Cloning and characterization of a pectin lyase gene from <it>Colletotrichum lindemuthianum </it>and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms

<p>Abstract</p> <p>Background</p> <p>Microorganisms produce cell-wall-degrading enzymes as part of their strategies for plant invasion/nutrition. Among these, pectin lyases (PNLs) catalyze the depolymerization of esterified pectin by a β-elimination mechanism. PNLs are...

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Main Authors: Lara-Márquez Alicia, Zavala-Páramo María G, López-Romero Everardo, Calderón-Cortés Nancy, López-Gómez Rodolfo, Conejo-Saucedo Ulises, Cano-Camacho Horacio
Format: Article
Language:English
Published: BMC 2011-12-01
Series:BMC Microbiology
Online Access:http://www.biomedcentral.com/1471-2180/11/260
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author Lara-Márquez Alicia
Zavala-Páramo María G
López-Romero Everardo
Calderón-Cortés Nancy
López-Gómez Rodolfo
Conejo-Saucedo Ulises
Cano-Camacho Horacio
author_facet Lara-Márquez Alicia
Zavala-Páramo María G
López-Romero Everardo
Calderón-Cortés Nancy
López-Gómez Rodolfo
Conejo-Saucedo Ulises
Cano-Camacho Horacio
author_sort Lara-Márquez Alicia
collection DOAJ
description <p>Abstract</p> <p>Background</p> <p>Microorganisms produce cell-wall-degrading enzymes as part of their strategies for plant invasion/nutrition. Among these, pectin lyases (PNLs) catalyze the depolymerization of esterified pectin by a β-elimination mechanism. PNLs are grouped together with pectate lyases (PL) in Family 1 of the polysaccharide lyases, as they share a conserved structure in a parallel β-helix. The best-characterized fungal pectin lyases are obtained from saprophytic/opportunistic fungi in the genera <it>Aspergillus </it>and <it>Penicillium </it>and from some pathogens such as <it>Colletotrichum gloeosporioides</it>.</p> <p>The organism used in the present study, <it>Colletotrichum lindemuthianum</it>, is a phytopathogenic fungus that can be subdivided into different physiological races with different capacities to infect its host, <it>Phaseolus vulgaris</it>. These include the non-pathogenic and pathogenic strains known as races 0 and 1472, respectively.</p> <p>Results</p> <p>Here we report the isolation and sequence analysis of the <it>Clpnl2 </it>gene, which encodes the pectin lyase 2 of <it>C. lindemuthianum</it>, and its expression in pathogenic and non-pathogenic races of <it>C. lindemuthianum </it>grown on different carbon sources. In addition, we performed a phylogenetic analysis of the deduced amino acid sequence of Clpnl2 based on reported sequences of PNLs from other sources and compared the three-dimensional structure of Clpnl2, as predicted by homology modeling, with those of other organisms. Both analyses revealed an early separation of bacterial pectin lyases from those found in fungi and oomycetes. Furthermore, two groups could be distinguished among the enzymes from fungi and oomycetes: one comprising enzymes from mostly saprophytic/opportunistic fungi and the other formed mainly by enzymes from pathogenic fungi and oomycetes. Clpnl2 was found in the latter group and was grouped together with the pectin lyase from <it>C. gloeosporioides</it>.</p> <p>Conclusions</p> <p>The <it>Clpnl2 </it>gene of <it>C. lindemuthianum </it>shares the characteristic elements of genes coding for pectin lyases. A time-course analysis revealed significant differences between the two fungal races in terms of the expression of <it>Clpnl2 </it>encoding for pectin lyase 2. According to the results, pectin lyases from bacteria and fungi separated early during evolution. Likewise, the enzymes from fungi and oomycetes diverged in accordance with their differing lifestyles. It is possible that the diversity and nature of the assimilatory carbon substrates processed by these organisms played a determinant role in this phenomenon.</p>
