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. 2010 Sep 19;2010:950230. doi: 10.4061/2010/950230

In Silico Characterization of Pectate Lyase Protein Sequences from Different Source Organisms

Amit Kumar Dubey 1, Sangeeta Yadav 1, Manish Kumar 1, Vinay Kumar Singh 2, Bijaya Ketan Sarangi 3, Dinesh Yadav 1,*
PMCID: PMC2962914  PMID: 21048874

Abstract

A total of 121 protein sequences of pectate lyases were subjected to homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis. The phylogenetic tree constructed revealed different clusters based on different source organisms representing bacterial, fungal, plant, and nematode pectate lyases. The multiple accessions of bacterial, fungal, nematode, and plant pectate lyase protein sequences were placed closely revealing a sequence level similarity. The multiple sequence alignment of these pectate lyase protein sequences from different source organisms showed conserved regions at different stretches with maximum homology from amino acid residues 439–467, 715–816, and 829–910 which could be used for designing degenerate primers or probes specific for pectate lyases. The motif analysis revealed a conserved Pec_Lyase_C domain uniformly observed in all pectate lyases irrespective of variable sources suggesting its possible role in structural and enzymatic functions.

1. Introduction

The enzymes hydrolyzing pectic substances ubiquitously present in the plant kingdom forming major components of middle lamella are referred as pectinases. The production, purification, biochemical characterization, and application of pectinases have been extensively reviewed [1–10]. The pectinases include polygalacturonases, pectic esterases, pectin lyases, and pectate lyases depending on their mode of action [1].

Pectate lyase (PL, EC 4.2.2.2) cleaves the α-1,4 glycosidic bonds of polygalacturonic acid via a β-elimination reaction producing unsaturated ∆4, 5 bond at the nonreducing end of the polysaccharide and generates 4,5-unsaturated oligogalacturonates. Pectate lyase is widely distributed in diverse families of microorganisms and plants. The important members of bacterial family include Erwinia carotovora, Bacillus polymyxa, Klebsiella, Yersinia, Cytophaga, Pseudomonas, and Xanthomonas while in fungi Aspergillus, Fusarium, and Penicillium are the most predominant source [9, 11–14].

A number of pectate lyase genes have been cloned, sequenced, and expressed from different source organism, namely, bacteria [15–22], fungi [23–25], yeast [26], nematode [27] and plants [14, 28].

The three-dimensional structures of various extracellular pectate lyase have been reported [29–36]. The pectate lyases, in general, have a parallel β-helix domain formed by parallel-strands folded into a large right-handed helix and a major loop region.

Amino acid sequence homology-based classification of pectate lyases into distinct families suggesting the possible evolution from different lineages has been reported [20, 35, 37–44]. In silico analysis of pectin lyase protein sequences has been recently reported [45].

This paper reports in silico characterization of pectate lyase protein sequences from different source organisms for homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis using various bioinformatics tools.

2. Materials and Methods

A total of 121 protein sequences of pectate lyases of different source organism available in GenBank were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/). The accession numbers of pectate lyases protein sequences along with the source organism are listed in Table 1.

Table 1.

List of pectate lyase protein sequences with respective accession number from different source organisms.

