Genome-Wide Analysis of PL7 Alginate Lyases in the Genus Zobellia

Abstract

We carried out a detailed investigation of PL7 alginate lyases across the Zobellia genus. The main findings were obtained using the methods of comparative genomics and spatial structure modeling, as well as a phylogenomic approach. Initially, in order to elucidate the alginolytic potential of Zobellia, we calculated the content of polysaccharide lyase (PL) genes in each genome. The genus-specific PLs were PL1, PL6, PL7 (the most abundant), PL14, PL17, and PL40. We revealed that PL7 belongs to subfamilies 3, 5, and 6. They may be involved in local and horizontal gene transfer and gene duplication processes. Most likely, an individual evolution of PL7 genes promotes the genetic variability of the Alginate Utilization System across Zobellia. Apparently, the PL7 alginate lyases may acquire a sub-functionalization due to diversification between in-paralogs.

Comparative genomics reveal distinct potential of Tamlana sp. S12 for algal polysaccharide degradation

“…According to the sequence identity of catalytic domains, the PL7 family is subdivided into seven subfamilies (SF1-SF7) (Lombard et al, 2010;Thomas et al, 2013;Pei et al, 2019;Chernysheva et al, 2021). Similarly, PL17 and PL6 are divided into two (SF1-SF2) and three (SF1-SF3) subfamilies, respectively (Mathieu et al, 2018;Violot et al, 2021).…”

“…PDB mainly comprises two classes: gammaproteobacteria in the phylum Proteobacteria and flavobacteria in the phylum Bacteroidetes. Marine bacteria have developed specific degradation mechanisms to utilize these polysaccharides, which differ significantly from the degradation of polysaccharides from terrestrial plants (Chernysheva et al, 2021). Marine flavobacteria are vital in the degradation of these complex polysaccharides (Thomas et al, 2017).…”

Genome Analysis of a Novel Polysaccharide-Degrading Bacterium Paenibacillus algicola and Determination of Alginate Lyases

“…Polysaccharide-degrading bacteria are key players in the global carbon cycle and algal biomass recycling. Many kinds of MPdegrading marine bacteria have been isolated and revealed as the key players in the algal biomass recycling and global carbon cycle, such as Pseudoalteromonas [7], Alteromonas [12], Agarivorans [13], Paenibacillus [14], Vibrio and Zobellia [15,16]. Members of genus Paenibacillus produce many kinds of extracellular enzymes, e.g., chitosanase [17], glucanase [18], cellulase/mannanase/xylanase [19], xanthanase [20] and chitinase [21], which can be used in a wide range of industrial fields.…”

“…CAZyme are the key to promoting carbohydrate catabolism in marine heterotrophic bacteria. Based on genome sequencing and functional annotation, the genomes of several alginate-degrading marine bacteria have been assembled and the CAZyme genes annotated; those such as Zobellia russellii and Z. barbeyronii [16], Flammeovirga pacifica WPAGA1 [1], Microbulbifer strain HZ11 [29] and Paenibacillus sp. str.…”

Editorial to the Special Issue: “Dedicated to the 55th Anniversary of G.B. Elyakov Pacific Institute of Bioorganic Chemistry of the Far Eastern Branch of the Russian Academy of Sciences”

“…As a result, the phenotypic heterogeneity of the Y. pseudotuberculosis population was found, manifested in the variable expression of the porin gene under the influence of carbenicillin. Chernysheva et al [ 17 ] carried out a detailed study of PL7 alginate lyase in the representatives of the genus Zobellia . PL7 was found to belong to subfamilies 3, 5, and 6, undergoing local and horizontal gene transfer and gene duplication processes.…”