Pectinolytic lyases: a comprehensive review of sources, category, property, structure, and catalytic mechanism of pectate lyases and pectin lyases.
Biochemical properties
Catalytic mechanism
Pectate lyase
Pectin lyase
Sequence analysis
Structure
Journal
Bioresources and bioprocessing
ISSN: 2197-4365
Titre abrégé: Bioresour Bioprocess
Pays: Germany
ID NLM: 101665551
Informations de publication
Date de publication:
23 Aug 2021
23 Aug 2021
Historique:
received:
03
08
2021
accepted:
16
08
2021
medline:
23
8
2021
pubmed:
23
8
2021
entrez:
23
4
2024
Statut:
epublish
Résumé
Pectate lyases and pectin lyases have essential roles in various biotechnological applications, such as textile industry, paper making, pectic wastewater pretreatment, juice clarification and oil extraction. They can effectively cleave the α-1,4-glycosidic bond of pectin molecules back bone by β-elimination reaction to produce pectin oligosaccharides. In this way, it will not generate highly toxic methanol and has the advantages of good enzymatic selectivity, less by-products, mild reaction conditions and high efficiency. However, numerous researches have been done for several decades; there are still no comprehensive reviews to summarize the recent advances of pectate lyases and pectin lyases. This review tries to fill this gap by providing all relevant information, including the substrate, origin, biochemical properties, sequence analysis, mode of action, the three-dimensional structure and catalytic mechanism.
Identifiants
pubmed: 38650254
doi: 10.1186/s40643-021-00432-z
pii: 10.1186/s40643-021-00432-z
doi:
Types de publication
Journal Article
Review
Langues
eng
Pagination
79Subventions
Organisme : national natural science foundation of china
ID : 31601410
Informations de copyright
© 2021. The Author(s).
Références
Abbott DW, Boraston AB (2007) A family 2 pectate lyase displays a rare fold and transition metal-assisted β-elimination. J Biol Chem 282(48):35328–35336
doi: 10.1074/jbc.M705511200
Anand G, Yadav S, Yadav D (2017) Production, purification and biochemical characterization of an exo-polygalacturonase from Aspergillus niger MTCC 478 suitable for clarification of orange juice. 3 Biotech 7(2):122
doi: 10.1007/s13205-017-0760-3
Bekli S, Aktas B, Gencer D, Aslim B (2019) Biochemical and molecular characterizations of a novel pH- and temperature-stable pectate lyase from Bacillus amyloliquefaciens S6 for industrial application. Mol Biotechnol 61(9):1–13
doi: 10.1007/s12033-019-00194-2
Bermúdez-Oria A, Rodríguez-Gutiérrez G, Rodríguez-Juan E, González-Benjumea A, Fernández-Bolaños J (2018) Molecular interactions between 3,4-dihydroxyphenylglycol and pectin and antioxidant capacity of this complex in vitro. Carbohydr Polym 197:260–268. https://doi.org/10.1016/j.carbpol.2018.05.089
doi: 10.1016/j.carbpol.2018.05.089
pubmed: 30007612
Boland WE, Henriksen ED, Doran-Peterson J (2010) Characterization of two Paenibacillus amylolyticus Strain 27C64 pectate lyases with activity on highly methylated pectin. Appl Environ Microbiol 76(17):6006–6009
doi: 10.1128/AEM.00043-10
Bonnin E, Ralet MC, Thibault JF, Schols HA (2009) Enzymes for the valorisation of fruit- and vegetable-based co-products. Handb Waste Manag Co Prod Recovery Food Process 27:257–285
Charnock SJ, Brown IE, Turkenburg JP, Black GW, Davies GJ (2002) Convergent evolution sheds light on the anti-beta -elimination mechanism common to family 1 and 10 polysaccharide lyases. Proc Natl Acad Sci USA 99(19):12067–12072. https://doi.org/10.1073/pnas.182431199