Group Total number Accession number (Source organism name)
Nematode 06 AAQ09004.1[Meloidogyne incognita], AAL66022.1|AF455757 1[Meloidogyne javanica], AAF80747.1[Globodera rostochiensis], BAE48375.1[Bursaphelenchus mucronatus], BAE48371.1[Bursaphelenchus xylophilus], BAI44500.1[Aphelenchus avenae]
Plant 17 CAA47630.1[Nicotiana tabacum], NP 001150723.1[Zea mays], AAA33398.1[Lilium longiflorum], CAA70735.1[Zinnia elegans], AAQ84042.1[Malus x domestica], BAE48664.1| Prunus mume], AAY85180.1[Gossypium hirsutum], AAF63756.1|AF243475 1[Vitis vinifera], BAB59066.1[Salix gilgiana], gi|1256509|emb|CAA63496.1[Musa acuminata], AAK66161.1[Fragaria x ananassa], BAF43573.1[Prunus persica], ACF40835.1[Manilkara zapota], ABG66729.2[Carica papaya], AAM63307.1[ Arabidopsis thaliana], ABR26682.1[Fragaria chiloensis], ABD47739.1[Eucalyptus globulus subsp. Globules
Fungi 10 AAA80568.1[Emericella nidulans], ABM60783.1[Penicillium citrinum], AAA75471.1[Glomerella cingulata], AAC64368.1[Fusarium oxysporum f. sp. lycopersici], ACS78057.1[ Fusarium oxysporum f. cubense], EEY55044.1[Phytophthora infestans T30-4], XP 749217.1[Aspergillus fumigatus Af293], AAA80568.1[Emericella nidulans], ABM60783.1[Penicillium citrinum], EEY23761.1[Verticillium albo-atrum VaMs.102]
Bacteria 87 AAB46398.1[Pseudomonas viridiflava], AAC60448.1[Pseudomonas marginalis], AAL56657.1[Pseudomonas syringae pv. glycinea], AAC41522.1[Xanthomonas campestris], AAM38405.1[Xanthomonas axonopodis pv citri str 306], YP 001915548.1|[Xanthomonas oryzae PXO99A], AAY50632.1|[Xanthomonas campestris pv campestris str 8004], YP 001314702.1[Sinorhizobium medicae WSM419], ZP 06003184.1[Selenomonas noxia ATCC 43541], ZP 04658159.1[Selenomonas flueggei ATCC 43531], ACH58409.1|[Bacillus subtilis], BAA05383.1[Bacillus sp. YA-14], ZP 05725973.1[Dickeya dadantii Ech586], NP 866630.1[Rhodopirellula baltica SH1], NP 228243.1[Thermotoga maritima MSB8], ACR10769.1[Teredinibacter turnerae T7901], ZP 04713986.1[Alteromonas macleodii ATCC 27126], ZP 04334947.1[Nocardiopsis dassonvillei subsp. dassonvillei DSM 43111], AAZ56201.1[Thermobifida fusca YX], AAW84086.1[Bacillus halodurans], ACD11362.1[Bacillus pumilus], AAC38059.1[Pseudonocardia sp.], ZP 04608172.1[Micromonospora sp ATCC 39149], ZP 05021985.1[Streptomyces sviceus ATCC 33406], YP 677777.1[Cytophaga hutchinsonii ATCC 33406], CAA43401.1[Pectobacterium carotovorum], CAA47821.1[Erwinia chrysanthemi], ABF59812.1[Erwinia sp. BTC105], NP 866628.1[Rhodopirellula baltica SH 1], ZP 01721007.1[Algoriphagus sp PR1], ZP 01851785.1[Planctomyces maris DSM 8797], ACL96719.1[Caulobacter crescentus NA1000], AAO79220.1[Bacteroides thetaiotaomicron VPI-5482], ABC76269.1[Syntrophus aciditrophicus SB], YP 618077.1[Sphingopyxis alaskensis RB2256], EER49733.1[Asticcacaulis excentricus CB 48], YP 527779.1[Saccharophagus degradans 2-40], YP 356933.1[Pelobacter carbinolicus DSM 2380], CAB40884.1[Paenibacillus barcinonensis BP23], YP 001615581.1[Sorangium cellulosum 'So