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Kholousi Adab F, Mehdi Yaghoobi M, Gharechahi J. Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme. Sci Rep 2024; 14:8560. [PMID: 38609443 PMCID: PMC11014956 DOI: 10.1038/s41598-024-59256-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/08/2024] [Indexed: 04/14/2024] Open
Abstract
Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.
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Affiliation(s)
- Faezeh Kholousi Adab
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mohammad Mehdi Yaghoobi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Javad Gharechahi
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Asadie M, Miri A, Badri T, Hosseini Nejad J, Gharechahi J. Dysregulated AEBP1 and COLEC12 Genes in Late-Onset Alzheimer's Disease: Insights from Brain Cortex and Peripheral Blood Analysis. J Mol Neurosci 2024; 74:37. [PMID: 38568322 DOI: 10.1007/s12031-024-02212-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/21/2024] [Indexed: 04/05/2024]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by memory and cognitive impairment, often accompanied by alterations in mood, confusion, and, ultimately, a state of acute mental disturbance. The cerebral cortex is considered a promising area for investigating the underlying causes of AD by analyzing transcriptional patterns, which could be complemented by investigating blood samples obtained from patients. We analyzed the RNA expression profiles of three distinct areas of the brain cortex, including the frontal cortex (FC), temporal cortex (TC), and entorhinal cortex (EC) in patients with AD. Functional enrichment analysis was performed on the differentially expressed genes (DEGs) across the three regions. The two genes with the most significant expression changes in the EC region were selected for assessing mRNA expression levels in the peripheral blood of late-onset AD patients using quantitative PCR (qPCR). We identified eight shared DEGs in these regions, including AEBP1 and COLEC12, which exhibited prominent changes in expression. Functional enrichment analysis uncovered a significant association of these DEGs with the transforming growth factor-β (TGF-β) signaling pathway and processes related to angiogenesis. Importantly, we established a robust connection between the up-regulation of AEBP1 and COLEC12 in both the brain and peripheral blood. Furthermore, we have demonstrated the potential of AEBP1 and COLEC12 genes as effective diagnostic tools for distinguishing between late-onset AD patients and healthy controls. This study unveils the intricate interplay between AEBP1 and COLEC12 in AD and underscores their potential as markers for disease detection and monitoring.
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Affiliation(s)
- Mohamadreza Asadie
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Miri
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Taleb Badri
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Javad Hosseini Nejad
- Neuroscience Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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Heidari S, Hajjaran H, Mohebali M, Akhoundi B, Gharechahi J. Recognition of Immunoreactive Proteins in Leishmania infantum Amastigote-Like and Promastigote Using Sera of Visceral Leishmaniasis Patients: a Preliminary Study. Acta Parasitol 2024:10.1007/s11686-023-00764-0. [PMID: 38227109 DOI: 10.1007/s11686-023-00764-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 11/22/2023] [Indexed: 01/17/2024]
Abstract
PURPOSE Visceral leishmaniasis (VL) is a systemic and parasitic disease that is usually fatal if left untreated. VL is endemic in different parts of Iran and is caused mainly by Leishmania infantum. This study aimed to recognition immunoreactive proteins in amastigote-like and promastigote stages of L. infantum (Iranian strain) by antibodies present in the sera of VL patients. METHODS Total protein extract from amastigote-like and promastigote cells was separated by two-dimensional electrophoresis (2DE). To detect the immunoreactive proteins, 2DE immunoblotting method was performed using different pools of VL patients' sera. RESULTS Approximately 390 and 430 protein spots could be separated in 2DE profiles of L. infantum amastigote-like and promastigote stages, respectively. In immunoblotting method, approximately 295 and 135 immunoreactive proteins of amastigotes-like reacted with high antibody titer serum pool and low antibody titer serum pool, respectively. Approximately 120 and 85 immunoreactive proteins of promastigote extract were recognized using the high antibody titer sera pool and low antibody titer sera, respectively. CONCLUSION The present study has recognized a number of antigenic diversity proteins based on the molecular weight and pH in amastigote-like and promastigote stages of L. infantum. These results provide us a new concept for further analysis development in the field of diagnosis biomarkers and vaccine targets.
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Affiliation(s)
- Soudabeh Heidari
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, P. O. Box: 1417613151, Tehran, Iran
| | - Homa Hajjaran
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, P. O. Box: 1417613151, Tehran, Iran.
| | - Mehdi Mohebali
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, P. O. Box: 1417613151, Tehran, Iran
- Center for Research of Endemic Parasites of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Behnaz Akhoundi
- Department of Medical Parasitology and Mycology, School of Public Health, Tehran University of Medical Sciences, P. O. Box: 1417613151, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Ariaeenejad S, Gharechahi J, Foroozandeh Shahraki M, Fallah Atanaki F, Han JL, Ding XZ, Hildebrand F, Bahram M, Kavousi K, Hosseini Salekdeh G. Precision enzyme discovery through targeted mining of metagenomic data. Nat Prod Bioprospect 2024; 14:7. [PMID: 38200389 PMCID: PMC10781932 DOI: 10.1007/s13659-023-00426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]
Abstract
Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.
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Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehdi Foroozandeh Shahraki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Fereshteh Fallah Atanaki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), Nairobi, 00100, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51, Uppsala, Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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Liang Z, Zhang J, Ahmad AA, Han J, Gharechahi J, Du M, Zheng J, Wang P, Yan P, Salekdeh GH, Ding X. Forage lignocellulose is an important factor in driving the seasonal dynamics of rumen anaerobic fungi in grazing yak and cattle. Microbiol Spectr 2023; 11:e0078823. [PMID: 37707448 PMCID: PMC10581131 DOI: 10.1128/spectrum.00788-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 07/20/2023] [Indexed: 09/15/2023] Open
Abstract
Anaerobic fungi (AF) inhabit the gastrointestinal tract of ruminants and play an important role in the degradation of fiber feed. However, limited knowledge is available on seasonal dynamics and inter-species differences in rumen AF community in yak and cattle under natural grazing systems. Using the random forests model, the null model, and structural equation model, we investigated the seasonal dynamics and key driving factors of fiber-associated rumen AF in grazing yak and cattle throughout the year on the Qinghai-Tibet Plateau (QTP). We found that the richness and diversity of rumen AF of grazing yak and cattle in cold season were significantly higher than those in warm season (P < 0.05). We identified 12 rumen AF genera, among which , Cyllamyces, and Orpinomyces were predominant in the rumen of both grazing yak and cattle. LEfSe and random forest analysis showed that Feramyces, Tahromyces, and Buwchfawromyces were important seasonal indicator of rumen AF in grazing yak (P < 0.05), and Caecomyces, Cyllamyces, and Piromyces in grazing cattle (P < 0.05). Null model analysis revealed that the dynamic changes of rumen AF community structure were mainly affected by deterministic factors. Notably, mantel test and structural equation model revealed that forage physical-chemical properties, including dry matter (DM), neutral detergent fiber (NDF), and hemicellulose contents (HC) were the key factors driving the seasonal variations of the rumen AF community (P < 0.05). The results revealed that forage lignocellulose was probably an important factor affecting the seasonal dynamics and inter-species differences of the rumen AF community under natural grazing conditions. IMPORTANCE The seasonal dynamics of rumen anaerobic fungi in nature grazing yak and cattle were determined during cold and warm seasons based on pasture nutritional quality and environmental data sets. The main driving factors of anaerobic fungi in yak and cattle rumen were explored by combining random forest and structural equation models. In addition, the dynamic differences in the composition of the anaerobic fungi community in the yak and cattle in different seasons were characterized. It was found that some rumen anaerobic fungi have contributed to high fiber degradation rate in yak. These novel findings improve our understanding of the association of environmental and dietary seasonal variations with anaerobic fungal community, facilitating yak adaptation to high altitude.
