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Chatterjee T, Guha D, Dhar J, Saha T, Paul D, Sa G, Chakrabarti P. Adenosine dialdehyde, a methyltransferase inhibitor, induces colorectal cancer cells apoptosis by regulating PIMT:p53 interaction. Biochem Biophys Res Commun 2023; 684:149134. [PMID: 37871521 DOI: 10.1016/j.bbrc.2023.149134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 10/25/2023]
Abstract
Post-translational modification (PTM) is important in controlling many biological processes by changing the structure and function of a protein. Protein methylation is an important PTM, and the role of methyltransferases has been implicated in numerous cellular functions. Protein L-isoaspartyl methyltransferase (PIMT) is ubiquitously expressed in almost all organisms and govern important cellular processes including apoptosis. Among other functions, PIMT has also been identified as a potent oncogene because it destabilizes the structure of the tumor suppressor p53 via methylation at the transactivation domain. In the present study we identified that out of the three methyltransferase inhibitors tested, namely, S-adenosyl-l-homocysteine (AdoHcy), adenosine and adenosine dialdehyde (AdOx), only AdOx augments p53 expression by destabilizing PIMT structure, as evident from far-UV CD. The effect of the inhibitors, AdOx in particular, to the structure of PIMT, and the binding of PIMT to the p53 transactivation domain have been investigated by docking and molecular dynamics simulations. AdOx significantly increases p53 accumulation and nuclear translocation in colon cancer cells, triggering the p53-mediated apoptotic pathway. To better understand the molecular mechanisms underlying p53 accumulation in colon cancer cells, we observed that the level of PIMT is considerably lower in AdOx-treated cells, reducing its association with p53, which stabilized p53. p53 then transactivated BAX, increasing the BAX: BCL-2 ratio and causing colon cancer cell death.
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Affiliation(s)
- Tanaya Chatterjee
- Department of Biochemistry, Bose Institute, P1/12, CIT Scheme VII M, Kolkata, 700054, India.
| | - Deblina Guha
- Division of Molecular Medicine, Bose Institute, P1/12, CIT Scheme VII M, Kolkata, 700054, India
| | - Jesmita Dhar
- Division of Molecular Medicine, Bose Institute, P1/12, CIT Scheme VII M, Kolkata, 700054, India
| | - Taniya Saha
- Division of Molecular Medicine, Bose Institute, P1/12, CIT Scheme VII M, Kolkata, 700054, India
| | - Debamita Paul
- Department of Biochemistry, Bose Institute, P1/12, CIT Scheme VII M, Kolkata, 700054, India
| | - Gaurisankar Sa
- Division of Molecular Medicine, Bose Institute, P1/12, CIT Scheme VII M, Kolkata, 700054, India.
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P1/12, CIT Scheme VII M, Kolkata, 700054, India
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Giri GR, Saxena P. Mycobacterial MMAR_2193 catalyzes O-methylation of diverse polyketide cores. PLoS One 2022; 17:e0262241. [PMID: 34986163 PMCID: PMC8730385 DOI: 10.1371/journal.pone.0262241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/20/2021] [Indexed: 11/18/2022] Open
Abstract
O-methylation of small molecules is a common modification widely present in most organisms. Type III polyketides undergo O-methylation at hydroxyl end to play a wide spectrum of roles in bacteria, plants, algae, and fungi. Mycobacterium marinum harbours a distinctive genomic cluster with a type III pks gene and genes for several polyketide modifiers including a methyltransferase gene, mmar_2193. This study reports functional analyses of MMAR_2193 and reveals multi-methylating potential of the protein. Comparative sequence analyses revealed conservation of catalytically important motifs in MMAR_2193 protein. Homology-based structure-function and molecular docking studies suggested type III polyketide cores as possible substrates for MMAR_2193 catalysis. In vitro enzymatic characterization revealed the capability of MMAR_2193 protein to utilize diverse polyphenolic substrates to methylate several hydroxyl positions on a single substrate molecule. High-resolution mass spectrometric analyses identified multi-methylations of type III polyketides in cell-free reconstitution assays. Notably, our metabolomics analyses identified some of these methylated molecules in biofilms of wild type Mycobacterium marinum. This study characterizes a novel mycobacterial O-methyltransferase protein with multi-methylating enzymatic ability that could be exploited to generate a palette of structurally distinct bioactive molecules.
