Pectin is one of the major components of the primary cell wall of plants and is also found in dividing cells and in the areas of contact between cells that have a secondary cell wall, including xylem and the fibrous cells of woody tissue. Pectin comprises approximately 35% of the primary cell wall of dicots and non-graminaceous monocots. Although its content in secondary walls is greatly reduced, it is believed that pectin plays an important role in the structure and function of both primary and secondary cell walls. The functions of pectin in cell walls are diverse and include plant growth and development, morphogenesis, defense, cell adhesion, cell wall structure, cellular expansion, porosity, ion binding, hydration of seeds, leaf abscission and fruit development, among others [1, 2]. In general, pectin is considered to be a group of polysaccharides that are rich in galacturonic acid (GalA) and present in the form of covalently linked structural domains: homogalacturonan (HG), xylogalacturonan (XGA), rhamnogalacturonan I (RG-I) and rhamnogalacturonan II (RG-II) [1, 2]. The main enzymes involved in the degradation of the HG backbone of pectin are polygalacturonases (PGA, E.C. 188.8.131.52 and XPG, E.C. 184.108.40.206), pectate lyases (PL, E.C. 220.127.116.11 and 18.104.22.168) and pectin lyases (PNL, E.C. 22.214.171.124) .
Pectin lyases (PNLs) catalyze the degradation of pectin through β-elimination; they remove a proton and generate an unsaturated bond between the C-4 and C-5 carbons of the non-reducing end of pectin, which is a neutral form of pectate in which the uronic acid moiety of galacturonic residues has been methyl-esterified. The activity of PNLs is highly dependent on the distribution of the methyl esters over the homogalacturonan backbone. PNLs exhibit pH optima in the range of 6.0-8.5 and, unlike PLs, their activity is independent of Ca2+ ions; it is believed, however, that the residue Arg236 plays a role similar to that of Ca+2 [4, 5]. Pectinase gene expression is regulated at the transcriptional level by the pH of the medium and by carbon sources, as it is induced by pectin and pectic components and repressed by glucose [6–8].
PNLs are grouped into Family 1 of the polysaccharide lyases  and into the pectate lyase superfamily that, in addition to pectin lyases and pectate lyases, also includes plant pollen/style proteins. The three-dimensional structures of five members of the pectate lyase superfamily have been determined. These include Erwinia chrysanthemi pectate lyase C (PELC)  and pectate lyase E (PELE) , Bacillus subtilis pectate lyase  and Aspergillus niger pectin lyase A (PLA)  and pectin lyase B (PLB) . These enzymes fold into a parallel β-helix, which is a topology in which parallel β-strands are wound into a large right-handed coil . Although PLs and PNLs exhibit a similar structural architecture and related catalysis mechanisms, they nonetheless diverge significantly in their carbohydrate binding strategy [4, 13]. Currently, strategies are available for developing functional information from three-dimensional images of enzymes. The growing number of databases on the structure of pectinolytic enzymes has facilitated the analysis of minor structural differences that are responsible for the specific recognition of a unique oligosaccharide sequence in a heterogeneous mixture .
Most of the available information about fungal PNLs and their corresponding encoding genes has been obtained from saprophytic/opportunistic fungi such as Aspergillus niger [16–19], A. orizae [20, 21], A. fumigatus , Penicillium griseoroseum , P. occitanis  and to a lesser extent from the phytopathogenic fungi Glomerella cingulata  and C. gloeosporioides .
The ascomycete C. lindemuthianum is an economically important phytopathogen, and along with its host Phaseolus vulgaris, it provides a convenient model to study the physiological and molecular bases of plant-pathogen interactions . It is an intracellular hemibiotrophic pathogen with physiological races that invade the plant in an interaction consistent to the gene-for-gene model , and monogenic dominant resistance in common bean cultivars leads to the appearance of localized necrotic spots typical of the hypersensitive response (HR) . After penetration of a host epidermal cell in a susceptible cultivar, the pathogenic races of C. lindemuthianum develop an infection vesicle and extend into adjacent cells by producing large primary hyphae, which invaginate without penetrating the host cell membrane and thus persist as a biotrophic interaction. Once a large area of the plant tissue has been colonized, necrotrophic hyphae develop , and this step closely correlates with the production of a number of host cell-wall-degrading enzymes that are characteristic of phytopathogenic fungi [30–32]. Up to know, race 0 is the only strain of C. lindemuthianum unable to infect P. vulgaris, which contrasts with 1472, one of the most virulent races isolated in México . This difference makes the two races an excellent model to investigate the role of pectinolytic enzymes in virulence of C. lindemuthianum. Previous results from this laboratory revealed significant differences between pathogenic (1472) and non-pathogenic (0) races of C. lindemuthianum in terms of growth and production of extracellular PNL activity on different carbon and nitrogen sources in liquid culture. Accordingly, race 1472 grew faster in media containing glucose or polygalacturonic acid, and on 92%-esterified pectin, it produced levels of PNL activity that were approximately 2-fold higher than those produced by race 0. In contrast, cell walls isolated from P. vulgaris hypocotyls and, to a lesser degree, from cellulose sustained the growth of both races but induced PNL only in the pathogenic race .
Here we report the isolation and sequence analysis of the Clpnl2 gene, which encodes pectin lyase 2 of C. lindemuthianum, and its expression in pathogenic and non-pathogenic races of C. lindemuthianum in response to cultivation on different carbon sources. To determine the relationship among the three-dimensional structures of PNLs and the lifestyle of PNL-producing microorganisms, we performed a phylogenetic analysis using protein sequences and deduced amino acid sequences reported for PNLs. A comparative analysis of the three-dimensional structure of the Clpnl2 protein predicted by homology modeling, covering the main body of the protein and the carbohydrate binding site, and the three-dimensional structures of the PNLs used in the phylogenetic analysis was also performed.