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Affiliation(s)
- Zeyi Liang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianbo Zhang
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Anum Ali Ahmad
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianlin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mei Du
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Juanshan Zheng
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Peng Wang
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
- Department of Molecular Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Xuezhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Key Laboratory of Veterinary Pharmaceutical Development, Ministry of Agricultural and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
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Heiat M, Rezaei E, Gharechahi J, Abbasi M, Behroozi J, Abyazi MA, Baradaran B. Knockdown of SIX4 inhibits pancreatic cancer cells via apoptosis induction. Med Oncol 2023; 40:287. [PMID: 37656231 DOI: 10.1007/s12032-023-02163-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
Sine oculis homeobox 4 (SIX4), a critical transcription factor modulating organ development, potentially participates in tumorigenesis through numerous pathways. Here, we investigated siRNA-mediated knockdown effects of SIX4 on pancreatic cancer cells and underlying molecular mechanisms. The expression of SIX4 in pancreatic cancer and adjacent tissues were investigated in clinical tissue samples and bioinformatically approved by gene expression omnibus (GEO) database. Appropriate siRNA transfected into PANC1 pancreatic cancer cells in order to SIX4 knockdown. The survival, migration, invasion, colony formation, mitochondrial membrane potential, apoptosis, autophagy, and cell cycle in the cancer cells were investigated after knockdown of SIX4. In addition, expression of genes involved in apoptosis and metastasis were assessed in the transfected cancer cells in mRNA and protein levels. High-throughput analysis using GEO database confirmed the overexpression of SIX4 in pancreatic cancer tissues by six independent pancreatic cancer microarrays. Knockdown of SIX4 by specific siRNA significantly decreased survival, colony formation, and mitochondrial membrane potential of the cancer cells. Further assessments demonstrated that knockdown of SIX4 increases the apoptosis and autophagy rates in the cancer cells through modifying the expression of related genes. Moreover, a significant decrease in migration and invasion rates were observed in SIX4 suppressed group. Furthermore, frequency of the cells transfected with SIX4 siRNA increased slightly in G1 and Sub-G1 phases of cell cycle. Our study suggested that siRNA-mediated knockdown of SIX4 increases the pancreatic cancer cells death and reduces the invasion and migration of the cancer cells through different molecular pathways.
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Affiliation(s)
- Mohammad Heiat
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases (BRCGL), Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ehsan Rezaei
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Masoumeh Abbasi
- Department of Microbiology, Malekan Branch, Islamic Azad University, Malekan, Iran
| | - Javad Behroozi
- Department of Genetics and Biotechnology, School of Medicine, AJA University of Medical Sciences, Tehran, Iran
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Abyazi
- Baqiyatallah Research Center for Gastroenterology and Liver Diseases (BRCGL), Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Gholghasht Ave, 5166614766, Tabriz, Iran.
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Miri A, Gharechahi J, Samiei Mosleh I, Sharifi K, Jajarmi V. Identification of co-regulated genes associated with doxorubicin resistance in the MCF-7/ADR cancer cell line. Front Oncol 2023; 13:1135836. [PMID: 37397367 PMCID: PMC10311417 DOI: 10.3389/fonc.2023.1135836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Accepted: 05/30/2023] [Indexed: 07/04/2023] Open
Abstract
Introduction The molecular mechanism of chemotherapy resistance in breast cancer is not well understood. The identification of genes associated with chemoresistance is critical for a better understanding of the molecular processes driving resistance. Methods This study used a co-expression network analysis of Adriamycin (or doxorubicin)-resistant MCF-7 (MCF-7/ADR) and its parent MCF-7 cell lines to explore the mechanisms of drug resistance in breast cancer. Genes associated with doxorubicin resistance were extracted from two microarray datasets (GSE24460 and GSE76540) obtained from the Gene Expression Omnibus (GEO) database using the GEO2R web tool. The candidate differentially expressed genes (DEGs) with the highest degree and/or betweenness in the co-expression network were selected for further analysis. The expression of major DEGs was validated experimentally using qRT-PCR. Results We identified twelve DEGs in MCF-7/ADR compared with its parent MCF-7 cell line, including 10 upregulated and 2 downregulated DEGs. Functional enrichment suggests a key role for RNA binding by IGF2BPs and epithelial-to-mesenchymal transition pathways in drug resistance in breast cancer. Discussion Our findings suggested that MMP1, VIM, CNN3, LDHB, NEFH, PLS3, AKAP12, TCEAL2, and ABCB1 genes play an important role in doxorubicin resistance and could be targeted for developing novel therapies by chemical synthesis approaches.
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Affiliation(s)
- Ali Miri
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Gharechahi
- Human Genetic Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Iman Samiei Mosleh
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Kazem Sharifi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Anesthesiology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Jajarmi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Gharechahi J, Vahidi MF, Sharifi G, Ariaeenejad S, Ding XZ, Han JL, Salekdeh GH. Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses. Environ Res 2023; 229:115925. [PMID: 37086884 DOI: 10.1016/j.envres.2023.115925] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/26/2023] [Accepted: 04/15/2023] [Indexed: 05/03/2023]
Abstract
Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- Animal Science Research Department, Qom Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Qom, Iran
| | - Golandam Sharifi
- Department of Basic Sciences, Encyclopedia Research Center, Institute for Humanities and Cultural Studies, Tehran, Iran
| | - Shohreh Ariaeenejad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), 00100, Nairobi, Kenya; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China.
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, And Extension Organization, Karaj, Iran; School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia.
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Gharechahi J, Sarikhan S, Han JL, Ding XZ, Salekdeh GH. Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates. NPJ Biofilms Microbiomes 2022; 8:46. [PMID: 35676509 PMCID: PMC9177762 DOI: 10.1038/s41522-022-00309-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/13/2022] [Indexed: 11/11/2022] Open
Abstract
Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.
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Jamiri Z, Khosravi R, Heidari MM, Kiani E, Gharechahi J. A nonsense mutation in MME gene associates with autosomal recessive late-onset Charcot-Marie-Tooth disease. Mol Genet Genomic Med 2022; 10:e1913. [PMID: 35212467 PMCID: PMC9034668 DOI: 10.1002/mgg3.1913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 01/02/2023] Open
Abstract
Background The genetic cause for the majority of patients with late‐onset axonal form of neuropathies have remained unknown. In this study we aimed to identify the causal mutation in a family with multiple affected individuals manifesting a range of phenotypic features consistent with late‐onset sensorimotor axonal polyneuropathy. Methods Whole exome sequencing (WES) followed by targeted variant screening and prioritization was performed to identify the candidate mutation. The co‐segregation of the mutation with the phenotype was confirmed by Sanger sequencing. Results We identified a nonsense mutation (c.1564C>T; p.Q522*) in membrane metalloendopeptidase (MME) gene as the cause of the disease condition. The mutation has a combined annotation‐ dependent depletion (CADD) score 45 and predicted to be deleterious based on various algorithms. The mutation was inherited in an autosomal recessive mode and further confirmed to co‐segregate with the disease phenotype in the family and showed to has the required criteria including rarity and deleteriousness to be considered as pathogenic. Conclusion The MME gene encodes for the membrane bound endopeptidase neprilysin (NEP) which is involved in processing of various peptide substrates. The identified mutation causes a complete loss of carboxy‐terminal region of the NEP protein which contains the zinc binding site and the catalytic domain and thus considered to be a loss‐of‐function mutation. The loss of NEP activity is likely associated with impaired myelination and axonal injury which is hallmark of CMT diseases.