doi: 10.1073/pnas.182431199
pubmed: 12221284
pmcid: 129399
Chen J, Liang R-H, Liu W, Li T, Liu C-M, Wu S-S, Wang Z-J (2013) Pectic-oligosaccharides prepared by dynamic high-pressure microfluidization and their in vitro fermentation properties. Carbohydr Polym 91(1):175–182. https://doi.org/10.1016/j.carbpol.2012.08.021
doi: 10.1016/j.carbpol.2012.08.021
pubmed: 23044120
Creze C, Castang S, Derivery E, Haser R, Hugouvieux-Cotte-Pattat N, Shevchik VE, Gouet P (2008) The crystal structure of pectate lyase peli from soft rot pathogen Erwinia chrysanthemi in complex with its substrate. J Biol Chem 283(26):18260–18268. https://doi.org/10.1074/jbc.M709931200
doi: 10.1074/jbc.M709931200
pubmed: 18430740
Damak N, Hadj-Taieb N, Bonnin E, Bacha AB, Gargouri A (2011) Purification and biochemical characterization of a novel thermoactive fungal pectate lyase from Penicillium occitanis. Process Biochem 46(4):888–893
doi: 10.1016/j.procbio.2010.12.014
Dong Z, Yang Y, Wang Z, Qin S, Zhao B (2011) Isolation, expression and comparison of a pectate lyase produced by Fusarium oxysporum f. sp. cubense race 1 and race 4. Afr J Biotechnol 9(53):8984–8990
Gang L, Lang R, Xue Y, Cheng Z, Ma Y (2010) Cloning, expression, and characterization of a highly active alkaline pectate lyase from alkaliphilic Bacillus sp. N16–5. J Microbiol Biotechnol 20(4):670
doi: 10.4014/jmb.0911.11019
Garron ML, Cygler M (2010) Structural and mechanistic classification of uronic acid-containing polysaccharide lyases. Glycobiology. https://doi.org/10.1093/glycob/cwq12
doi: 10.1093/glycob/cwq12
pubmed: 20805221
Gómez B, Yáñez R, Parajó J, Alonso JL (2014) Production of pectin-derived oligosaccharides from lemon peels by extraction, enzymatic hydrolysis and membrane filtration. J Chem Technol Biotechol 91(1):234–247
doi: 10.1002/jctb.4569
Hamdy HS (2005) Purification and characterization of the pectin lyase produced by Rhizopus oryzae grown on orange peels. Ann Microbiol 55(3):205–211
Heffron SE, Henrissat B, Yoder M, Lietzke SE, Jurnak F (1995) Structure-based multiple alignment of extracellular pectate lyase sequences. Mol Plant Microbe Interact 8(2):331–334
doi: 10.1094/MPMI-8-0331
Jayani RS, Saxena S, Gupta R (2005) Microbial pectinolytic enzymes: a review. Process Biochem 40(9):2931–2944
doi: 10.1016/j.procbio.2005.03.026
Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, Pickersgill RW (2004) The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi. J Biol Chem 279(10):9139–9145
doi: 10.1074/jbc.M311390200
Kamijo J, Sakai K, Suzuki H, Suzuki K, Kunitake E, Shimizu M, Kato M (2019) Identification and characterization of a thermostable pectate lyase from Aspergillus luchuensis var. saitoi. Food Chem 276:503–510. https://doi.org/10.1016/j.foodchem.2018.10.059
doi: 10.1016/j.foodchem.2018.10.059
pubmed: 30409626
Kang HJ, Jo C, Kwon JH, Son JH, An BJ, Byun MW (2006) Antioxidant and cancer cell proliferation inhibition effect of citrus pectin-oligosaccharide prepared by irradiation. J Med Food 9(3):313–320. https://doi.org/10.1089/jmf.2006.9.313
doi: 10.1089/jmf.2006.9.313
pubmed: 17004892
Kashyap DR, Vohra PK, Chopra S, Tewari R (2001) Applications of pectinases in the commercial sector: a review. Bioresour Technol 77(3):215–227
doi: 10.1016/S0960-8524(00)00118-8
Kikuchi T, Shibuya H, Aikawa T, Jones JT (2006) Cloning and characterization of pectate lyases expressed in the esophageal gland of the pine wood nematode Bursaphelenchus xylophilus. Mol Plant Microbe Interact 19(3):280–287
doi: 10.1094/MPMI-19-0280