ce 56'], YP 002573715.1[Anaerocellum thermophilum DSM 6725], ACU58213.1[Chitinophaga pinensis DSM 2588], ZP 00943832.1[Ralstonia solanacearum UW 551], CAG74004.1[Pectobacterium atrosepticum SCRI1043], YP 432149.1[Hahella chejuensis KCTC 2396], ZP 05805856.1[Streptomyces flavogriseus ATCC 33331], ZP 05542020.1[Streptomyces griseoflavus Tu4000], ZP 04688982.1[Streptomyces ghanaensis ATCC 14672], ZP 05530610.1[Streptomyces viridochromogenes DSM 40736], NP 827559.1[Streptomyces avermitilis MA-4680], BAH85845.1| [Streptomyces thermocarboxydus], ZP 05514668.1[Streptomyces hygroscopicus ATCC 53653], YP 001506642.1[Frankia sp EAN1pec], ZP 05011753.1[Streptomyces pristinaespiralis ATCC 25486], ACV08000.1[Jonesia denitrificans DSM 20603], ZP 04367351.1[Cellulomonas flavigena DSM 20109]
YP 001106556.1[Saccharopolyspora erythraea NRRL 2338], ACU38032.1[Actinosynnema mirum DSM 43827], AAL51034.1|AF454849 1[Klebsiella oxytoca], NP 149220.1[Clostridium acetobutylicum ATCC 824], YP 003248772.1[Fibrobacter_succinogenes ssp succinogens], ZP 04805707.1[Clostridium_cellulovorans_743B], YP002505581.1[Clostridium_cellulolyticum_H10], ZP 05495790.1[Clostridium_papyrosolvens_DSM_2782], AAG24437.1|AF303225 1[Bacillus alcalophilus], BAD63679.1[Bacillus_clausii_KSM-K16], YP 003091439.1[Pedobacter_heparinus_DSM_2366], EER72050.1[Sphingobacterium_spiritivorum_ATCC_33861], ZP 06173220.1[Brevundimonas subvibrioides ATCC15264], ABJ82092.1[Candidatus solibacter usitatus Ellin6076], EEX43407.1[Bacteroides finegoldii DSM 17565], ZP 06083351.1[Bacteroides sp. 2 1 22], YP 001196575.1[Flavobacterium johnsoniae UW101], ACU08313.1[Flavobacteriaceae bacterium 3519-10], YP 001817270.1[Opitutus terrae PB90-1], YP 003003775.1[Dickeya zeae Ech1591], AAD25394.1[Azospirillum irakense], EER49094.1[Asticcacaulis excentricus CB 48], YP 003061197.1[Hirschia baltica ATCC 49814], AAG29353.1|AF279264 1[Cellvibrio japonicus], ZP 02927550.1[Verrucomicrobium spinosum DSM 4136], ZP 03725417.1[Opitutaceae bacterium TAV2], YP 003259879.1[Pectobacterium wasabiae WPP163], ACT13209.1[Pectobacterium carotovorum subsp. carotovorum PC1], AAM87379.1|AE013987 2[Yersinia pestis KIM 10], YP 001175221.1[Enterobacter sp.638], ABR71284.1[Marinomonas sp.MWYL1], YP 003243108.1[Geobacillus sp. Y412MC10], YP 001018637.1[prochlorococcus marinus str MIT 9303], YP 382660.1[Synechococcus sp. CC9605]
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The program ClustalW [46] was used for multiple sequence alignment. Mega 4 was used for dendrogram construction by Neighbor-Joining (NJ) method [47]. For domain search, the Pfam site (http://www.sanger.ac.uk/software/pfam/search.html) was used. Domain analysis was done using MEME (http://meme.sdsc.edu/meme/meme.html) [48]. The conserved protein motifs deduced by MEME were characterized for biological function analysis using protein BLAST, and domains were studied with Interproscan providing the best possible match based on highest similarity score.