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Affiliation(s)
- Zeinab Jamiri
- Department of Biology, Faculty of Science, Yazd University, Yazd, Iran
| | - Rana Khosravi
- Department of Biology, Faculty of Science, University of Zabol, Zabol, Iran
| | | | - Ebrahim Kiani
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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11
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Bayranvand M, Akbarinia M, Salehi Jouzani G, Gharechahi J, Baldrian P. Distribution of Soil Extracellular Enzymatic, Microbial, and Biological Functions in the C and N-Cycle Pathways Along a Forest Altitudinal Gradient. Front Microbiol 2021; 12:660603. [PMID: 34539590 PMCID: PMC8447401 DOI: 10.3389/fmicb.2021.660603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 07/23/2021] [Indexed: 11/23/2022] Open
Abstract
The diverse chemical, biological, and microbial properties of litter and organic matter (OM) in forest soil along an altitudinal gradient are potentially important for nutrient cycling. In the present study, we sought to evaluate soil chemical, biological, microbial, and enzymatic characteristics at four altitude levels (0, 500, 1,000, and 1,500 m) in northern Iran to characterize nutrient cycling in forest soils. The results showed that carbon (C) and nitrogen (N) turnover changed with altitude along with microbial properties and enzyme activity. At the lowest altitude with mixed forest and no beech trees, the higher content of N in litter and soil, higher pH and microbial biomass nitrogen (MBN), and the greater activities of aminopeptidases affected soil N cycling. At elevations above 1,000 m, where beech is the dominant tree species, the higher activities of cellobiohydrolase, arylsulfatase, β-xylosidase, β-galactosidase, endoglucanase, endoxylanase, and manganese peroxidase (MnP) coincided with higher basal respiration (BR), substrate-induced respiration (SIR), and microbial biomass carbon (MBC) and thus favored conditions for microbial entropy and C turnover. The low N content and high C/N ratio at 500-m altitude were associated with the lowest microbial and enzyme activities. Our results support the view that the plain forest with mixed trees (without beech) had higher litter quality and soil fertility, while forest dominated by beech trees had the potential to store higher C and can potentially better mitigate global warming.
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Affiliation(s)
- Mohammad Bayranvand
- Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Tehran, Iran.,Laboratory of Environmental Microbiology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
| | - Moslem Akbarinia
- Faculty of Natural Resources and Marine Sciences, Tarbiat Modares University, Tehran, Iran
| | - Gholamreza Salehi Jouzani
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Javad Gharechahi
- Human Genetics Research Centre, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology, Czech Academy of Sciences, Prague, Czechia
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12
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Bayranvand M, Akbarinia M, Salehi Jouzani G, Gharechahi J, Kooch Y, Baldrian P. Composition of soil bacterial and fungal communities in relation to vegetation composition and soil characteristics along an altitudinal gradient. FEMS Microbiol Ecol 2021; 97:5918382. [PMID: 33021633 DOI: 10.1093/femsec/fiaa201] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/01/2020] [Indexed: 11/12/2022] Open
Abstract
The objective of the present study was to evaluate how altitudinal gradients shape the composition of soil bacterial and fungal communities, humus forms and soil properties across six altitude levels in Hyrcanian forests. Soil microbiomes were characterized by sequencing amplicons of selected molecular markers. Soil chemistry and plant mycorrhizal type were the two dominant factors explaining variations in bacterial and fungal diversity, respectively. The lowest altitude level had more favorable conditions for the formation of mull humus and exhibited higher N and Ca contents. These conditions were also associated with a higher proportion of Betaproteobacteria, Acidimicrobia, Acidobacteria and Nitrospirae. Low soil and forest floor quality as well as lower bacterial and fungal diversity characterized higher altitude levels, along with a high proportion of shared bacterial (Thermoleophilia, Actinobacteria and Bacilli) and fungal (Eurotiomycetes and Mortierellomycota) taxa. Beech-dominated sites showed moderate soil quality and high bacterial (Alphaproteobacteria, Acidobacteria, Planctomycetes and Bacteroidetes) and fungal (Basidiomycota) diversity. Particularly, the Basidiomycota were well represented in pure beech forests at an altitude of 1500 m. In fertile and nitrogen rich soils with neutral pH, soil quality decreased along the altitudinal gradient, indicating that microbial diversity and forest floor decomposition were likely constrained by climatic conditions.
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Affiliation(s)
- Mohammad Bayranvand
- Faculty of Natural Resources & Marine Sciences; Tarbiat Modares University (TMU), Imam Reza Blvd., 46614-356, Noor, Mazandaran, Iran
| | - Moslem Akbarinia
- Faculty of Natural Resources & Marine Sciences; Tarbiat Modares University (TMU), Imam Reza Blvd., 46614-356, Noor, Mazandaran, Iran
| | - Gholamreza Salehi Jouzani
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Fahmideh Blvd., P.O. Box:31535-1897, Karaj, Iran
| | - Javad Gharechahi
- Human Genetics Research Centre, Baqiyatallah University of Medical Sciences, Vanak Square, Shahid Nosrati Alley, P.O. Box: 1435916471, Tehran, Iran
| | - Yahya Kooch
- Faculty of Natural Resources & Marine Sciences; Tarbiat Modares University (TMU), Imam Reza Blvd., 46614-356, Noor, Mazandaran, Iran
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, Praha 4 14220, Czech Republic
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13
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Gharechahi J, Vahidi MF, Bahram M, Han JL, Ding XZ, Salekdeh GH. Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen. ISME J 2021; 15:1108-1120. [PMID: 33262428 PMCID: PMC8114923 DOI: 10.1038/s41396-020-00837-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 11/03/2020] [Accepted: 11/11/2020] [Indexed: 02/08/2023]
Abstract
Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle's diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.
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Affiliation(s)
- Javad Gharechahi
- grid.411521.20000 0000 9975 294XHuman Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- grid.473705.20000 0001 0681 7351Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Mohammad Bahram
- grid.6341.00000 0000 8578 2742Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden ,grid.10939.320000 0001 0943 7661Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, 51005 Tartu, Estonia
| | - Jian-Lin Han
- grid.419369.00000 0000 9378 4481Livestock Genetics Program, International Livestock Research Institute (ILRI), 00100 Nairobi, Kenya ,grid.410727.70000 0001 0526 1937CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), 100193 Beijing, China
| | - Xue-Zhi Ding
- grid.410727.70000 0001 0526 1937Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), 730050 Lanzhou, China
| | - Ghasem Hosseini Salekdeh
- grid.473705.20000 0001 0681 7351Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran ,grid.1004.50000 0001 2158 5405Department of Molecular Sciences, Macquarie University, North Ryde, NSW Australia
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14
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Vahidi MF, Gharechahi J, Behmanesh M, Ding XZ, Han JL, Hosseini Salekdeh G. Diversity of microbes colonizing forages of varying lignocellulose properties in the sheep rumen. PeerJ 2021; 9:e10463. [PMID: 33510967 PMCID: PMC7808268 DOI: 10.7717/peerj.10463] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 11/10/2020] [Indexed: 01/13/2023] Open
Abstract
Background The rumen microbiota contributes strongly to the degradation of ingested plant materials. There is limited knowledge about the diversity of taxa involved in the breakdown of lignocellulosic biomasses with varying chemical compositions in the rumen. Method We aimed to assess how and to what extent the physicochemical properties of forages influence the colonization and digestion by rumen microbiota. This was achieved by placing nylon bags filled with candidate materials in the rumen of fistulated sheep for a period of up to 96 h, followed by measuring forage's chemical characteristics and community structure of biofilm-embedded microbiota. Results Rumen degradation for all forages appeared to have occurred mainly during the first 24 h of their incubation, which significantly slowed down after 48 h of rumen incubation, depending on their chemical properties. Random Forest analysis predicted the predominant role of Treponema and Butyrivibrio in shaping microbial diversity attached to the forages during the course of rumen incubation. Exploring community structure and composition of fiber-attached microbiota revealed significant differential colonization rates of forages depending on their contents for NDF and cellulose. The correlation analysis highlighted the significant contribution of Lachnospiraceae and Veillonellaceae to fiber degradation in the sheep rumen. Conclusion Our findings suggested that forage cellulose components are critical in shaping the pattern of microbial colonization and thus their final digestibility in the rumen.
