1
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Ashraf RA, Bureik M, Marchisio MA. Design and engineering of logic genetic-enzymatic gates based on the activity of the human CYP2C9 enzyme in permeabilized Saccharomyces cerevisiae cells. Synth Syst Biotechnol 2024; 9:406-415. [PMID: 38590712 PMCID: PMC10999488 DOI: 10.1016/j.synbio.2024.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/10/2024] [Accepted: 03/17/2024] [Indexed: 04/10/2024] Open
Abstract
Gene circuits allow cells to carry out complex functions such as the precise regulation of biological metabolic processes. In this study, we combined, in the yeast S. cerevisiae, genetic regulatory elements with the enzymatic reactions of the human CYP2C9 and its redox partner CPR on luciferin substrates and diclofenac. S. cerevisiae cells were permeabilized and used as enzyme bags in order to host these metabolic reactions. We engineered three different (genetic)-enzymatic basic Boolean gates (YES, NOT, and N-IMPLY). In the YES and N-IMPLY gates, human CYP2C9 was expressed under the galactose-inducible GAL1 promoter. The carbon monoxide releasing molecule CORM-401 was used as an input in the NOT and N-IMPLY gates to impair CYP2C9 activity through inhibition of the Fe+2- heme prosthetic group in the active site of the human enzyme. Our study provides a new approach in designing synthetic bio-circuits and optimizing experimental conditions to favor the heterologous expression of human drug metabolic enzymes over their endogenous counterparts. This new approach will help study precise metabolic attributes of human P450s.
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Affiliation(s)
- Rana Azeem Ashraf
- School of Pharmaceutical Science and Technology, Tianjin University, 300072, Tianjin, China
| | - Matthias Bureik
- School of Pharmaceutical Science and Technology, Tianjin University, 300072, Tianjin, China
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, 300072, Tianjin, China
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2
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Li W, Hu J, Song F, Yu J, Peng X, Zhang S, Wang L, Hu M, Liu JC, Wei Y, Xiao X, Li Y, Li D, Wang H, Zhou BR, Dai L, Mou Z, Zhou M, Zhang H, Zhou Z, Zhang H, Bai Y, Zhou JQ, Li W, Li G, Zhu P. Structural basis for linker histone H5-nucleosome binding and chromatin fiber compaction. Cell Res 2024:10.1038/s41422-024-01009-z. [PMID: 39103524 DOI: 10.1038/s41422-024-01009-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/20/2024] [Indexed: 08/07/2024] Open
Abstract
The hierarchical packaging of chromatin fibers plays a critical role in gene regulation. The 30-nm chromatin fibers, a central-level structure bridging nucleosomal arrays to higher-order organizations, function as the first level of transcriptional dormant chromatin. The dynamics of 30-nm chromatin fiber play a crucial role in biological processes related to DNA. Here, we report a 3.6-angstrom resolution cryogenic electron microscopy structure of H5-bound dodecanucleosome, i.e., the chromatin fiber reconstituted in the presence of linker histone H5, which shows a two-start left-handed double helical structure twisted by tetranucleosomal units. An atomic structural model of the H5-bound chromatin fiber, including an intact chromatosome, is built, which provides structural details of the full-length linker histone H5, including its N-terminal domain and an HMG-motif-like C-terminal domain. The chromatosome structure shows that H5 binds the nucleosome off-dyad through a three-contact mode in the chromatin fiber. More importantly, the H5-chromatin structure provides a fine molecular basis for the intra-tetranucleosomal and inter-tetranucleosomal interactions. In addition, we systematically validated the physiological functions and structural characteristics of the tetranucleosomal unit through a series of genetic and genomic studies in Saccharomyces cerevisiae and in vitro biophysical experiments. Furthermore, our structure reveals that multiple structural asymmetries of histone tails confer a polarity to the chromatin fiber. These findings provide structural and mechanistic insights into how a nucleosomal array folds into a higher-order chromatin fiber with a polarity in vitro and in vivo.
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Affiliation(s)
- Wenyan Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jie Hu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feng Song
- New Cornerstone Science Laboratory, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shangdong, China
| | - Juan Yu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xin Peng
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuming Zhang
- Department of Public Health Laboratory Sciences, West China School of Public Health, Sichuan University, Chengdu, Sichuan, China
| | - Lin Wang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mingli Hu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Cheng Liu
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yu Wei
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xue Xiao
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Dongyu Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui Wang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Linchang Dai
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zongjun Mou
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Zhou
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Haonan Zhang
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zheng Zhou
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huidong Zhang
- Research Center for Environment and Female Reproductive Health, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jin-Qiu Zhou
- The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Wei Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- National Laboratory for Condensed Matter Physics and Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Guohong Li
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- New Cornerstone Science Laboratory, Frontier Science Center for Immunology and Metabolism, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei, China.
| | - Ping Zhu
- Key Laboratory of Epigenetic Regulation and Intervention, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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3
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Haase MAB, Lazar-Stefanita L, Ólafsson G, Wudzinska A, Shen MJ, Truong DM, Boeke JD. macroH2A1 drives nucleosome dephasing and genome instability in histone humanized yeast. Cell Rep 2024; 43:114472. [PMID: 38990716 DOI: 10.1016/j.celrep.2024.114472] [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: 05/01/2023] [Revised: 01/15/2024] [Accepted: 06/24/2024] [Indexed: 07/13/2024] Open
Abstract
In addition to replicative histones, eukaryotic genomes encode a repertoire of non-replicative variant histones, providing additional layers of structural and epigenetic regulation. Here, we systematically replace individual replicative human histones with non-replicative human variant histones using a histone replacement system in yeast. We show that variants H2A.J, TsH2B, and H3.5 complement their respective replicative counterparts. However, macroH2A1 fails to complement, and its overexpression is toxic in yeast, negatively interacting with yeast's native histones and kinetochore genes. To isolate yeast with macroH2A1 chromatin, we uncouple the effects of its macro and histone fold domains, revealing that both domains suffice to override native nucleosome positioning. Furthermore, both uncoupled constructs of macroH2A1 exhibit lower nucleosome occupancy, decreased short-range chromatin interactions (<20 kb), disrupted centromeric clustering, and increased chromosome instability. Our observations demonstrate that lack of a canonical histone H2A dramatically alters chromatin organization in yeast, leading to genome instability and substantial fitness defects.
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Affiliation(s)
- Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Vilcek Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY 10016, USA
| | - Luciana Lazar-Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Aleksandra Wudzinska
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Michael J Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - David M Truong
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA; Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA.
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4
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Kelliher JL, Folkerts ML, Shen KV, Song W, Tengler K, Stiefel CM, Lee SO, Dray E, Zhao W, Koss B, Pannunzio NR, Leung JW. Evolved histone tail regulates 53BP1 recruitment at damaged chromatin. Nat Commun 2024; 15:4634. [PMID: 38821984 PMCID: PMC11143218 DOI: 10.1038/s41467-024-49071-w] [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: 11/02/2023] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
The master DNA damage repair histone protein, H2AX, is essential for orchestrating the recruitment of downstream mediator and effector proteins at damaged chromatin. The phosphorylation of H2AX at S139, γH2AX, is well-studied for its DNA repair function. However, the extended C-terminal tail is not characterized. Here, we define the minimal motif on H2AX for the canonical function in activating the MDC1-RNF8-RNF168 phosphorylation-ubiquitination pathway that is important for recruiting repair proteins, such as 53BP1 and BRCA1. Interestingly, H2AX recruits 53BP1 independently from the MDC1-RNF8-RNF168 pathway through its evolved C-terminal linker region with S139 phosphorylation. Mechanistically, 53BP1 recruitment to damaged chromatin is mediated by the interaction between the H2AX C-terminal tail and the 53BP1 Oligomerization-Tudor domains. Moreover, γH2AX-linker mediated 53BP1 recruitment leads to camptothecin resistance in H2AX knockout cells. Overall, our study uncovers an evolved mechanism within the H2AX C-terminal tail for regulating DNA repair proteins at damaged chromatin.
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Affiliation(s)
- Jessica L Kelliher
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Melissa L Folkerts
- Department of Medicine, Division of Hematology/Oncology, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92626, USA
| | - Kaiyuan V Shen
- Department of Medicine, Division of Hematology/Oncology, University of California, Irvine, Irvine, CA, 92697, USA
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92626, USA
| | - Wan Song
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Kyle Tengler
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Clara M Stiefel
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Seong-Ok Lee
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Eloise Dray
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Weixing Zhao
- Department of Biochemistry and Structural Biology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA
| | - Brian Koss
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Nicholas R Pannunzio
- Department of Medicine, Division of Hematology/Oncology, University of California, Irvine, Irvine, CA, 92697, USA.
| | - Justin W Leung
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
- Department of Radiation Oncology, University of Texas Health and Science Center, San Antonio, TX, 78229, USA.
