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Mobarra N, Gholamalizadeh H, Abdulhussein KA, Raji S, Taheri Asl F, Mirvahabi MS, Rafiee M, Pakzad R. Serum level and tumor tissue expression of Ribonucleotide-diphosphate Reductase subunit M2 B: a potential biomarker for colorectal cancer. Mol Biol Rep 2022; 49:3657-3663. [DOI: 10.1007/s11033-022-07205-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 01/26/2022] [Indexed: 10/19/2022]
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2
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DNA Damage Response and Metabolic Reprogramming in Health and Disease. Trends Genet 2020; 36:777-791. [PMID: 32684438 DOI: 10.1016/j.tig.2020.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 01/08/2023]
Abstract
Nuclear DNA damage contributes to cellular malfunction and the premature onset of age-related diseases, including cancer. Until recently, the canonical DNA damage response (DDR) was thought to represent a collection of nuclear processes that detect, signal and repair damaged DNA. However, recent evidence suggests that beyond nuclear events, the DDR rewires an intricate network of metabolic circuits, fine-tunes protein synthesis, trafficking, and secretion as well as balances growth with defense strategies in response to genotoxic insults. In this review, we discuss how the active DDR signaling mobilizes extranuclear and systemic responses to promote cellular homeostasis and organismal survival in health and disease.
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Du M, Kodner S, Bai L. Enhancement of LacI binding in vivo. Nucleic Acids Res 2019; 47:9609-9618. [PMID: 31396617 PMCID: PMC6765135 DOI: 10.1093/nar/gkz698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 07/11/2019] [Accepted: 07/30/2019] [Indexed: 11/30/2022] Open
Abstract
Transcription factors (TFs) bind to specific sequences in DNA to regulate transcription. Despite extensive measurements of TFs’ dissociation constant (Kd) in vitro, their apparent Kdin vivo are usually unknown. LacI, a bacterial TF, is often used to artificially recruit proteins onto eukaryotic genomes. As LacI binds tightly to its recognition site (LacO) in vitro with a Kd about 10 picomolar (pM), it is often assumed that LacI also has high affinity to LacO in vivo. In this work, we measured LacI binding in living yeast cells using a fluorescent repressor operator system and found an apparent Kd of ∼0.6 μM, four orders of magnitude higher than that in vitro. By genetically altering (i) GFP-LacI structure, (ii) GFP-LacI stability, (iii) chromosome accessibility and (iv) LacO sequence, we reduced the apparent Kd to <10 nM. It turns out that the GFP tagging location and the fusion protein stability have a large effect on LacI binding, but surprisingly, chromosome accessibility only plays a mild role. These findings contribute to our quantitative understanding of the features that affect the apparent Kd of TF in cells. They also provide guidance for future design of more specific chromosomal recruitment through high-affinity TFs.
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Affiliation(s)
- Manyu Du
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.,Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Seth Kodner
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.,Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Physics, The Pennsylvania State University, University Park, PA 16802, USA
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Pasnuri N, Khuntia P, Mazumder A. Single transcript imaging to assay gene expression in wholemount Drosophila melanogaster tissues. Mech Dev 2018; 153:10-16. [PMID: 30118816 DOI: 10.1016/j.mod.2018.08.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 10/28/2022]
Abstract
Single molecule Fluorescence in situ Hybridization (smFISH) for mRNA provides a powerful quantitative handle on expression from endogenous gene loci. While the method has been widely applied in cells in culture, applications to primary tissue samples remain fewer, and often use involved cryosectioning. Even apart from quantitative access to absolute transcript counts in specific tissue volumes, many other advantages of smFISH can be envisaged in tissue samples. Primary among these are the ability to report on subtle differences in expression among different cell types within a tissue, and the ability to correlate the expression from different target genes. Here, we present a modified method of smFISH applicable on various primary wholemount tissues from the fruit fly Drosophila melanogaster, and show the efficacy of the method in a variety of larval and adult tissue, and embryos. We also combine smFISH in tissue with immunofluorescence to demonstrate the possibility of capturing transcriptional and translational aspects of gene expression in the same tissue. Given the widespread use of Drosophila melanogaster as a model system in Developmental Biology and Genetics, such methods are likely to be of wide interest and could yield rich information about gene expression in tissues from this organism.
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Affiliation(s)
- Nikhita Pasnuri
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500107, Telangana, India
| | - Purnati Khuntia
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500107, Telangana, India
| | - Aprotim Mazumder
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research Hyderabad, 36/P, Gopanpally, Serlingampally Mandal, Hyderabad 500107, Telangana, India.
