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Genomic Comparison of Rhizobium Species using in Silico AFLP-PCR Endonuclease Restrictions and Ampylating Enzymes

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Author: MUHAMMAD AMJAD QURESHI

Citable URI : https://vspace.vu.edu.pk/detail.aspx?id=107

Publisher : Virtual University of Pakistan

Date Issued: 11/13/2017 12:00:00 AM

Abstract

Characterizing genomic differences at species level is key to understand evolutionary and phylogenetic relationships, morphological and functional diversities and, above all, meaningful and precise taxonomic classifications. The techniques widely used in molecular biology like Amplified fragment length polymorphism-PCR (AFLP-PCR), endonuclease restrictions followed by Pulsed Field Gel Electrophoresis are the techniques mainly used to differentiate species of microbes for many years. These techniques are very useful in determining genomic differences arisen from point mutations, insertion-deletions and inversions. These differences may represent functional dissimilarities in studied organisms. AMPylation enzymes might reveal the changes occurring in proteome of organisms having similar genomes that may further explain the functional diversity of these organisms. The whole genome sequences of nine Rhizobium species were evaluated with different in-silico molecular techniques such as AFLP-PCR, endonuclease restrictions and AMPylating enzymes diversity for genome comparison. The entire genome sequences of Rhizobium species were retrieved from NCBI and aligned with Progressive Mauve and visualizedas Phylogenetic tree.The AFLP-PCR was carried out in-silico from the insilico.ehu.es, different combinations of restriction enzymes with different nucleotides to generate the AFLP bands to draw phylogeny. Different set of restriction enzymes were used for Restriction Digest and PFGE in silico for scoring of binary scores and analyzed. The post-translational modification (PTM) and ampylating enzymes diversity from the proteome of Rhizobium species were determined from novPTMenzy. The phylogenetic treesbased on AFLP-PCR and PFGE were compared with the tree on whole genome basis and slight variations were observed in the AFLP and PFGE based trees. Results clearly demonstrated the presence of PTM’s i.e. AMPylation, Hydroxylation, Sulfation and Deamidation with their specific domains (ampylating enzymes) GS-ATasE (GlnE), Fic, Doc (Phosphorylation); Aspargine_hydroxylase, Collagen_prolyl_lysyl_hydroxylase; Sulfotransferase and CNF (Cytotoxic Necrotizing Factors), respectively were observed in different Rhizobium species. The results pertaining to post translational modifications are discussed with relation to functional diversities reported in these species.


URI : https://vspace.vu.edu.pk/details.aspx?id=107

Citation: Qureshi, M. A. (2017). Genomic Comparison of Rhizobium Species using in Silico AFLP-PCR Endonuclease Restrictions and Ampylating Enzymes, Virtual University of Pakistan, (Lahore, Pakistan).

Version : Final Version

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