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Rathore M, Thakur A, Saran S. Deletion of Dictyostelium tpc2 gene forms multi-tipped structures, regulates autophagy and cell-type patterning. Biol Cell 2024; 116:e2300067. [PMID: 38537110 DOI: 10.1111/boc.202300067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 03/04/2024] [Accepted: 03/08/2024] [Indexed: 05/09/2024]
Abstract
BACKGROUND INFORMATION Two pore channels (TPCs) are voltage-gated ion channel superfamily members that release Ca2+ from acidic intracellular stores and are ubiquitously present in both animals and plants. Starvation initiates multicellular development in Dictyostelium discoideum. Increased intracellular calcium levels bias Dictyostelium cells towards the stalk pathway and thus we decided to analyze the role of TPC2 in development, differentiation, and autophagy. RESULTS We showed TPC2 protein localizes in lysosome-like acidic vesicles and the in situ data showed stalk cell biasness. Deletion of tpc2 showed defective and delayed development with formation of multi-tipped structures attached to a common base, while tpc2OE cells showed faster development with numerous small-sized aggregates and wiry fruiting bodies. The tpc2OE cells showed higher intracellular cAMP levels as compared to the tpc2- cells while pinocytosis was found to be higher in the tpc2- cells. Also, TPC2 regulates cell-substrate adhesion and cellular morphology. Under nutrient starvation, deletion of tpc2 reduced autophagic flux as compared to Ax2. During chimera formation, tpc2- cells showed a bias towards the prestalk/stalk region while tpc2OE cells showed a bias towards the prespore/spore region. tpc2 deficient strain exhibits aberrant cell-type patterning and loss of distinct boundary between the prestalk/prespore regions. CONCLUSION TPC2 is required for effective development and differentiation in Dictyostelium and supports autophagic cell death and cell-type patterning. SIGNIFICANCE Decreased calcium due to deletion of tpc2 inhibit autophagic flux.
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Affiliation(s)
- Madhubala Rathore
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ashima Thakur
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shweta Saran
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Fatima T, Hadem IKH, Saran S. Metabolic signals influence cell-fate decisions in Dictyostelium discoideum. Cell Biochem Funct 2023; 41:1514-1525. [PMID: 38014740 DOI: 10.1002/cbf.3892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/29/2023]
Abstract
Nutrient-sensing plays a crucial role in maintaining cellular energy and metabolic homeostasis. Perturbations in sensing pathways are associated with a wide variety of pathologies, especially metabolic diseases. Very little is understood about sensing fluctuations in nutrients and how this information is integrated into physiological and metabolic adaptation that could further affect cell-fate decisions during differentiation in Dictyostelium discoideum (henceafter, Dictyostelium). Glucose is the primary metabolic fuel among all nutrients. Carbohydrates, lipids and proteins ultimately breakdown into glucose, which is further used for providing energy. The maintenance of optimum glucose levels is important for efficient cell-survival. Glucose is not only a nutrient, but also a signaling molecule influencing cell growth and differentiation in Dictyostelium. Modulation of endogenous glucose levels either by varying exogenous glucose levels or genetic overexpression or deletion of genes involved in glucose signaling lead to changes in endogenous metabolite levels such as ADP/ATP ratio, NAD+ /NADH ratio, cAMP and ROS levels which further influence cell-fate decisions. Here, we show that AMPKα and Sir2D are components of glucose-signaling pathway in Dictyostelium which adjust cell metabolism interdependently in response to nutrient-status and promote cell-fate decisions.