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Affiliation(s)
- Mohammad Farhad Vahidi
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya.,CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China, Institute of Animal Science, Beijing, China
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
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15
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Gharechahi J, Vahidi MF, Ding XZ, Han JL, Salekdeh GH. Temporal changes in microbial communities attached to forages with different lignocellulosic compositions in cattle rumen. FEMS Microbiol Ecol 2020; 96:5822058. [PMID: 32304321 DOI: 10.1093/femsec/fiaa069] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/15/2020] [Indexed: 01/22/2023] Open
Abstract
The attachment of rumen microbes to feed particles is critical to feed fermentation, degradation and digestion. However, the extent to which the physicochemical properties of feeds influence the colonization by rumen microbes is still unclear. We hypothesized that rumen microbial communities may have differential preferences for attachments to feeds with varying lignocellulose properties. To this end, the structure and composition of microbial communities attached to six common forages with different lignocellulosic compositions were analyzed following in situ rumen incubation in male Taleshi cattle. The results showed that differences in lignocellulosic compositions significantly affected the inter-sample diversity of forage-attached microbial communities in the first 24 h of rumen incubation, during which the highest dry matter degradation was achieved. However, extension of the incubation to 96 h resulted in the development of more uniform microbial communities across the forages. Fibrobacteres were significantly overrepresented in the bacterial communities attached to the forages with the highest neutral detergent fiber contents. Ruminococcus tended to attach to the forages with low acid detergent lignin contents. The extent of dry matter fermentation was significantly correlated with the populations of Fibrobacteraceae, unclassified Bacteroidales, Ruminococcaceae and Spirochaetacea. Our findings suggested that lignocellulosic compositions, and more specifically the cellulose components, significantly affected the microbial attachment to and thus the final digestion of the forages.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mohammad Farhad Vahidi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
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16
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Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH. Plant-Microbe Symbiosis: What Has Proteomics Taught Us? Proteomics 2020; 19:e1800105. [PMID: 31218790 DOI: 10.1002/pmic.201800105] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/04/2019] [Indexed: 11/08/2022]
Abstract
Beneficial microbes have a positive impact on the productivity and fitness of the host plant. A better understanding of the biological impacts and underlying mechanisms by which the host derives these benefits will help to address concerns around global food production and security. The recent development of omics-based technologies has broadened our understanding of the molecular aspects of beneficial plant-microbe symbiosis. Specifically, proteomics has led to the identification and characterization of several novel symbiosis-specific and symbiosis-related proteins and post-translational modifications that play a critical role in mediating symbiotic plant-microbe interactions and have helped assess the underlying molecular aspects of the symbiotic relationship. Integration of proteomic data with other "omics" data can provide valuable information to assess hypotheses regarding the underlying mechanism of symbiosis and help define the factors affecting the outcome of symbiosis. Herein, an update is provided on the current and potential applications of symbiosis-based "omic" approaches to dissect different aspects of symbiotic plant interactions. The application of proteomics, metaproteomics, and secretomics as enabling approaches for the functional analysis of plant-associated microbial communities is also discussed.
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Affiliation(s)
- Behnam Khatabi
- Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD, 21853, USA
| | - Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran
| | - Dilin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, P. R. China.,Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou, P. R. China
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Matthew J McKay
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Mehdi Mirzaei
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia.,Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, 2109, Australia
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran.,Department of Molecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
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17
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Khatabi B, Gharechahi J, Ghaffari MR, Liu D, Haynes PA, McKay MJ, Mirzaei M, Salekdeh GH. Front Cover: Plant–Microbe Symbiosis: What Has Proteomics Taught Us? Proteomics 2019. [DOI: 10.1002/pmic.201970141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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18
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Khalili Ghadikolaei K, Gharechahi J, Haghbeen K, Akbari Noghabi K, Hosseini Salekdeh G, Shahbani Zahiri H. A cold-adapted endoglucanase from camel rumen with high catalytic activity at moderate and low temperatures: an anomaly of truly cold-adapted evolution in a mesophilic environment. Extremophiles 2018; 22:315-326. [PMID: 29330650 DOI: 10.1007/s00792-018-0999-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 12/23/2017] [Indexed: 11/25/2022]
Abstract
Endoglucanases are important enzymes in plant biomass degradation. They have current and potential applications in various industrial sectors including human and animal food processing, textile, paper, and renewable biofuel production. It is assumed that the cold-active endoglucanases, with high catalytic rates in moderate and cold temperatures, can improve the cost-effectiveness of industrial processes by lowering the need for heating and, thus, energy consumption. In this study, the endoglucanase CelCM3 was procured from a camel rumen metagenome via gene cloning and expression in Escherichia coli BL21 (DE3). The maximum activity of the enzyme on carboxymethyl cellulose (CMC) was obtained at pH 5 and 30 °C with a Vmax and Km of 339 U/mg and 2.57 mg/ml, respectively. The enzyme with an estimated low melting temperature of 45 °C and about 50% activity at 4 °C was identified to be cold-adapted. A thermodynamic analysis corroborated that CelCM3 with an activation energy (Ea), enthalpy of activation (ΔH), and Gibb's free energy (ΔG) of, respectively, 18.47 kJ mol-1, 16.12 kJ mol-1, and 56.09 kJ mol-1 is a cold-active endoglucanase. In addition, CelCM3 was tolerant of metal ions, non-ionic detergents, urea, and organic solvents. Given these interesting characteristics, CelCM3 shows promise to meet the requirements of industrial applications.
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Affiliation(s)
- Kamran Khalili Ghadikolaei
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Kamahldin Haghbeen
- Department of Plant Bioproducts, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Kambiz Akbari Noghabi
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | - Hossein Shahbani Zahiri
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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19
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Gharechahi J, Salekdeh GH. A metagenomic analysis of the camel rumen's microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation. Biotechnol Biofuels 2018; 11:216. [PMID: 30083229 PMCID: PMC6071333 DOI: 10.1186/s13068-018-1214-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 07/24/2018] [Indexed: 05/02/2023]
Abstract
BACKGROUND The diverse microbiome present in the rumen of ruminant animals facilitates the digestion of plant-based fiber. In this study, a shotgun metagenomic analysis of the microbes adhering to plant fiber in the camel rumen was undertaken to identify the key species contributing to lignocellulose degradation and short chain volatile fatty acids (VFA) fermentation. RESULTS The density of genes in the metagenome encoding glycoside hydrolases was estimated to be 25 per Mbp of assembled DNA, which is significantly greater than what has been reported in other sourced metagenomes, including cow rumen. There was also a substantial representation of sequences encoding scaffoldins, dockerins and cohesins, indicating the potential for cellulosome-mediated lignocellulose degradation. Binning of the assembled metagenome has enabled the definition of 65 high-quality genome bins which showed high diversity for lignocellulose degrading enzymes. Species associated to Bacteroidetes showed a high proportion of genes for debranching and oligosaccharide degrading enzymes, while those belonging to Firmicutes and Fibrobacteres were rich in cellulases and hemicellulases and thus these lineages were probably the key for ensuring the degradation of lignocellulose. The presence of many "polysaccharide utilization loci" (PULs) in Bacteroidetes genomes indicates their broad substrate specificity and high potential carbohydrate degradation ability. An analysis of VFA biosynthesis pathways showed that genes required for the synthesis of acetate were present in a range of species, except for Elusimicrobiota and Euryarchaeota. The production of propionate, exclusively via the succinate pathway, was carried out by species belonging to the phyla Bacteroidetes, Firmicutes, Spirochaetes and Fibrobacteres. Butyrate was generated via the butyrylCoA: acetate CoA-transferase pathway by Bacteroidetes and Lentisphaerae species, but generally via the butyrate kinase pathway by Firmicutes species. CONCLUSION The analysis confirmed the camel rumen's microbiome as a dense and yet largely untapped source of enzymes with the potential to be used in a range of biotechnological processes including biofuel, fine chemicals and food processing industries.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research Education, and Extension Organization, Karaj, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, NSW Australia
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20
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Bakhshi B, Fard EM, Gharechahi J, Safarzadeh M, Nikpay N, Fotovat R, Azimi MR, Salekdeh GH. The contrasting microRNA content of a drought tolerant and a drought susceptible wheat cultivar. J Plant Physiol 2017; 216:35-43. [PMID: 28575745 DOI: 10.1016/j.jplph.2017.05.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/14/2017] [Accepted: 05/17/2017] [Indexed: 05/08/2023]
Abstract
Drought stress represents one of the most common stresses affecting the productivity of crop plants. A rather recently discovered component of the plant response to drought is the cellular population of microRNAs. Here, the microRNA content was revealed of two bread wheat cultivars contrasting strongly with respect to the ability to withstand drought stress. A total of 1813 miRNAs was identified, grouped into 106 families. Some 104 of these miRNAs were predicted to match 212 novel miRNA precursors. In the drought tolerant cultivar (SM), 105 (33 known and 72 novel) miRNAs were altered in abundance by the imposition of drought stress, while the equivalent number in the more sensitive cultivar (SW) was 51 (20 and 31). An in silico analysis predicted that these miRNAs target at least 1959 genes in SM and 1111 in SW, suggesting their broad contribution to the drought stress response. Among the target genes were several known stress-related genes, encoding, for example, superoxide dismutase, various MYB transcription factors, various ABA signaling proteins and various MADS-box transcription factors. In many cases, the more susceptible cultivar SW behaved in a contrasting manner. The suggestion is that miRNAs represent an important aspect of the drought stress response, post-transcriptionally regulating a range of stress-related genes.