Kita N, Boyd CM, Garrett MR, Jurnak F, Keen NT (1996) Differential effect of site-directed mutations in pelC on pectate lyase activity, plant tissue maceration, and elicitor activity. J Biol Chem 271(43):26529–26535
doi: 10.1074/jbc.271.43.26529
Kohli P, Gupta R (2015) Alkaline pectinases: a review. Biocatal Agric Biotechnol 4(3):S1878818115000821
doi: 10.1016/j.bcab.2015.07.001
Lee D-W, Kang JS, Jung CS, Han HR, Moon YS, Park SJ, Koh YH (2013) Identification and biochemical analysis of a novel pectate lyase 3 gene in Bursaphelenchus xylophilus. J Asia Pac Entomol 16(3):335–342. https://doi.org/10.1016/j.aspen.2013.04.016
doi: 10.1016/j.aspen.2013.04.016
Li P-J, Xia J-L, Nie Z-Y, Shan Y (2016) Pectic oligosaccharides hydrolyzed from orange peel by fungal multi-enzyme complexes and their prebiotic and antibacterial potentials. LWT Food Sci Technol 69:203–210. https://doi.org/10.1016/j.lwt.2016.01.042
doi: 10.1016/j.lwt.2016.01.042
Liang C, Gui X, Cheng Z, Xue Y, Tang SY (2014) Improving the thermoactivity and thermostability of pectate lyase from Bacillus pumilus for ramie degumming. Appl Microbiol Biotechol 99(6):2673–2682
doi: 10.1007/s00253-014-6091-y
Lietzke SE, Scavetta RD, Yoder MD, Jurnak F (1996) The refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi at 2.2 A resolution. Plant Physiol 111(1):73–92
doi: 10.1104/pp.111.1.73
Lima JO, Pereira JF, Araújo EF, Queiroz MV (2017) Pectin lyase overproduction by Penicillium griseoroseum mutants resistant to catabolite repression. Braz J Microbiol. https://doi.org/10.1016/j.bjm.2016.12.009
doi: 10.1016/j.bjm.2016.12.009
pubmed: 29107584
pmcid: 5913826
Liu M-Q, Huo W-K, Dai X, Dang Y-H (2018) Preparation of low-molecular-weight citrus pectin by recombinant Bacillus subtilis pectate lyase and promotion of growth of Bifidobacterium longum. Catal Commun 107:39–42. https://doi.org/10.1016/j.catcom.2018.01.017
doi: 10.1016/j.catcom.2018.01.017
Ma G, Zhu W, Liu Y (2016) QM/MM studies on the calcium-assisted β-elimination mechanism of pectate lyase from Bacillus subtilis. Proteins. https://doi.org/10.1002/prot.25103
doi: 10.1002/prot.25103
pubmed: 27802576
pmcid: 5313341
Michener W, Bomble YJ, Lunin E (2015) The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase. Acta Crystallogr D Biol Crystallogr. https://doi.org/10.1107/S1399004715013760
doi: 10.1107/S1399004715013760
pubmed: 26327384
pmcid: 4556314
Novoa de Armas H, Verboven C, De Ranter C, Desair J, Vande Broek A, Vanderleyden J, Rabijns A (2004) Azospirillum irakense pectate lyase displays a toroidal fold. Acta Crystallogr D Biol Crystallogr 60(6):999–1007
doi: 10.1107/S090744490400602X
Ogawa A, Sawada K, Saito K, Hakamada Y, Ito S (2000) A new high-alkaline and high-molecular-weight pectate lyase from a Bacillus isolate: enzymatic properties and cloning of the gene for the enzyme. Biosci Biotechnol Bioch 64(6):1133–1141
doi: 10.1271/bbb.64.1133
Olano-martin E, Gibson GR, Rastall RA (2002) Comparison of the in vitro bifidogenic properties of pectins and pectic, ligosaccharides. J Appl Microbiol 93(3):505
doi: 10.1046/j.1365-2672.2002.01719.x
Pérez S, Mazeau K, Penhoat CH (2000) The three-dimensional structures of the pectic polysaccharides. Plant Physiol Bioch 38(1–2):37–55
doi: 10.1016/S0981-9428(00)00169-8
Pickersgill R, Jenkins J, Harris G, Nasser W, Robert-Baudouy J (1994) The structure of Bacillus subtilis pectate lyase in complex with calcium. Nat Struct Mol Biol 1(10):717–723
doi: 10.1038/nsb1094-717
