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Ravi, Kumar A, Bhattacharyya S, Singh J. Thiol reductive stress activates the hypoxia response pathway. EMBO J 2023; 42:e114093. [PMID: 37902464 PMCID: PMC10646554 DOI: 10.15252/embj.2023114093] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/31/2023] Open
Abstract
Owing to their capability to disrupt the oxidative protein folding environment in the endoplasmic reticulum (ER), thiol antioxidants, such as dithiothreitol (DTT), are used as ER-specific stressors. We recently showed that thiol antioxidants modulate the methionine-homocysteine cycle by upregulating an S-adenosylmethionine-dependent methyltransferase, rips-1, in Caenorhabditis elegans. However, the changes in cellular physiology induced by thiol stress that modulate the methionine-homocysteine cycle remain uncharacterized. Here, using forward genetic screens in C. elegans, we discover that thiol stress enhances rips-1 expression via the hypoxia response pathway. We demonstrate that thiol stress activates the hypoxia response pathway. The activation of the hypoxia response pathway by thiol stress is conserved in human cells. The hypoxia response pathway enhances thiol toxicity via rips-1 expression and confers protection against thiol toxicity via rips-1-independent mechanisms. Finally, we show that DTT might activate the hypoxia response pathway by producing hydrogen sulfide. Our studies reveal an intriguing interaction between thiol-mediated reductive stress and the hypoxia response pathway and challenge the current model that thiol antioxidant DTT disrupts only the ER milieu in the cell.
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Affiliation(s)
- Ravi
- Department of Biological SciencesIndian Institute of Science Education and ResearchMohaliIndia
| | - Ajay Kumar
- Department of BiophysicsPostgraduate Institute of Medical Education and ResearchChandigarhIndia
| | - Shalmoli Bhattacharyya
- Department of BiophysicsPostgraduate Institute of Medical Education and ResearchChandigarhIndia
| | - Jogender Singh
- Department of Biological SciencesIndian Institute of Science Education and ResearchMohaliIndia
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Dileep D, Syed TA, Sloan TFW, Dhandapany PS, Siddiqi K, Sirajuddin M. Cardiomyocyte orientation recovery at micrometer scale reveals long-axis fiber continuum in heart walls. EMBO J 2023; 42:e113288. [PMID: 37671467 PMCID: PMC10548172 DOI: 10.15252/embj.2022113288] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 08/01/2023] [Accepted: 08/06/2023] [Indexed: 09/07/2023] Open
Abstract
Coordinated cardiomyocyte contraction drives the mammalian heart to beat and circulate blood. No consensus model of cardiomyocyte geometrical arrangement exists, due to the limited spatial resolution of whole heart imaging methods and the piecemeal nature of studies based on histological sections. By combining microscopy and computer vision, we produced the first-ever three-dimensional cardiomyocyte orientation reconstruction across mouse ventricular walls at the micrometer scale, representing a gain of three orders of magnitude in spatial resolution. We recovered a cardiomyocyte arrangement aligned to the long-axis direction of the outer ventricular walls. This cellular network lies in a thin shell and forms a continuum with longitudinally arranged cardiomyocytes in the inner walls, with a complex geometry at the apex. Our reconstruction methods can be applied at fine spatial scales to further understanding of heart wall electrical function and mechanics, and set the stage for the study of micron-scale fiber remodeling in heart disease.
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Affiliation(s)
- Drisya Dileep
- Centre for Cardiovascular Biology and DiseaseInstitute for Stem Cell Science and Regenerative MedicineBengaluruIndia
- The University of Trans‐Disciplinary Health Sciences and Technology (TDU)BengaluruIndia
| | - Tabish A Syed
- School of Computer Science and Centre for Intelligent MachinesMcGill University, and MILA – Québec AI InstituteMontréalQCCanada
| | | | - Perundurai S Dhandapany
- Centre for Cardiovascular Biology and DiseaseInstitute for Stem Cell Science and Regenerative MedicineBengaluruIndia
| | - Kaleem Siddiqi
- School of Computer Science and Centre for Intelligent MachinesMcGill University, and MILA – Québec AI InstituteMontréalQCCanada
| | - Minhajuddin Sirajuddin
- Centre for Cardiovascular Biology and DiseaseInstitute for Stem Cell Science and Regenerative MedicineBengaluruIndia
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3
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Ansari S, Gupta N, Verma R, Singh ON, Gupta J, Kumar A, Yadav MK, Binayke A, Tiwari M, Periwal N, Sood V, Mani S, Awasthi A, Shalimar, Nayak B, Ranjith‐Kumar CT, Surjit M. Antiviral activity of the human endogenous retrovirus‐R envelope protein against SARS‐CoV‐2. EMBO Rep 2023; 24:e55900. [PMCID: PMC10328075 DOI: 10.15252/embr.202255900] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 08/04/2022] [Revised: 03/31/2023] [Accepted: 04/26/2023] [Indexed: 09/29/2023] Open
Abstract
Coronavirus‐induced disease‐19 (COVID‐19), caused by SARS‐CoV‐2, is still a major global health challenge. Human endogenous retroviruses (HERVs) represent retroviral elements that were integrated into the ancestral human genome. HERVs are important in embryonic development as well as in the manifestation of diseases, including cancer, inflammation, and viral infections. Here, we analyze the expression of several HERVs in SARS‐CoV‐2‐infected cells and observe increased activity of HERV‐E, HERV‐V, HERV‐FRD, HERV‐MER34, HERV‐W, and HERV‐K‐HML2. In contrast, the HERV‐R envelope is downregulated in cell‐based models and PBMCs of COVID‐19 patients. Overexpression of HERV‐R inhibits SARS‐CoV‐2 replication, suggesting its antiviral activity. Further analyses demonstrate the role of the extracellular signal‐regulated kinase (ERK) in regulating HERV‐R antiviral activity. Lastly, our data indicate that the crosstalk between ERK and p38 MAPK controls the synthesis of the HERV‐R envelope protein, which in turn modulates SARS‐CoV‐2 replication. These findings suggest the role of the HERV‐R envelope as a prosurvival host factor against SARS‐CoV‐2 and illustrate a possible advantage of integration and evolutionary maintenance of retroviral elements in the human genome.