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5
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Camellato BR, Brosh R, Ashe HJ, Maurano MT, Boeke JD. Synthetic reversed sequences reveal default genomic states. Nature 2024; 628:373-380. [PMID: 38448583 PMCID: PMC11006607 DOI: 10.1038/s41586-024-07128-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
Abstract
Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or 'noise'1-4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in 'default genomic states' between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.
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Affiliation(s)
| | - Ran Brosh
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Pathology, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA.
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York, NY, USA.
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6
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Haase MAB, Steenwyk JL, Boeke JD. Gene loss and cis-regulatory novelty shaped core histone gene evolution in the apiculate yeast Hanseniaspora uvarum. Genetics 2024; 226:iyae008. [PMID: 38271560 PMCID: PMC10917516 DOI: 10.1093/genetics/iyae008] [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: 08/28/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
Core histone genes display a remarkable diversity of cis-regulatory mechanisms despite their protein sequence conservation. However, the dynamics and significance of this regulatory turnover are not well understood. Here, we describe the evolutionary history of core histone gene regulation across 400 million years in budding yeasts. We find that canonical mode of core histone regulation-mediated by the trans-regulator Spt10-is ancient, likely emerging between 320 and 380 million years ago and is fixed in the majority of extant species. Unexpectedly, we uncovered the emergence of a novel core histone regulatory mode in the Hanseniaspora genus, from its fast-evolving lineage, which coincided with the loss of 1 copy of its paralogous core histone genes. We show that the ancestral Spt10 histone regulatory mode was replaced, via cis-regulatory changes in the histone control regions, by a derived Mcm1 histone regulatory mode and that this rewiring event occurred with no changes to the trans-regulator, Mcm1, itself. Finally, we studied the growth dynamics of the cell cycle and histone synthesis in genetically modified Hanseniaspora uvarum. We find that H. uvarum divides rapidly, with most cells completing a cell cycle within 60 minutes. Interestingly, we observed that the regulatory coupling between histone and DNA synthesis was lost in H. uvarum. Our results demonstrate that core histone gene regulation was fixed anciently in budding yeasts, however it has greatly diverged in the Hanseniaspora fast-evolving lineage.
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Affiliation(s)
- Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 435 E 30th St, New York, NY 10016, USA
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jacob L Steenwyk
- Howards Hughes Medical Institute and the Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 435 E 30th St, New York, NY 10016, USA
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7
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Gaikani HK, Stolar M, Kriti D, Nislow C, Giaever G. From beer to breadboards: yeast as a force for biological innovation. Genome Biol 2024; 25:10. [PMID: 38178179 PMCID: PMC10768129 DOI: 10.1186/s13059-023-03156-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
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Affiliation(s)
- Hamid Kian Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Monika Stolar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
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8
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Ólafsson G, Haase MAB, Boeke JD. Humanization reveals pervasive incompatibility of yeast and human kinetochore components. G3 (BETHESDA, MD.) 2023; 14:jkad260. [PMID: 37962556 PMCID: PMC10755175 DOI: 10.1093/g3journal/jkad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 06/29/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023]
Abstract
Kinetochores assemble on centromeres to drive chromosome segregation in eukaryotic cells. Humans and budding yeast share most of the structural subunits of the kinetochore, whereas protein sequences have diverged considerably. The conserved centromeric histone H3 variant, CenH3 (CENP-A in humans and Cse4 in budding yeast), marks the site for kinetochore assembly in most species. A previous effort to complement Cse4 in yeast with human CENP-A was unsuccessful; however, co-complementation with the human core nucleosome was not attempted. Previously, our lab successfully humanized the core nucleosome in yeast; however, this severely affected cellular growth. We hypothesized that yeast Cse4 is incompatible with humanized nucleosomes and that the kinetochore represented a limiting factor for efficient histone humanization. Thus, we argued that including the human CENP-A or a Cse4-CENP-A chimera might improve histone humanization and facilitate kinetochore function in humanized yeast. The opposite was true: CENP-A expression reduced histone humanization efficiency, was toxic to yeast, and disrupted cell cycle progression and kinetochore function in wild-type (WT) cells. Suppressors of CENP-A toxicity included gene deletions of subunits of 3 conserved chromatin remodeling complexes, highlighting their role in CenH3 chromatin positioning. Finally, we attempted to complement the subunits of the NDC80 kinetochore complex, individually and in combination, without success, in contrast to a previous study indicating complementation by the human NDC80/HEC1 gene. Our results suggest that limited protein sequence similarity between yeast and human components in this very complex structure leads to failure of complementation.
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Affiliation(s)
- Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 14 11201, USA
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9
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Zhang X, Fawwal DV, Spangle JM, Corbett AH, Jones CY. Exploring the Molecular Underpinnings of Cancer-Causing Oncohistone Mutants Using Yeast as a Model. J Fungi (Basel) 2023; 9:1187. [PMID: 38132788 PMCID: PMC10744705 DOI: 10.3390/jof9121187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Understanding the molecular basis of cancer initiation and progression is critical in developing effective treatment strategies. Recently, mutations in genes encoding histone proteins that drive oncogenesis have been identified, converting these essential proteins into "oncohistones". Understanding how oncohistone mutants, which are commonly single missense mutations, subvert the normal function of histones to drive oncogenesis requires defining the functional consequences of such changes. Histones genes are present in multiple copies in the human genome with 15 genes encoding histone H3 isoforms, the histone for which the majority of oncohistone variants have been analyzed thus far. With so many wildtype histone proteins being expressed simultaneously within the oncohistone, it can be difficult to decipher the precise mechanistic consequences of the mutant protein. In contrast to humans, budding and fission yeast contain only two or three histone H3 genes, respectively. Furthermore, yeast histones share ~90% sequence identity with human H3 protein. Its genetic simplicity and evolutionary conservation make yeast an excellent model for characterizing oncohistones. The power of genetic approaches can also be exploited in yeast models to define cellular signaling pathways that could serve as actionable therapeutic targets. In this review, we focus on the value of yeast models to serve as a discovery tool that can provide mechanistic insights and inform subsequent translational studies in humans.
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Affiliation(s)
- Xinran Zhang
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
| | - Dorelle V. Fawwal
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Jennifer M. Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Anita H. Corbett
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Celina Y. Jones
- Department of Biology, Emory University, Atlanta, GA 30322, USA; (X.Z.); (D.V.F.); (A.H.C.)
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
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10
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Goldberg GW, Kogenaru M, Keegan S, Haase MAB, Kagermazova L, Arias MA, Onyebeke K, Adams S, Fenyö D, Noyes MB, Boeke JD. Engineered transcription-associated Cas9 targeting in eukaryotic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558319. [PMID: 37781609 PMCID: PMC10541143 DOI: 10.1101/2023.09.18.558319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
DNA targeting Class 2 CRISPR-Cas effector nucleases, including the well-studied Cas9 proteins, evolved protospacer-adjacent motif (PAM) and guide RNA interactions that sequentially license their binding and cleavage activities at protospacer target sites. Both interactions are nucleic acid sequence specific but function constitutively; thus, they provide intrinsic spatial control over DNA targeting activities but naturally lack temporal control. Here we show that engineered Cas9 fusion proteins which bind to nascent RNAs near a protospacer can facilitate spatiotemporal coupling between transcription and DNA targeting at that protospacer: Transcription-associated Cas9 Targeting (TraCT). Engineered TraCT is enabled when suboptimal PAM interactions limit basal activity in vivo and when one or more nascent RNA substrates are still tethered to the actively transcribing target DNA in cis. We further show that this phenomenon can be exploited for selective editing at one of two identical targets in distinct gene loci, or, in diploid allelic loci that are differentially transcribed. Our work demonstrates that temporal control over Cas9's targeting activity at specific DNA sites may be engineered without modifying Cas9's core domains and guide RNA components or their expression levels. More broadly, it establishes RNA binding in cis as a mechanism that can conditionally stimulate CRISPR-Cas DNA targeting in eukaryotes.