3. Results and Discussion

A total of 121 pectate lyases sequences from different source organisms subjected to phylogenetic tree construction revealed major clusters of bacterial, fungal, plant, and nematode pectate lyases. The pectate lyase from bacterial source was the predominant comprising of 87 accession numbers. The different accession of bacterial pectate lyase formed three major clusters as shown in Figure 1. The plant, fungal, and nematode pectate lyases formed separate clusters signifying the sequence-based similarity with reference to different source organisms. The multiple accessions of bacterial, fungal, plant, and nematode pectate lyases were placed closely in the clusters signifying the greater degree of sequence level similarity. Similar phylogenetic tree revealing clustering of pectin lyases protein sequences based on different source organism has been reported [45].

Figure 1.

Figure 1

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Phylogenetic tree of pectate lyase protein sequences from different source organism constructed by NJ method.

The multiple sequence alignment of these protein sequences revealed conserved regions at different stretches, namely, from 439–467, 715–816, and 829–918 amino acid residues (Figures 2(a), 2(b), and 2(c)). This region could be used for designing degenerate primers or probes for PCR-based amplification or hybridization-based detection of pectate lyase sequences from different source organisms.

Figure 2.

Figure 2

Figure 2

Figure 2

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(a) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 439–467. (b) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 715–816. (c) Multiple sequence alignment of pectate lyase protein sequences showing maximum homology from amino acid residues 829–910.

A total of five motifs labelled as 1, 2, 3, 4, and 5 were observed in only 91 sequences when subjected to MEME. The distribution of these motifs among 92 pectate lyase accession number is shown in Table 2.

Table 2.

Distribution of motifs among 91 pectate lyase proteins sequences from different source organisms.

S. no. Accession no. Motif 1 Motif 2 Motif 3 Motif 4 Motif 5
1 AAB46398 + +
2 CAB40884 +
3 CAA47630 + + + +
4 CAA70735 + + + +
5 CAA43401 +
6 CAA47821 +
7 NP866630 + + +
8 YP003003775 +
9 ZP05725973 + +
10 NP866628 + + + +
11 ZP05805856 +
12 YP002573715 +
13 YP001506642 +
14 NP001150723 + + + +
15 BAE48375 +
16 BAE48371 +
17 AAD25394 +
18 ACV08000 +
19 ACU58213 ++
20 AAC60448 + + +
21 BAI44500 +
22 YP001314702 + +
23 AAQ09004 +
24 AAL66022.1|AF455757_1 +
25 AAF80747 +
26 AAC64368 +
27 AAA33398 + + + +
28 ACU38032 +
29 ACR10769 + + +
30 ACU08313 +
31 BAH85845 +
32 ACS78057 +
33 ZP04367351 +
34 AAW84086 + +
35 AAL56657 + + + +
36 AAK66161 + + + +
37 AAQ84042 + + + +
38 AAC41522 + +
39 AAA80568 + + +
40 ZP06003184 + +
41 ACH58409 + + +
42 AAF63756.1|AF243475_1 + + + +
43 ZP04713986 +
44 ZP04334947 + +
45 ABG66729 + + + +
46 ABR26682 + + + +
47 ACD11362 + +
48 XP749217 + +
49 BAA05383 + +
50 BAB59066 + + + +
51 ZP01851785 + + +
52 ABM60783 + + +
53 BAF43573 + + + +
54 ABF59812 +
55 AAY85180 + + + +
56 EEY55044 +
57 EEY23761 + +
58 YP001615581 + +
59 ZP05542020 +
60 ZP05530610 +
61 ZP05514668 +
62 ZP05011753 +
63 ZP04688982 +
64 YP001106556 +
65 NP827559 +
66 YP432149 +
67 ABD47739 + + +
68 ZP00943832 +
69 AAM63307 + + + +
70 AAC38059 + + +
71 AAA75471 + +
72 ACL96719 + +
73 AAZ56201 + +
74 AAY50632 + + +
75 AAM38405 + +
76 YP618077 + +
77 ZP04608172 + +
78 ZP05021985 + +
79 ZP04658159 + +
80 YP001915548 + +
81 NP228243 + + +
82 YP356933 +
83 YP677777 + +
84 ACF40835 + + + +
85 CAA63496 + + + +
86 AAO79220 + + +
87 ABC76269 + +
88 ZP01721007 + +
89 BAE48664 + + + +
90 EER49733 + +
91 AAL51034.1|AF454849_1 +
92 YP527779.1| +
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The motifs with width and best possible match amino acid sequences are shown in Table 3. All these motifs showed similarity with pec_lyase_C domain which is quite prevalent in pectin lyase sequences as reported earlier [45]. As the mechanism of pectin lyase and pectate lyase is quite similar, it is expected to show similar motifs. The motif 1 of 29 amino acid residues with sequence IAFNHFGEGLVQRMPRCRHGYFHVVNNDY and motif 4 of 50 amino acid residues with a sequence HNSLSNCHDGLIDAIHGSTAITISNNYMTHHDKVMLLGHSDSYTQDKNMQ were observed in 47 and 39 pectate lyase protein sequences (Table 3) signifying their possible role in the structural and catalytic attributes of pectate lyases.