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Affiliation(s)
- Gorkha Raj Giri
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, India
| | - Priti Saxena
- Chemical Biology Group, Faculty of Life Sciences and Biotechnology, South Asian University, Akbar Bhawan, Chanakyapuri, New Delhi, India
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3
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Chatterjee T, Das G, Ghosh S, Chakrabarti P. Effect of gold nanoparticles on the structure and neuroprotective function of protein L-isoaspartyl methyltransferase (PIMT). Sci Rep 2021; 11:14296. [PMID: 34253804 PMCID: PMC8275801 DOI: 10.1038/s41598-021-93752-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 06/01/2021] [Indexed: 02/06/2023] Open
Abstract
Fibrillation of peptides and proteins is implicated in various neurodegenerative diseases and is a global concern. Aging leads to the formation of abnormal isoaspartate (isoAsp) residues from isomerization of normal aspartates in proteins, triggering fibril formation that leads to neurodegenerative diseases. Protein L-isoaspartyl methyltransferase (PIMT) is a repair enzyme which recognizes and converts altered isoAsp residues back to normal aspartate. Here we report the effect of gold nanoparticles (AuNPs) of different sizes on the structure and function of PIMT. Spherical AuNPs, viz. AuNS5, AuNS50 and AuNS100 (the number indicating the diameter in nm) stabilize PIMT, with AuNS100 exhibiting the best efficacy, as evident from various biophysical experiments. Isothermal titration calorimetry (ITC) revealed endothermic, but entropy driven mode of binding of PIMT with all the three AuNSs. Methyltransferase activity assay showed enhanced activity of PIMT in presence of all AuNSs, the maximum being with AuNS100. The efficacy of PIMT in presence of AuNS100 was further demonstrated by the reduction of fibrillation of Aβ42, the peptide that is implicated in Alzheimer's disease. The enhancement of anti-fibrillation activity of PIMT with AuNS100 was confirmed from cell survival assay with PC12 derived neuronal cells against Aβ42 induced neurotoxicity.
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Affiliation(s)
- Tanaya Chatterjee
- grid.418423.80000 0004 1768 2239Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata, 700054 India
| | - Gaurav Das
- grid.417635.20000 0001 2216 5074Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India ,grid.417635.20000 0001 2216 5074Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032 India
| | - Surajit Ghosh
- grid.417635.20000 0001 2216 5074Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032 India ,grid.469887.c0000 0004 7744 2771Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India ,grid.417635.20000 0001 2216 5074Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032 India ,grid.462385.e0000 0004 1775 4538Present Address: Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, Rajasthan, 342037 India
| | - Pinak Chakrabarti
- grid.418423.80000 0004 1768 2239Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata, 700054 India
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PROTEIN l-ISOASPARTYL METHYLTRANSFERASE (PIMT) in plants: regulations and functions. Biochem J 2020; 477:4453-4471. [PMID: 33245750 DOI: 10.1042/bcj20200794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023]
Abstract
Proteins are essential molecules that carry out key functions in a cell. However, as a result of aging or stressful environments, the protein undergoes a range of spontaneous covalent modifications, including the formation of abnormal l-isoaspartyl residues from aspartyl or asparaginyl residues, which can disrupt the protein's inherent structure and function. PROTEIN l-ISOASPARTYL METHYLTRANSFERASE (PIMT: EC 2.1.1.77), an evolutionarily conserved ancient protein repairing enzyme (PRE), converts such abnormal l-isoaspartyl residues to normal l-aspartyl residues and re-establishes the protein's native structure and function. Although originally discovered in animals as a PRE, PIMT emerged as a key PRE in plants, particularly in seeds, in which PIMT plays a predominant role in preserving seed vigor and viability for prolonged periods of time. Interestingly, higher plants encode a second PIMT (PIMT2) protein which possesses a unique N-terminal extension, and exhibits several distinct features and far more complexity than non-plant PIMTs. Recent studies indicate that the role of PIMT is not restricted to preserving seed vigor and longevity but is also implicated in enhancing the growth and survivability of plants under stressful environments. Furthermore, expression studies indicate the tantalizing possibility that PIMT is involved in various physiological processes apart from its role in seed vigor, longevity and plant's survivability under abiotic stress. This review article particularly describes new insights and emerging interest in all facets of this enzyme in plants along with a concise comparative overview on isoAsp formation, and the role and regulation of PIMTs across evolutionary diverse species. Additionally, recent methods and their challenges in identifying isoaspartyl containing proteins (PIMT substrates) are highlighted.