Saharan R, Sharma KP (2019) Production, purification and characterization of pectin lyase from Bacillus subtilis isolated from moong beans leaves (Vigna radiata). Biocatal Agric Biotechnol 21:101306. https://doi.org/10.1016/j.bcab.2019.101306
doi: 10.1016/j.bcab.2019.101306
Sakiyama C, Paula EM, Pereira PC, Borges AC, Silva DO (2010) Characterization of pectin lyase produced by an endophytic strain isolated from coffee cherries. Lett Appl Microbiol 33(2):117–121
doi: 10.1046/j.1472-765x.2001.00961.x
Sassi AH, Trigui-Lahiani H, Abdeljalil S, Gargouri A (2017) Enhancement of solubility, purification and inclusion-bodies-refolding of an active pectin lyase from Penicillium occitanis expressed in Escherichia coli. Int J Biol Macromol 95:256–262
doi: 10.1016/j.ijbiomac.2016.11.036
Scavetta RD (1999) Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell 11(6):1081–1092
doi: 10.1105/tpc.11.6.1081
Scavetta RD, Herron SR, Hotchkiss AT, Kita N, Keen NT, Benen JA, Jurnak F (1999) Structure of a plant cell wall fragment complexed to pectate lyase C. Plant Cell 11(6):1081–1092. https://doi.org/10.1105/tpc.11.6.1081
doi: 10.1105/tpc.11.6.1081
pubmed: 10368179
pmcid: 144236
Seyedarabi A, To TT, Ali S, Hussain S, Fries M, Madsen R, Pickersgill RW (2010) Structural insights into substrate specificity and the anti beta-elimination mechanism of pectate lyase. Biochemistry 49(3):539–546. https://doi.org/10.1021/bi901503g
doi: 10.1021/bi901503g
pubmed: 20000851
Sharma HP, Patel H, Sugandha S (2016) Enzymatic extraction and clarification of juice from various fruits: a review. Crit Rev Food Sci Nutr. https://doi.org/10.1080/10408398.2014.977434
doi: 10.1080/10408398.2014.977434
pubmed: 25830555
Sinitsyna OA, Fedorova EA, Semenova MV, Gusakov AV, Sokolova LM, Bubnova TM, Sinitsyn AP (2007) Isolation and characterization of extracellular pectin lyase from Penicillium canescens. Biochemistry 72(5):565–571. https://doi.org/10.1134/s0006297907050148
doi: 10.1134/s0006297907050148
pubmed: 17573712
Tang Q, Liu YP, Ren ZG, Yan XX, Zhang LQ (2013) 1.37 Å Crystal structure of pathogenic factor pectate lyase from Acidovorax citrulli. Proteins 81(8):1485–1490
doi: 10.1002/prot.24298
Tobias W, Anna N, Stefan C-L (2017) Reassessment of chitosanase substrate specificities and classification. Nat Commun. https://doi.org/10.1038/s41467-017-01667-1
doi: 10.1038/s41467-017-01667-1
pubmed: 29123117
pmcid: 5680334
Trollinger D, Berry S, Belser W, Keen NT (1989) Cloning and characterization of a pectate lyase gene from Erwinia carotovora EC153. Mol Plant Microbe Interact 2(1):17–25
doi: 10.1094/MPMI-2-017
Vasco-Correa J, Zapata Zapata AD (2017) Enzymatic extraction of pectin from passion fruit peel (Passiflora edulis f. flavicarpa) at laboratory and bench scale. LWT Food Sci Technol 80:280–285
doi: 10.1016/j.lwt.2017.02.024
Vincent L, Hemalatha GR, Elodie D, Coutinho PM, Bernard H (2013) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res. https://doi.org/10.1093/nar/gkt1178
doi: 10.1093/nar/gkt1178
pubmed: 23361466
pmcid: 3597676
Vitali J, Schick B, Kester HC, Visser J, Jurnak F (1998) The three-dimensional structure of Aspergillus niger pectin lyase B at 1.7-Å resolution. Plant Physiol 116(1):69–80
doi: 10.1104/pp.116.1.69
Wang H, Li X, Ma Y, Song J (2014) Characterization and high-level expression of a metagenome-derived alkaline pectate lyase in recombinant Escherichia coli. Process Biochem 49(1):69–76. https://doi.org/10.1016/j.procbio.2013.10.001
doi: 10.1016/j.procbio.2013.10.001