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Affiliation(s)
- Gregory W. Goldberg
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Manjunatha Kogenaru
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Denotes equivalent contribution to the work
| | - Max A. B. Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Denotes equivalent contribution to the work
| | - Larisa Kagermazova
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Mauricio A. Arias
- Courant Institute of Mathematical Sciences, New York University, New York, NY 10012, USA
| | - Kenenna Onyebeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Samantha Adams
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Marcus B. Noyes
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn NY 11201
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11
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Sultana S, Abdullah M, Li J, Hochstrasser M, Kachroo AH. Species-specific protein-protein interactions govern the humanization of the 20S proteasome in yeast. Genetics 2023; 225:iyad117. [PMID: 37364278 PMCID: PMC10471208 DOI: 10.1093/genetics/iyad117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/28/2023] Open
Abstract
Yeast and humans share thousands of genes despite a billion years of evolutionary divergence. While many human genes can functionally replace their yeast counterparts, nearly half of the tested shared genes cannot. For example, most yeast proteasome subunits are "humanizable," except subunits comprising the β-ring core, including β2c (HsPSMB7, a constitutive proteasome subunit). We developed a high-throughput pipeline to humanize yeast proteasomes by generating a large library of Hsβ2c mutants and screening them for complementation of a yeast β2 (ScPup1) knockout. Variants capable of replacing ScPup1 included (1) those impacting local protein-protein interactions (PPIs), with most affecting interactions between the β2c C-terminal tail and the adjacent β3 subunit, and (2) those affecting β2c proteolytic activity. Exchanging the full-length tail of human β2c with that of ScPup1 enabled complementation. Moreover, wild-type human β2c could replace yeast β2 if human β3 was also provided. Unexpectedly, yeast proteasomes bearing a catalytically inactive HsPSMB7-T44A variant that blocked precursor autoprocessing were viable, suggesting an intact propeptide stabilizes late assembly intermediates. In contrast, similar modifications in human β2i (HsPSMB10), an immunoproteasome subunit and the co-ortholog of yeast β2, do not enable complementation in yeast, suggesting distinct interactions are involved in human immunoproteasome core assembly. Broadly, our data reveal roles for specific PPIs governing functional replaceability across vast evolutionary distances.
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Affiliation(s)
- Sarmin Sultana
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H3G 1M8, Canada
| | - Mudabir Abdullah
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H3G 1M8, Canada
| | - Jianhui Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Aashiq H Kachroo
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC H3G 1M8, Canada
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12
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Jia X, Lin W, Wang W. Regulation of chromatin organization during animal regeneration. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:19. [PMID: 37259007 DOI: 10.1186/s13619-023-00162-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/21/2023] [Indexed: 06/02/2023]
Abstract
Activation of regeneration upon tissue damages requires the activation of many developmental genes responsible for cell proliferation, migration, differentiation, and tissue patterning. Ample evidence revealed that the regulation of chromatin organization functions as a crucial mechanism for establishing and maintaining cellular identity through precise control of gene transcription. The alteration of chromatin organization can lead to changes in chromatin accessibility and/or enhancer-promoter interactions. Like embryogenesis, each stage of tissue regeneration is accompanied by dynamic changes of chromatin organization in regeneration-responsive cells. In the past decade, many studies have been conducted to investigate the contribution of chromatin organization during regeneration in various tissues, organs, and organisms. A collection of chromatin regulators were demonstrated to play critical roles in regeneration. In this review, we will summarize the progress in the understanding of chromatin organization during regeneration in different research organisms and discuss potential common mechanisms responsible for the activation of regeneration response program.
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Affiliation(s)
- Xiaohui Jia
- National Institute of Biological Sciences, Beijing, 102206, China
- China Agricultural University, Beijing, 100083, China
| | - Weifeng Lin
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
| | - Wei Wang
- National Institute of Biological Sciences, Beijing, 102206, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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13
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Abdullah M, Greco BM, Laurent JM, Garge RK, Boutz DR, Vandeloo M, Marcotte EM, Kachroo AH. Rapid, scalable, combinatorial genome engineering by marker-less enrichment and recombination of genetically engineered loci in yeast. CELL REPORTS METHODS 2023; 3:100464. [PMID: 37323580 PMCID: PMC10261898 DOI: 10.1016/j.crmeth.2023.100464] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/30/2023] [Accepted: 04/12/2023] [Indexed: 06/17/2023]
Abstract
A major challenge to rationally building multi-gene processes in yeast arises due to the combinatorics of combining all of the individual edits into the same strain. Here, we present a precise and multi-site genome editing approach that combines all edits without selection markers using CRISPR-Cas9. We demonstrate a highly efficient gene drive that selectively eliminates specific loci by integrating CRISPR-Cas9-mediated double-strand break (DSB) generation and homology-directed recombination with yeast sexual assortment. The method enables marker-less enrichment and recombination of genetically engineered loci (MERGE). We show that MERGE converts single heterologous loci to homozygous loci at ∼100% efficiency, independent of chromosomal location. Furthermore, MERGE is equally efficient at converting and combining multiple loci, thus identifying compatible genotypes. Finally, we establish MERGE proficiency by engineering a fungal carotenoid biosynthesis pathway and most of the human α-proteasome core into yeast. Therefore, MERGE lays the foundation for scalable, combinatorial genome editing in yeast.
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Affiliation(s)
- Mudabir Abdullah
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
| | - Brittany M. Greco
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
| | - Jon M. Laurent
- Institute of Systems Genetics, NYU Langone Health, New York, NY, USA
| | - Riddhiman K. Garge
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Daniel R. Boutz
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Michelle Vandeloo
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
| | - Edward M. Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Aashiq H. Kachroo
- Centre for Applied Synthetic Biology, Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
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14
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Haase MAB, Lazar-Stefanita L, Ólafsson G, Wudzinska A, Shen MJ, Truong DM, Boeke JD. Human macroH2A1 drives nucleosome dephasing and genome instability in histone-humanized yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.538725. [PMID: 37205538 PMCID: PMC10187286 DOI: 10.1101/2023.05.06.538725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In addition to replicative histones, eukaryotic genomes encode a repertoire of non-replicative variant histones providing additional layers of structural and epigenetic regulation. Here, we systematically replaced individual replicative human histones with non-replicative human variant histones using a histone replacement system in yeast. Variants H2A.J, TsH2B, and H3.5 complemented for their respective replicative counterparts. However, macroH2A1 failed to complement and its expression was toxic in yeast, negatively interacting with native yeast histones and kinetochore genes. To isolate yeast with "macroH2A1 chromatin" we decoupled the effects of its macro and histone fold domains, which revealed that both domains sufficed to override native yeast nucleosome positioning. Furthermore, both modified constructs of macroH2A1 exhibited lower nucleosome occupancy that correlated with decreased short-range chromatin interactions (<20 Kb), disrupted centromeric clustering, and increased chromosome instability. While supporting viability, macroH2A1 dramatically alters chromatin organization in yeast, leading to genome instability and massive fitness defects.
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Affiliation(s)
- Max A. B. Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY, 10016, USA
| | - Luciana Lazar-Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Aleksandra Wudzinska
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Michael J. Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - David M. Truong
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
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15
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Haase MAB, Ólafsson G, Flores RL, Boakye‐Ansah E, Zelter A, Dickinson MS, Lazar‐Stefanita L, Truong DM, Asbury CL, Davis TN, Boeke JD. DASH/Dam1 complex mutants stabilize ploidy in histone-humanized yeast by weakening kinetochore-microtubule attachments. EMBO J 2023; 42:e112600. [PMID: 36651597 PMCID: PMC10106983 DOI: 10.15252/embj.2022112600] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 01/19/2023] Open
Abstract
Forcing budding yeast to chromatinize their DNA with human histones manifests an abrupt fitness cost. We previously proposed chromosomal aneuploidy and missense mutations as two potential modes of adaptation to histone humanization. Here, we show that aneuploidy in histone-humanized yeasts is specific to a subset of chromosomes that are defined by their centromeric evolutionary origins but that these aneuploidies are not adaptive. Instead, we find that a set of missense mutations in outer kinetochore proteins drives adaptation to human histones. Furthermore, we characterize the molecular mechanism underlying adaptation in two mutants of the outer kinetochore DASH/Dam1 complex, which reduce aneuploidy by suppression of chromosome instability. Molecular modeling and biochemical experiments show that these two mutants likely disrupt a conserved oligomerization interface thereby weakening microtubule attachments. We propose a model through which weakened microtubule attachments promote increased kinetochore-microtubule turnover and thus suppress chromosome instability. In sum, our data show how a set of point mutations evolved in histone-humanized yeasts to counterbalance human histone-induced chromosomal instability through weakening microtubule interactions, eventually promoting a return to euploidy.