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Affiliation(s)
- Behnam Bakhshi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran
| | - Ehsan Mohseni Fard
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahdieh Safarzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran
| | - Nava Nikpay
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran
| | - Reza Fotovat
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Mohammad Reza Azimi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Tehran, Iran; Department of Molecular Systems Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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21
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Khorrami A, Sharif Bagheri M, Tavallaei M, Gharechahi J. The functional significance of 14-3-3 proteins in cancer: focus on lung cancer. Horm Mol Biol Clin Investig 2017; 32:/j/hmbci.ahead-of-print/hmbci-2017-0032/hmbci-2017-0032.xml. [PMID: 28779564 DOI: 10.1515/hmbci-2017-0032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 07/03/2017] [Indexed: 02/07/2023]
Abstract
The 14-3-3 family proteins are phosphoserine/phosphothreonine binding proteins constituting a conserved class of proteins which are detected in all eukaryotic cells. In mammalians, 14-3-3 proteins have seven distinct isoforms (β, γ, ε, η, ζ, σ and τ/θ) which are involved in various cellular processes including signal transduction, cell cycle, cell proliferation, apoptosis, differentiation and survival. 14-3-3 proteins do not have a distinct catalytic activity and often regulate the activity, stability, subcellular localization and interactions of other proteins. The 14-3-3 family proteins function through interacting with their client proteins or facilitating the interaction of other proteins likely as adaptor proteins. The versatile functions of these proteins in the regulation of cell growth, cell division, cell death and cell migration make them candidate proteins for which an important role in cancer development could be envisioned. Indeed, analysis of cancer cell lines and tumor-derived tissues have indicated the differential abundance or post-translational modification of some 14-3-3 isoforms. In this review, we aimed to show how deregulation of 14-3-3 proteins contributes to initiation, establishment and progression of cancers with a particular emphasis on lung cancer. The role of these proteins in cancer-relevant processes including cell cycle, cell migration, cell-cell communication and programmed cell death will be discussed in detail.
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Affiliation(s)
- Afshin Khorrami
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahyar Sharif Bagheri
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mahmood Tavallaei
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
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Gharechahi J, Kharazian ZA, Sarikhan S, Jouzani GS, Aghdasi M, Hosseini Salekdeh G. The dynamics of the bacterial communities developed in maize silage. Microb Biotechnol 2017; 10:1663-1676. [PMID: 28696065 PMCID: PMC5658587 DOI: 10.1111/1751-7915.12751] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 05/26/2017] [Accepted: 05/28/2017] [Indexed: 02/01/2023] Open
Abstract
Ensilage provides an effective means of conserving summer‐grown green forage to supply as winter feed to ruminants. The fermentation process involved in the ensilage process relies on lactic acid bacteria (LAB). Here, 16S ribosomal DNA amplicon pyrosequencing was used to follow the dynamic behaviour of the LAB community during the ensilage of maize biomass, with a view to identify the key species involved in the process. The biomass used for ensilage was a single‐cross maize hybrid, harvested at the milk‐line stage. The crop was grown at three contrasting locations. Aspects of the physico‐chemical composition of the material and the LAB species present were sampled at 0, 3, 6, 14, 21 and 32 days after ensilage was initiated. In all three cases, members of the Leuconostocaceae family dominated the epiphytic bacterial community, notably Leuconostoc and Weissella, but some variation was noted in the abundance of certain Leuconostocaceae and Lactobacillaceae species, as well as that of some Acetobacteraceae, Enterobacteriaceae and Moraxellaceae species. The constellation of the microbiome which developed during the ensilage process differed markedly from that of the epiphytic one, with Lactobacillaceae, particularly Lactobacillus and Pediococcus spp. dominating. The abundance of heterofermentative Leuconostocaceae spp. in the epiphytic community and the extent of the transition from hetero‐ to homo‐fermentation during the initial ensilage period are important factors in determining silage quality.
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Affiliation(s)
- Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Science, Tehran, Iran
| | | | - Sajjad Sarikhan
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Gholamreza Salehi Jouzani
- Department of Microbial Biotechnology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Mahnaz Aghdasi
- Department of Biology, Faculty of Science, Golestan University, Gorgan, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
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Hashemi A, Gharechahi J, Nematzadeh G, Shekari F, Hosseini SA, Salekdeh GH. Two-dimensional blue native/SDS-PAGE analysis of whole cell lysate protein complexes of rice in response to salt stress. J Plant Physiol 2016; 200:90-101. [PMID: 27362847 DOI: 10.1016/j.jplph.2016.05.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 05/22/2016] [Accepted: 05/25/2016] [Indexed: 06/06/2023]
Abstract
To understand the biology of a plant in response to stress, insight into protein-protein interactions, which almost define cell behavior, is thought to be crucial. Here, we provide a comparative complexomics analysis of leaf whole cell lysate of two rice genotypes with contrasting responses to salt using two-dimensional blue native/SDS-PAGE (2D-BN/SDS-PAGE). We aimed to identify changes in subunit composition and stoichiometry of protein complexes elicited by salt. Using mild detergent for protein complex solubilization, we were able to identify 9 protein assemblies as hetero-oligomeric and 30 as homo-oligomeric complexes. A total of 20 proteins were identified as monomers in the 2D-BN/SDS-PAGE gels. In addition to identifying known protein complexes that confirm the technical validity of our analysis, we were also able to discover novel protein-protein interactions. Interestingly, an interaction was detected for glycolytic enzymes enolase (ENO1) and triosephosphate isomerase (TPI) and also for a chlorophyll a-b binding protein and RuBisCo small subunit. To show changes in subunit composition and stoichiometry of protein assemblies during salt stress, the differential abundance of interacting proteins was compared between salt-treated and control plants. A detailed exploration of some of the protein complexes provided novel insight into the function, composition, stoichiometry and dynamics of known and previously uncharacterized protein complexes in response to salt stress.