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Dhuppar S, Mazumder A. Measuring cell cycle-dependent DNA damage responses and p53 regulation on a cell-by-cell basis from image analysis. Cell Cycle 2018; 17:1358-1371. [PMID: 29963960 DOI: 10.1080/15384101.2018.1482136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
DNA damage in cells occurs from both endogenous and exogenous sources, and failure to repair such damage is associated with the emergence of different cancers, neurological disorders and aging. DNA damage responses (DDR) in cells are closely associated with the cell cycle. While most of our knowledge of DDR comes from bulk biochemistry, such methods require cells to be arrested at specific stages for cell cycle studies, potentially altering measured responses; nor is cell to cell variability in DDR or direct cell-level correlation of two response metrics measured in such methods. To overcome these limitations we developed a microscopy-based assay for determining cell cycle stages over large cell numbers. This method can be used to study cell-cycle-dependent DDR in cultured cells without the need for cell synchronization. Upon DNA damage γH2A.X induction was correlated to nuclear enrichment of p53 on a cell-by-cell basis and in a cell cycle dependent manner. Imaging-based cell cycle staging was combined with single molecule P53 mRNA detection and immunofluorescence for p53 protein in the very same cells to reveal an intriguing repression of P53 transcript numbers due to reduced transcription across different stages of the cell cycle during DNA damage. Our study hints at an unexplored mechanism for p53 regulation and underscores the importance of measuring single cell level responses to DNA damage.
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Affiliation(s)
- Shivnarayan Dhuppar
- a TIFR Centre for Interdisciplinary Sciences , TIFR Hyderabad , Hyderabad , India
| | - Aprotim Mazumder
- a TIFR Centre for Interdisciplinary Sciences , TIFR Hyderabad , Hyderabad , India
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6
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Ouenzar F, Lalonde M, Laprade H, Morin G, Gallardo F, Tremblay-Belzile S, Chartrand P. Cell cycle-dependent spatial segregation of telomerase from sites of DNA damage. J Cell Biol 2017. [PMID: 28637749 PMCID: PMC5551704 DOI: 10.1083/jcb.201610071] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Telomerase can generate a novel telomere at a DNA break, with potentially lethal consequences for the cell. Ouenzar et al. reveal novel roles for Pif1, Rad52, and Siz1-dependent sumoylation in the spatial exclusion of telomerase from sites of DNA repair during the cell cycle. Telomerase can generate a novel telomere at DNA double-strand breaks (DSBs), an event called de novo telomere addition. How this activity is suppressed remains unclear. Combining single-molecule imaging and deep sequencing, we show that the budding yeast telomerase RNA (TLC1 RNA) is spatially segregated to the nucleolus and excluded from sites of DNA repair in a cell cycle–dependent manner. Although TLC1 RNA accumulates in the nucleoplasm in G1/S, Pif1 activity promotes TLC1 RNA localization in the nucleolus in G2/M. In the presence of DSBs, TLC1 RNA remains nucleolar in most G2/M cells but accumulates in the nucleoplasm and colocalizes with DSBs in rad52Δ cells, leading to de novo telomere additions. Nucleoplasmic accumulation of TLC1 RNA depends on Cdc13 localization at DSBs and on the SUMO ligase Siz1, which is required for de novo telomere addition in rad52Δ cells. This study reveals novel roles for Pif1, Rad52, and Siz1-dependent sumoylation in the spatial exclusion of telomerase from sites of DNA repair.
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Affiliation(s)
- Faissal Ouenzar
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Maxime Lalonde
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Hadrien Laprade
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Geneviève Morin
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Franck Gallardo
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Samuel Tremblay-Belzile
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
| | - Pascal Chartrand
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Quebec, Canada
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Stratz S, Dittrich PS. A Microfluidic Device for Immunoassay-Based Protein Analysis of Single E. coli Bacteria. Methods Mol Biol 2016; 1346:11-25. [PMID: 26542712 DOI: 10.1007/978-1-4939-2987-0_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
We present a method suitable for quantitative analysis of intracellular proteins, metabolites and secondary messengers of single bacterial cells. The method integrates the concept of immunoassays on a microfluidic device that facilitates single cell trapping and isolating in a small volume of a few tens of picoliters. Combination of the benefits of microfluidic systems for single cell analysis with the high analytical selectivity and sensitivity of immunoassays enables the detection of even low abundant intracellular analytes which occur only at a few hundred copies per bacterium.
