabinose is associated with the chemical recognition of the reducing end of the substrate imposed by steric impediments at the aglycone-binding site. By structure-guided rational design, ARN3 was converted into a classical endo enzyme, confirming the role of the extended Arg(203)-Ala(230) loop in determining its action mode. These results reveal novel molecular aspects concerning the functioning of GH43 ABNs and provide new strategies for arabinan degradation.
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23
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Design of thermostable rhamnogalacturonan lyase mutants from Bacillus licheniformis by combination of targeted single point mutations. Appl Microbiol Biotechnol 2014; 98:4521-31. [DOI: 10.1007/s00253-013-5483-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 12/17/2013] [Accepted: 12/20/2013] [Indexed: 11/26/2022]
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24
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Di Donato P, Poli A, Taurisano V, Nicolaus B. Polysaccharides: Applications in Biology and Biotechnology/Polysaccharides from Bioagro-Waste New Biomolecules-Life. POLYSACCHARIDES 2014. [DOI: 10.1007/978-3-319-03751-6_16-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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25
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Rozeboom HJ, Beldman G, Schols HA, Dijkstra BW. Crystal structure of endo-xylogalacturonan hydrolase fromAspergillus tubingensis. FEBS J 2013; 280:6061-9. [DOI: 10.1111/febs.12524] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 09/10/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Henriëtte J. Rozeboom
- Laboratory of Biophysical Chemistry; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; The Netherlands
| | - Gerrit Beldman
- Laboratory of Food Chemistry; Wageningen University; The Netherlands
| | - Henk A. Schols
- Laboratory of Food Chemistry; Wageningen University; The Netherlands
| | - Bauke W. Dijkstra
- Laboratory of Biophysical Chemistry; Groningen Biomolecular Sciences and Biotechnology Institute; University of Groningen; The Netherlands
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26
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Gapper NE, McQuinn RP, Giovannoni JJ. Molecular and genetic regulation of fruit ripening. PLANT MOLECULAR BIOLOGY 2013; 82:575-91. [PMID: 23585213 DOI: 10.1007/s11103-013-0050-3] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2013] [Accepted: 03/23/2013] [Indexed: 05/21/2023]
Abstract
Fleshy fruit undergo a novel developmental program that ends in the irreversible process of ripening and eventual tissue senescence. During this maturation process, fruit undergo numerous physiological, biochemical and structural alterations, making them more attractive to seed dispersal organisms. In addition, advanced or over-ripening and senescence, especially through tissue softening and eventual decay, render fruit susceptible to invasion by opportunistic pathogens. While ripening and senescence are often used interchangeably, the specific metabolic activities of each would suggest that ripening is a distinct process of fleshy fruits that precedes and may predispose the fruit to subsequent senescence.
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Affiliation(s)
- Nigel E Gapper
- Department of Horticulture, Cornell University, Ithaca, NY 14853, USA
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27
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Li B, Wang W, Zong Y, Qin G, Tian S. Exploring pathogenic mechanisms of Botrytis cinerea secretome under different ambient pH based on comparative proteomic analysis. J Proteome Res 2012; 11:4249-60. [PMID: 22746291 DOI: 10.1021/pr300365f] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Botrytis cinerea causes gray mold rot on over 200 plant species worldwide, resulting in great economic loss every year. Cooperation of proteins secreted by B. cinerea plays an important role in its successful infection to host plants. The ambient pH, as one of the most important environmental parameters, can regulate expression of secreted proteins in various fungal pathogens. In the present study, we mainly investigated the effect of ambient pH on secretome of B. cinerea strain B05.10 with a comparative proteomic method based on 2-DE. Distinct differences in secretome of B. cinerea were found between pH 4 and 6 treatments, and 47 differential spots, corresponding to 21 unique proteins, were identified using MALDI-TOF/TOF. At pH 4, more proteins related to proteolysis were induced, whereas most of up-accumulated proteins were cell wall degrading enzymes at pH 6. Analysis of gene expression using quantitative real-time PCR suggests that production of most of these proteins was regulated at the level of transcription. These findings indicate that B. cinerea can adjust protein profile of secretome responding to different ambient pH values and provide evidence to deeply understand the complicated infecting mechanisms of B. cinerea on a wide range of plant hosts.
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Affiliation(s)
- Boqiang Li
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
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28
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Konozy EHE, Causse M, Faurobert M. Cell wall glycosidase activities and protein content variations during fruit development and ripening in three texture contrasted tomato cultivars. Saudi J Biol Sci 2012; 19:277-83. [PMID: 23961187 DOI: 10.1016/j.sjbs.2012.04.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 04/09/2012] [Accepted: 04/23/2012] [Indexed: 11/28/2022] Open
Abstract
Excessive softening is the main factor limiting fruit shelf life and storage. It is generally acceptable now that softening of fruit which occurs during the ripening is due to synergistic actions of several enzymes on cell wall polysaccharides. As a subject for this study, we have assayed some glycosidase activities using three tomato species (Lycopersicon esculentum) contrasted for their texture phenotypes; the cherry tomato line Cervil (Solanum lycopersicum var. cerasiforme), a common taste tomato line Levovil (S. lycopersicum Mill.) and VilB a modern line, large, firmer and with good storage capability. Four glycosidase activities namely α-galactosidase, β-galactosidase, β-mannosidase and β-glucosidase were extracted from tomato's cell wall of the three species. Cell wall protein from fruits pericarp was extracted and compared among the three cultivars at the following stages; 14 days post anthesis (14DPA) fruit; 21 days post anthesis (21DPA), turning (breaker), red and over ripe. When glycolytic activities were also compared among these cultivars at the precited development stages, gross variations were noticed from stage to stage and also from species to species in accordance with the fruit firmness status. Interestingly, VilB cultivar, the firmer among the other two, though possessed the highest total protein content, exhibited the lowest enzymatic activities. Taken together, these results may therefore allow us to conclude that studies of glycolytic activities in a single tomato cultivar cannot be generalized to all species. On the other hand, relating fruit development to glycosidase activities should logically be coupled to these enzymes from cell wall compartment.