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Buongiorno J, Sipes K, Wasmund K, Loy A, Lloyd KG. Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment. PLoS One 2020; 15:e0234839. [PMID: 32853201 PMCID: PMC7451513 DOI: 10.1371/journal.pone.0234839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/04/2020] [Indexed: 11/30/2022] Open
Abstract
Distinct lineages of Gammaproteobacteria clade Woeseiales are globally distributed in marine sediments, based on metagenomic and 16S rRNA gene analysis. Yet little is known about why they are dominant or their ecological role in Arctic fjord sediments, where glacial retreat is rapidly imposing change. This study combined 16S rRNA gene analysis, metagenome-assembled genomes (MAGs), and genome-resolved metatranscriptomics uncovered the in situ abundance and transcriptional activity of Woeseiales with burial in four shallow sediment sites of Kongsfjorden and Van Keulenfjorden of Svalbard (79°N). We present five novel Woeseiales MAGs and show transcriptional evidence for metabolic plasticity during burial, including sulfur oxidation with reverse dissimilatory sulfite reductase (dsrAB) down to 4 cm depth and nitrite reduction down to 6 cm depth. A single stress protein, spore protein SP21 (hspA), had a tenfold higher mRNA abundance than any other transcript, and was a hundredfold higher on average than other transcripts. At three out of the four sites, SP21 transcript abundance increased with depth, while total mRNA abundance and richness decreased, indicating a shift in investment from metabolism and other cellular processes to build-up of spore protein SP21. The SP21 gene in MAGs was often flanked by genes involved in membrane-associated stress response. The ability of Woeseiales to shift from sulfur oxidation to nitrite reduction with burial into marine sediments with decreasing access to overlying oxic bottom waters, as well as enter into a dormant state dominated by SP21, may account for its ubiquity and high abundance in marine sediments worldwide, including those of the rapidly shifting Arctic.
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Affiliation(s)
- Joy Buongiorno
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Katie Sipes
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Kenneth Wasmund
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Alexander Loy
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
- Austrian Polar Research Institute, Vienna, Austria
| | - Karen G. Lloyd
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, United States of America
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Chatterjee T, Das G, Chatterjee BK, Dhar J, Ghosh S, Chakrabarti P. The role of isoaspartate in fibrillation and its prevention by Protein-L-isoaspartyl methyltransferase. Biochim Biophys Acta Gen Subj 2019; 1864:129500. [PMID: 31785325 DOI: 10.1016/j.bbagen.2019.129500] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/21/2019] [Accepted: 11/25/2019] [Indexed: 01/16/2023]
Abstract
BACKGROUND Isomerization of aspartate to isoaspartate (isoAsp) on aging causes protein damage and malfunction. Protein-L-isoaspartyl methyltransferase (PIMT) performs a neuroprotective role by repairing such residues. A hexapeptide, Val-Tyr-Pro-(isoAsp)-His-Ala (VA6), a substrate of PIMT, is shown to form fibrils, while the normal Asp-containing peptide does not. Considering the role of PIMT against epileptic seizure, the combined effect of PIMT and two antiepileptic drugs (AEDs) (valproic acid and stiripentol) was investigated for anti-fibrillation activity. METHODS Structural/functional modulations due to the binding of AEDs to PIMT were investigated using biophysical techniques. Thioflavin T (ThT) fluorescence assay and microscopic methods were employed to study fibril formation by VA6. In vitro experiments with PC12 cells were carried out with PIMT/AEDs. RESULTS ThT assay indicated reduction of fibrillation of VA6 by PIMT. AEDs stabilize PIMT, bind close to the cofactor binding site, possibly exerting allosteric effect, increase the enzymatic activity, and anti-fibrillation efficacy. Furthermore, Aβ42, implicated in Alzheimer's disease, undergoes β-sheet to α-helix transition in presence of PIMT. Studies with PC12 derived neurons showed that PIMT and PIMT/AEDs exerted neuroprotective effect against anti-NGF induced neurotoxicity. This was further validated against neurotoxicity induced by Aβ42 in primary rat cortical neurons. CONCLUSIONS The study provides a new perspective to the role isoAsp in protein fibrillation, PIMT in its prevention and AEDs in enhancing the activity of the enzyme. GENERAL SIGNIFICANCE IsoAsp, with an additional C atom in the main-chain of polypeptide chain, may make it more susceptible to fibrillation. PIMT alone, or in association with AEDs prevents this.