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Affiliation(s)
- Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
- Vilcek Institute of Graduate Biomedical SciencesNYU School of MedicineNew YorkNYUSA
| | - Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
| | - Rachel L Flores
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | | | - Alex Zelter
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | | | - Luciana Lazar‐Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
| | - David M Truong
- Department of Biomedical EngineeringNYU Tandon School of EngineeringBrooklynNYUSA
- Department of PathologyNYU Langone HealthNew YorkNYUSA
| | - Charles L Asbury
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
- Department of Physiology and BiophysicsUniversity of WashingtonSeattleWAUSA
| | - Trisha N Davis
- Department of BiochemistryUniversity of WashingtonSeattleWAUSA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
- Department of Biomedical EngineeringNYU Tandon School of EngineeringBrooklynNYUSA
- Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
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16
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Gleason RJ, Guo Y, Semancik CS, Ow C, Lakshminarayanan G, Chen X. Developmentally programmed histone H3 expression regulates cellular plasticity at the parental-to-early embryo transition. SCIENCE ADVANCES 2023; 9:eadh0411. [PMID: 37027463 PMCID: PMC10081851 DOI: 10.1126/sciadv.adh0411] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
During metazoan development, the marked change in developmental potential from the parental germline to the embryo raises an important question regarding how the next life cycle is reset. As the basic unit of chromatin, histones are essential for regulating chromatin structure and function and, accordingly, transcription. However, the genome-wide dynamics of the canonical, replication-coupled (RC) histones during gametogenesis and embryogenesis remain unknown. In this study, we use CRISPR-Cas9-mediated gene editing in Caenorhabditis elegans to investigate the expression pattern and role of individual RC histone H3 genes and compare them to the histone variant, H3.3. We report a tightly regulated epigenome landscape change from the germline to embryos that are regulated through differential expression of distinct histone gene clusters. Together, this study reveals that a change from a H3.3- to H3-enriched epigenome during embryogenesis restricts developmental plasticity and uncovers distinct roles for individual H3 genes in regulating germline chromatin.
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Affiliation(s)
- Ryan J. Gleason
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yanrui Guo
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Cindy Ow
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
- University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gitanjali Lakshminarayanan
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Dana-Farber Cancer Institute, Boston, MA 02215 USA
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
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17
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Storchová Z. The adaptive strategies of cells in the face of CIN. EMBO J 2023; 42:e113766. [PMID: 36939036 PMCID: PMC10106979 DOI: 10.15252/embj.2023113766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/08/2023] [Indexed: 03/21/2023] Open
Abstract
An increased frequency of chromosome segregation errors, known as chromosomal instability (CIN), leads to accumulation of aneuploid cells with abnormal chromosomal numbers, which impairs viability through negative effects on survival and proliferation under most conditions. Two recent papers find by independent approaches that the key to surviving high levels of CIN is reducing the instability itself, showcasing the remarkable adaptability of the chromosome segregation machinery, in particular the microtubule-kinetochore interface, and highlighting the crucial role that maintaining chromosomal stability plays in cell proliferation.
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Affiliation(s)
- Zuzana Storchová
- Department of Molecular Genetics, RPTU Kaiserslautern-Landau, Kaiserslautern, Germany
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18
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Lazar-Stefanita L, Luo J, Haase MAB, Zhang W, Boeke JD. Two differentially stable rDNA loci coexist on the same chromosome and form a single nucleolus. Proc Natl Acad Sci U S A 2023; 120:e2219126120. [PMID: 36821584 PMCID: PMC9992848 DOI: 10.1073/pnas.2219126120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/20/2023] [Indexed: 02/24/2023] Open
Abstract
The nucleolus is the most prominent membraneless compartment within the nucleus-dedicated to the metabolism of ribosomal RNA. Nucleoli are composed of hundreds of ribosomal DNA (rDNA) repeated genes that form large chromosomal clusters, whose high recombination rates can cause nucleolar dysfunction and promote genome instability. Intriguingly, the evolving architecture of eukaryotic genomes appears to have favored two strategic rDNA locations-where a single locus per chromosome is situated either near the centromere (CEN) or the telomere. Here, we deployed an innovative genome engineering approach to cut and paste to an ectopic chromosomal location-the ~1.5 mega-base rDNA locus in a single step using CRISPR technology. This "megablock" rDNA engineering was performed in a fused-karyotype strain of Saccharomyces cerevisiae. The strategic repositioning of this locus within the megachromosome allowed experimentally mimicking and monitoring the outcome of an rDNA migratory event, in which twin rDNA loci coexist on the same chromosomal arm. We showed that the twin-rDNA yeast readily adapts, exhibiting wild-type growth and maintaining rRNA homeostasis, and that the twin loci form a single nucleolus throughout the cell cycle. Unexpectedly, the size of each rDNA array appears to depend on its position relative to the CEN, in that the locus that is CEN-distal undergoes size reduction at a higher frequency compared to the CEN-proximal counterpart. Finally, we provided molecular evidence supporting a mechanism called paralogous cis-rDNA interference, which potentially explains why placing two identical repeated arrays on the same chromosome may negatively affect their function and structural stability.
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Affiliation(s)
- Luciana Lazar-Stefanita
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY10016
| | - Jingchuan Luo
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY10016
| | - Max A. B. Haase
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY10016
- Vilcek Institute of Graduate Biomedical Sciences at NYU School of Medicine, New York, NY10016
| | - Weimin Zhang
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY10016
| | - Jef D. Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY10016
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY11201
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19
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Corcoran ET, Jacob Y. Direct assessment of histone function using histone replacement. Trends Biochem Sci 2023; 48:53-70. [PMID: 35853806 PMCID: PMC9789166 DOI: 10.1016/j.tibs.2022.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 02/09/2023]
Abstract
Histones serve many purposes in eukaryotic cells in the regulation of diverse genomic processes, including transcription, replication, DNA repair, and chromatin organization. As such, experimental systems to assess histone function are fundamental resources toward elucidating the regulation of activities occurring on chromatin. One set of important tools for investigating histone function are histone replacement systems, in which endogenous histone expression can be partially or completely replaced with a mutant histone. Histone replacement systems allow systematic screens of histone regulatory functions and the direct assessment of functions for histone residues. In this review, we describe existing histone replacement systems in model organisms, the benefits and limitations of these systems, and opportunities for future research with histone replacement strategies.
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Affiliation(s)
- Emma Tung Corcoran
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CT 06511, USA
| | - Yannick Jacob
- Yale University, Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, 260 Whitney Avenue, New Haven, CT 06511, USA.
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20
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Stenback KE, Flyckt KS, Hoang T, Campbell AA, Nikolau BJ. Modifying the yeast very long chain fatty acid biosynthetic machinery by the expression of plant 3-ketoacyl CoA synthase isozymes. Sci Rep 2022; 12:13235. [PMID: 35918413 PMCID: PMC9346008 DOI: 10.1038/s41598-022-17080-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/20/2022] [Indexed: 11/09/2022] Open
Abstract
Eukaryotes express a multi-component fatty acid elongase to produce very long chain fatty acids (VLCFAs), which are building blocks of diverse lipids. Elongation is achieved by cyclical iteration of four reactions, the first of which generates a new carbon-carbon bond, elongating the acyl-chain. This reaction is catalyzed by either ELONGATION DEFECTIVE LIKE (ELO) or 3-ketoacyl-CoA synthase (KCS) enzymes. Whereas plants express both ELO and KCS enzymes, other eukaryotes express only ELOs. We explored the Zea mays KCS enzymatic redundancies by expressing each of the 26 isozymes in yeast strains that lacked endogenous ELO isozymes. Expression of the 26 maize KCS isozymes in wild-type, scelo2 or scelo3 single mutants did not affect VLCFA profiles. However, a complementation screen of each of the 26 KCS isozymes revealed five that were capable of complementing the synthetically lethal scelo2; scelo3 double mutant. These rescued strains express novel VLCFA profiles reflecting the different catalytic capabilities of the KCS isozymes. These novel strains offer a platform to explore the relationship between VLCFA profiles and cellular physiology.
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Affiliation(s)
- Kenna E Stenback
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School Blavatnik Institute, Boston, MA, USA
| | - Kayla S Flyckt
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.,Corteva Agriscience, Johnston, IA, USA
| | - Trang Hoang
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.,Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Alexis A Campbell
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA.,School of Education, Iowa State University, Ames, IA, USA
| | - Basil J Nikolau
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA. .,Center for Metabolic Biology, Iowa State University, Ames, IA, USA.
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21
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Wu D, Zhang Y, Tang Z, Chen X, Ling X, Li L, Cao W, Zheng W, Wu J, Tang H, Liu X, Luo X, Liu T. Creation of a Yeast Strain with Co‐Translationally Acylated Nucleosomes. Angew Chem Int Ed Engl 2022; 61:e202205570. [DOI: 10.1002/anie.202205570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Dan Wu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yunfeng Zhang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhiheng Tang
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaoxu Chen
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Longtu Li
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Wenbing Cao
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Wei Zheng
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Jiale Wu
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Hongting Tang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Xiaoyun Liu
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- CAS Key Laboratory of Quantitative Engineering Biology Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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22
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Boonekamp FJ, Knibbe E, Vieira-Lara MA, Wijsman M, Luttik MAH, van Eunen K, Ridder MD, Bron R, Almonacid Suarez AM, van Rijn P, Wolters JC, Pabst M, Daran JM, Bakker BM, Daran-Lapujade P. Full humanization of the glycolytic pathway in Saccharomyces cerevisiae. Cell Rep 2022; 39:111010. [PMID: 35767960 DOI: 10.1016/j.celrep.2022.111010] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/03/2022] [Accepted: 06/07/2022] [Indexed: 12/22/2022] Open
Abstract
Although transplantation of single genes in yeast plays a key role in elucidating gene functionality in metazoans, technical challenges hamper humanization of full pathways and processes. Empowered by advances in synthetic biology, this study demonstrates the feasibility and implementation of full humanization of glycolysis in yeast. Single gene and full pathway transplantation revealed the remarkable conservation of glycolytic and moonlighting functions and, combined with evolutionary strategies, brought to light context-dependent responses. Human hexokinase 1 and 2, but not 4, required mutations in their catalytic or allosteric sites for functionality in yeast, whereas hexokinase 3 was unable to complement its yeast ortholog. Comparison with human tissues cultures showed preservation of turnover numbers of human glycolytic enzymes in yeast and human cell cultures. This demonstration of transplantation of an entire essential pathway paves the way for establishment of species-, tissue-, and disease-specific metazoan models.
