Evolutionary Analysis of Pectin Lyases of the Genus Colletotrichum
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Pectin lyases (PNLs) are important enzymes that are involved in plant cell wall degradation during the infection process. Colletotrichum is a diverse genus of fungi, which allows the study of the evolution of PNLs and their possible role in pathogen–host interactions and lifestyle adaptations. The phylogenetic reconstruction of PNLs from Colletotrichum and analysis of selection pressures showed the formation of protein lineages by groups of species with different selection pressures and specific patterns. The analysis of positive selection at individual sites using different methods allowed for the identification of three codons with evidence of positive selection in the oligosaccharide-binding region and two codons on the antiparallel sheet, which may influence the interaction with the substrate. Seven codons on the surface of the protein, mainly in the peripheral helices of the PNLs, could have an important function in evasion of plant defenses, as has been proposed in other enzymes. According to our results, it is possible that events of genetic duplication occurred in ancestral lines, followed by episodes of genetic diversification and gene loss, probably influenced by differences in the composition of the host cell wall. Additionally, different patterns of evolution in Colletotrichum appear to be molded by a strong purifying selection and positive selection episodes that forged the observed evolutionary patterns, possibly influenced by host interaction or substrate specificity. This work represents a starting point for the study of sites that may be important for evasion of plant defenses and biotechnological purposes.
KeywordsPectin lyase Colletotrichum sp. Positive selection Molecular evolution
The authors thank the financial support provided by Secretaría de Educación Pública-Consejo Nacional de Ciencia y Tecnología (SEP-CONACyT), México (project 2012-01-182755 to María G. Zavala-Páramo); Coordinación de la Investigación, Universidad Michoacana de San Nicolás de Hidalgo (project 2014–2015 to Horacio Cano-Camacho); Universidad Nacional Autónoma de México (for post-doctoral fellowship program 2012–14 granted to Alicia Lara-Márquez); and Consejo Nacional de Ciencia y Tecnología, México (for scholarship number 209148 granted to Ulises Conejo-Saucedo and scholarship number 233565 granted to Maria G. Villa-Rivera).
- Barrus MF (1911) Variation of varieties of beans in their susceptibility to anthracnose. Phytopathology 1:190–195Google Scholar
- Cooper JA (1983) The mechanisms and significance of enzymic degradation of host cell walls by parasites. In: Callow JA (ed) Biochemical plant pathology. Wiley, Chichester, pp 101–137Google Scholar
- Crouch J, O’Connell R, Gan P et al (2014) The genomics of Colletotrichum. In: Genomics of plant-associated fungi: monocot pathogens. Springer, Berlin, pp 69–102Google Scholar
- D’Ovidio R, Raiola A, Capodicasa C et al (2004) Characterization of the complex locus of bean encoding polygalacturonase-inhibiting proteins reveals subfunctionalization for defense against fungi and insects. Plant Physiol 135:2424–2435. doi: 10.1104/pp.104.044644 CrossRefPubMedPubMedCentralGoogle Scholar
- Damm U, Woudenberg JHC, Cannon PF, Crous PW (2009) Colletotrichum species with curved conidia from herbaceous hosts. Fungal Divers 39:45–87Google Scholar
- Gan P, Kumakura N, Narusaka M et al (2016) Genus-wide comparative genome analyses of Colletotrichum species reveal specific gene family losses and gains during adaptation to specific infection lifestyles. Genome Biol Evol 8:1467–1481. doi: 10.1093/gbe/evw089 CrossRefPubMedPubMedCentralGoogle Scholar
- Leckie F, Mattei B, Capodicasa C et al (1999) The specificity of polygalacturonase-inhibiting protein (PGIP): a single amino acid substitution in the solvent-exposed β-strand/β-turn region of the leucine-rich repeats (LRRs) confers a new recognition capability. EMBO J 18:2352–2363. doi: 10.1093/emboj/18.9.2352 CrossRefPubMedPubMedCentralGoogle Scholar
- Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, New YorkGoogle Scholar
- Nuss L, Mahé A, Clark AJ et al (1996) Differential accumulation of PGIP (polygalacturonase-inhibiting protein) mRNA in two near-isogenic lines of Phaseolus vulgaris L. upon infection with Colletotrichum lindemuthianum. Physiol Mol Plant Pathol 48:83–89. doi: 10.1006/pmpp.1996.0008 CrossRefGoogle Scholar
- Wang Y-T, Lo H-S, Wang P-H (2008) Endophytic fungi from taxus mairei in Taiwan: first report of Colletotrichum gloeosporioides as an endophyte of Taxus mairei. Bot Stud 39:39–43Google Scholar