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Zbieralski K, Staszewski J, Konczak J, Lazarewicz N, Nowicka-Kazmierczak M, Wawrzycka D, Maciaszczyk-Dziubinska E. Multilevel Regulation of Membrane Proteins in Response to Metal and Metalloid Stress: A Lesson from Yeast. Int J Mol Sci 2024; 25:4450. [PMID: 38674035 PMCID: PMC11050377 DOI: 10.3390/ijms25084450] [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: 03/07/2024] [Revised: 04/06/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
In the face of flourishing industrialization and global trade, heavy metal and metalloid contamination of the environment is a growing concern throughout the world. The widespread presence of highly toxic compounds of arsenic, antimony, and cadmium in nature poses a particular threat to human health. Prolonged exposure to these toxins has been associated with severe human diseases, including cancer, diabetes, and neurodegenerative disorders. These toxins are known to induce analogous cellular stresses, such as DNA damage, disturbance of redox homeostasis, and proteotoxicity. To overcome these threats and improve or devise treatment methods, it is crucial to understand the mechanisms of cellular detoxification in metal and metalloid stress. Membrane proteins are key cellular components involved in the uptake, vacuolar/lysosomal sequestration, and efflux of these compounds; thus, deciphering the multilevel regulation of these proteins is of the utmost importance. In this review, we summarize data on the mechanisms of arsenic, antimony, and cadmium detoxification in the context of membrane proteome. We used yeast Saccharomyces cerevisiae as a eukaryotic model to elucidate the complex mechanisms of the production, regulation, and degradation of selected membrane transporters under metal(loid)-induced stress conditions. Additionally, we present data on orthologues membrane proteins involved in metal(loid)-associated diseases in humans.
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Affiliation(s)
| | | | | | | | | | | | - Ewa Maciaszczyk-Dziubinska
- Department of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wroclaw, 50-328 Wroclaw, Poland; (K.Z.); (J.S.); (J.K.); (N.L.); (M.N.-K.); (D.W.)
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Saha E, Fanfani V, Mandros P, Ben-Guebila M, Fischer J, Hoff-Shutta K, Glass K, DeMeo DL, Lopes-Ramos C, Quackenbush J. Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.16.567119. [PMID: 38014256 PMCID: PMC10680741 DOI: 10.1101/2023.11.16.567119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Gene regulatory networks (GRNs) are effective tools for inferring complex interactions between molecules that regulate biological processes and hence can provide insights into drivers of biological systems. Inferring co-expression networks is a critical element of GRN inference as the correlation between expression patterns may indicate that genes are coregulated by common factors. However, methods that estimate co-expression networks generally derive an aggregate network representing the mean regulatory properties of the population and so fail to fully capture population heterogeneity. To address these concerns, we introduce BONOBO (Bayesian Optimized Networks Obtained By assimilating Omics data), a scalable Bayesian model for deriving individual sample-specific co-expression networks by recognizing variations in molecular interactions across individuals. For every sample, BONOBO assumes a Gaussian distribution on the log-transformed centered gene expression and a conjugate prior distribution on the sample-specific co-expression matrix constructed from all other samples in the data. Combining the sample-specific gene expression with the prior distribution, BONOBO yields a closed-form solution for the posterior distribution of the sample-specific co-expression matrices, thus making the method extremely scalable. We demonstrate the utility of BONOBO in several contexts, including analyzing gene regulation in yeast transcription factor knockout studies, prognostic significance of miRNA-mRNA interaction in human breast cancer subtypes, and sex differences in gene regulation within human thyroid tissue. We find that BONOBO outperforms other sample-specific co-expression network inference methods and provides insight into individual differences in the drivers of biological processes.
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Affiliation(s)
- Enakshi Saha
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Viola Fanfani
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Panagiotis Mandros
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Marouen Ben-Guebila
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Jonas Fischer
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Katherine Hoff-Shutta
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
| | - Kimberly Glass
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Dawn Lisa DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Camila Lopes-Ramos
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
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Recio PS, Mitra NJ, Shively CA, Song D, Jaramillo G, Lewis KS, Chen X, Mitra R. Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode. Nucleic Acids Res 2023; 51:5006-5021. [PMID: 37125648 PMCID: PMC10250231 DOI: 10.1093/nar/gkad320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 05/02/2023] Open
Abstract
Gene expression changes are orchestrated by transcription factors (TFs), which bind to DNA to regulate gene expression. It remains surprisingly difficult to predict basic features of the transcriptional process, including in vivo TF occupancy. Existing thermodynamic models of TF function are often not concordant with experimental measurements, suggesting undiscovered biology. Here, we analyzed one of the most well-studied TFs, the yeast zinc cluster Gal4, constructed a Shea-Ackers thermodynamic model to describe its binding, and compared the results of this model to experimentally measured Gal4p binding in vivo. We found that at many promoters, the model predicted no Gal4p binding, yet substantial binding was observed. These outlier promoters lacked canonical binding motifs, and subsequent investigation revealed Gal4p binds unexpectedly to DNA sequences with high densities of its half site (CGG). We confirmed this novel mode of binding through multiple experimental and computational paradigms; we also found most other zinc cluster TFs we tested frequently utilize this binding mode, at 27% of their targets on average. Together, these results demonstrate a novel mode of binding where zinc clusters, the largest class of TFs in yeast, bind DNA sequences with high densities of half sites.
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Affiliation(s)
- Pamela S Recio
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Nikhil J Mitra
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Christian A Shively
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - David Song
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Grace Jaramillo
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Kristine Shady Lewis
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Xuhua Chen
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
| | - Robi D Mitra
- Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
- McDonnell Genome Institute, Washington University School of Medicine in St. Louis, St. Louis, MO 63108, USA
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Li M, Yao T, Lin W, Hinckley WE, Galli M, Muchero W, Gallavotti A, Chen JG, Huang SSC. Double DAP-seq uncovered synergistic DNA binding of interacting bZIP transcription factors. Nat Commun 2023; 14:2600. [PMID: 37147307 PMCID: PMC10163045 DOI: 10.1038/s41467-023-38096-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 04/15/2023] [Indexed: 05/07/2023] Open
Abstract
Many eukaryotic transcription factors (TF) form homodimer or heterodimer complexes to regulate gene expression. Dimerization of BASIC LEUCINE ZIPPER (bZIP) TFs are critical for their functions, but the molecular mechanism underlying the DNA binding and functional specificity of homo- versus heterodimers remains elusive. To address this gap, we present the double DNA Affinity Purification-sequencing (dDAP-seq) technique that maps heterodimer binding sites on endogenous genomic DNA. Using dDAP-seq we profile twenty pairs of C/S1 bZIP heterodimers and S1 homodimers in Arabidopsis and show that heterodimerization significantly expands the DNA binding preferences of these TFs. Analysis of dDAP-seq binding sites reveals the function of bZIP9 in abscisic acid response and the role of bZIP53 heterodimer-specific binding in seed maturation. The C/S1 heterodimers show distinct preferences for the ACGT elements recognized by plant bZIPs and motifs resembling the yeast GCN4 cis-elements. This study demonstrates the potential of dDAP-seq in deciphering the DNA binding specificities of interacting TFs that are key for combinatorial gene regulation.
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Affiliation(s)
- Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Tao Yao
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wanru Lin
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Will E Hinckley
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA
| | - Mary Galli
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854-8020, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Shao-Shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, 10003, USA.
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