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Affiliation(s)
| | - Javad Gharechahi
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Ghorbanali Nematzadeh
- Faculty of Agronomy, University of Agricultural Sciences and Natural Resources of Sari, Sari, Iran
| | - Faezeh Shekari
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Seyed Abdollah Hosseini
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education, and Extension Organization, Karaj, Iran; Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
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Vahdat S, Mousavi SA, Omrani G, Gholampour M, Sotoodehnejadnematalahi F, Ghazizadeh Z, Gharechahi J, Baharvand H, Salekdeh GH, Aghdami N. Cellular and molecular characterization of human cardiac stem cells reveals key features essential for their function and safety. Stem Cells Dev 2016; 24:1390-404. [PMID: 25867933 DOI: 10.1089/scd.2014.0222] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cell therapy of heart diseases is emerging as one of the most promising known treatments in recent years. Transplantation of cardiac stem cells (CSCs) may be one of the best strategies to cure adult or pediatric heart diseases. As these patient-derived stem cells need to be isolated from small heart biopsies, it is important to select the best isolation method and CSC subpopulation with the best cardiogenic functionality. We employed three different protocols including c-KIT(+) cell sorting, clonogenic expansion, and explants culture to isolate c-KIT(+) cells, clonogenic expansion-derived cells (CEDCs), and cardiosphere-derived cells (CDCs), respectively. Evaluation of isolated CSC characteristics in vitro and after rat myocardial infarction (MI) model transplantation revealed that although c-KIT(+) and CDCs had higher MI regenerative potential, CEDCs had more commitment into cardiomyocytes and needed lower passages that were essential to reach a definite cell count. Furthermore, genome-wide expression analysis showed that subsequent passages caused changes in characteristics of cells, downregulation of cell cycle-related genes, and upregulation of differentiation and carcinogenic genes, which might lead to senescence, commitment, and possible tumorigenicity of the cells. Because of different properties of CSC subpopulations, we suggest that appropriate CSCs subpopulation should be chosen based on their experimental or clinical use.
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Affiliation(s)
- Sadaf Vahdat
- 1Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,2Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Seyed Ahmad Mousavi
- 3Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Gholamreza Omrani
- 4Department of Cardiac Surgery, Rajaei Cardiovascular Medical Research Center, Tehran University of Medical Science, Tehran, Iran
| | - Maziar Gholampour
- 4Department of Cardiac Surgery, Rajaei Cardiovascular Medical Research Center, Tehran University of Medical Science, Tehran, Iran
| | - Fattah Sotoodehnejadnematalahi
- 1Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Zaniar Ghazizadeh
- 1Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Javad Gharechahi
- 3Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hossein Baharvand
- 1Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,5Department of Developmental Biology, University of Science and Culture, ACECR, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- 3Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,6Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | - Nasser Aghdami
- 1Department of Stem Cells and Developmental Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.,7Department of Regenerative Biomedicine at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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Faghani E, Gharechahi J, Komatsu S, Mirzaei M, Ali Khavarinejad R, Najafi F, Karimi Farsad L, Hosseini Salekdeh G. Data in support of comparative physiology and proteomic analysis of two wheat genotypes contrasting in drought tolerance. Data Brief 2015. [PMID: 26217700 PMCID: PMC4459561 DOI: 10.1016/j.dib.2014.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Here, we present the data from a comparative physiology and proteomics approach used to analyze the response of two wheat genotypes (SERI M 82 (SE) and SW89.5193/kAu2 (SW)) with contrasting responses to drought stress. Proteomic analysis resulted in identification of 49 unique proteins with significant change in abundance (2-fold) under water shortage in roots and leaves. Gene ontology analysis of drought-responsive proteins (DRPs) suggested an induction of proteins related to cell wall biogenesis, ATP synthesis, photosynthesis, and carbohydrate/energy metabolism in leaves under stress condition. A large fraction of root proteins were identified to be involved in defense and oxidative stress response. In addition, a significant change was detected in proteins related to protein synthesis, ATP synthesis, and germin-like proteins in response to drought stress. A detailed analysis of this data may be obtained from Ref. [1].
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Affiliation(s)
- Elham Faghani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | - Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | - Setsuko Komatsu
- National Institute of Crop Science, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | | | | | - Laleh Karimi Farsad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem cell Biology and Technology, ACECR, Tehran, Iran
- Corresponding author at: Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran. Tel.: +98 263 2703536; fax: +98 263 2704539.
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Mardi M, Karimi Farsad L, Gharechahi J, Salekdeh GH. In-Depth Transcriptome Sequencing of Mexican Lime Trees Infected with Candidatus Phytoplasma aurantifolia. PLoS One 2015; 10:e0130425. [PMID: 26132073 PMCID: PMC4489016 DOI: 10.1371/journal.pone.0130425] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 05/20/2015] [Indexed: 12/31/2022] Open
Abstract
Witches' broom disease of acid lime greatly affects the production of Mexican lime in Iran. It is caused by a phytoplasma (Candidatus Phytoplasma aurantifolia). However, the molecular mechanisms that underlie phytoplasma pathogenicity and the mode of interactions with host plants are largely unknown. Here, high-throughput transcriptome sequencing was conducted to explore gene expression signatures associated with phytoplasma infection in Mexican lime trees. We assembled 78,185 unique transcript sequences (unigenes) with an average length of 530 nt. Of these, 41,805 (53.4%) were annotated against the NCBI non-redundant (nr) protein database using a BLASTx search (e-value ≤ 1e-5). When the abundances of unigenes in healthy and infected plants were compared, 2,805 transcripts showed significant differences (false discovery rate ≤ 0.001 and log2 ratio ≥ 1.5). These differentially expressed genes (DEGs) were significantly enriched in 43 KEGG metabolic and regulatory pathways. The up-regulated DEGs were mainly categorized into pathways with possible implication in plant-pathogen interaction, including cell wall biogenesis and degradation, sucrose metabolism, secondary metabolism, hormone biosynthesis and signalling, amino acid and lipid metabolism, while down-regulated DEGs were predominantly enriched in ubiquitin proteolysis and oxidative phosphorylation pathways. Our analysis provides novel insight into the molecular pathways that are deregulated during the host-pathogen interaction in Mexican lime trees infected by phytoplasma. The findings can be valuable for unravelling the molecular mechanisms of plant-phytoplasma interactions and can pave the way for engineering lime trees with resistance to witches' broom disease.
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Affiliation(s)
- Mohsen Mardi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran
| | - Laleh Karimi Farsad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran
| | - Javad Gharechahi
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Tehran, Iran
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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Abdollah Hosseini S, Gharechahi J, Heidari M, Koobaz P, Abdollahi S, Mirzaei M, Nakhoda B, Hosseini Salekdeh G. Comparative proteomic and physiological characterisation of two closely related rice genotypes with contrasting responses to salt stress. Funct Plant Biol 2015; 42:527-542. [PMID: 32480698 DOI: 10.1071/fp14274] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 02/07/2015] [Indexed: 06/11/2023]
Abstract
Salinity is a limiting factor affecting crop growth. We evaluated the responses of a salt-tolerant recombinant inbred rice (Oryza sativa L.) line, FL478, and the salt-sensitive IR29. Seedlings were exposed to salt stress and the growth rate was monitored to decipher the effect of long-term stress. At Day 16, IR29 produced lower shoot biomass than FL478. Significant differences for Na+ and K+ concentrations and Na+ : K+ ratios in roots and shoots were observed between genotypes. Changes in the proteomes of control and salt-stressed plants were analysed, identifying 59 and 39 salt-responsive proteins in roots and leaves, respectively. Proteomic analysis showed greater downregulation of proteins in IR29. In IR29, proteins related to pathways involved in salt tolerance (e.g. oxidative stress response, amino acid biosynthesis, polyamine biosynthesis, the actin cytoskeleton and ion compartmentalisation) changed to combat salinity. We found significant downregulation of proteins related to photosynthetic electron transport in IR29, indicating that photosynthesis was influenced, probably increasing the risk of reactive oxygen species formation. The sensitivity of IR29 might be related to its inability to exclude salt from its transpiration stream, to compartmentalise excess ions and to maintain a healthy photosynthetic apparatus during salt stress, or might be because of the leakiness of its roots, allowing excess salt to enter apoplastically. In FL478, superoxide dismutase, ferredoxin thioredoxin reductase, fibre protein and inorganic pyrophosphatase, which may participate in salt tolerance, increased in abundance. Our analyses provide novel insights into the mechanisms behind salt tolerance and sensitivity in genotypes with close genetic backgrounds.