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Affiliation(s)
- Francine J Boonekamp
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Ewout Knibbe
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Marcel A Vieira-Lara
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Melanie Wijsman
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Karen van Eunen
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Maxime den Ridder
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Reinier Bron
- Department of Biomedical Engineering-FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ana Maria Almonacid Suarez
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Patrick van Rijn
- Department of Biomedical Engineering-FB40, W.J. Kolff Institute for Biomedical Engineering and Materials Science-FB41, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Justina C Wolters
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands
| | - Barbara M Bakker
- Laboratory of Pediatrics, Section Systems Medicine and Metabolic Signalling, Center for Liver, Digestive and Metabolic Disease, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pascale Daran-Lapujade
- Department of Biotechnology, Delft University of Technology, Van Der Maasweg 9, 2629 Delft, the Netherlands.
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23
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Genome-Wide Analysis of Yeast Metabolic Cycle through Metabolic Network Models Reveals Superiority of Integrated ATAC-seq Data over RNA-seq Data. mSystems 2022; 7:e0134721. [PMID: 35695574 PMCID: PMC9239220 DOI: 10.1128/msystems.01347-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Saccharomyces cerevisiae undergoes robust oscillations to regulate its physiology for adaptation and survival under nutrient-limited conditions. Environmental cues can induce rhythmic metabolic alterations in order to facilitate the coordination of dynamic metabolic behaviors. Of such metabolic processes, the yeast metabolic cycle enables adaptation of the cells to varying nutritional status through oscillations in gene expression and metabolite production levels. In this process, yeast metabolism is altered between diverse cellular states based on changing oxygen consumption levels: quiescent (reductive charging [RC]), growth (oxidative [OX]), and proliferation (reductive building [RB]) phases. We characterized metabolic alterations during the yeast metabolic cycle using a variety of approaches. Gene expression levels are widely used for condition-specific metabolic simulations, whereas the use of epigenetic information in metabolic modeling is still limited despite the clear relationship between epigenetics and metabolism. This prompted us to investigate the contribution of epigenomic information to metabolic predictions for progression of the yeast metabolic cycle. In this regard, we determined altered pathways through the prediction of regulated reactions and corresponding model genes relying on differential chromatin accessibility levels. The predicted metabolic alterations were confirmed via data analysis and literature. We subsequently utilized RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) data sets in the contextualization of the yeast model. The use of ATAC-seq data considerably enhanced the predictive capability of the model. To the best of our knowledge, this is the first attempt to use genome-wide chromatin accessibility data in metabolic modeling. The preliminary results showed that epigenomic data sets can pave the way for more accurate metabolic simulations. IMPORTANCE Dynamic chromatin organization mediates the emergence of condition-specific phenotypes in eukaryotic organisms. Saccharomyces cerevisiae can alter its metabolic profile via regulation of genome accessibility and robust transcriptional oscillations under nutrient-limited conditions. Thus, both epigenetic information and transcriptomic information are crucial in the understanding of condition-specific metabolic behavior in this organism. Based on genome-wide alterations in chromatin accessibility and transcription, we investigated the yeast metabolic cycle, which is a remarkable example of coordinated and dynamic yeast behavior. In this regard, we assessed the use of ATAC-seq and RNA-seq data sets in condition-specific metabolic modeling. To our knowledge, this is the first attempt to use chromatin accessibility data in the reconstruction of context-specific metabolic models, despite the extensive use of transcriptomic data. As a result of comparative analyses, we propose that the incorporation of epigenetic information is a promising approach in the accurate prediction of metabolic dynamics.
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24
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Wu D, Zhang Y, Tang Z, Chen X, Ling X, Li L, Cao W, Zheng W, Wu J, Tang H, Liu X, Luo X, Liu T. Creation of a Yeast Strain with Co‐Translationally Acylated Nucleosomes. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dan Wu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Yunfeng Zhang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Zhiheng Tang
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaoxu Chen
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xinyu Ling
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Longtu Li
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Wenbing Cao
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Wei Zheng
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Jiale Wu
- Key Laboratory of Protein and Plant Gene Research School of Life Sciences and Peking-Tsinghua Center for Life Science Peking University Beijing 100871 China
| | - Hongting Tang
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Xiaoyun Liu
- Department of Microbiology School of Basic Medical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
- CAS Key Laboratory of Quantitative Engineering Biology Institute of Synthetic Biology Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China
| | - Tao Liu
- State Key Laboratory of Natural and Biomimetic Drugs Chemical Biology Center Department of Molecular and Cellular, Pharmacology, Pharmaceutical Sciences Peking University 38 Xueyuan Road, Haidian District Beijing 100191 China
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25
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Kachroo AH, Vandeloo M, Greco BM, Abdullah M. Humanized yeast to model human biology, disease and evolution. Dis Model Mech 2022; 15:275614. [PMID: 35661208 PMCID: PMC9194483 DOI: 10.1242/dmm.049309] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
For decades, budding yeast, a single-cellular eukaryote, has provided remarkable insights into human biology. Yeast and humans share several thousand genes despite morphological and cellular differences and over a billion years of separate evolution. These genes encode critical cellular processes, the failure of which in humans results in disease. Although recent developments in genome engineering of mammalian cells permit genetic assays in human cell lines, there is still a need to develop biological reagents to study human disease variants in a high-throughput manner. Many protein-coding human genes can successfully substitute for their yeast equivalents and sustain yeast growth, thus opening up doors for developing direct assays of human gene function in a tractable system referred to as 'humanized yeast'. Humanized yeast permits the discovery of new human biology by measuring human protein activity in a simplified organismal context. This Review summarizes recent developments showing how humanized yeast can directly assay human gene function and explore variant effects at scale. Thus, by extending the 'awesome power of yeast genetics' to study human biology, humanizing yeast reinforces the high relevance of evolutionarily distant model organisms to explore human gene evolution, function and disease.
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26
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Singh NP, Krumlauf R. Diversification and Functional Evolution of HOX Proteins. Front Cell Dev Biol 2022; 10:798812. [PMID: 35646905 PMCID: PMC9136108 DOI: 10.3389/fcell.2022.798812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 04/08/2022] [Indexed: 01/07/2023] Open
Abstract
Gene duplication and divergence is a major contributor to the generation of morphological diversity and the emergence of novel features in vertebrates during evolution. The availability of sequenced genomes has facilitated our understanding of the evolution of genes and regulatory elements. However, progress in understanding conservation and divergence in the function of proteins has been slow and mainly assessed by comparing protein sequences in combination with in vitro analyses. These approaches help to classify proteins into different families and sub-families, such as distinct types of transcription factors, but how protein function varies within a gene family is less well understood. Some studies have explored the functional evolution of closely related proteins and important insights have begun to emerge. In this review, we will provide a general overview of gene duplication and functional divergence and then focus on the functional evolution of HOX proteins to illustrate evolutionary changes underlying diversification and their role in animal evolution.
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Affiliation(s)
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, United States
- Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, KS, United States
- *Correspondence: Robb Krumlauf,
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27
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Fukushima Y, Hatazawa S, Hirai S, Kujirai T, Ehara H, Sekine SI, Takizawa Y, Kurumizaka H. Structural and biochemical analyses of the nucleosome containing Komagataella pastoris histones. J Biochem 2022; 172:79-88. [PMID: 35485963 DOI: 10.1093/jb/mvac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Komagataella pastoris is a methylotrophic yeast that is commonly used as a host cell for protein production. In the present study, we reconstituted the nucleosome with K. pastoris histones, and determined the structure of the nucleosome core particle by cryogenic electron microscopy. In the K. pastoris nucleosome, the histones form an octamer, and the DNA is left-handedly wrapped around it. Micrococcal nuclease assays revealed that the DNA ends of the K. pastoris nucleosome are somewhat more accessible, as compared to those of the human nucleosome. In vitro transcription assays demonstrated that the K. pastoris nucleosome is transcribed by the K. pastoris RNA polymerase II more efficiently than the human nucleosome, while the RNA polymerase II pausing positions of the K. pastoris nucleosome are the same as those of the human nucleosome. These results suggested that the DNA end flexibility may enhance the transcription efficiency in the nucleosome, but minimally affect the nucleosomal pausing positions of RNA polymerase II.
