Molecular insights into cold active polygalacturonase enzyme for its potential application in food processing

Abstract

Pectin is a complex structural heteropolysaccharide that require numerous pectinolytic enzymes for its complete degradation. Polygalacturonase from mesophilic or thermophilic origin are being widely used in fruit and vegetable processing in the recent decades to degrade pectic substances. Recently cold active pectinases are finding added advantages over meso and thermophilic counterparts, to use in industrial scale particularly in food processing industry. They facilitate in conservation of several properties of foods so that the end product retains its naturality and also generates economic benefits. In the present study, Pseudoalteromonas haloplanktis, a well reported marine psychrophile is taken as a model organism for cold active polygalacturonase and is evaluated in comparision to the routinely used mesophilic and thermophilic enzymes by insicio approach. Polygalacturonase sequences from industrially important microbial sources were subjected to MEME and Pfam wherein motifs and domains involved in the conservation were analyzed. Dendrogram revealed sequence level similarity and motifs showed uniform distribution of conserved regions that are involved in important functions. It was also observed through clustalW analysis that the amount of arginine content of psychrophiles is less when compared with thermophiles. Finally, all the modeled enzyme structures were subjected to docking studies using Autodock 4.2 with the substrate polygalacturonic acid and binding energies were found to be -5.73, -6.22 and -7.27 KCals/mole for meso, thermo and psychrophiles respectively which indicates the efficiency of psychrophilic enzymes when compared with its counterparts giving scope for further experimentation to find their better usage in various food industry applications.

Keywords: Cold active enzymes; Pectin; Polygalacturonase; Pseudoalteromonas haloplanktis; Psychrophile.

Fig. 1

a: 2D structure of PGA. b: 3D structure of PGA

Fig. 2

Multiple sequence alignment of polygalacturonase sequences from meso, thermo and psychrophiles. Arrows represent the most important residues of the active site of the enzyme

Fig. 3

Combined block diagram of motifs in polygalacturonase sequences from various sources

Fig. 4

Phylogenetic tree of polygalacturonase sequences of different organisms constructed by maximum likelihood method

Fig. 5

Structure of Polygalacturonase enzyme from a Erwinia carotovora b Thermotoga maritima

Fig. 6

Modeled Polygalacturonase enzyme from Pseudoalteromonas haloplanktis

Fig. 7

Polygalacturonase from Erwinia carotovorum docked with PGA

Fig. 8

Polygalacturonase from Pseudoalteromonas haloplanktis docked with PGA

Fig. 9

Polygalacturonase from Thermotoga maritima docked with PGA

Fig. 10

Enzyme Polygalacturonic acid docked with PGA (in mesh) from Erwinia carotovora

Fig. 11

Enzyme Polygalacturonic acid docked with PGA (in spheres) from Pseudoalteromonas haloplanktis

Fig. 12

Enzyme Polygalacturonic acid docked with PGA (in mesh) from Thermatogo maritima