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Affiliation(s)
- Seyed Abdollah Hosseini
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
| | - Javad Gharechahi
- Chemical Injuries Research Center, Baqiyatallah University of Medical Sciences, PO Box 19395-5478, Tehran 1435916471, Iran
| | - Manzar Heidari
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
| | - Parisa Koobaz
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
| | - Shapour Abdollahi
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Babak Nakhoda
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, PO Box 31535-1897, Karaj 3135933151, Iran
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Gharechahi J, Hajirezaei MR, Salekdeh GH. Comparative proteomic analysis of tobacco expressing cyanobacterial flavodoxin and its wild type under drought stress. J Plant Physiol 2015; 175:48-58. [PMID: 25506766 DOI: 10.1016/j.jplph.2014.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 11/05/2014] [Accepted: 11/13/2014] [Indexed: 05/02/2023]
Abstract
Tobacco plants expressing cyanobacterial flavodoxin (Fld) show enhanced tolerance to a wide range of abiotic stresses including drought, temperature and UV. The mechanisms of adaptation to stress conditions under Fld expression are largely unknown. Here, we applied comparative proteomic analysis to uncover the changes in the proteome profile of Fld-expressing plants in response to drought stress. Using high-resolution two-dimensional gel electrophoresis, we were able to detect 930 protein spots and compare their abundance. We found changes up to 1.5 fold for 52 spots under drought in transgenic and/or wild type plants. Using combined MALDI-TOF/TOF and ESI-Q/TOF analysis 39 (24 in wild type, 11 in transgenic, and 4 in both) drought-responsive proteins (DRPs) could be identified. The majority of DRPs are known to be involved in photosynthesis, carbohydrate and energy metabolism, amino acid and protein synthesis and processing, and oxidative stress responses. Among candidate DRPs, the abundance of remurin, ferredoxin-NADP reductase, chloroplast manganese stabilizing protein-II, phosphoglycerate mutase, and glutathione S-transferase decreased in drought stressed Fld-tobacco while S-formylglutathione hydrolase and pyridoxine biosynthesis protein abundance increased. In wild type plants, drought caused a reduction of proteins related to carbohydrate metabolism. These results suggest that the stress tolerance conferred by Fld expression is strongly related to control mechanisms regarding carbohydrate and energy metabolism as well as oxidative stress responses.
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Affiliation(s)
- Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | - Mohammad-Reza Hajirezaei
- Leibniz Institute of Plant Genetics and Crop Plant Research (Leibniz-IPK), Corrensstraße 3, 06466 Gatersleben, Germany
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran.
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Gharechahi J, Zahiri HS, Noghabi KA, Salekdeh GH. In-depth diversity analysis of the bacterial community resident in the camel rumen. Syst Appl Microbiol 2015; 38:67-76. [DOI: 10.1016/j.syapm.2014.09.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/25/2014] [Accepted: 09/26/2014] [Indexed: 10/24/2022]
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Faghani E, Gharechahi J, Komatsu S, Mirzaei M, Khavarinejad RA, Najafi F, Farsad LK, Salekdeh GH. Comparative physiology and proteomic analysis of two wheat genotypes contrasting in drought tolerance. J Proteomics 2014; 114:1-15. [PMID: 25449836 DOI: 10.1016/j.jprot.2014.10.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/28/2014] [Accepted: 10/26/2014] [Indexed: 10/24/2022]
Abstract
UNLABELLED Comparative physiology and proteomic analyses were conducted to monitor the stress response of two wheat genotypes (SERI M 82 (SE) and SW89.5193/kAu2 (SW)) with contrasting responses to drought stress. Under stress condition, the tolerant genotype (SE) produced higher shoot and root biomasses, longer roots and accumulated higher level of ABA in leaves. Physiological measurements suggested that the SE genotype was more efficient in water absorption and could preserve more water presumably by controlling stomata closure. Proteomic analysis showed an increased abundance of proteins related to defense and oxidative stress responses such as GLPs, GST, and SOD, and those related to protein processing such as small HSPs in roots of both genotypes in response to drought stress. Interestingly, the abundance of proteins such as endo-1,3-beta-glucosidase, peroxidase, SAMS, and MDH significantly increased in roots or leaves of the SE genotype and decreased in that of the SW one. In addition, an increased abundance of APX was detected in leaves and roots of the SE genotype and a decreased abundance of 14-3-3 and ribosomal proteins were noted in the SW one in response to drought stress. Our findings led to a better understanding about the integrated physiology and proteome responses of wheat genotypes with nearly contrasting responses to drought stress. BIOLOGICAL SIGNIFICANCE We applied a comparative physiology and proteomic analysis to decipher the differential responses of two contrasting wheat genotypes to drought stress. Based on physiological measurements the tolerant genotype (SE) showed better drought response by developing deep root system, higher root and shoot biomasses, and higher level of ABA in leaves. Proteomic analysis showed an increased abundance of proteins related to defense and oxidative stress responses such as GLPs, GST, and SOD, and those related to protein processing such as small HSPs in roots of both genotypes in response to drought stress. In addition, the abundance of proteins such as glucan endo-1,3-beta-glucosidase, peroxidases, SAMS, and MDH increased in roots or leaves of the tolerant genotype (SE) and decreased in that of the sensitive genotype (SW). Overall, proteins related to oxidative stress, protein processing and photosynthesis showed decreased abundance to a greater extent in the sensitive genotype (SW).
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Affiliation(s)
- Elham Faghani
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | - Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | - Setsuko Komatsu
- National Institute of Crop Science, Kannondai 2-1-18, Tsukuba 305-8518, Japan
| | - Mehdi Mirzaei
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | | | | | - Laleh Karimi Farsad
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran
| | - Ghasem Hosseini Salekdeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Karaj, Iran; Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem cell Biology and Technology, ACECR, Tehran, Iran.
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Gharechahi J, Alizadeh H, Naghavi MR, Sharifi G. A proteomic analysis to identify cold acclimation associated proteins in wild wheat (Triticum urartu L.). Mol Biol Rep 2014; 41:3897-905. [PMID: 24535272 DOI: 10.1007/s11033-014-3257-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Accepted: 02/08/2014] [Indexed: 01/19/2023]
Abstract
To gain a better understanding of cold acclimation process in wheat, we applied a 2-DE based proteomic approach to discover changes in proteome profile of a diploid wild wheat (Triticum urartu L.) during prolonged cold stress treatment. To this end, plants were grown in pots and the growing seedlings (4-leaf stage) were exposed to cold stress. After 4 weeks of cold acclimation (4-6 °C) and subsequent treatment for 12 h at -2 °C, samples were collected from control and stressed plants and were subjected to proteome pattern analysis. Among approximately 450 reproducible protein spots displayed in each given 2-DE gels, 34 proteins changed significantly in abundance in response to cold stress. Among them, 25 and 9 proteins were up and down-regulated under stress condition, respectively. Analysis by matrix-assisted laser desorption ionization time of flight/time of flight mass spectrometry coupled with non-redundant protein database search allowed the identification of 20 cold-induced proteins. Integrated proteomic and database survey resulted in identification of several cold stress related proteins such as pathogenesis related protein, cold regulated protein, cold-responsive LEA/RAB-related COR protein, oxygen-evolving enhancer protein and oxalate oxidase. The presumed functions of the identified proteins were mostly related to cold acclimation, oxidative stress and photosynthesis. The possible implications of differentially accumulated proteins in acquiring systemic tolerance to freezing stress following exposure to prolonged low temperature will be discussed.
