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Ashraf A, Majeed Y, Gul I, Banday M, Ramzan K, Fazili KM. Elucidating the EXOSC3-IRE1α interaction: a convergent study incorporating computational, in vitro and in vivo studies. J Biomol Struct Dyn 2024:1-11. [PMID: 38407190 DOI: 10.1080/07391102.2024.2320252] [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: 11/10/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
The Unfolded protein response (UPR) is an adaptive signalling pathway which is triggered by accumulation of unfolded/misfolded protein in ER lumen. The UPR consist of three transmembrane proteins-IRE1α, PERK and ATF6 that sense ER stress which leads to activation and downstream signaling from ER lumen to cytosol to restore homeostasis. IRE1α is an evolutionary conserved arm of UPR and acts as an interaction platform for many potential proteins that become activated under ER stress conditions. We investigated potential partners of IRE1 α through MS studies and found EXOSC3 as one of the binding partner of IRE1α. Exosomal complex proteins have 3'5' exonuclease properties (EXOSC3) that play an important role in mRNA surveillance. This property of exosomal proteins coincides with IRE1α ribonuclease activities and its mechanism of action is similar to that of IRE1α-RIDD pathway which degrades any unstable mRNA that disrupts cellular homeostasis. At the same time, studies have shown that knockdown of EXOSC3 causes ER stress in human cells, so we speculated that there might be a functional crosstalk between IRE1α and EXOSC3 under ER stress conditions. Therefore, we employed computational tools to predict and explore the stability and dynamics of the IRE1α-EXOSC3 complex. The analysis indicates that IRE1α and EXOSC3 exhibit potential interaction with the involvement of ScanNet, predicting binding pockets between the two proteins. Further, the interaction was validated via co-immunoprecipitation and yeast two-hybrid assays, thus suggesting EXOSC3 as a component of the UPRosome complex. Hence, this functional crosstalk might influence the dynamic functional output of IRE1α.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ariha Ashraf
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Younis Majeed
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Irfan Gul
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Mariam Banday
- Department of Biotechnology, University of Kashmir, Srinagar, India
| | - Khalida Ramzan
- Department of Biotechnology, University of Kashmir, Srinagar, India
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Banday M, Qureshi M, Patel K, Movval N, Sharma N. Endothelial Derived IL-33 Induces Fibrogenesis and is Associated with CLAD. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.1679] [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: 04/05/2023] Open
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Banday M, Patel K, Qureshi M, Movval N, Sharma N. Distinct Airway Virome Signatures are Associated with CLAD and Modulate Airway Interferon Responses. J Heart Lung Transplant 2023. [DOI: 10.1016/j.healun.2023.02.054] [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: 04/05/2023] Open
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Bashir S, Banday M, Qadri O, Pal D, Bashir A, Hilal N, Altaf M, Fazili KM. The Bcl-2 family protein bid interacts with the ER stress sensor IRE1 to differentially modulate its RNase activity. FEBS Lett 2023; 597:962-974. [PMID: 36723387 DOI: 10.1002/1873-3468.14593] [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: 09/20/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 02/02/2023]
Abstract
IRE1 is a transmembrane signalling protein that activates the unfolded protein response under endoplasmic reticulum stress. IRE1 is endowed with kinase and endoribonuclease activities. The ribonuclease activity of IRE1 can switch substrate specificities to carry out atypical splicing of Xbp1 mRNA or trigger the degradation of specific mRNAs. The mechanisms regulating the distinct ribonuclease activities of IRE1 have yet to be fully understood. Here, we report the Bcl-2 family protein Bid as a novel recruit of the IRE1 complex, which directly interacts with the cytoplasmic domain of IRE1. Bid binding to IRE1 leads to a decrease in IRE1 phosphorylation in a way that it can only perform Xbp1 splicing while mRNA degradation activity is repressed. The RNase outputs of IRE1 have been found to regulate the homeostatic-apoptotic switch. This study, thus, provides insight into IRE1-mediated cell survival.
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Affiliation(s)
- Samirul Bashir
- Department of Biotechnology, University of Kashmir, Hazratbal J&K, India
| | - Mariam Banday
- Department of Biotechnology, University of Kashmir, Hazratbal J&K, India
| | - Ozaira Qadri
- Department of Biotechnology, University of Kashmir, Hazratbal J&K, India
| | - Debnath Pal
- Department of Computational and Data Science (CDS), Indian Institute of Science (IISc), Bengaluru, India
| | - Arif Bashir
- Department of Biotechnology, University of Kashmir, Hazratbal J&K, India
| | - Nazia Hilal
- Department of Biotechnology, University of Kashmir, Hazratbal J&K, India
| | - Mohammad Altaf
- Department of Biotechnology, University of Kashmir, Hazratbal J&K, India
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Bashir S, Pal D, Qadri O, Banday M, Fazili K. Quaternary structure analysis of IRE1. MicroPubl Biol 2023; 2023:10.17912/micropub.biology.000763. [PMID: 37065768 PMCID: PMC10091119 DOI: 10.17912/micropub.biology.000763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 02/22/2023] [Accepted: 03/27/2023] [Indexed: 04/18/2023]
Abstract
IRE1 belongs to a type I transmembrane protein family harboring two functional domains, cytoplasmic domain with kinase and RNAse catalytic activity, and the luminal domain, which is involved in the sensing of unfolded proteins. IRE1 molecule undergoes dimerization in the lumenal domain, which functionally activates the catalytic C-terminal domain. IRE1 activation is directly related to transition between monomeric and dimeric forms. We have deduced two quaternary structures from the published crystal structure of IRE1. One structure with a large stable interface that requires large activation and deactivation energy to active IRE1. The other quaternary structure has low dissociation energy and is more suitable for IRE1 oligomeric transition.