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Affiliation(s)
- Yutaro Fukushima
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Suguru Hatazawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Seiya Hirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Haruhiko Ehara
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shun-Ichi Sekine
- RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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28
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Khan SU, Khan MU, Kalsoom F, Khan MI, Gao S, Unar A, Zubair M, Bilal M. Mechanisms of gene regulation by histone degradation in adaptation of yeast: an overview of recent advances. Arch Microbiol 2022; 204:287. [PMID: 35482104 DOI: 10.1007/s00203-022-02897-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/12/2022] [Accepted: 04/04/2022] [Indexed: 02/07/2023]
Abstract
Histones are important component of eukaryotic cells chromatin and consist of arginine and lysine residues. Histones play an important role in the protection of DNA. Their contents significantly affect high-level chromatin structure formation, gene expression, DNA replication, and other important life activities. Protein degradation is an important regulatory mechanism of histone content. Recent studies have revealed that modification of amino acid sequence is directly related to histone breakdown. In addition, histone degradation is closely related to covalent modifications, such as ubiquitination and acetylation, which are considered to be driving factors in gene regulation. Gene regulation is an important mechanism in adaptation to the environment and survival of species. With the introduction of highly efficient technology, various mutations in histones have been identified in yeast. In the field of epigenetics and the transmission of chromatin states, two widely used model organisms are the budding yeast Saccharomyces cerevisiae and Schizosaccharomyces pombe. Higher eukaryotes can use their silent loci to maintain their epigenetic states and providing the base to investigate mechanisms underlying development. Therfore, both species have contributed a plethora of information on these mechanisms in both yeast and higher eukaryotes. This study focuses on the role of histone modifications in controlling telomeric silencing in Saccharomyces cerevisiae and centromeric silencing in S. pombe as examples of genetic loci that demonstrate epigenetic inheritance. In view of recent advances, this review focuses on the post-translational modification of histone amino acid residues and reviews the relationship between histone degradation and amino acid residue modification.
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Affiliation(s)
- Safir Ullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Munir Ullah Khan
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Fadia Kalsoom
- Department of Microbiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Muhammad Imran Khan
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Hefei National Laboratory for Physical Sciences at Microscale and the Center for Biomedical Engineering, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Department of Pathology, District headquarters hospital, Jhang, 35200, Punjab Province, Islamic Republic of Pakistan.
| | - Shuang Gao
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Ahsanullah Unar
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Muhammad Zubair
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, People's Republic of China.
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29
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Iida T, Kobayashi T. Establishment of an "in saccharo" experimental system. Genes Genet Syst 2021; 96:107-118. [PMID: 34108346 DOI: 10.1266/ggs.21-00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Many proteins form complexes that function in reaction pathways. Therefore, to understand protein function, it is necessary to reconstitute complexes and pathways in vitro. However, it is not straightforward to achieve full activity in reconstituted systems. To address this problem, we present a yeast system named "in saccharo" analysis, which uses budding yeast for simultaneous expression and analysis of many kinds of non-host proteins, such as human proteins. For this purpose, vectors that can accommodate many genes are required. Here, we describe the construction of a chromosome vector by insertion of unique barcode sequences (BCs) into the ribosomal RNA gene repeat (rDNA). Each unit of the rDNA has a BC that is used as the target for integration of an external gene. Because rDNA is naturally capable of maintaining many repetitive copies, the vector is expected to retain the numerous external genes that may be required for reconstitution of functional protein complexes and reaction pathways. Consistent with this prediction, we were able to clone three human genes that form the RNA silencing pathway, which has no functional equivalent in budding yeast, and to demonstrate functionality in this in saccharo analysis system.
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Affiliation(s)
- Tetsushi Iida
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences (IQB), The University of Tokyo
| | - Takehiko Kobayashi
- Laboratory of Genome Regeneration, Institute for Quantitative Biosciences (IQB), The University of Tokyo.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo
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30
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Oncohistone mutations enhance chromatin remodeling and alter cell fates. Nat Chem Biol 2021; 17:403-411. [PMID: 33649601 PMCID: PMC8174649 DOI: 10.1038/s41589-021-00738-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022]
Abstract
Whole genome sequencing data mining efforts have revealed numerous histone mutations in a wide range of cancer types. These occur in all four core histones in both the tail and globular domains and remain largely uncharacterized. Here we used two high-throughput approaches, a DNA-barcoded mononucleosome library and a humanized yeast library, to profile the biochemical and cellular effects of these mutations. We identified cancer-associated mutations in the histone globular domains that enhance fundamental chromatin remodeling processes, histone exchange and nucleosome sliding, and are lethal in yeast. In mammalian cells, these mutations upregulate cancer-associated gene pathways and inhibit cellular differentiation by altering expression of lineage-specific transcription factors. This work represents a comprehensive functional analysis of the histone mutational landscape in human cancers and leads to a model in which histone mutations that perturb nucleosome remodeling may contribute to disease development and/or progression.
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31
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Valencia-Sánchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ. Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation. Science 2021; 371:371/6527/eabc6663. [PMID: 33479126 DOI: 10.1126/science.abc6663] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/27/2020] [Indexed: 12/30/2022]
Abstract
Dot1 (disruptor of telomeric silencing-1), the histone H3 lysine 79 (H3K79) methyltransferase, is conserved throughout evolution, and its deregulation is found in human leukemias. Here, we provide evidence that acetylation of histone H4 allosterically stimulates yeast Dot1 in a manner distinct from but coordinating with histone H2B ubiquitination (H2BUb). We further demonstrate that this stimulatory effect is specific to acetylation of lysine 16 (H4K16ac), a modification central to chromatin structure. We provide a mechanism of this histone cross-talk and show that H4K16ac and H2BUb play crucial roles in H3K79 di- and trimethylation in vitro and in vivo. These data reveal mechanisms that control H3K79 methylation and demonstrate how H4K16ac, H3K79me, and H2BUb function together to regulate gene transcription and gene silencing to ensure optimal maintenance and propagation of an epigenetic state.
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Affiliation(s)
- Marco Igor Valencia-Sánchez
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Pablo De Ioannes
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Miao Wang
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - David M Truong
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA
| | - Rachel Lee
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jef D Boeke
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
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32
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Nucleosome Positioning and Spacing: From Mechanism to Function. J Mol Biol 2021; 433:166847. [PMID: 33539878 DOI: 10.1016/j.jmb.2021.166847] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023]
Abstract
Eukaryotes associate their genomes with histone proteins, forming nucleosome particles. Nucleosomes regulate and protect the genetic information. They often assemble into evenly spaced arrays of nucleosomes. These regular nucleosome arrays cover significant portions of the genome, in particular over genes. The presence of these evenly spaced nucleosome arrays is highly conserved throughout the entire eukaryotic domain. Here, we review the mechanisms behind the establishment of this primary structure of chromatin with special emphasis on the biogenesis of evenly spaced nucleosome arrays. We highlight the roles that transcription, nucleosome remodelers, DNA sequence, and histone density play towards the formation of evenly spaced nucleosome arrays and summarize our current understanding of their cellular functions. We end with key unanswered questions that remain to be explored to obtain an in-depth understanding of the biogenesis and function of the nucleosome landscape.
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33
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Ray-Gallet D, Almouzni G. The Histone H3 Family and Its Deposition Pathways. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1283:17-42. [PMID: 33155135 DOI: 10.1007/978-981-15-8104-5_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Within the cell nucleus, the organization of the eukaryotic DNA into chromatin uses histones as components of its building block, the nucleosome. This chromatin organization contributes to the regulation of all DNA template-based reactions impacting genome function, stability, and plasticity. Histones and their variants endow chromatin with unique properties and show a distinct distribution into the genome that is regulated by dedicated deposition machineries. The histone variants have important roles during early development, cell differentiation, and chromosome segregation. Recent progress has also shed light on how mutations and transcriptional deregulation of these variants participate in tumorigenesis. In this chapter we introduce the organization of the genome in chromatin with a focus on the basic unit, the nucleosome, which contains histones as the major protein component. Then we review our current knowledge on the histone H3 family and its variants-in particular H3.3 and CenH3CENP-A-focusing on their deposition pathways and their dedicated histone chaperones that are key players in histone dynamics.
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Affiliation(s)
- Dominique Ray-Gallet
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France.,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France
| | - Geneviève Almouzni
- Institut Curie, PSL Research University, CNRS UMR3664, Paris, France. .,Institut Curie, Sorbonne Université, CNRS UMR3664, Paris, France.