Table 3.

Different motifs commonly observed in pectate lyases protein sequences with best possible match amino acid sequences.

Motif number Width Sequence Occurrence in pectate lyase protein sequences
1 29 IAFNHFGEGLVQRMPRCRHGYFHVVNNDY 47
2 50 NPRPGTLRHAVIQDEPLWIVFKRDMVIQLKQELIMNSFKTIDGRGVNVHI 16
3 50 CITIQFVTNIIIHGIHIHDCKPTGNAMVRSSPSHYGWRTMADGDGISIFG 16
4 50 HNSLSNCHDGLIDAIHGSTAITISNNYMTHHDKVMLLGHSDSYTQDKNMQ 39
5 49 SSSQTMTVDGGGARYAHDKVFQHNGPGTFVIKNFQVQDFGKLYRSCGNC 27
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Further when the motif best possible match amino acid sequence was subjected to BLAST to reveal its identity, it was observed that the motifs 1, 2, 3, and 4 represents Pec_Lyase_C superfamily while motif 5 represents pectate lyase superfamily. The exact function of these motifs in influencing the catalytic activity of the pectate lyase needs to be investigated.

The in silico characterization of pectate lyases protein sequences from different source organisms has revealed sequence level similarity specific for different groups which could be utilized for designing strategy for cloning the putative genes based on PCR amplification using degenerate primers.

Acknowledgments

The authors wish to acknowledge Head, Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur for providing the infrastructural facilities. The facilities provided by DBT-funded SUB-DIC, Bioinformatics centre, School of Biotechnology, BHU, Varanasi are also thankfully acknowledged. The financial support by UGC, India in the form of UGC- Major Project (F. no.37-133/2009-SR) to D. Yadav and by DST, India in the form of Fast Track Young Scientist Fellowship (FT/LS-125/2008) to S. Yadav is duly acknowledged.