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Affiliation(s)
- Tasneem Fatima
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Shweta Saran
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Romano PS, Akematsu T, Besteiro S, Bindschedler A, Carruthers VB, Chahine Z, Coppens I, Descoteaux A, Alberto Duque TL, He CY, Heussler V, Le Roch KG, Li FJ, de Menezes JPB, Menna-Barreto RFS, Mottram JC, Schmuckli-Maurer J, Turk B, Tavares Veras PS, Salassa BN, Vanrell MC. Autophagy in protists and their hosts: When, how and why? AUTOPHAGY REPORTS 2023; 2:2149211. [PMID: 37064813 PMCID: PMC10104450 DOI: 10.1080/27694127.2022.2149211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/15/2022] [Indexed: 03/12/2023]
Abstract
Pathogenic protists are a group of organisms responsible for causing a variety of human diseases including malaria, sleeping sickness, Chagas disease, leishmaniasis, and toxoplasmosis, among others. These diseases, which affect more than one billion people globally, mainly the poorest populations, are characterized by severe chronic stages and the lack of effective antiparasitic treatment. Parasitic protists display complex life-cycles and go through different cellular transformations in order to adapt to the different hosts they live in. Autophagy, a highly conserved cellular degradation process, has emerged as a key mechanism required for these differentiation processes, as well as other functions that are crucial to parasite fitness. In contrast to yeasts and mammals, protist autophagy is characterized by a modest number of conserved autophagy-related proteins (ATGs) that, even though, can drive the autophagosome formation and degradation. In addition, during their intracellular cycle, the interaction of these pathogens with the host autophagy system plays a crucial role resulting in a beneficial or harmful effect that is important for the outcome of the infection. In this review, we summarize the current state of knowledge on autophagy and other related mechanisms in pathogenic protists and their hosts. We sought to emphasize when, how, and why this process takes place, and the effects it may have on the parasitic cycle. A better understanding of the significance of autophagy for the protist life-cycle will potentially be helpful to design novel anti-parasitic strategies.
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Affiliation(s)
- Patricia Silvia Romano
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
| | - Takahiko Akematsu
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | | | | | - Vern B Carruthers
- Department of Microbiology and Immunology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Zeinab Chahine
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology. Department of Molecular Microbiology and Immunology. Johns Hopkins Malaria Research Institute. Johns Hopkins University Bloomberg School of Public Health. Baltimore 21205, MD, USA
| | - Albert Descoteaux
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, Laval, QC
| | - Thabata Lopes Alberto Duque
- Autophagy Inflammation and Metabolism Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA; Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Cynthia Y He
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Volker Heussler
- Institute of Cell Biology.University of Bern. Baltzerstr. 4 3012 Bern
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, CA, USA
| | - Feng-Jun Li
- Department of Biological Sciences, National University of Singapore, Singapore
| | | | | | - Jeremy C Mottram
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | | | - Boris Turk
- Department of Biochemistry and Molecular and Structural Biology, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Patricia Sampaio Tavares Veras
- Laboratory of Host-Parasite Interaction and Epidemiology, Gonçalo Moniz Institute, Fiocruz-Bahia
- National Institute of Science and Technology of Tropical Diseases - National Council for Scientific Research and Development (CNPq)
| | - Betiana Nebai Salassa
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
| | - María Cristina Vanrell
- Laboratorio de Biología de Trypanosoma cruzi y de la célula hospedadora. Instituto de Histología y Embriología de Mendoza. Universidad Nacional de Cuyo. (IHEM-CONICET-UNCUYO). Facultad de Ciencias Médicas. Universidad Nacional de Cuyo. Av. Libertador 80 (5500), Mendoza, Argentina
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Kumar R, Kumar R, Goel H, Tanwar P. Computational investigation reveals that the mutant strains of SARS-CoV2 have differential structural and binding properties. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 215:106594. [PMID: 34968787 PMCID: PMC8685290 DOI: 10.1016/j.cmpb.2021.106594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/12/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND AND OBJECTIVES Remarkable infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV2) is due to the rapid emergence of various strains which enable the virus to ruling the world. Over the course of SARS-CoV2 pandemic, the scientific communities worldwide are responding to newly emerging genetic variants. However, mechanism behind the persistent infection of these variants is still not known due to the paucity of study of these variants at molecular level. In this scenario, computational methods have immense utility in understanding the molecular and functional properties of different variants. METHODS The various mutants (MTs) of SpikeS1 receptor binding domain (RBD) of highly infectious SARS-CoV2 strains were manifested and elucidated the protein structure and binding strength using molecular dynamics (MD) simulation and protein-protein docking approaches. RESULTS MD simulation study showed that all MTs exhibited stable structures with altered functional properties. Furthermore, the binding strength of different MTs along with WT (wildtype) was revealed that MTs showed differential binding affinities to host protein with high binding strength exhibited by V367F and V483A MTs. CONCLUSION Hence, this study shed light on the molecular basis of infection caused by different variants of SARS-CoV2, which might play an important role in to cease the transmission and pathogenesis of virus and also implicate in rational designing of a specific drug.