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Formosa T, Winston F. The role of FACT in managing chromatin: disruption, assembly, or repair? Nucleic Acids Res 2020; 48:11929-11941. [PMID: 33104782 PMCID: PMC7708052 DOI: 10.1093/nar/gkaa912] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/20/2022] Open
Abstract
FACT (FAcilitates Chromatin Transcription) has long been considered to be a transcription elongation factor whose ability to destabilize nucleosomes promotes RNAPII progression on chromatin templates. However, this is just one function of this histone chaperone, as FACT also functions in DNA replication. While broadly conserved among eukaryotes and essential for viability in many organisms, dependence on FACT varies widely, with some differentiated cells proliferating normally in its absence. It is therefore unclear what the core functions of FACT are, whether they differ in different circumstances, and what makes FACT essential in some situations but not others. Here, we review recent advances and propose a unifying model for FACT activity. By analogy to DNA repair, we propose that the ability of FACT to both destabilize and assemble nucleosomes allows it to monitor and restore nucleosome integrity as part of a system of chromatin repair, in which disruptions in the packaging of DNA are sensed and returned to their normal state. The requirement for FACT then depends on the level of chromatin disruption occurring in the cell, and the cell's ability to tolerate packaging defects. The role of FACT in transcription would then be just one facet of a broader system for maintaining chromatin integrity.
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Affiliation(s)
- Tim Formosa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Fred Winston
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Schindler D. Genetic Engineering and Synthetic Genomics in Yeast to Understand Life and Boost Biotechnology. Bioengineering (Basel) 2020; 7:E137. [PMID: 33138080 PMCID: PMC7711850 DOI: 10.3390/bioengineering7040137] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/26/2020] [Accepted: 10/28/2020] [Indexed: 02/07/2023] Open
Abstract
The field of genetic engineering was born in 1973 with the "construction of biologically functional bacterial plasmids in vitro". Since then, a vast number of technologies have been developed allowing large-scale reading and writing of DNA, as well as tools for complex modifications and alterations of the genetic code. Natural genomes can be seen as software version 1.0; synthetic genomics aims to rewrite this software with "build to understand" and "build to apply" philosophies. One of the predominant model organisms is the baker's yeast Saccharomyces cerevisiae. Its importance ranges from ancient biotechnologies such as baking and brewing, to high-end valuable compound synthesis on industrial scales. This tiny sugar fungus contributed greatly to enabling humankind to reach its current development status. This review discusses recent developments in the field of genetic engineering for budding yeast S. cerevisiae, and its application in biotechnology. The article highlights advances from Sc1.0 to the developments in synthetic genomics paving the way towards Sc2.0. With the synthetic genome of Sc2.0 nearing completion, the article also aims to propose perspectives for potential Sc3.0 and subsequent versions as well as its implications for basic and applied research.
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Affiliation(s)
- Daniel Schindler
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043 Marburg, Germany; ; Tel.: +49-6421-178533
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Kim S, Park J, Kim T, Lee JS. The functional study of human proteins using humanized yeast. J Microbiol 2020; 58:343-349. [PMID: 32342338 DOI: 10.1007/s12275-020-0136-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/13/2020] [Accepted: 04/13/2020] [Indexed: 12/18/2022]
Abstract
The functional and optimal expression of genes is crucial for survival of all living organisms. Numerous experiments and efforts have been performed to reveal the mechanisms required for the functional and optimal expression of human genes. The yeast Saccharomyces cerevisiae has evolved independently of humans for billions of years. Nevertheless, S. cerevisiae has many conserved genes and expression mechanisms that are similar to those in humans. Yeast is the most commonly used model organism for studying the function and expression mechanisms of human genes because it has a relatively simple genome structure, which is easy to manipulate. Many previous studies have focused on understanding the functions and mechanisms of human proteins using orthologous genes and biological systems of yeast. In this review, we mainly introduce two recent studies that replaced human genes and nucleosomes with those of yeast. Here, we suggest that, although yeast is a relatively small eukaryotic cell, its humanization is useful for the direct study of human proteins. In addition, yeast can be used as a model organism in a broader range of studies, including drug screening.
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Affiliation(s)
- Seho Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Juhee Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Taekyung Kim
- Department of Biology Education, Pusan National University, Busan, 26241, Republic of Korea.
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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Histone variant H3.3 residue S31 is essential for Xenopus gastrulation regardless of the deposition pathway. Nat Commun 2020; 11:1256. [PMID: 32152320 PMCID: PMC7062693 DOI: 10.1038/s41467-020-15084-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 02/09/2020] [Indexed: 01/04/2023] Open
Abstract
Vertebrates exhibit specific requirements for replicative H3 and non-replicative H3.3 variants during development. To disentangle whether this involves distinct modes of deposition or unique functions once incorporated into chromatin, we combined studies in Xenopus early development with chromatin assays. Here we investigate the extent to which H3.3 mutated at residues that differ from H3.2 rescue developmental defects caused by H3.3 depletion. Regardless of the deposition pathway, only variants at residue 31-a serine that can become phosphorylated-failed to rescue endogenous H3.3 depletion. Although an alanine substitution fails to rescue H3.3 depletion, a phospho-mimic aspartate residue at position 31 rescues H3.3 function. To explore mechanisms involving H3.3 S31 phosphorylation, we identified factors attracted or repulsed by the presence of aspartate at position 31, along with modifications on neighboring residues. We propose that serine 31-phosphorylated H3.3 acts as a signaling module that stimulates the acetylation of K27, providing a chromatin state permissive to the embryonic development program.
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Hamza A, Driessen MRM, Tammpere E, O'Neil NJ, Hieter P. Cross-Species Complementation of Nonessential Yeast Genes Establishes Platforms for Testing Inhibitors of Human Proteins. Genetics 2020; 214:735-747. [PMID: 31937519 PMCID: PMC7054014 DOI: 10.1534/genetics.119.302971] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/13/2020] [Indexed: 01/09/2023] Open
Abstract
Cross-species complementation can be used to generate humanized yeast, which is a valuable resource with which to model and study human biology. Humanized yeast can be used as an in vivo platform to screen for chemical inhibition of human protein drug targets. To this end, we report the systematic complementation of nonessential yeast genes implicated in chromosome instability (CIN) with their human homologs. We identified 20 human-yeast complementation pairs that are replaceable in 44 assays that test rescue of chemical sensitivity and/or CIN defects. We selected a human-yeast pair (hFEN1/yRAD27), which is frequently overexpressed in cancer and is an anticancer therapeutic target, to perform in vivo inhibitor assays using a humanized yeast cell-based platform. In agreement with published in vitro assays, we demonstrate that HU-based PTPD is a species-specific hFEN1 inhibitor. In contrast, another reported hFEN1 inhibitor, the arylstibonic acid derivative NSC-13755, was determined to have off-target effects resulting in a synthetic lethal phenotype with yRAD27-deficient strains. Our study expands the list of human-yeast complementation pairs to nonessential genes by defining novel cell-based assays that can be utilized as a broad resource to study human drug targets.
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Affiliation(s)
- Akil Hamza
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Maureen R M Driessen
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Erik Tammpere
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Nigel J O'Neil
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
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Agmon N, Temple J, Tang Z, Schraink T, Baron M, Chen J, Mita P, Martin JA, Tu BP, Yanai I, Fenyö D, Boeke JD. Phylogenetic debugging of a complete human biosynthetic pathway transplanted into yeast. Nucleic Acids Res 2020; 48:486-499. [PMID: 31745563 PMCID: PMC7145547 DOI: 10.1093/nar/gkz1098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 11/04/2019] [Accepted: 11/16/2019] [Indexed: 12/30/2022] Open
Abstract
Cross-species pathway transplantation enables insight into a biological process not possible through traditional approaches. We replaced the enzymes catalyzing the entire Saccharomyces cerevisiae adenine de novo biosynthesis pathway with the human pathway. While the 'humanized' yeast grew in the absence of adenine, it did so poorly. Dissection of the phenotype revealed that PPAT, the human ortholog of ADE4, showed only partial function whereas all other genes complemented fully. Suppressor analysis revealed other pathways that play a role in adenine de-novo pathway regulation. Phylogenetic analysis pointed to adaptations of enzyme regulation to endogenous metabolite level 'setpoints' in diverse organisms. Using DNA shuffling, we isolated specific amino acids combinations that stabilize the human protein in yeast. Thus, using adenine de novo biosynthesis as a proof of concept, we suggest that the engineering methods used in this study as well as the debugging strategies can be utilized to transplant metabolic pathway from any origin into yeast.