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Affiliation(s)
- Simone Stratz
- Department of Biosystems Science and Engineering, ETH Zurich, Vladimir-Prelog-Weg 3, Zurich, 8091, Switzerland
| | - Petra S Dittrich
- Department of Biosystems Science and Engineering, ETH Zurich, Vladimir-Prelog-Weg 3, Zurich, 8091, Switzerland.
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Heath JR, Ribas A, Mischel PS. Single-cell analysis tools for drug discovery and development. Nat Rev Drug Discov 2016; 15:204-16. [PMID: 26669673 PMCID: PMC4883669 DOI: 10.1038/nrd.2015.16] [Citation(s) in RCA: 323] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The genetic, functional or compositional heterogeneity of healthy and diseased tissues presents major challenges in drug discovery and development. Such heterogeneity hinders the design of accurate disease models and can confound the interpretation of biomarker levels and of patient responses to specific therapies. The complex nature of virtually all tissues has motivated the development of tools for single-cell genomic, transcriptomic and multiplex proteomic analyses. Here, we review these tools and assess their advantages and limitations. Emerging applications of single cell analysis tools in drug discovery and development, particularly in the field of oncology, are discussed.
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Affiliation(s)
- James R Heath
- California Institute of Technology Division of Chemistry and Chemical Engineering, MC 127-72, 1200 East California Boulevard, Pasadena, California 91125, USA
| | - Antoni Ribas
- Department of Medicine, University of California, Los Angeles, 10833 Le Conte Avenue, Los Angeles, California 90095, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research San Diego, Department of Pathology and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
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9
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Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis. Cell 2015; 161:1413-24. [DOI: 10.1016/j.cell.2015.04.051] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 02/05/2015] [Accepted: 04/09/2015] [Indexed: 02/06/2023]
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10
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Guarino E, Salguero I, Kearsey SE. Cellular regulation of ribonucleotide reductase in eukaryotes. Semin Cell Dev Biol 2014; 30:97-103. [PMID: 24704278 DOI: 10.1016/j.semcdb.2014.03.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/26/2014] [Indexed: 12/22/2022]
Abstract
Synthesis of deoxynucleoside triphosphates (dNTPs) is essential for both DNA replication and repair and a key step in this process is catalyzed by ribonucleotide reductases (RNRs), which reduce ribonucleotides (rNDPs) to their deoxy forms. Tight regulation of RNR is crucial for maintaining the correct levels of all four dNTPs, which is important for minimizing the mutation rate and avoiding genome instability. Although allosteric control of RNR was the first discovered mechanism involved in regulation of the enzyme, other controls have emerged in recent years. These include regulation of expression of RNR genes, proteolysis of RNR subunits, control of the cellular localization of the small RNR subunit, and regulation of RNR activity by small protein inhibitors. This review will focus on these additional mechanisms of control responsible for providing a balanced supply of dNTPs.
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Affiliation(s)
- Estrella Guarino
- Tinbergen Building, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
| | - Israel Salguero
- Tinbergen Building, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
| | - Stephen E Kearsey
- Tinbergen Building, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
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Mazumder A, Pesudo LQ, McRee S, Bathe M, Samson LD. Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae. Nucleic Acids Res 2013; 41:9310-24. [PMID: 23935119 PMCID: PMC3814357 DOI: 10.1093/nar/gkt715] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An effective response to DNA damaging agents involves modulating numerous facets of cellular homeostasis in addition to DNA repair and cell-cycle checkpoint pathways. Fluorescence microscopy-based imaging offers the opportunity to simultaneously interrogate changes in both protein level and subcellular localization in response to DNA damaging agents at the single-cell level. We report here results from screening the yeast Green Fluorescent Protein (GFP)-fusion library to investigate global cellular protein reorganization on exposure to the alkylating agent methyl methanesulfonate (MMS). Broad groups of induced, repressed, nucleus- and cytoplasm-enriched proteins were identified. Gene Ontology and interactome analyses revealed the underlying cellular processes. Transcription factor (TF) analysis identified principal regulators of the response, and targets of all major stress-responsive TFs were enriched amongst the induced proteins. An unexpected partitioning of biological function according to the number of TFs targeting individual genes was revealed. Finally, differential modulation of ribosomal proteins depending on methyl methanesulfonate dose was shown to correlate with cell growth and with the translocation of the Sfp1 TF. We conclude that cellular responses can navigate different routes according to the extent of damage, relying on both expression and localization changes of specific proteins.
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Affiliation(s)
- Aprotim Mazumder
- Department of Biological Engineering, Center for Environmental Health Sciences, Laboratory for Computational Biology and Biophysics, Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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