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Affiliation(s)
- Javad Gharechahi
- Chemical Injures Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran,
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Gharechahi J, Pakzad M, Mirshavaladi S, Sharifitabar M, Baharvand H, Salekdeh GH. The effect of Rho-associated kinase inhibition on the proteome pattern of dissociated human embryonic stem cells. Mol BioSyst 2014; 10:640-52. [DOI: 10.1039/c3mb70255c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Ghaffari A, Gharechahi J, Nakhoda B, Salekdeh GH. Physiology and proteome responses of two contrasting rice mutants and their wild type parent under salt stress conditions at the vegetative stage. J Plant Physiol 2014; 171:31-44. [PMID: 24094368 DOI: 10.1016/j.jplph.2013.07.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/13/2013] [Accepted: 07/22/2013] [Indexed: 05/21/2023]
Abstract
Salinity is one of the major environmental limiting factors that affects growth and productivity of rice (Oryza sativa L.) worldwide. Rice is among the most sensitive crops to salinity, especially at early vegetative stages. In order to get a better understanding of molecular pathways affected in rice mutants showing contrasting responses to salinity, we exploited the power of 2-DE based proteomics to explore the proteome changes associated with salt stress response. Our physiological observations showed that standard evaluation system (SES) scores, Na+ and K+ concentrations in shoots and Na+/K+ ratio were significantly different in contrasting mutants under salt stress condition. Proteomics analysis showed that, out of 854 protein spots which were reproducibly detected, 67 protein spots showed significant responses to salt stress. The tandem mass spectrometry analysis of these significantly differentially accumulated proteins resulted in identification of 34 unique proteins. These proteins are involved in various molecular processes including defense to oxidative stresses, metabolisms, photosynthesis, protein synthesis and processing, signal transduction. Several of the identified proteins were emerged as key participants in salt stress tolerance. The possible implication of salt responsive proteins in plant adaptation to salt stress is discussed.
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Affiliation(s)
- Akram Ghaffari
- Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
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Majidzadeh-A K, Gharechahi J. Plasma proteomics analysis of tamoxifen resistance in breast cancer. Med Oncol 2013; 30:753. [DOI: 10.1007/s12032-013-0753-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 10/15/2013] [Indexed: 02/08/2023]
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Gharechahi J, Khalili M, Hasanloo T, Salekdeh GH. An integrated proteomic approach to decipher the effect of methyl jasmonate elicitation on the proteome of Silybum marianum L. hairy roots. Plant Physiol Biochem 2013; 70:115-22. [PMID: 23771036 DOI: 10.1016/j.plaphy.2013.05.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 05/21/2013] [Indexed: 06/02/2023]
Abstract
Jasmonate and its methyl derivative, methyl jasmonate (MeJA), are naturally occurring compounds that mediate several plant physiological processes in response to pathogen attack, wounding, and ozone. Exogenous application of jasmonates triggers defense responses that resemble those initiated by pathogen infection and also modulates the production of certain secondary metabolites in a variety of plant species. In this study, we treated the hairy root cultures of Silybum marianum L. with 100 μM MeJA and then measured the content of Silymarin (SLM). We observed that the SLM content increased significantly after 48 h of MeJA treatment and remained constant for 120 h. However, MeJA treatment caused a significant growth reduction after 96 h incubation. The activity of lipoxygenase as a key enzyme in the jasmonate biosynthesis pathway and anti-oxidative enzymes; peroxidase and ascorbate peroxidase was also significantly increased after MeJA treatment. To elucidate the global effect of jasmonate on gene expression of S. marianum, we employed high resolution two-dimensional gel electrophoresis coupled with tandem mass spectrometry. Out of 670 reproducibly detected protein spots which were analyzed on each given gel, 32 spots were up- or down regulated upon MeJA treatment. Of them, ten proteins such as ER binding protein, glutamine synthetase, pathogenesis-related protein, caffeoyl CoA O-methyltransferase, and profilin-1 could be identified by mass spectrometry analysis. The possible implications of the identified proteins on physiological outcome of MeJA application in S. marianum hairy root culture will be discussed.
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Affiliation(s)
- Javad Gharechahi
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran.
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Moniri Javadhesari S, Gharechahi J, Hosseinpour Feizi MA, Montazeri V, Halimi M. Transcriptional Expression Analysis of Survivin Splice Variants Reveals Differential Expression of Survivin-3α in Breast Cancer. Genet Test Mol Biomarkers 2013; 17:314-20. [DOI: 10.1089/gtmb.2012.0411] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | - Javad Gharechahi
- Department of Molecular Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
- Department of Genetics, Iranian Center for Breast Cancer, Academic Center for Education, Culture and Research, Tehran, Iran
| | | | - Vahid Montazeri
- Department of Surgery, School of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Monireh Halimi
- Department of Pathology, School of Medicine, Tabriz University of Medical Science, Tabriz, Iran
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Sharifi G, Ebrahimzadeh H, Ghareyazie B, Gharechahi J, Vatankhah E. Identification of differentially accumulated proteins associated with embryogenic and non-embryogenic calli in saffron (Crocus sativus L.). Proteome Sci 2012; 10:3. [PMID: 22243837 PMCID: PMC3349542 DOI: 10.1186/1477-5956-10-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Accepted: 01/13/2012] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Somatic embryogenesis (SE) is a complex biological process that occurs under inductive conditions and causes fully differentiated cells to be reprogrammed to an embryo like state. In order to get a better insight about molecular basis of the SE in Crocus sativus L. and to characterize differentially accumulated proteins during the process, a proteomic study based on two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization time of flight mass spectrometry has been carried out. RESULTS We have compared proteome profiles of non-embryogenic and embryogenic calli with native corm explants. Total soluble proteins were phenol-extracted and loaded on 18 cm IPG strips for the first dimension and 11.5% sodium dodecyl sulfate-polyacrylamide gels for the second dimension. Fifty spots with more than 1.5-fold change in abundance were subjected to mass spectrometry analysis for further characterization. Among them 36 proteins could be identified, which are classified into defense and stress response, protein synthesis and processing, carbohydrate and energy metabolism, secondary metabolism, and nitrogen metabolism. CONCLUSION Our results showed that diverse cellular and molecular processes were affected during somatic to embryogenic transition. Differential proteomic analysis suggests a key role for ascorbate metabolism during early stage of SE, and points to the possible role of ascorbate-glutathione cycle in establishing somatic embryos.
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Affiliation(s)
- Golandam Sharifi
- Department of Basic Sciences, Iranian Encyclopedia Compiling Foundation, Tehran, Iran
- Department of Botany, Faculty of Science, University of Tehran, Tehran, Iran
| | - Hassan Ebrahimzadeh
- Department of Botany, Faculty of Science, University of Tehran, Tehran, Iran
| | - Behzad Ghareyazie
- Department of Genomics, Agricultural Biotechnology Research Institute of Iran, Karaj, Iran
| | - Javad Gharechahi
- Department of Molecular Genetics, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Elaheh Vatankhah
- Department of Botany, Faculty of Science, University of Tehran, Tehran, Iran
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Faradonbeh MZ, Gharechahi J, Mollamohammadi S, Pakzad M, Taei A, Rassouli H, Baharvand H, Salekdeh GH. An orthogonal comparison of the proteome of human embryonic stem cells with that of human induced pluripotent stem cells of different genetic background. Mol BioSyst 2012; 8:1833-40. [DOI: 10.1039/c2mb25018g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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