Abstract
A total of 48 full-length protein sequences of pectin lyases from different source organisms available in NCBI were subjected to multiple sequence alignment, domain analysis, and phylogenetic tree construction. A phylogenetic tree constructed on the basis of the protein sequences revealed two distinct clusters representing pectin lyases from bacterial and fungal sources. Similarly, the multiple accessions of different source organisms representing bacterial and fungal pectin lyases also formed distinct clusters, showing sequence level homology. The sequence level similarities among different groups of pectinase enzymes, viz. pectin lyase, pectate lyase, polygalacturonase, and pectin esterase, were also analyzed by subjecting a single protein sequence from each group with common source organism to tree construction. Four distinct clusters representing different groups of pectinases with common source organisms were observed, indicating the existing sequence level similarity among them. Multiple sequence alignment of pectin lyase protein sequence of different source organisms along with pectinases with common source organisms revealed a conserved region, indicating homology at sequence level. A conserved domain Pec_Lyase_C was frequently observed in the protein sequences of pectin lyases and pectate lyases, while Glyco_hydro_28 domains and Pectate lyase-like β-helix clan domain are frequently observed in polygalacturonases and pectin esterases, respectively. The signature amino acid sequence of 41 amino acids, i.e. TYDNAGVLPITVN-SNKSLIGEGSKGVIKGKGLRIVSGAKNI, related with the Pec_Lyase_C is frequently observed in pectin lyase protein sequences and might be related with the structure and enzymatic function.
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Abbreviations
- MEME:
-
Multiple EM for Motif Elicitation
- NCBI:
-
National Center for Biotechnology Information
- NJ:
-
Neighbor-Joining method
- PCR:
-
polymerase chain reaction
- PE:
-
pectin esterase
- PG:
-
polygalacturonase
- PL:
-
pectate lyase
- PNL:
-
pectin lyase
- UPGMA method:
-
Unweighted Pair Group method with Arithmetic Mean method
References
Yadav, S., Yadav, P. K., Yadav, D., and Yadav, K. D. S. (2009) Process Biochem., 44, 1–10.
Visser, J., Bussink, H. J., and Witteveen, C. (2004) in Gene Expression in Recombinant Microorganisms (Smith, A., ed.) Marcel Dekker, Inc., New York, pp. 241–306.
Cosgrove, D. J. (1997) Ann. Rev. Cell. Dev. Biol., 13, 171–201.
Prade, R. A., Zohan, D., Ayoubi, P., and Mort, A. J. (1999) Biotechnol. Gene Eng. Rev., 16, 361–391.
Jayani, S. R., Saxena, S., and Gupta, R. (2005) Process Biochem., 40, 2931–2944.
Luh, B. S., and Phaff, H. J. (1951) Arch. Biochem. Biophys., 33, 212–227.
Gysler, C., Harmsen, J. A. M., Kester, H. C. M., Visser, J., and Heim, J. (1990) Gene, 89, 101–108.
Someren, M. A. K., Harmsen, J. A. M., Kester, H. C. M., and Visser, J. (1991) Curr. Gen., 20, 293–299.
Someren, M. A. K., Flipphi, M., de Graaff, L., van den Broeck, H., Kester, H., Hinnen, A., and Visser, J. (1992) Mol. Gen. Genom., 234, 113–120.
Kitamoto, N., Yasuda, Y. S., Ohmiya, K., and Tsukagoshi, N. (2001) Biosci. Biotechnol. Biochem., 65, 209–212.
Templeton, M. D., Sharrock, K. R., Bowen, J. K., Crowhurst, R. N., and Rikkerink, E. H. (1994) Gene, 142, 141–146.
Kilara, A. (1982) Process Biochem., 23, 35–41.
Naidu, G. S. N., and Panda, T. (1998) Bioprocess. Eng., 9, 355–361.
Alkorta, I., Garbisu, G., Llama, M. J., and Serra, J. L. (1998) Process Biochem., 33, 21–28.
Blanco, P., Sieiro, C., Reboredo, N. M., and Villa, T. G. (1997) Arch. Microbiol., 167, 284–288.
Takebe, I., Otsuki, Y., and Aoki, S. (1968) Plant Cell Physiol., 9, 115–124.
Beldman, G., Rombouts, F. M., Voragen, A. G. J., and Pilnik, W. (1984) Enz. Microb. Technol., 6, 503–507.
Whitaker, J. R. (1991) in Microbial Enzymes and Biotechnology (Fogarty, W. M., and Kelly, C. T., eds.) Elsevier Applied Science, London-New York, pp. 133–175.
Mayans, O., Scott, M., Connerton, I., Gravesen, T., Benen, J., Visser, J., Pickersgill, R., and Jenkins, J. (1997) Structure, 5, 677–689.
Vitali, J., Schick, B., Kester, H. C. M., Visser, J., and Jurnak, F. (1998) Plant Physiol., 116, 69–80.
Lassmann, T., and Sonnhammer, E. L. (2006) Nucleic Acids Res., 34 (Web Server Issue), W596-9.
Kumar, S., Tamura, K., and Nei, M. (2004) Brief. Bioinformatics, 5, 150–163.
Saitou, N., and Nei, M. (1987) Mol. Biol. Evol., 4, 406–425.
Shi, G. Y., Jie, T. Y., Bing, T. H., Hua, W. K., and Wei, C. K. (2007) Chin. J. Agric. Biotechnol., 4, 33–38.
Timothy, L. B., and Gribskov, M. (1997) J. Comp. Biol., 4, 45–59.
Timothy, L. B., and Gribskov, M. (1998) Bioinformatics, 14, 48–54.
Yoder, M. D., Keen, N. T., and Jurnak, F. (1993) Science, 260, 1503–1507.
Lietzke, S. E., Yoder, M. D., Keen, N. T., and Jurnak, F. (1994) Plant Physiol., 106, 849–862.
Pickersgill, R., Jenkins, J., Harris, G., Nasser, W., and Robert-Baudouy, J. (1994) Nat. Struct. Biol., 1, 717–723.
Herron, S. R., Benen, J. A. E., Scavetta, R. D., Visser, J., and Jurnak, F. (2000) Proc. Natl. Acad. Sci. USA, 97, 8762–8769.
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Published in Russian in Biokhimiya, 2009, Vol. 74, No. 9, pp. 1286–1293.
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Yadav, P.K., Singh, V.K., Yadav, S. et al. In silico analysis of pectin lyase and pectinase sequences. Biochemistry Moscow 74, 1049–1055 (2009). https://doi.org/10.1134/S0006297909090144
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DOI: https://doi.org/10.1134/S0006297909090144