References

  • 1.Alkorta I, Garbisu C, Llama MJ, Serra JL. Industrial applications of pectic enzymes: a review. Process Biochemistry. 1998;33(1):21–28. [Google Scholar]
  • 2.Naidu GSN, Panda T. Production of pectolytic enzymes—a review. Bioprocess Engineering. 1998;19(5):355–361. [Google Scholar]
  • 3.Lang C, Dörnenburg H. Perspectives in the biological function and the technological application of polygalacturonases. Applied Microbiology and Biotechnology. 2000;53(4):366–375. doi: 10.1007/s002530051628. [DOI] [PubMed] [Google Scholar]
  • 4.Kashyap DR, Vohra PK, Chopra S, Tewari R. Applications of pectinases in the commercial sector: a review. Bioresource Technology. 2001;77(3):215–227. doi: 10.1016/s0960-8524(00)00118-8. [DOI] [PubMed] [Google Scholar]
  • 5.Hoondal G, Tiwari R, Tewari R, Dahiya N, Beg Q. Microbial alkaline pectinases and their industrial applications: a review. Applied Microbiology and Biotechnology. 2002;59(4-5):409–418. doi: 10.1007/s00253-002-1061-1. [DOI] [PubMed] [Google Scholar]
  • 6.Gummadi SN, Panda T. Purification and biochemical properties of microbial pectinases—a review. Process Biochemistry. 2003;38(7):987–996. [Google Scholar]
  • 7.Jayani RS, Saxena S, Gupta R. Microbial pectinolytic enzymes: a review. Process Biochemistry. 2005;40(9):2931–2944. [Google Scholar]
  • 8.Gummadi SN, Kumar DS. Microbial pectic transeliminases. Biotechnology Letters. 2005;27(7):451–458. doi: 10.1007/s10529-005-2197-8. [DOI] [PubMed] [Google Scholar]
  • 9.Payasi A, Sanwal R, Sanwal GG. Microbial pectate lyases: characterization and enzymological properties. World Journal of Microbiology and Biotechnology. 2008;25(1):1–14. [Google Scholar]
  • 10.Yadav S, Yadav PK, Yadav D, Yadav KDS. Pectin lyase: a review. Process Biochemistry. 2009;44(1):1–10. [Google Scholar]
  • 11.Marín-Rodríguez MC, Orchard J, Seymour GB. Pectate lyases, cell wall degradation and fruit softening. Journal of Experimental Botany. 2002;53(377):2115–2119. doi: 10.1093/jxb/erf089. [DOI] [PubMed] [Google Scholar]
  • 12.Marín-Rodríguez MC, Smith DL, Manning K, Orchard J, Seymour GB. Pectate lyase gene expression and enzyme activity in ripening banana fruit. Plant Molecular Biology. 2003;51(6):851–857. doi: 10.1023/a:1023057202847. [DOI] [PubMed] [Google Scholar]
  • 13.Payasi A, Sanwal GG. Pectate lyase activity during ripening of banana fruit. Phytochemistry. 2003;63(3):243–248. doi: 10.1016/s0031-9422(03)00027-x. [DOI] [PubMed] [Google Scholar]
  • 14.Payasi A, Misra PC, Sanwal GG. Purification and characterization of pectate lyase from banana (Musa acuminata) fruits. Phytochemistry. 2006;67(9):861–869. doi: 10.1016/j.phytochem.2006.02.003. [DOI] [PubMed] [Google Scholar]
  • 15.Soriano M, Blanco A, Díaz P, Pastor FIJ. An unusual pectate lyase from a Bacillus sp. with high activity on pectin: cloning and characterization. Microbiology. 2002;146(1):89–95. doi: 10.1099/00221287-146-1-89. [DOI] [PubMed] [Google Scholar]
  • 16.Sawada K, Ogawa A, Ozawa T, et al. Nucleotide and amino-acid sequences of a new-type pectate lyase from an alkaliphilic strain of Bacillus . European Journal of Biochemistry. 2000;267(5):1510–1515. doi: 10.1046/j.1432-1327.2000.01146.x. [DOI] [PubMed] [Google Scholar]
  • 17.Truong LV, Tuyen H, Helmke E, Binh LT, Schweder T. Cloning of two pectate lyase genes from the marine Antarctic bacterium Pseudoalteromonas haloplanktis strain ANT/505 and characterization of the enzymes. Extremophiles. 2001;5(1):35–44. doi: 10.1007/s007920000170. [DOI] [PubMed] [Google Scholar]
  • 18.Matsumoto T, Katsura D, Kondo A, Fukuda H. Efficient secretory overexpression of Bacillus subtilis pectate lyase in Escherichia coli and single-step purification. Biochemical Engineering Journal. 2002;12(3):175–179. [Google Scholar]