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Affiliation(s)
- Emadeldin H E Konozy
- INRA, Unité de Génétique et Amélioration des Fruits et Légumes, Montfavet BP94, France
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29
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Kim YS, Lim YR, Oh DK. l-Arabinose production from sugar beet arabinan by immobilized endo- and exo-arabinanases from Caldicellulosiruptor saccharolyticus in a packed-bed reactor. J Biosci Bioeng 2012; 113:239-41. [DOI: 10.1016/j.jbiosc.2011.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 10/11/2011] [Accepted: 10/12/2011] [Indexed: 12/01/2022]
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30
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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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31
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Fungal enzyme sets for plant polysaccharide degradation. Appl Microbiol Biotechnol 2011; 91:1477-92. [PMID: 21785931 PMCID: PMC3160556 DOI: 10.1007/s00253-011-3473-2] [Citation(s) in RCA: 347] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Revised: 06/27/2011] [Accepted: 07/10/2011] [Indexed: 02/01/2023]
Abstract
Enzymatic degradation of plant polysaccharides has many industrial applications, such as within the paper, food, and feed industry and for sustainable production of fuels and chemicals. Cellulose, hemicelluloses, and pectins are the main components of plant cell wall polysaccharides. These polysaccharides are often tightly packed, contain many different sugar residues, and are branched with a diversity of structures. To enable efficient degradation of these polysaccharides, fungi produce an extensive set of carbohydrate-active enzymes. The variety of the enzyme set differs between fungi and often corresponds to the requirements of its habitat. Carbohydrate-active enzymes can be organized in different families based on the amino acid sequence of the structurally related catalytic modules. Fungal enzymes involved in plant polysaccharide degradation are assigned to at least 35 glycoside hydrolase families, three carbohydrate esterase families and six polysaccharide lyase families. This mini-review will discuss the enzymes needed for complete degradation of plant polysaccharides and will give an overview of the latest developments concerning fungal carbohydrate-active enzymes and their corresponding families.
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Nakkeeran E, Umesh-Kumar S, Subramanian R. Aspergillus carbonarius polygalacturonases purified by integrated membrane process and affinity precipitation for apple juice production. BIORESOURCE TECHNOLOGY 2011; 102:3293-3297. [PMID: 21051226 DOI: 10.1016/j.biortech.2010.10.048] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2010] [Revised: 10/08/2010] [Accepted: 10/11/2010] [Indexed: 05/30/2023]
Abstract
Aspergillus carbonarius, when grown by submerged and solid-state fermentation, produces different molecular forms of polygalacturonase (PG; EC 3.2.1.15), among them a 42 kDa PG with a high specific activity of 7000 U/mg protein. When the enzymes were purified by integrated membrane process (IMP) and alginate affinity precipitation (AAP), the two processes concentrated different forms of the enzyme. The AAP process selectively purified and concentrated the high active PG whereas the IMP yielded different PGs and also amylase and protease. Evaluation of the AAP enzyme preparations for apple juice preparation under conditions usually employed commercially demonstrated that the high activity PG did not result in good juice clarity. With IMP processed enzymes, juice yields and clarity were similar to that obtained with commercial PG from A. niger.
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Affiliation(s)
- Ekambaram Nakkeeran
- Department of Food Engineering, Central Food Technological Research Institute, CSIR, Mysore, India
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Seo ES, Lim YR, Kim YS, Park CS, Oh DK. Characterization of a recombinant endo-1,5-α-l-arabinanase from the isolated bacterium Bacillus licheniformis. BIOTECHNOL BIOPROC E 2010. [DOI: 10.1007/s12257-009-3138-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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34
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Feng B, Huang HZ, Zhou WB, Kang LP, Zou P, Liu YX, Yu HS, Han BQ, Li YY, Zhang LL, Zhang T, Ma BP. Substrate specificity, purification and identification of a novel pectinase with the specificity of hydrolyzing the α-1,4-glycosyl residue in steroidal saponin. Process Biochem 2010. [DOI: 10.1016/j.procbio.2010.05.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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35
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Hong MR, Park CS, Oh DK. Characterization of a thermostable endo-1,5-α-l-arabinanase from Caldicellulorsiruptor saccharolyticus. Biotechnol Lett 2009; 31:1439-43. [DOI: 10.1007/s10529-009-0019-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Revised: 04/13/2009] [Accepted: 04/28/2009] [Indexed: 10/20/2022]
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36
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Duvetter T, Sila D, Van Buggenhout S, Jolie R, Van Loey A, Hendrickx M. Pectins in Processed Fruit and Vegetables: Part I-Stability and Catalytic Activity of Pectinases. Compr Rev Food Sci Food Saf 2009. [DOI: 10.1111/j.1541-4337.2009.00070.x] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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37
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Cloning and characterization of a novel exo-α-1,5-L-arabinanase gene and the enzyme. Appl Microbiol Biotechnol 2008; 79:941-9. [DOI: 10.1007/s00253-008-1504-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 04/04/2008] [Accepted: 04/14/2008] [Indexed: 10/22/2022]
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