scholarly journals In silico characterization of MTP1 gene associated with Zn homeostasis across different dicot plant species

2020 ◽  
Author(s):  
Ahmad Humayan Kabir
Keyword(s):  
Plant Species ◽  
In Silico ◽  
Metal Ion ◽  
Metal Tolerance ◽  
Critical Role ◽  
Alpha Helix ◽  
Motif Analysis ◽  
Zn Homeostasis ◽  
Metal Tolerance Protein ◽  
Cadmium Zinc

ABSTRACTZinc (Zn) is tightly regulated in plants. The MTP1/ZAT (metal tolerance protein) plays a critical role in adjusting Zn homeostasis upon Zn fluctuation in plants. This study characterizes MTP1 homologs with particular emphasis on AtMT1 in various dicot plants. The protein BLAST search was used to identify a total of 21 MTP1 proteins. Generally, all these MTP1 proteins showed around 400 residues long, six transmembrane helices, stable instability index along with cation transmembrane transporter activity (GO:0008324). These physio-chemical features of MTP1 can be utilized as a benchmark in the prediction of Zn uptake and tolerance in plants. These MTP1 homologs were located on chromosomes 2, 7, and 14 with one exon. Motif analysis showed conserved sequences of 41-50 residues belonging to the family of cation efflux, which may be helpful for binding sites targeting and transcription factor analysis. Phylogenetic studies revealed close similarities of AtZAT with Glycine max and Medicago trunculata that may infer a functional relationship in Zn tolerance or uptake across different plant species. Further, interactome analysis suggests that AtZAT is closely linked cadmium/zinc-transporting ATPase and ZIP metal ion transporter, which could provide essential background for functional genomics studies in plants. The network of AtZAT is predominantly connected to cadmium/zinc-transporting ATPase (HMA2, HMA3, HMA4), cation efflux protein (MTP11), and metal tolerance protein C3 (AT4G58060). The Genevestigator platform further predicts the high expression potential of AtMTP1 in root tissue at the germination and grain filling stage. The structural analysis of MTP1 proteins suggests the conserved N-glyco motifs as well as similar hydrophobicity, net charge and nonpolar residues, alpha-helix in all MTP1 proteins. Altogether, these in silico characterization features of MTP1 and its orthologs will provide an essential theoretical background to perform wet-lab experiments and to better understand Zn homeostasis aiming to develop genetically engineered plants.

In Silico Study of 1, 4 Alpha Glucan Branching Enzyme and Substrate Docking Studies

2020 ◽  
Vol 17 (1) ◽  
pp. 40-50
Author(s):  
Farzane Kargar ◽  
Amir Savardashtaki ◽  
Mojtaba Mortazavi ◽  
Masoud Torkzadeh Mahani ◽  
Ali Mohammad Amani ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
In Silico ◽  
Alpha Helix ◽  
In Silico Analysis ◽  
Glycogen Storage ◽  
Docking Studies ◽  
Random Coil ◽  
Special Topic ◽  
Industrial Biotechnology ◽  
In Silico Study

Background: The 1,4-alpha-glucan branching protein (GlgB) plays an important role in the glycogen biosynthesis and the deficiency in this enzyme has resulted in Glycogen storage disease and accumulation of an amylopectin-like polysaccharide. Consequently, this enzyme was considered a special topic in clinical and biotechnological research. One of the newly introduced GlgB belongs to the Neisseria sp. HMSC071A01 (Ref.Seq. WP_049335546). For in silico analysis, the 3D molecular modeling of this enzyme was conducted in the I-TASSER web server. Methods: For a better evaluation, the important characteristics of this enzyme such as functional properties, metabolic pathway and activity were investigated in the TargetP software. Additionally, the phylogenetic tree and secondary structure of this enzyme were studied by Mafft and Prabi software, respectively. Finally, the binding site properties (the maltoheptaose as substrate) were studied using the AutoDock Vina. Results: By drawing the phylogenetic tree, the closest species were the taxonomic group of Betaproteobacteria. The results showed that the structure of this enzyme had 34.45% of the alpha helix and 45.45% of the random coil. Our analysis predicted that this enzyme has a potential signal peptide in the protein sequence. Conclusion: By these analyses, a new understanding was developed related to the sequence and structure of this enzyme. Our findings can further be used in some fields of clinical and industrial biotechnology.

Identification and characterization of a tobacco metal tolerance protein, NtMTP2

Metallomics ◽  
2020 ◽  
Author(s):  
Anna Papierniak-Wygladala ◽  
Katarzyna Kozak ◽  
Anna Barabasz ◽  
Małgorzata Palusińska ◽  
Małgorzata Całka ◽  
...  
Keyword(s):  
Metal Tolerance ◽  
Efflux Transporter ◽  
Metal Tolerance Protein ◽  
Identification And Characterization

Metal Tolerance Protein 2 from N. tabacum (NtMTP2) is a tonoplast-localized Co and Ni efflux transporter. As an housekeeping protein controls optimal micronutrients concentration in the cytoplasm, and sequesters metal excess specifically in leaves.