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Affiliation(s)
- Tanaya Chatterjee
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.
| | - Gaurav Das
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Barun K Chatterjee
- Department of Physics, Bose Institute, 93/1 A.P.C. Road, Kolkata 700009, India
| | - Jesmita Dhar
- Bioinformatics Center, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Pinak Chakrabarti
- Department of Biochemistry, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India; Bioinformatics Center, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata 700054, India.
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Mishra PKK, Mahawar M. PIMT-Mediated Protein Repair: Mechanism and Implications. BIOCHEMISTRY (MOSCOW) 2019; 84:453-463. [PMID: 31234761 DOI: 10.1134/s0006297919050018] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Amino acids undergo many covalent modifications, but only few amino acid repair enzymes have been identified. Protein-L-isoaspartate (D-aspartate) O-methyltransferase (PIMT), also known as L-isoaspartyl/D-aspartyl protein carboxyl methyltransferase (PCMT), methylates covalently modified isoaspartate (isoAsp) residues accumulated in proteins via Asn deamidation and Asp hydrolysis. This cytoplasmic reaction occurs through the formation of succinimide cyclical intermediate and generates either isoAsp or Asp from succinimide. Succinimide conversion into Asp is spontaneous, while isoAsp is restored by PIMT using S-adenosylmethionine as a methyl donor. PIMT transforms isoAsp into succinimide, thereby creating an opportunity for the later to be converted into Asp. Apart from normal cell physiology, formation of isoAsp in proteins is promoted by various stress conditions. The resulting isoAsp can form a kink or bend in the protein backbone thus making the protein conformationally and functionally distorted. Many PIMT-interacting proteins (proteins with isoAsp residues) have been reported in eukaryotes, but only few of them have been found in prokaryotes. Extensive studies in mice have shown the importance of PIMT in neurodegeneration. Detail elucidation of PIMT function can create a platform for addressing various disorders such as Alzheimer's disease and cancer.
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Affiliation(s)
- P K K Mishra
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
| | - M Mahawar
- Division of Biochemistry, Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh, 243122, India.
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Rivera-Millot A, Lesne E, Solans L, Coutte L, Bertrand-Michel J, Froguel P, Dhennin V, Hot D, Locht C, Antoine R, Jacob-Dubuisson F. Characterization of a Bvg-regulated fatty acid methyl-transferase in Bordetella pertussis. PLoS One 2017; 12:e0176396. [PMID: 28493897 PMCID: PMC5426589 DOI: 10.1371/journal.pone.0176396] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/10/2017] [Indexed: 12/22/2022] Open
Abstract
The whooping cough agent Bordetella pertussis controls the expression of its large virulence regulon in a coordinated manner through the two-component signal transduction system BvgAS. In addition to the genes coding for bona fide virulence factors, the Bvg regulon comprises genes of unknown function. In this work, we characterized a new Bvg-activated gene called BP2936. Homologs of BP2936 are found in other pathogenic Bordetellae and in several other species, including plant pathogens and environmental bacteria. We showed that the gene product of BP2936 is a membrane-associated methyl-transferase of free fatty acids. We thus propose to name it FmtB, for fatty acid methyl-transferase of Bordetella. The role of this protein was tested in cellular and animal models of infection, but the loss of BP2936 did not appear to affect host-pathogen interactions in those assays. The high level of conservation of BP2936 among B. pertussis isolates nevertheless argues that it probably plays a role in the life cycle of this pathogen.
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Affiliation(s)
- Alex Rivera-Millot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019- UMR 8204-CIIL-Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Elodie Lesne
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019- UMR 8204-CIIL-Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Luis Solans
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019- UMR 8204-CIIL-Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Loic Coutte
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019- UMR 8204-CIIL-Centre d’Infection et d’Immunité de Lille, Lille, France
| | | | - Philippe Froguel
- University of Lille, CNRS, Institut Pasteur de Lille, UMR 8199, European Genomic Institute for Diabetes, Lille, France
- Department of Genomics of Common Diseases, School of Public Health, Imperial College London, Hammersmith Hospital, London, United Kingdom
| | - Véronique Dhennin
- University of Lille, CNRS, Institut Pasteur de Lille, UMR 8199, European Genomic Institute for Diabetes, Lille, France
| | - David Hot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019- UMR 8204-CIIL-Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Camille Locht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019- UMR 8204-CIIL-Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019- UMR 8204-CIIL-Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Françoise Jacob-Dubuisson
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019- UMR 8204-CIIL-Centre d’Infection et d’Immunité de Lille, Lille, France
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