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Affiliation(s)
- Shabnam Ansari
- Virology LaboratoryTranslational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
| | - Nidhi Gupta
- Virology LaboratoryTranslational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
- Present address:
Department of BiochemistryAll India Institute of Medical SciencesNew DelhiIndia
| | - Rohit Verma
- Virology LaboratoryTranslational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
| | - Oinam N Singh
- Virology LaboratoryTranslational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
| | - Jyoti Gupta
- Virology LaboratoryTranslational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
| | - Amit Kumar
- Virology LaboratoryTranslational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
| | - Mukesh Kumar Yadav
- Virology LaboratoryTranslational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
| | - Akshay Binayke
- Immunobiology LaboratoryTranslational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
| | - Mahima Tiwari
- Translational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
| | - Neha Periwal
- Department of Biochemistry, School of Chemical and Life SciencesJamia Hamdard UniversityNew DelhiIndia
| | - Vikas Sood
- Department of Biochemistry, School of Chemical and Life SciencesJamia Hamdard UniversityNew DelhiIndia
| | - Shailendra Mani
- Translational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
| | - Amit Awasthi
- Immunobiology LaboratoryTranslational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
| | - Shalimar
- Department of GastroenterologyAll India Institute of Medical SciencesNew DelhiIndia
| | - Baibaswata Nayak
- Department of GastroenterologyAll India Institute of Medical SciencesNew DelhiIndia
| | - CT Ranjith‐Kumar
- University School of Biotechnology, Guru Gobind Singh Indraprastha UniversityNew DelhiIndia
| | - Milan Surjit
- Virology LaboratoryTranslational Health Science and Technology Institute, NCR Biotech Science ClusterFaridabadIndia
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Yoganand KN, Muralidharan M, Nimkar S, Anand B. Fidelity of prespacer capture and processing is governed by the PAM-mediated interactions of Cas1-2 adaptation complex in CRISPR-Cas type I-E system. J Biol Chem 2019; 294:20039-20053. [PMID: 31748409 PMCID: PMC6937570 DOI: 10.1074/jbc.ra119.009438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 11/18/2019] [Indexed: 12/11/2022] Open
Abstract
Prokaryotes deploy CRISPR-Cas-based RNA-guided adaptive immunity to fend off mobile genetic elements such as phages and plasmids. During CRISPR adaptation, which is the first stage of CRISPR immunity, the Cas1-2 integrase complex captures invader-derived prespacer DNA and specifically integrates it at the leader-repeat junction as spacers. For this integration, several variants of CRISPR-Cas systems use Cas4 as an indispensable nuclease for selectively processing the protospacer adjacent motif (PAM) containing prespacers to a defined length. Surprisingly, however, a few CRISPR-Cas systems, such as type I-E, are bereft of Cas4. Despite the absence of Cas4, how the prespacers show impeccable conservation for length and PAM selection in type I-E remains intriguing. Here, using in vivo and in vitro integration assays, deep sequencing, and exonuclease footprinting, we show that Cas1-2/I-E-via the type I-E-specific extended C-terminal tail of Cas1-displays intrinsic affinity for PAM containing prespacers of variable length in Escherichia coli Although Cas1-2/I-E does not prune the prespacers, its binding protects the prespacer boundaries from exonuclease action. This ensures the pruning of exposed ends by exonucleases to aptly sized substrates for integration into the CRISPR locus. In summary, our work reveals that in a few CRISPR-Cas variants, such as type I-E, the specificity of PAM selection resides with Cas1-2, whereas the prespacer processing is co-opted by cellular non-Cas exonucleases, thereby offsetting the need for Cas4.
