Volume 8, Issue 31 (7-2018)
NCMBJ 2018, 8(31): 39-48 |
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Samiei K, Sohrabi S M. Identification of potential protein targets in P. syringae using bioinformatic analysis to control this pathogen. NCMBJ 2018; 8 (31) :39-48
URL: http://ncmbjpiau.ir/article-1-1127-en.html
URL: http://ncmbjpiau.ir/article-1-1127-en.html
Faculty Members of Agriculture, Islamic Azad University kangavar branch, Kangavar, I.R. of Iran , kamransamiei@yahoo.com
Abstract: (5030 Views)
Aim and Background: P. syringae have different pathological variants and causes disease in a wide range of plants. Annually, this pathogen causes high damage to tomato crops. Despite the different methods, the control of this pathogen still depends to chemicals. Due to similarity of chemical targets in pathogens to non-target organisms such as humans, these chemicals have harmful side effects on human, other organism and environment. Therefore, identification of specific targets in each pathogen is necessary to prevent the harmful effects of chemicals. In this study, using a homology-based bioinformatic approach, proteome of P. syringae were compared with tomato and other host plants proteomes and a number of proteins were selected as potential targets.
Material and Methods: In the first stage of the study, proteome of P. syringae were compared with host plants and non-similar proteins were selected. In the second stage, these proteins were compared with human, gastrointestinal microbial flora and non-target organisms (including vertebrates, arthropods and molluscs) proteomes and non-similar proteins were selected. In the third stage, selected proteins were compared with essential genes and resulting proteins were considered as potential targets. In the final stage, the potential targets were subjected to various qualitative analyzes, including subcellular localization search, metabolic pathways search and broad-spectrum analysis.
Results: Results of analyses identified 95 proteins as unique targets. Of 95 proteins, 22 proteins were broad-spectrum and 73 proteins were specific to P. syringae. Some targets involved in metabolism of carbohydrate, energy, fat, nucleotides, amino acids, other amines, glycans, vitamins, cofactors and secondary metabolites. Some targets involved in genetic and environmental information processing and some have played role in cellular processes. Of 95 proteins, 59 proteins are localized in cytoplasm, 15 proteins in inner membrane, 17 proteins in periplasmic space, 3 proteins in outer membrane and 1 protein in extracellular of P. syringae.
Conclusion: Identified proteins in this study are very effective targets and targeting of such proteins can efficiently control the P.syringae pathogen. Also, design and production of chemicals against these target proteins, along with the effective control of this pathogen, can control a wide range of pathogens and prevents the harmful effects on the human, non-target organisms and environment.
Material and Methods: In the first stage of the study, proteome of P. syringae were compared with host plants and non-similar proteins were selected. In the second stage, these proteins were compared with human, gastrointestinal microbial flora and non-target organisms (including vertebrates, arthropods and molluscs) proteomes and non-similar proteins were selected. In the third stage, selected proteins were compared with essential genes and resulting proteins were considered as potential targets. In the final stage, the potential targets were subjected to various qualitative analyzes, including subcellular localization search, metabolic pathways search and broad-spectrum analysis.
Results: Results of analyses identified 95 proteins as unique targets. Of 95 proteins, 22 proteins were broad-spectrum and 73 proteins were specific to P. syringae. Some targets involved in metabolism of carbohydrate, energy, fat, nucleotides, amino acids, other amines, glycans, vitamins, cofactors and secondary metabolites. Some targets involved in genetic and environmental information processing and some have played role in cellular processes. Of 95 proteins, 59 proteins are localized in cytoplasm, 15 proteins in inner membrane, 17 proteins in periplasmic space, 3 proteins in outer membrane and 1 protein in extracellular of P. syringae.
Conclusion: Identified proteins in this study are very effective targets and targeting of such proteins can efficiently control the P.syringae pathogen. Also, design and production of chemicals against these target proteins, along with the effective control of this pathogen, can control a wide range of pathogens and prevents the harmful effects on the human, non-target organisms and environment.
Type of Study: Research Article |
Subject:
Cellular and molecular
Received: 2018/09/5 | Accepted: 2018/09/5 | Published: 2018/09/5
Received: 2018/09/5 | Accepted: 2018/09/5 | Published: 2018/09/5
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