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Affiliation(s)
- Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jasmine Temple
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Zuojian Tang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tobias Schraink
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Maayan Baron
- Institute for Computational Medicine and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jun Chen
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Paolo Mita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - James A Martin
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Benjamin P Tu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Itai Yanai
- Institute for Computational Medicine and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
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Yeast Models for Amyloids and Prions: Environmental Modulation and Drug Discovery. Molecules 2019; 24:molecules24183388. [PMID: 31540362 PMCID: PMC6767215 DOI: 10.3390/molecules24183388] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/10/2019] [Accepted: 09/16/2019] [Indexed: 12/11/2022] Open
Abstract
Amyloids are self-perpetuating protein aggregates causing neurodegenerative diseases in mammals. Prions are transmissible protein isoforms (usually of amyloid nature). Prion features were recently reported for various proteins involved in amyloid and neural inclusion disorders. Heritable yeast prions share molecular properties (and in the case of polyglutamines, amino acid composition) with human disease-related amyloids. Fundamental protein quality control pathways, including chaperones, the ubiquitin proteasome system and autophagy are highly conserved between yeast and human cells. Crucial cellular proteins and conditions influencing amyloids and prions were uncovered in the yeast model. The treatments available for neurodegenerative amyloid-associated diseases are few and their efficiency is limited. Yeast models of amyloid-related neurodegenerative diseases have become powerful tools for high-throughput screening for chemical compounds and FDA-approved drugs that reduce aggregation and toxicity of amyloids. Although some environmental agents have been linked to certain amyloid diseases, the molecular basis of their action remains unclear. Environmental stresses trigger amyloid formation and loss, acting either via influencing intracellular concentrations of the amyloidogenic proteins or via heterologous inducers of prions. Studies of environmental and physiological regulation of yeast prions open new possibilities for pharmacological intervention and/or prophylactic procedures aiming on common cellular systems rather than the properties of specific amyloids.
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41
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Haase MAB, Truong DM, Boeke JD. Superloser: A Plasmid Shuffling Vector for Saccharomyces cerevisiae with Exceedingly Low Background. G3 (BETHESDA, MD.) 2019; 9:2699-2707. [PMID: 31213518 PMCID: PMC6686923 DOI: 10.1534/g3.119.400325] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 06/14/2019] [Indexed: 11/18/2022]
Abstract
Here we report a new plasmid shuffle vector for forcing budding yeast (Saccharomyces cerevisiae) to incorporate a new genetic pathway in place of a native pathway - even an essential one - while maintaining low false positive rates (less than 1 in 108 per cell). This plasmid, dubbed "Superloser," was designed with reduced sequence similarity to commonly used yeast plasmids (i.e., pRS400 series) to limit recombination, a process that in our experience leads to retention of the yeast gene(s) instead of the desired gene(s). In addition, Superloser utilizes two orthogonal copies of the counter-selectable marker URA3 to reduce spontaneous 5-fluoroorotic acid resistance. Finally, the CEN/ARS sequence is fused to the GAL1-10 promoter, which disrupts plasmid segregation in the presence of the sugar galactose, causing Superloser to rapidly be removed from a population of cells. We show one proof-of-concept shuffling experiment: swapping yeast's core histones out for their human counterparts. Superloser is especially useful for forcing yeast to use highly unfavorable genes, such as human histones, as it enables plating a large number of cells (1.4x109) on a single 10 cm petri dish while maintaining a very low background. Therefore, Superloser is a useful tool for yeast geneticists to effectively shuffle low viability genes and/or pathways in yeast that may arise in as few as 1 in 108 cells.
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Affiliation(s)
- Max A B Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, 10016 and
- Sackler Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY, 10016
| | - David M Truong
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, 10016 and
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, 10016 and
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42
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Tackling Cancer with Yeast-Based Technologies. Trends Biotechnol 2019; 37:592-603. [DOI: 10.1016/j.tibtech.2018.11.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/24/2018] [Accepted: 11/30/2018] [Indexed: 12/19/2022]
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Ravikumar A, Arzumanyan GA, Obadi MKA, Javanpour AA, Liu CC. Scalable, Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds. Cell 2018; 175:1946-1957.e13. [PMID: 30415839 PMCID: PMC6343851 DOI: 10.1016/j.cell.2018.10.021] [Citation(s) in RCA: 146] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/16/2018] [Accepted: 10/04/2018] [Indexed: 11/17/2022]
Abstract
Directed evolution is a powerful approach for engineering biomolecules and understanding adaptation. However, experimental strategies for directed evolution are notoriously labor intensive and low throughput, limiting access to demanding functions, multiple functions in parallel, and the study of molecular evolution in replicate. We report OrthoRep, an orthogonal DNA polymerase-plasmid pair in yeast that stably mutates ∼100,000-fold faster than the host genome in vivo, exceeding the error threshold of genomic replication that causes single-generation extinction. User-defined genes in OrthoRep continuously and rapidly evolve through serial passaging, a highly straightforward and scalable process. Using OrthoRep, we evolved drug-resistant malarial dihydrofolate reductases (DHFRs) in 90 independent replicates. We uncovered a more complex fitness landscape than previously realized, including common adaptive trajectories constrained by epistasis, rare outcomes that avoid a frequent early adaptive mutation, and a suboptimal fitness peak that occasionally traps evolving populations. OrthoRep enables a new paradigm of routine, high-throughput evolution of biomolecular and cellular function.
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Affiliation(s)
- Arjun Ravikumar
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Garri A Arzumanyan
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Muaeen K A Obadi
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Alex A Javanpour
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Chang C Liu
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA; Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA.
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Hofer S, Kainz K, Zimmermann A, Bauer MA, Pendl T, Poglitsch M, Madeo F, Carmona-Gutierrez D. Studying Huntington's Disease in Yeast: From Mechanisms to Pharmacological Approaches. Front Mol Neurosci 2018; 11:318. [PMID: 30233317 PMCID: PMC6131589 DOI: 10.3389/fnmol.2018.00318] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disorder that leads to progressive neuronal loss, provoking impaired motor control, cognitive decline, and dementia. So far, HD remains incurable, and available drugs are effective only for symptomatic management. HD is caused by a mutant form of the huntingtin protein, which harbors an elongated polyglutamine domain and is highly prone to aggregation. However, many aspects underlying the cytotoxicity of mutant huntingtin (mHTT) remain elusive, hindering the efficient development of applicable interventions to counteract HD. An important strategy to obtain molecular insights into human disorders in general is the use of eukaryotic model organisms, which are easy to genetically manipulate and display a high degree of conservation regarding disease-relevant cellular processes. The budding yeast Saccharomyces cerevisiae has a long-standing and successful history in modeling a plethora of human maladies and has recently emerged as an effective tool to study neurodegenerative disorders, including HD. Here, we summarize some of the most important contributions of yeast to HD research, specifically concerning the elucidation of mechanistic features of mHTT cytotoxicity and the potential of yeast as a platform to screen for pharmacological agents against HD.
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Affiliation(s)
- Sebastian Hofer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Katharina Kainz
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Andreas Zimmermann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Maria A. Bauer
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Tobias Pendl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Michael Poglitsch
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Frank Madeo
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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Kuznetsov VI, Haws SA, Fox CA, Denu JM. General method for rapid purification of native chromatin fragments. J Biol Chem 2018; 293:12271-12282. [PMID: 29794135 PMCID: PMC6078465 DOI: 10.1074/jbc.ra118.002984] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/10/2018] [Indexed: 11/06/2022] Open
Abstract
Biochemical, proteomic, and epigenetic studies of chromatin rely on the ability to efficiently isolate native nucleosomes in high yield and purity. However, isolation of native chromatin suitable for many downstream experiments remains a challenging task. This is especially true for the budding yeast Saccharomyces cerevisiae, which continues to serve as an important model organism for the study of chromatin structure and function. Here, we developed a time- and cost-efficient universal protocol for isolation of native chromatin fragments from yeast, insect, and mammalian cells. The resulting protocol preserves histone posttranslational modification in the native chromatin state and is applicable for both parallel multisample spin-column purification and large-scale isolation. This protocol is based on the efficient and stable purification of polynucleosomes and features a combination of optimized cell lysis and purification conditions, three options for chromatin fragmentation, and a novel ion-exchange chromatographic purification strategy. The procedure will aid chromatin researchers interested in isolating native chromatin material for biochemical studies and serve as a mild, acid- and detergent-free sample preparation method for MS analysis.
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Affiliation(s)
- Vyacheslav I Kuznetsov
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715; Wisconsin Institute for Discovery, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715
| | - Spencer A Haws
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715; Wisconsin Institute for Discovery, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715
| | - Catherine A Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715.
| | - John M Denu
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715; Wisconsin Institute for Discovery, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715; Morgridge Institute for Research, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715.
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46
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Humanized yeast—erasing 1.3 billion years of evolution. Nat Methods 2018. [DOI: 10.1038/nmeth.4598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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