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spelling doaj.art-a801ff649eeb4fb89c69c7851afc81af2022-12-21T21:05:06ZengBMCBMC Microbiology1471-21802011-12-0111126010.1186/1471-2180-11-260Cloning and characterization of a pectin lyase gene from <it>Colletotrichum lindemuthianum </it>and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganismsLara-Márquez AliciaZavala-Páramo María GLópez-Romero EverardoCalderón-Cortés NancyLópez-Gómez RodolfoConejo-Saucedo UlisesCano-Camacho Horacio<p>Abstract</p> <p>Background</p> <p>Microorganisms produce cell-wall-degrading enzymes as part of their strategies for plant invasion/nutrition. Among these, pectin lyases (PNLs) catalyze the depolymerization of esterified pectin by a β-elimination mechanism. PNLs are grouped together with pectate lyases (PL) in Family 1 of the polysaccharide lyases, as they share a conserved structure in a parallel β-helix. The best-characterized fungal pectin lyases are obtained from saprophytic/opportunistic fungi in the genera <it>Aspergillus </it>and <it>Penicillium </it>and from some pathogens such as <it>Colletotrichum gloeosporioides</it>.</p> <p>The organism used in the present study, <it>Colletotrichum lindemuthianum</it>, is a phytopathogenic fungus that can be subdivided into different physiological races with different capacities to infect its host, <it>Phaseolus vulgaris</it>. These include the non-pathogenic and pathogenic strains known as races 0 and 1472, respectively.</p> <p>Results</p> <p>Here we report the isolation and sequence analysis of the <it>Clpnl2 </it>gene, which encodes the pectin lyase 2 of <it>C. lindemuthianum</it>, and its expression in pathogenic and non-pathogenic races of <it>C. lindemuthianum </it>grown on different carbon sources. In addition, we performed a phylogenetic analysis of the deduced amino acid sequence of Clpnl2 based on reported sequences of PNLs from other sources and compared the three-dimensional structure of Clpnl2, as predicted by homology modeling, with those of other organisms. Both analyses revealed an early separation of bacterial pectin lyases from those found in fungi and oomycetes. Furthermore, two groups could be distinguished among the enzymes from fungi and oomycetes: one comprising enzymes from mostly saprophytic/opportunistic fungi and the other formed mainly by enzymes from pathogenic fungi and oomycetes. Clpnl2 was found in the latter group and was grouped together with the pectin lyase from <it>C. gloeosporioides</it>.</p> <p>Conclusions</p> <p>The <it>Clpnl2 </it>gene of <it>C. lindemuthianum </it>shares the characteristic elements of genes coding for pectin lyases. A time-course analysis revealed significant differences between the two fungal races in terms of the expression of <it>Clpnl2 </it>encoding for pectin lyase 2. According to the results, pectin lyases from bacteria and fungi separated early during evolution. Likewise, the enzymes from fungi and oomycetes diverged in accordance with their differing lifestyles. It is possible that the diversity and nature of the assimilatory carbon substrates processed by these organisms played a determinant role in this phenomenon.</p>http://www.biomedcentral.com/1471-2180/11/260
spellingShingle Lara-Márquez Alicia
Zavala-Páramo María G
López-Romero Everardo
Calderón-Cortés Nancy
López-Gómez Rodolfo
Conejo-Saucedo Ulises
Cano-Camacho Horacio
Cloning and characterization of a pectin lyase gene from <it>Colletotrichum lindemuthianum </it>and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms
BMC Microbiology
title Cloning and characterization of a pectin lyase gene from <it>Colletotrichum lindemuthianum </it>and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms
title_full Cloning and characterization of a pectin lyase gene from <it>Colletotrichum lindemuthianum </it>and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms
title_fullStr Cloning and characterization of a pectin lyase gene from <it>Colletotrichum lindemuthianum </it>and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms
title_full_unstemmed Cloning and characterization of a pectin lyase gene from <it>Colletotrichum lindemuthianum </it>and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms
title_short Cloning and characterization of a pectin lyase gene from <it>Colletotrichum lindemuthianum </it>and comparative phylogenetic/structural analyses with genes from phytopathogenic and saprophytic/opportunistic microorganisms
title_sort cloning and characterization of a pectin lyase gene from it colletotrichum lindemuthianum it and comparative phylogenetic structural analyses with genes from phytopathogenic and saprophytic opportunistic microorganisms
url http://www.biomedcentral.com/1471-2180/11/260
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