23
DOI: https://doi.org/10.1186/s43141-022-00404-6
English
eng
Nene, Takio
Contributor
<div id="abs0005" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0010" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Background</h3><div class="u-margin-s-bottom" id="sp0075" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/catalase" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Catalase</a> (EC 1.11.1.6) is a heme-containing tetrameric </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/enzyme" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">enzyme</a><span style="margin: 0px; padding: 0px;"> that plays a critical role in signaling and hydrogen peroxide metabolism. It was the first enzyme to be crystallized and isolated. <a href="https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/catalase" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Catalase</a> is a well-known </span></span><a href="https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/industrial-enzyme" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">industrial enzyme</a> used in diagnostic and analytical methods in the form of biomarkers and biosensors, as well as in the textile, paper, food, and pharmaceutical industries. In silico </span><em style="margin: 0px; padding: 0px;">analysis</em><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"> of CAT genes and proteins has gained increased interest, emphasizing the development of biomarkers and <a href="https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/drug-development" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">drug designs</a>. The present work aims to understand the catalase evolutionary relationship of plant species and analyze its physicochemical characteristics, homology, </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/phylogenetic-tree" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">phylogenetic tree</a> construction, </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/protein-secondary-structure" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">secondary structure prediction</a><span style="margin: 0px; padding: 0px;">, and 3D modeling of <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/peptide-sequence" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">protein sequences</a> and its validation using a variety of conventional computational methods to assist researchers in better understanding the structure of proteins.</span></span></div></div><div id="abs0010" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0015" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Results</h3><div class="u-margin-s-bottom" id="sp0080" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;">Around 65 plant catalase sequences were computationally evaluated and subjected to bioinformatics assessment for physicochemical characterization, multiple sequence alignment, <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/phylogeny" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">phylogenetic</a> construction, motif and domain identification, and secondary and </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/tertiary-structure" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">tertiary structure</a> prediction. The phylogenetic tree revealed six unique clusters where diversity of plant catalases was found to be the largest for </span><em style="margin: 0px; padding: 0px;">Oryza sativa</em><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;">. The <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/thermostability" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">thermostability</a> and hydrophilic nature of these proteins were primarily observed, as evidenced by a relatively high aliphatic index and negative GRAVY value. The distribution of 5 </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/sequence-motif" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">sequence motifs</a> was uniformly distributed with a width length of 50 with the best possible amino residue sequences that resemble the plant catalase PLN02609 superfamily. Using SOPMA, the predicted secondary structure of the protein sequences revealed the predominance of the random coil. The predicted 3D CAT model from </span><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/arabidopsis-thaliana" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Arabidopsis thaliana</a></span></span><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"><span style="margin: 0px; padding: 0px;"> was a <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/homotetramer" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">homotetramer</a>, thermostable protein with 59-KDa weight, and its structural validation was confirmed by PROCHECK, ERRAT, Verify3D, and </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/ramachandran-plot" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">Ramachandran plot</a>. The functional relationships of our query sequence revealed the </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/glutathione-reductase" class="topic-link" style="margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration-line: underline; text-decoration-thickness: 1px; text-decoration-color: rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">glutathione reductase</a> as the closest interacting protein of query protein.</span></div></div><div id="abs0015" style="margin: 0px; padding: 0px; color: rgb(31, 31, 31); font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif; font-size: 16px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0020" style="margin-right: 0px; margin-left: 0px; padding: 0px; margin-top: 24px !important; margin-bottom: 8px !important; font-size: 20px !important; line-height: 30px !important;">Conclusions</h3><div class="u-margin-s-bottom" id="sp0085" style="margin-top: 0px; margin-right: 0px; margin-left: 0px; padding: 0px; margin-bottom: 16px !important;">This theoretical plant catalases in silico analysis provide insight into its physiochemical characteristics and functional and structural understanding and its evolutionary behavior and exploring protein structure-function relationships when crystal structures are unavailable.</div></div>
Elsevier
December 2022
pdf
Journal of Genetic Engineering and Biotechnology
Plant catalase in silico characterization and phylogenetic analysis with structural modeling
mixed material
Elsevier