Diversity of Glycoside Hydrolase 10 Family Xylanases Found in Rumen Metagenome and Selection of Sequences with Biotechnological Potential
Gabriella Cavazzini Pavarina1, Natália Sarmanho Monteiro Lima1,2, Claudio Damasceno Pavani1, Eliana Gertrudes de Macedo Lemos1,2, João Martins Pizauro Junior1 and Adriano Marques Gonçalves3,4*
1Technology Department, Sao Paulo State University (Unesp), Faculty of Agricultural and Veterinary Sciences, Brazil
2Molecular Biology Laboratory, Bioenergy Research Institute (IPBEN), Jaboticabal, Sao Paulo, Unesp, Brazil
3Department of Biological and Health Sciences, University of Araraquara (UNIARA), Brazil
4Department of Biochemistry and Organic Chemistry, Chemistry Institute, Sao Paulo State University (UNESP), Brazil
*Corresponding Author: Adriano Marques Gonçalves, Professor, Department of Biological and Health Sciences, University of Araraquara (UNIARA), Araraquara, SP, Brazil.
Received: June 01, 2021 ; Published: June 17, 2021
Metagenomics is an important tool for mining and discovering new enzymes, making it possible to explore the diversity of environments, which could not be explored with conventional methods of cultivating microorganisms. Therefore, this strategy can be used to prospect for xylanases, which degrades lignocellulosic biomass, an important and strategic source of renewable energy of great economic interest. The aim of the work was to identify and investigate the diversity of xylanases of the GH10 family present in the rumen metagenome of Nelore cattle and to prospect molecules with good potential for biotechnological application through in silico analyzes. Pfam was used for the initial selection of GH10 sequences, then the physical and chemical parameters were computed using the ProtParam tool, SignalP-5.0 server was used to predict signal peptides and cleavage location, transmembrane helices prediction was made in TMHMM server, version 2.0 and domain annotation was performed with dbCAN meta server. In addition, identity comparison was performed with NCBI BLAST webtool, sequences were aligned with ClustalW and Neighbor-Joining Tree and pairwise analysis were performed. The metagenomics analysis from Nelore cattle rumen returned 38 sequences with the GH10 domain, CE1, GH43 and CBM6 were also identified in these sequences. Analysis of Neighbor-Joining Tree and proteins identity enabled to differentiate 6 groups with, at least, two proteins with identity higher than 70%. Based on the analysis, 13 sequences were considered unappropriated for biotechnological application for either for being unstable or having transmembrane helices. In this sense, based on the in silico analyzes, 25 of the 38 sequences presented good characteristics for in vitro studies. Thus, in addition to the identification of the 38 sequences with GH10 domain, a workflow of in silico methodologies was suggested to assist the selection of sequences that will guide future in vitro studies.
Keywords: Metagenomics; Xylanase; In silico Studies; Lignocellulose; Protein Biotechnology; Lignocellulose Degrading Enzymes
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