  • 19.Kluskens LD, Van Alebeek G-JWM, Voragen AGJ, De Vos WM, van der Oost J. Molecular and biochemical characterization of the thermoactive family 1 pectate lyase from the hyperthermophilic bacterium Thermotoga maritima . Biochemical Journal. 2003;370(2):651–659. doi: 10.1042/BJ20021595. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Soriano M, Diaz P, Pastor FIJ. Pectate lyase C from Bacillus subtilis: a novel endo-cleaving enzyme with activity on highly methylated pectin. Microbiology. 2006;152(3):617–625. doi: 10.1099/mic.0.28562-0. [DOI] [PubMed] [Google Scholar]
  • 21.Kaewnum S, Prathuangwong S, Burr TJ. A pectate lyase homolog, xagP, in Xanthomonas axonopodis pv. glycines is associated with hypersensitive response induction on tobacco. Phytopathology. 2006;96(11):1230–1236. doi: 10.1094/PHYTO-96-1230. [DOI] [PubMed] [Google Scholar]
  • 22.Xiao Z, Bergeron H, Grosse S, et al. Improvement of the thermostability and activity of a pectate lyase by single amino acid substitutions, using a strategy based on melting-temperature-guided sequence alignment. Applied and Environmental Microbiology. 2008;74(4):1183–1189. doi: 10.1128/AEM.02220-07. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 23.Shih J, Wei Y, Goodwin PH. A comparison of the pectate lyase genes, pel-1 and pel-2, of Colletotrichum gloeosporioides f.sp. malvae and the relationship between their expression in culture and during necrotrophic infection. Gene. 2000;243(1-2):139–150. doi: 10.1016/s0378-1119(99)00546-6. [DOI] [PubMed] [Google Scholar]
  • 24.De Vries RP, Jansen J, Aguilar G, et al. Expression profiling of pectinolytic genes from Aspergillus niger . FEBS Letters. 2002;530(1–3):41–47. doi: 10.1016/s0014-5793(02)03391-4. [DOI] [PubMed] [Google Scholar]
  • 25.Zhao Q, Yuan S, Zhang Y, et al. Expression, purification and characterization of pectate lyase a from Aspergillus nidulans in Escherichia coli . World Journal of Microbiology and Biotechnology. 2008;23(8):1057–1064. [Google Scholar]
  • 26.Margesin R, Fauster V, Fonteyne P-A. Characterization of cold-active pectate lyases from psychrophilic Mrakia frigida . Letters in Applied Microbiology. 2005;40(6):453–459. doi: 10.1111/j.1472-765X.2005.01704.x. [DOI] [PubMed] [Google Scholar]
  • 27.Doyle EA, Lambert KN. Cloning and characterization of an esophageal-gland-specific pectate lyase from the root-knot nematode Meloidogyne javanica . Molecular Plant-Microbe Interactions. 2002;15(6):549–556. doi: 10.1094/MPMI.2002.15.6.549. [DOI] [PubMed] [Google Scholar]
  • 28.Medina-Escobar N, Cárdenas J, Moyano E, Caballero JL, Muñoz-Blanco J. Cloning, molecular characterization and expression pattern of a strawberry ripening-specific cDNA with sequence homology to pectate lyase from higher plants. Plant Molecular Biology. 1997;34(6):867–877. doi: 10.1023/a:1005847326319. [DOI] [PubMed] [Google Scholar]
  • 29.Yoder MD, Keen NT, Jurnak F. New domain motif: the structure of pectate lyase C, a secreted plant virulence factor. Science. 1993;260(5113):1503–1507. doi: 10.1126/science.8502994. [DOI] [PubMed] [Google Scholar]
  • 30.Lietzke SE, Yoder MD, Keen NT, Jurnak F. The three-dimensional structure of pectate lyase E, a plant virulence factor from Erwinia chrysanthemi . Plant Physiology. 1994;106(3):849–852. doi: 10.1104/pp.106.3.849. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Pickersgill R, Jenkins J, Harris G, Nasser W, Robert-Baudouy J. The structure of Bacillus subtilis pectate lyase in complex with calcium. Nature Structural Biology. 1994;1(10):717–723. doi: 10.1038/nsb1094-717. [DOI] [PubMed] [Google Scholar]
  • 32.Mayans O, Scott M, Connerton I, et al. Two crystal structures of pectin lyase A from Aspergillus reveal a pH driven conformational change and striking divergence in the substrate-binding clefts of pectin and pectate lyases. Structure. 1997;5(5):677–689. doi: 10.1016/s0969-2126(97)00222-0. [DOI] [PubMed] [Google Scholar]