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Affiliation(s)
- Rakesh Kumar
- Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Rahul Kumar
- Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Harsh Goel
- Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Pranay Tanwar
- Dr. B.R.A. Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi 110029, India.
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Wang H, Wang A, Wang X, Zeng X, Xing H. AMPK/PPAR-γ/NF-κB axis participates in ROS-mediated apoptosis and autophagy caused by cadmium in pig liver. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 294:118659. [PMID: 34896222 DOI: 10.1016/j.envpol.2021.118659] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 11/19/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
The experiment was conducted to investigate the effects of Cadmium (Cd) on growth performance, blood biochemical parameters, oxidative stress, hepatocyte apoptosis and autophagy of weaned piglets. A total of 12 healthy weaned piglets were randomly assigned to the control and the Cd group, which were fed with a basal diet and the basal diet supplemented with 15 ± 0.242 mg/kg CdCl2 for 30 d, respectively. Our results demonstrated that Cd significantly decreased final body weight, average daily feed intake (ADFI), average daily gain (ADG) and increased feed-to-gain (F/G) ratio (P < 0.05). For blood biochemical parameters, Cd treatment significantly decreased the red blood cell (RBC), hemoglobin (HGB), hematocrit (HCT), total protein, albumin, copper content and iron content (P < 0.05). In addition, liver injury was observed in the Cd-exposed group. Our results also demonstrated that Cd exposure contributed to the production of ROS, activated the AMPK/PPAR-γ/NF-κB pathway (increasing the expressions of P-AMPK/AMPK, NF-κB, I-κB-β, COX-2, and iNOS, decreasing the expressions of PPAR-γ and I-κB-α), finally induced autophagy (increasing the expressions of Beclin-1, the ratio of LC3-II/LC3-I and p62), and apoptosis (increasing the expressions of Bax, Bak, Caspase-9, and Caspase-3, decreasing the expression of Bcl-2). Overall, these findings revealed the vital role of AMPK/PPAR-γ/NF-κB pathway in Cd-induced liver apoptosis and autophagy, which provided deeper insights into a better understanding of Cd-induced hepatotoxicity.
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Affiliation(s)
- Huan Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Anqi Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Xinqiao Wang
- College of Chemical Engineering and Environment, China University of Petroleum, Beijing, 102249, People's Republic of China
| | - Xiangyin Zeng
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Houjuan Xing
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
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Joshi K, Kaur S, Kumar R. Cytochrome P450 2C19 gene polymorphisms (CYP2C19*2 and CYP2C19*3) in chronic myeloid leukemia patients: in vitro and in silico studies. J Biomol Struct Dyn 2021; 40:9389-9402. [PMID: 34060427 DOI: 10.1080/07391102.2021.1929491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Polymorphisms in the CYP2C19 have a huge impact on drug processing, out of which CYP2C19*2 and CYP2C19*3 are the most common variants associated with reduced metabolism of drugs. Mechanism by which two variants contribute in poor metabolization of drugs and cancer is not well understood. Here, we hypothesized that the mutations in CYP2C19 gene might affect the risk of chronic myeloid leukemia patients (CML). Present study has two main objectives: first to investigate the allele frequencies of CYP2C19*2 and CYP2C19*3 associated gene polymorphisms in CML patients and to elucidate the structural stability, conformation and functions of protein encoded by such variants. Genotyping of CYP2C19 was performed in 103 CML patients and 103 matched healthy controls. Heterozygous genotype of CYP2C19*2 was higher in CML patients (13.59%) than the controls (4.85%). Whereas, CYP2C19*3 allele frequency was not observed in cases as well as in controls. Furthermore, molecular dynamics (MD) simulation was applied to monitor the structural and conformational effect of above mutants. MD simulation results demonstrated that these mutants formed unstable proteins with distorted conformations, altered residues network and affected drug binding site which led to malfunction of mutant proteins. Hence, the study provides the role of CYP2C19 gene polymorphisms in susceptibility to CML population and explored the molecular basis of malignancies caused which may aid in the development of precise medicine or adjusting the drug dosages so as to reduce the chemotherapeutic side effects.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kaishiv Joshi