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Affiliation(s)
- Samirul Bashir
- University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Debnath Pal
- Indian Institute of Science Bangalore, Bengaluru, Karnataka, India
| | - Ozaira Qadri
- University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Mariam Banday
- University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Khalid Fazili
- University of Kashmir, Srinagar, Jammu and Kashmir, India
- Correspondence to: Khalid Fazili (
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Qaiser KN, Shah IA, Khan PA, Rather TA, Banday M, Dar MUD. Mapping and economic evaluation of traditional wicker willow in the plains of Kashmir Himalaya, India. CURR SCI INDIA 2022. [DOI: 10.18520/cs/v122/i12/1385-1391] [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: 11/15/2022]
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Bashir S, Banday M, Qadri O, Bashir A, Hilal N, Nida-I-Fatima, Rader S, Fazili KM. The molecular mechanism and functional diversity of UPR signaling sensor IRE1. Life Sci 2020; 265:118740. [PMID: 33188833 DOI: 10.1016/j.lfs.2020.118740] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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: 08/20/2020] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 02/06/2023]
Abstract
The endoplasmic reticulum is primarily responsible for protein folding and maturation. However, the organelle is subject to varied stress conditions from time to time, which lead to the activation of a signaling program known as the Unfolded Protein Response (UPR) pathway. This pathway, upon sensing any disturbance in the protein-folding milieu sends signals to the nucleus and cytoplasm in order to restore homeostasis. One of the prime UPR signaling sensors is Inositol-requiring enzyme 1 (IRE1); an ER membrane embedded protein with dual enzyme activities, kinase and endoribonuclease. The ribonuclease activity of IRE1 results in Xbp1 splicing in mammals or Hac1 splicing in yeast. However, IRE1 can switch its substrate specificity to the mRNAs that are co-transnationally transported to the ER, a phenomenon known as Regulated IRE1 Dependent Decay (RIDD). IRE1 is also reported to act as a principal molecule that coordinates with other proteins and signaling pathways, which in turn might be responsible for its regulation. The current review highlights studies on IRE1 explaining the structural features and molecular mechanism behind its ribonuclease outputs. The emphasis is also laid on the molecular effectors, which directly or indirectly interact with IRE1 to either modulate its function or connect it to other pathways. This is important in understanding the functional pleiotropy of IRE1, by which it can switch its activity from pro-survival to pro-apoptotic, thus determining the fate of cells.
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Affiliation(s)
- Samirul Bashir
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Mariam Banday
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Ozaira Qadri
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Arif Bashir
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Nazia Hilal
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Nida-I-Fatima
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India
| | - Stephen Rader
- Department of Chemistry, University of Northern British Columbia, Prince George, BC, Canada
| | - Khalid Majid Fazili
- Department of Biotechnology, University of Kashmir, Srinagar, Jammu and Kashmir, India.
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Banday M, Kumar A, Patel K, Sharma N. Gammaproteobacteria Dominant Lung Microbiome Induces Epithelial to Mesenchymal Transition and is Associated with CLAD. J Heart Lung Transplant 2020. [DOI: 10.1016/j.healun.2020.01.793] [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: 10/24/2022] Open
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Bashir A, Hazari YM, Bashir S, Hilal N, Banday M, Iqbal MK, Jan TR, Farooq SS, Shah NN, Fazili KM. SERPINA1 Hepatocyte-Specific Promoter Polymorphism Associate with Chronic Obstructive Pulmonary Disease in a Study of Kashmiri Ancestry Individuals. Lung 2018; 196:447-454. [PMID: 29804144 DOI: 10.1007/s00408-018-0124-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 01/13/2018] [Accepted: 05/13/2018] [Indexed: 02/05/2023]
Abstract
PURPOSE Different mutations in coding and non-coding sequences of the SERPINA1 gene have been implicated in the pathogenesis of COPD. However, - 10T/C mutation in the hepatocyte-directed promoter region has not been associated with COPD pathogenesis so far. Here, we report an increased frequency of - 10C genotype that is associated with decreased levels of serum alpha1-antitrypsin (α1AT) in COPD patients. METHODS The quantification of serum α1AT was done by ELISA, the phenol-chloroform method was used for DNA extraction, PCR products were directly sequenced. The IBM SPSS Statistics v21 software was used for statistical analyses of the data. RESULTS The mean serum α1AT level was found to be 1.203+0.239 and 3.162+0.160 g/L in COPD cases and in control, respectively. The - 10C allele is associated with an increased risk of COPD [OR, 3.50 (95%CI, 1.86-6.58); p < 0.001]. The combined variant genotype (TT+CC) was significantly found associated with an increased risk of COPD [OR, 3.20 (95% CI, 1.47-6.96); p = 0.003]. A significant association of the family history with COPD (overall p value= 0.0331) suggests that genetics may play an important role in the pathogenesis of COPD. CONCLUSION The polymorphism associated with hepatocyte-specific promoter region (- 10T/C) is likely to be associated with the pathogenesis of COPD. It is quite possible that the change of the base in the hepatocyte-specific promoter of the SERPINA1 gene can modulate its strength, thereby driving the reduced expression of α1AT.