  • 33.Vitali J, Schick B, Kester HCM, Visser J, Jurnak F. The three-dimensional structure of Aspergillus niger pectin lyase b at 1.7-Å resolution. Plant Physiology. 1998;116(1):69–80. doi: 10.1104/pp.116.1.69. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Yoder MD, Jurnak F. The refined three-dimensional structure of pectate lyase C from Erwinia chrysanthemi at 2.2 Å resolution. Plant Physiology. 1994;107(2):349–364. doi: 10.1104/pp.107.2.349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Herron SR, Benen JAE, Scavetta RD, Visser J, Jurnak F. Structure and function of pectic enzymes: virulence factors of plant pathogens. Proceedings of the National Academy of Sciences of the United States of America. 2000;97(16):8762–8769. doi: 10.1073/pnas.97.16.8762. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Jenkins J, Shevchik VE, Hugouvieux-Cotte-Pattat N, Pickersgill RW. The crystal structure of pectate lyase Pel9A from Erwinia chrysanthemi . Journal of Biological Chemistry. 2004;279(10):9139–9145. doi: 10.1074/jbc.M311390200. [DOI] [PubMed] [Google Scholar]
  • 37.Gonzalez-Candelas L, Kolattukudy PE. Isolation and analysis of a novel inducible pectate lyase gene from the phytopathogenic fungus Fusarium solani f. sp. pisi (Nectria haematococca, mating population VI) Journal of Bacteriology. 1992;174(20):6343–6349. doi: 10.1128/jb.174.20.6343-6349.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 38.Bekri MA, Desair J, Keijers V, et al. Azospirillum irakense produces a novel type of pectate lyase. Journal of Bacteriology. 1999;181(8):2440–2447. doi: 10.1128/jb.181.8.2440-2447.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Shevchik VE, Robert-Baudouy J, Hugouvieux-Cotte-Pattat N. Pectate lyase PelI of Erwinia chrysanthemi 3937 belongs to a new family. Journal of Bacteriology. 1997;179(23):7321–7330. doi: 10.1128/jb.179.23.7321-7330.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 40.Hatada Y, Kobayashi T, Ito S. Enzymatic properties of the highly thermophilic and alkaline pectate lyase Pel-4B from alkaliphilic Bacillus sp. strain P-4-N and the entire nucleotide and amino acid sequences. Extremophiles. 2001;5(2):127–133. doi: 10.1007/s007920100182. [DOI] [PubMed] [Google Scholar]
  • 41.Zhai C, Cao J, Wang Y. Cloning and expression of a pectate lyase gene from Bacillus alcalophillus NTT33. Enzyme and Microbial Technology. 2003;33(2-3):173–178. [Google Scholar]
  • 42.Dehdashti SJ, Doan CN, Chao KL, Yoder MD. Effect of mutations in the T1.5 loop of pectate lyase A from Erwinia chrysanthemi EC16. Acta Crystallographica. 2003;59(7):1339–1342. doi: 10.1107/s0907444903011491. [DOI] [PubMed] [Google Scholar]
  • 43.Berensmeier S, Singh SA, Meens J, Buchholz K. Cloning of the pelA gene from Bacillus licheniformis 14A and biochemical characterization of recombinant, thermostable, high-alkaline pectate lyase. Applied Microbiology and Biotechnology. 2004;64(4):560–567. doi: 10.1007/s00253-003-1446-9. [DOI] [PubMed] [Google Scholar]
  • 44.Guo W, Gonzalez-Candelas L, Kolattukudy PE. Cloning of a novel constitutively expressed pectate lyase gene pelB from Fusarium solani f. sp. pisi (Nectria haematococca, mating type VI) and characterization of the gene product expressed in Pichia pastoris . Journal of Bacteriology. 1995;177(24):7070–7077. doi: 10.1128/jb.177.24.7070-7077.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 45.Yadav PK, Singh VK, Yadav S, Yadav KDS, Yadav D. In silico analysis of pectin lyase and pectinase sequences. Biochemistry. 2009;74(9):1049–1055. doi: 10.1134/s0006297909090144. [DOI] [PubMed] [Google Scholar]
  • 46.Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: fexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research. 1997;25(24):4876–4882. doi: 10.1093/nar/25.24.4876. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 47.Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution. 2007;24(8):1596–1599. doi: 10.1093/molbev/msm092. [DOI] [PubMed] [Google Scholar]
  • 48.Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In: Proceedings of the 2nd International Conference on Intelligent Systems for Molecular Biology; 1994; AAAI Press; pp. 28–36. [PubMed] [Google Scholar]

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