In silico profiling and structural insights of zinc metal ion on O6-methylguanine methyl transferase and its interactions using molecular dynamics approach

2021 ◽  
Vol 27 (2) ◽  
Author(s):  
Marzieh Gharouni ◽  
Hamid Mosaddeghi ◽  
Jamshid Mehrzad ◽  
Ali Es-haghi ◽  
Alireza Motavalizadehkakhky
Keyword(s):  
Molecular Dynamics ◽  
In Silico ◽  
Metal Ion ◽  
Methyl Transferase ◽  
Zinc Metal ◽  
Structural Insights

Identification and characterization of Metal Tolerance Protein (MTP) family in Glycyrrhiza uralensis

Biologia ◽  
2021 ◽  
Author(s):  
Zahra Shirazi ◽  
Samaneh Samavat ◽  
Mahnaz Nezamivand Chegini ◽  
Yousef Mohammadi ◽  
Farzad Banaei-Asl
Keyword(s):  
Metal Tolerance ◽  
Glycyrrhiza Uralensis ◽  
Metal Tolerance Protein ◽  
Identification And Characterization

scholarly journals Corrigendum to: Metal tolerance protein MTP6 affects mitochondrial iron and manganese homeostasis in cucumber

2018 ◽  
Vol 70 (1) ◽  
pp. 369-369
Author(s):  
Magdalena Migocka ◽  
Ewa Maciaszczyk-Dziubinska ◽  
Karolina Małas ◽  
Ewelina Posyniak ◽  
Arnold Garbiec
Keyword(s):  
Metal Tolerance ◽  
Mitochondrial Iron ◽  
Metal Tolerance Protein ◽  
Iron And Manganese

scholarly journals Silicon flow from root to shoot in pepper: a comprehensive in silico analysis reveals a potential linkage between gene expression and hormone signaling that stimulates plant growth and metabolism

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10053
Author(s):  
Fernando Carlos Gómez-Merino ◽  
Libia Iris Trejo-Téllez ◽  
Atonaltzin García-Jiménez ◽  
Hugo Fernando Escobar-Sepúlveda ◽  
Sara Monzerrat Ramírez-Olvera
Keyword(s):  
Plant Growth ◽  
Plant Species ◽  
In Silico ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Plant Tissues ◽  
Promoter Regions ◽  
Root Cells ◽  
Physiological Processes ◽  
Silico Analysis

Background Silicon (Si) is categorized as a quasi-essential element for plants thanks to the benefits on growth, development and metabolism in a hormetic manner. Si uptake is cooperatively mediated by Lsi1 and Lsi2. Nevertheless, Lsi channels have not yet been identified and characterized in pepper (Capsicum annuum), while genes involved in major physiological processes in pepper are Si-regulated. Furthermore, Si and phytohormones may act together in regulating plant growth, metabolism and tolerance against stress. Our aim was to identify potential synergies between Si and phytohormones stimulating growth and metabolism in pepper, based on in silico data. Methods We established a hydroponic system to test the effect of Si (0, 60, 125 and 250 mg L−1 Si) on the concentrations of this element in different pepper plant tissues. We also performed an in silico analysis of putative Lsi genes from pepper and other species, including tomato (Solanum lycopersicum), potato (Solanum tuberosum) and Arabidopsis thaliana, to look for cis-acting elements responsive to phytohormones in their promoter regions. With the Lsi1 and Lsi2 protein sequences from various plant species, we performed a phylogenetic analysis. Taking into consideration the Lsi genes retrieved from tomato, potato and Arabidopsis, an expression profiling analysis in different plant tissues was carried out. Expression of Si-regulated genes was also analyzed in response to phytohormones and different plant tissues and developmental stages in Arabidopsis. Results Si concentrations in plant tissues exhibited the following gradient: roots > stems > leaves. We were able to identify 16 Lsi1 and three Lsi2 genes in silico in the pepper genome, while putative Lsi homologs were also found in other plant species. They were mainly expressed in root tissues in the genomes analyzed. Both Lsi and Si-regulated genes displayed cis-acting elements responsive to diverse phytohormones. In Arabidopsis, Si-regulated genes were transcriptionally active in most tissues analyzed, though at different expressed levels. From the set of Si-responsive genes, the NOCS2 gene was highly expressed in germinated seeds, whereas RABH1B, and RBCS-1A, were moderately expressed in developed flowers. All genes analyzed showed responsiveness to phytohormones and phytohormone precursors. Conclusion Pepper root cells are capable of absorbing Si, but small amounts of this element are transported to the upper parts of the plant. We could identify putative Si influx (Lsi1) and efflux (Lsi2) channels that potentially participate in the absorption and transport of Si, since they are mainly expressed in roots. Both Lsi and Si-regulated genes exhibit cis-regulatory elements in their promoter regions, which are involved in phytohormone responses, pointing to a potential connection among Si, phytohormones, plant growth, and other vital physiological processes triggered by Si in pepper.

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