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Affiliation(s)
- Arif Bashir
- Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Younis M Hazari
- Institute of Biomedical Sciences, University of Chile, 8380453, Santiago, Chile
| | - Samirul Bashir
- Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Nazia Hilal
- Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Mariam Banday
- Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Mir Khurshid Iqbal
- Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Tariq Rashid Jan
- Department of Statistics, University of Kashmir, Srinagar, J&K, 190006, India
| | - Syed Suraiya Farooq
- Department of Chest Medicine, Government Medical College, Srinagar, J&K, 190006, India
| | - Naveed Nazir Shah
- Department of Chest Medicine, Government Medical College, Srinagar, J&K, 190006, India.
| | - Khalid Majid Fazili
- Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India.
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Bashir A, Shah NN, Hazari YM, Habib M, Bashir S, Hilal N, Banday M, Asrafuzzaman S, Fazili KM. Novel variants of SERPIN1A gene: Interplay between alpha1-antitrypsin deficiency and chronic obstructive pulmonary disease. Respir Med 2016; 117:139-49. [DOI: 10.1016/j.rmed.2016.06.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 04/18/2016] [Accepted: 06/06/2016] [Indexed: 12/31/2022]
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Naqash S, Sarmast AH, Showkat HI, Wani M, Besina S, Banday M, Shah M. Fungating extramedullary plasmocytoma of breast; a unique case presentation. Indian J Cancer 2016; 52:43-4. [PMID: 26837969 DOI: 10.4103/0019-509x.175600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
| | - A H Sarmast
- Department of Gen Surgery, Skims Srinagar Jammu and Kashmir, India
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Naqash S, Sarmast AH, Showkat HI, Wani M, Besina S, Banday M, Shah M. An unusual breast malignancy. Gulf J Oncolog 2015; 1:7-9. [PMID: 26003097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2015] [Indexed: 06/04/2023]
Abstract
We describe an extramedullary plasmacytoma of both breasts in a 35-year-old woman. No other involvement was detected in the bone marrow or in any other site . Extramedullary plasmacytomas of the breast are extremely rare, especially those that are not associated with multiple myeloma.
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Affiliation(s)
- S Naqash
- Dept. of General Surgery, SKIMS, Srinagar Jammu and Kashmir, India
| | - A H Sarmast
- Dept. of General Surgery, SKIMS, Srinagar Jammu and Kashmir, India
| | - H I Showkat
- Dept. of Medical Oncology, SKIMS, Srinagar Jammu and Kashmir, India
| | - M Wani
- Dept. of General Surgery, SKIMS, Srinagar Jammu and Kashmir, India
| | - S Besina
- Dept. of Pathology, SKIMS, Srinagar Jammu and Kashmir, India
| | - M Banday
- Dept. of Medical Oncology, SKIMS, Srinagar Jammu and Kashmir, India
| | - M Shah
- Dept. of General Surgery, SKIMS, Srinagar Jammu and Kashmir, India
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Hamadani H, Khan A, Banday M, Ashraf I, Handoo N, Shah A, Hamadani A. Bovine Mastitis - A Disease of Serious Concern for Dairy Farmers. ACTA ACUST UNITED AC 2013. [DOI: 10.5455/ijlr.20130213091143] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Khuroo MS, Mahajan R, Zargar SA, Javid G, Banday M. Epidemiology of acute viral hepatitis in northern India: role of hepatitis D virus and hepatitis non-A, non-B superinfections. Indian J Gastroenterol 1989; 8:119-20. [PMID: 2496026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Khuroo MS, Mahajan R, Zargar SA, Javid G, Banday M. Endoscopic vs surgical drainage of biliary tract in acute pyogenic cholangitis: a controlled study. Indian J Gastroenterol 1989; 8:119. [PMID: 2707842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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