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Affiliation(s)
- Kakimani Nagarajan Yoganand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Manasasri Muralidharan
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Siddharth Nimkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
| | - Baskaran Anand
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
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Kumar S, Sharma C, Kaushik SR, Kulshreshtha A, Chaturvedi S, Nanda RK, Bhaskar A, Chattopadhyay D, Das G, Dwivedi VP. The phytochemical bergenin as an adjunct immunotherapy for tuberculosis in mice. J Biol Chem 2019; 294:8555-8563. [PMID: 30975902 PMCID: PMC6544861 DOI: 10.1074/jbc.ra119.008005] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/20/2019] [Indexed: 12/12/2022] Open
Abstract
The widespread availability and use of modern synthetic therapeutic agents have led to a massive decline in ethnomedical therapies. However, these synthetic agents often possess toxicity leading to various adverse effects. For instance, anti-tubercular treatment (ATT) is toxic, lengthy, and severely impairs host immunity, resulting in posttreatment vulnerability to reinfection and reactivation of tuberculosis (TB). Incomplete ATT enhances the risk for the generation of multidrug- or extensively drug-resistant (MDR or XDR, respectively) variants of Mycobacterium tuberculosis (M. tb), the TB-causing microbe. Therefore, a new therapeutic approach that minimizes these risks is urgently needed to combat this deadly disease and prevent future TB epidemics. Previously, we have shown that the phytochemical bergenin induces T helper 1 (Th1)- and Th17 cell-based protective immune responses and potently inhibits mycobacterial growth in a murine model of M. tb infection, suggesting bergenin as a potential adjunct agent to TB therapy. Here, we combined ATT therapy with bergenin and found that this combination reduces immune impairment and the length of treatment in mice. We observed that co-treatment with the anti-TB drug isoniazid and bergenin produces additive effects and significantly reduces bacterial loads compared with isoniazid treatment alone. The bergenin co-treatment also reduced isoniazid-induced immune impairment; promoted long-lasting, antigen-specific central memory T cell responses; and acted as a self-propelled vaccine. Of note, bergenin treatment significantly reduced the bacterial burden of a multidrug-resistant TB strain. These observations suggest that bergenin is a potent immunomodulatory agent that could be further explored as a potential adjunct to TB therapy.
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Affiliation(s)
- Santosh Kumar
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | - Chetan Sharma
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | - Sandeep Rai Kaushik
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | | | - Shivam Chaturvedi
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | - Ranjan Kumar Nanda
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India
| | - Ashima Bhaskar
- Signal Transduction Laboratory-1, National Institute of Immunology, New Delhi 110 067, India
| | | | - Gobardhan Das
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110 067, India.
| | - Ved Prakash Dwivedi
- International Centre for Genetic Engineering and Biotechnology, New Delhi 110 067, India.
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Kempaiah Nagappa L, Satha P, Govindaraju T, Balaram H. Phosphoglycolate phosphatase is a metabolic proofreading enzyme essential for cellular function in Plasmodium berghei. J Biol Chem 2019; 294:4997-5007. [PMID: 30700551 PMCID: PMC6442027 DOI: 10.1074/jbc.ac118.007143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/28/2019] [Indexed: 11/06/2022] Open
Abstract
Plasmodium falciparum (Pf) 4-nitrophenylphosphatase has been shown previously to be involved in vitamin B1 metabolism. Here, conducting a BLASTp search, we found that 4-nitrophenylphosphatase from Pf has significant homology with phosphoglycolate phosphatase (PGP) from mouse, human, and yeast, prompting us to reinvestigate the biochemical properties of the Plasmodium enzyme. Because the recombinant PfPGP enzyme is insoluble, we performed an extended substrate screen and extensive biochemical characterization of the recombinantly expressed and purified homolog from Plasmodium berghei (Pb), leading to the identification of 2-phosphoglycolate and 2-phospho-L-lactate as the relevant physiological substrates of PbPGP. 2-Phosphoglycolate is generated during repair of damaged DNA ends, 2-phospho-L-lactate is a product of pyruvate kinase side reaction, and both potently inhibit two key glycolytic enzymes, triosephosphate isomerase and phosphofructokinase. Hence, PGP-mediated clearance of these toxic metabolites is vital for cell survival and functioning. Our results differ significantly from those in a previous study, wherein the PfPGP enzyme has been inferred to act on 2-phospho-D-lactate and not on the L isomer. Apart from resolving the substrate specificity conflict through direct in vitro enzyme assays, we conducted PGP gene knockout studies in P. berghei, confirming that this conserved metabolic proofreading enzyme is essential in Plasmodium In summary, our findings establish PbPGP as an essential enzyme for normal physiological function in P. berghei and suggest that drugs that specifically inhibit Plasmodium PGP may hold promise for use in anti-malarial therapies.
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Affiliation(s)
| | - Pardhasaradhi Satha
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, Karnataka 560064, India
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