In silico identification and analysis of phytoene synthase genes in plants

Han, Yujun; Qs, Zheng; Yp, Wei; Chen, J; R, Liu; Hj, Wan

doi:10.4238/2015.august.14.5

Cited by 15 publications

(16 citation statements)

References 25 publications

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“…The PSY proteins used in this study have a wide range of pI values from 5. inter-domain similarity concerning pI values which is similar to previous reports of plant origin phytoene synthases showing a wide range of pI values (Iwata-Reuyl et al 2003;Lao et al 2011;Han et al 2015).…”

Section: Isoelectric Point (Pi)supporting

confidence: 89%

Comparative analysis of structural and functional aspects of phytoene synthase from Meiothermus taiwanensis strain RP

Mukherjee

Mukhopadhyay

2020

Ann Microbiol

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Purpose: The aim of this study is the in silico characterization of the structure and function of the phytoene synthase (PSY) of a red carotenoid producing thermophile Meiothermus taiwanensis strain RP with a comparative approach. Methods: PSYs from M. taiwanensis strain RP and other groups of thermophilic, mesophilic and psychrophilic bacteria, plants, protozoa, and algae were analyzed by ExPASy ProtParam, NCBI Conserved Domain Search, SOPMA, PSIPRED, Robetta server, ProQ, and QMEAN, with the superposition of 3-D structures in PyMOL.Results: RP PSY shows the highest (97.5 %) similarity with M. ruber and the lowest with the psychrophile Gelidibacter algens (36.7 %). The amino acid sequence of RP PSY is one of the shortest, with 275 residues. The instability index of RP PSY is much lower compared with plant sequences. Alanine, arginine, glycine, and leucine residues are the highest in Meiothermus sp., and they have a high amount of alpha-helix. Most of the 32 active site residues are conserved in all the sequences. However, some residues are more prone to substitutions in other PSYs except M. ruber. The three-dimensional structures of M. taiwanensis strain RP, Gelidibacter algens, Thermus thermophiles, Meiothermus ruber, and Brassica napus PSYs were homology modeled, validated, and submitted to Protein Model Databank. The superposition of the 3-D structures shows that their active site region structure is identical.Conclusion: RP PSY is one of the most stable PSYs and knowledge of its individual properties, similarities, and dissimilarities with other PSYs may be useful for genetic engineering and purification of the protein for improved carotenoid production.

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Section: Isoelectric Point (Pi)supporting

confidence: 89%

Comparative analysis of structural and functional aspects of phytoene synthase from Meiothermus taiwanensis strain RP

Mukherjee

Mukhopadhyay

2020

Ann Microbiol

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“…Bioinformatics analysis can play a vital role in the interpretation of proteomic data. These methodologies have been extensively used for predicting function and structure of proteins from its amino acid sequences 24,27,28,52,53,55 . The identification of the characteristics of these proteins during parasitism can serve as an important tool in the construction of control strategies for root-knot nematodes and its interactions with their host plants.…”

Section: Discussionmentioning

confidence: 99%

“…This type of experimentation represents a low cost alternative for studies on biological functions with very precise computational models when compared with laboratory conditions. Computational analyzes have been used in the characterization of several proteins and enzymes in both eukaryotes and prokaryotes, in search of genes linked to parasitism and resistance in host species [25][26][27][28][29][30][31] . The identification of proteins involved in the relationship of parasitism of nematodes and plants can provide important tools for research that develop plant species with resistant genes and in the search for mechanisms that avoid the breakdown of this resistance by phytonematodes.…”

Section: Introductionmentioning

confidence: 99%

In Silico Characterization of Meloidogyne Genus Nematode Cellulose Binding Proteins

Menezes

Cavalcanti

Martins

et al. 2019

Braz. arch. biol. technol.

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Root-knot nematodes are a group of endoparasites species that induce the formation of giant cells in the hosts, by which they guarantee their feeding and development. Meloidogyne species infect over 2000 plant species, and are highly destructive, causing damage to many crops around the world. M. enterolobii is considered the most aggressive species in tropical regions, such as Africa and South America. Phytonematodes are able to penetrate and migrate within plant tissues, establishing a sophisticated interaction with their hosts through parasitism factors, which include a series of cell wall degradation enzymes and plant cell modification. Among the parasitism factors documented in the M. enterolobii species, cellulose binding protein (CBP), a nematode excretion protein that appears to be associated with the breakdown of cellulose present in the plant cell wall. In silico analysis can be of great importance for the identification, structural and functional characterization of genomic sequences, besides making possible the prediction of structures and functions of proteins. The present work characterized 12 sequences of the CBP protein of nematodes of the genus Meloidogyne present in genomic databases. The results showed that all CBP sequences had signal peptide and that, after their removal, they had an isoelectric point that characterized them as unstable in an acid medium. The values of the average hydrophilicity demonstrated the hydrophilic character of the analyzed sequences. Phylogenetic analyzes were also consistent with the taxonomic classification of the nematode species of this study. Five motifs were identified, which are present in all sequences analyzed. These results may provide theoretical grounds for future studies of plant resistance to nematode infection. HIGHLIGHTS• CBPs are remarkably conserved between Meloidogyne species • CBPs exhibit two to three functional domains related to signal binding and cellulose hydrolase activities Menezes, A.M.F.; et al.

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“…Several research groups have identified a number of genes including WRKY genes, Ascorbate Peroxidase, PSY, etc. using different bioinformatics tools [38][39][40].…”

Section: Analysis Of Regulatory Elementsmentioning

confidence: 99%

Bioinformatics: A Way Forward to Explore “Plant Omics”

Rahman¹,

Shaheen²,

Rahman³

et al. 2016

Bioinformatics - Updated Features and Applications

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"ioinformatics, a computer-assisted science aiming at managing a huge volume of genomic data, is an emerging discipline that combines the power of computers, mathematical algorithms, and statistical concepts to solve multiple genetic/biological puzzles. This science has progressed parallel to the evolution of genome-sequencing tools, for example, the next-generation sequencing technologies, that resulted in arranging and analyzing the genome-sequencing information of large genomes. Synergism of plant omics and bioinformatics set a firm foundation for deducing ancestral karyotype of multiple plant families, predicting genes, etc. Second, the huge genomic data can be assembled to acquire maximum information from a voluminous omics data. The science of bioinformatics is handicapped due to lack of appropriate computational procedures in assembling sequencing reads of the homologs occurring in complex genomes like cotton n = x = , wheat n = x = , etc., and shortage of multidisciplinary-oriented trained manpower. In addition, the rapid expansion of sequencing data restricts the potential of acquisitioning, storing, distributing, and analyzing the genomic information. In future, inventions of high-tech computational tools and skills together with improved biological expertise would provide better insight into the genomes, and this information would be helpful in sustaining crop productivities on this planet.

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In silico identification and analysis of phytoene synthase genes in plants

Cited by 15 publications

References 25 publications

Comparative analysis of structural and functional aspects of phytoene synthase from Meiothermus taiwanensis strain RP

Comparative analysis of structural and functional aspects of phytoene synthase from Meiothermus taiwanensis strain RP

In Silico Characterization of Meloidogyne Genus Nematode Cellulose Binding Proteins

Bioinformatics: A Way Forward to Explore “Plant Omics”

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