Wang Z, Xu B, Luo H, Meng K, Tu T (2019) Production pectin oligosaccharides using Humicola insolens Y1-derived unusual pectate lyase. J Biosci Bioeng 129(1):16
doi: 10.1016/j.jbiosc.2019.07.005
Wu P, Yang S, Zhan Z, Zhang G (2020) Origins and features of pectate lyases and their applications in industry. Appl Microbiol Biotechnol. https://doi.org/10.1007/s00253-020-10769-8
doi: 10.1007/s00253-020-10769-8
pubmed: 33216160
pmcid: 7347694
Yadav S, Yadav PK, Yadav D, Yadav K (2008a) Purification and characterisation of an acidic pectin lyase produced by Aspergillus ficuum strain MTCC 7591 suitable for clarification of fruit juices. Ann Microbiol 58(1):61–65
doi: 10.1007/BF03179446
Yadav S, Yadav PK, Yadav D, Yadav KD (2008b) Purification and characterization of an alkaline pectin lyase from Aspergillus flavus. Process Biochem 43(5):547–552. https://doi.org/10.1016/j.procbio.2008.01.015
doi: 10.1016/j.procbio.2008.01.015
Yadav S, Yadav PK, Yadav D, Yadav K (2009a) Purification and characterization of pectin lyase produced by Aspergillus terricola and its application in retting of natural fibers. Appl Biochem Biotechnol 159(1):270–283
doi: 10.1007/s12010-008-8471-1
Yadav S, Yadav PK, Yadav D, Yadav KDS (2009b) Pectin lyase: a review. Process Biochem 44(1):1–10
doi: 10.1016/j.procbio.2008.09.012
Yan Z, Ye Y, Xinyu Z (2018) Screening of a novel polysaccharide lyase family 10 pectate lyase from Paenibacillus polymyxa KF-1: cloning expression and characterization. Molecules. https://doi.org/10.3390/molecules23112774
doi: 10.3390/molecules23112774
pubmed: 30586897
pmcid: 6337326
Yang G, Chen W, Tan H, Li K, Li J, Yin H (2020) Biochemical characterization and evolutionary analysis of a novel pectate lyase from Aspergillus parasiticus. Int J Biol Macromol 152:180–188. https://doi.org/10.1016/j.ijbiomac.2020.02.279
doi: 10.1016/j.ijbiomac.2020.02.279
pubmed: 32109469
Yoder MD, Keen NT, Jurnak F (1993) New domain motif: the structure of pectate lyase C, a secreted plant virulence factor. Science 260(5113):1503
doi: 10.1126/science.8502994
Yuan P, Meng K, Wang Y, Luo H, Shi P, Huang H, Yao B (2012) A low-temperature-active alkaline pectate lyase from Xanthomonas campestris ACCC 10048 with high activity over a wide pH range. Appl Biochem Biotechnol 168(6):1489–1500
doi: 10.1007/s12010-012-9872-8
Zhai C, Cao J, Wang Y (2003) Cloning and expression of a pectate lyase gene from Bacillus alcalophillus NTT33. Enzyme MicrobTechnol 33(2–3):173–178
doi: 10.1016/S0141-0229(03)00091-7
Zheng Y, Huang CH, Liu W, Ko TP, Xue Y, Zhou C, Ma Y (2012) Crystal structure and substrate-binding mode of a novel pectate lyase from Alkaliphilic Bacillus sp. N16–5. Biochem Biophys Res Commun 420(2):274
doi: 10.1016/j.bbrc.2012.02.148
Zhou C, Xue Y, Ma Y (2017a) Characterization and overproduction of a thermo-alkaline pectate lyase from alkaliphilic Bacillus licheniformis with potential in ramie degumming. Process Biochem 54:49–58. https://doi.org/10.1016/j.procbio.2017.01.010
doi: 10.1016/j.procbio.2017.01.010
Zhou Z, Liu Y, Chang Z, Wang H, Leier A, Marquez-Lago TT, Song J (2017b) Structure-based engineering of a pectate lyase with improved specific activity for ramie degumming. Appl Microbiol Biotechnol 101(7):2919–2929
doi: 10.1007/s00253-016-7994-6
Zhu R, Wang C, Zhang L, Wang Y, Chen G, Fan J, Ning C (2019) Pectin oligosaccharides from fruit of Actinidia arguta: structure-activity relationship of prebiotic and antiglycation potentials. Carbohydr Polym 217:90–97. https://doi.org/10.1016/j.carbpol.2019.04.032
doi: 10.1016/j.carbpol.2019.04.032
pubmed: 31079689