- Department of Human Genetics, Punjabi University, Patiala, India
| | - Satbir Kaur
- Department of Human Genetics, Punjabi University, Patiala, India
| | - Rakesh Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Kumar R, Mukherjee PK. Trichoderma virens Bys1 may competitively inhibit its own effector protein Alt a 1 to stabilize the symbiotic relationship with plant-evidence from docking and simulation studies. 3 Biotech 2021; 11:144. [PMID: 33708467 PMCID: PMC7910336 DOI: 10.1007/s13205-021-02652-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/09/2021] [Indexed: 12/14/2022] Open
Abstract
The filamentous fungi Trichoderma spp. are widely used for plant growth promotion and disease control. They form stable symbiosis-like relationship with roots. Unlike plant pathogens and mycorrhizae, the molecular events leading to the development of this association is not well understood. Pathogens deploy effector proteins to suppress or evade plant defence. Indirect evidences suggest that Trichoderma spp. can also deploy effector-like proteins to suppress plant defence favouring colonization of roots. Here, using computer simulation, we provide evidence that Trichoderma virens may deploy analogues of host defence proteins to "neutralize" its own effector protein to minimize damage to host tissues, as one of the mechanisms to achieve a stable symbiotic relationship with plants. We provide evidence that T. virens Bys1 protein has a structure similar to plant PR5/thaumatin-like protein and can bind Alt a 1 with a very high affinity, which might lead to the inactivation of its own effector protein. We have, for the first time, predicted a fungal protein that is a competitive inhibitor of a fungal effector protein deployed by many pathogenic fungi to suppress plant defence, and this protein/gene can potentially be used to enhance plant defence through transgenic or other approaches. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-02652-8.
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Affiliation(s)
- Rakesh Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Prasun K. Mukherjee
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085 India
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Kumar R, Maurya R, Saran S. Investigating the Role of Translationally Control Tumor Protein in Growth, Development and Differentiation of Dictyostelium discoideum. Front Cell Dev Biol 2020; 8:742. [PMID: 32850852 PMCID: PMC7426469 DOI: 10.3389/fcell.2020.00742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/16/2020] [Indexed: 12/31/2022] Open
Abstract
Translationally controlled tumor protein (TCTP) is a multifunctional protein implicated in various types of cellular processes involving growth and development of an organism. Here, we identified tctp gene in Dictyostelium discoideum and unraveled its function. The sequence analysis of D. discoideum TCTP (DdTCTP) showed its conservation among eukaryotes. Transcript of DdTCTP was highly expressed at the initial time points of development and protein is localized both in the cytoplasm and nucleus. Disruption of tctp was achieved by BSR cassette using double homologous recombination method. Abrogation of tctp resulted in reduced cell proliferation but increased cell size. Additionally, development was delayed by 4 h wherein small-sized aggregates and fruiting bodies were produced by tctp– cells while larger aggregates and fruiting bodies were produced by tctpOE cells concordant with the fact that TCTP regulates prestalk/prespore ratio and cell-type differentiation. tctp– cells produced round spores with reduced viability and stalk cells are arranged in septate pattern as compared to polyhedral manner of wild type. Abrogation of tctp resulted in aberrant localization of cell type specific markers and show low proclivity toward prespore/spore region, in presence of wild type cells.
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Affiliation(s)
- Rakesh Kumar
- Cell and Developmental Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Ranjana Maurya
- Cell and Developmental Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shweta Saran
- Cell and Developmental Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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