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Hamali B, Amine AAA, Al-Sady B. Regulation of the heterochromatin spreading reaction by trans-acting factors. Open Biol 2023; 13:230271. [PMID: 37935357 PMCID: PMC10645111 DOI: 10.1098/rsob.230271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 10/03/2023] [Indexed: 11/09/2023] Open
Abstract
Heterochromatin is a gene-repressive protein-nucleic acid ultrastructure that is initially nucleated by DNA sequences. However, following nucleation, heterochromatin can then propagate along the chromatin template in a sequence-independent manner in a reaction termed spreading. At the heart of this process are enzymes that deposit chemical information on chromatin, which attracts the factors that execute chromatin compaction and transcriptional or co/post-transcriptional gene silencing. Given that these enzymes deposit guiding chemical information on chromatin they are commonly termed 'writers'. While the processes of nucleation and central actions of writers have been extensively studied and reviewed, less is understood about how the spreading process is regulated. We discuss how the chromatin substrate is prepared for heterochromatic spreading, and how trans-acting factors beyond writer enzymes regulate it. We examine mechanisms by which trans-acting factors in Suv39, PRC2, SETDB1 and SIR writer systems regulate spreading of the respective heterochromatic marks across chromatin. While these systems are in some cases evolutionarily and mechanistically quite distant, common mechanisms emerge which these trans-acting factors exploit to tune the spreading reaction.
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Affiliation(s)
- Bulut Hamali
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
- College of Dentistry, The Ohio State University, Columbus, OH, USA
| | - Ahmed A A Amine
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA 94143, USA
- The G. W. Hooper Foundation, San Francisco, CA 94143, USA
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Hsu P, Cheng Y, Liao C, Litan RRR, Jhou Y, Opoc FJG, Amine AAA, Leu J. Rapid evolutionary repair by secondary perturbation of a primary disrupted transcriptional network. EMBO Rep 2023; 24:e56019. [PMID: 37009824 PMCID: PMC10240213 DOI: 10.15252/embr.202256019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
The discrete steps of transcriptional rewiring have been proposed to occur neutrally to ensure steady gene expression under stabilizing selection. A conflict-free switch of a regulon between regulators may require an immediate compensatory evolution to minimize deleterious effects. Here, we perform an evolutionary repair experiment on the Lachancea kluyveri yeast sef1Δ mutant using a suppressor development strategy. Complete loss of SEF1 forces cells to initiate a compensatory process for the pleiotropic defects arising from misexpression of TCA cycle genes. Using different selective conditions, we identify two adaptive loss-of-function mutations of IRA1 and AZF1. Subsequent analyses show that Azf1 is a weak transcriptional activator regulated by the Ras1-PKA pathway. Azf1 loss-of-function triggers extensive gene expression changes responsible for compensatory, beneficial, and trade-off phenotypes. The trade-offs can be alleviated by higher cell density. Our results not only indicate that secondary transcriptional perturbation provides rapid and adaptive mechanisms potentially stabilizing the initial stage of transcriptional rewiring but also suggest how genetic polymorphisms of pleiotropic mutations could be maintained in the population.
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Affiliation(s)
- Po‐Chen Hsu
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | - Yu‐Hsuan Cheng
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
- Present address:
Morgridge Institute for ResearchMadisonWIUSA
- Present address:
Howard Hughes Medical InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Chia‐Wei Liao
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | | | - Yu‐Ting Jhou
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
| | | | | | - Jun‐Yi Leu
- Institute of Molecular BiologyAcademia SinicaTaipeiTaiwan
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Amine AAA, Liao CW, Hsu PC, Opoc FJG, Leu JY. Experimental evolution improves mitochondrial genome quality control in Saccharomyces cerevisiae and extends its replicative lifespan. Curr Biol 2021; 31:3663-3670.e4. [PMID: 34192514 DOI: 10.1016/j.cub.2021.06.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/18/2021] [Accepted: 06/09/2021] [Indexed: 01/22/2023]
Abstract
The mitochondrion is an ancient endosymbiotic organelle that performs many essential functions in eukaryotic cells.1-3 Mitochondrial impairment often results in physiological defects or diseases.2-8 Since most mitochondrial genes have been copied into the nuclear genome during evolution,9 the regulatory and interaction mechanisms between the mitochondrial and nuclear genomes are very complex. Multiple mechanisms, including antioxidant, DNA repair, mitophagy, and mitochondrial biogenesis pathways, have been shown to monitor the quality and quantity of mitochondria.10-12 Nonetheless, it remains unclear if these pathways can be further modified to enhance mitochondrial stability. Previously, experimental evolution has been used to adapt cells to novel growth conditions. By analyzing the resulting evolved populations, insights have been gained into the underlying molecular mechanisms.13 Here, we experimentally evolved yeast cells under conditions that selected for efficient respiration while continuously assaulting the mitochondrial genome (mtDNA) with ethidium bromide (EtBr). We found that the ability to maintain functional mtDNA was enhanced in most of the evolved lines when challenged with mtDNA-damaging reagents. We identified mutations of the mitochondrial NADH dehydrogenase NDE1 in most of the evolved lines, but other pathways are also involved. Finally, we show that cells displaying enhanced mtDNA retention also exhibit a prolonged replicative lifespan. Our work reveals potential evolutionary trajectories by which cells can maintain functional mitochondria in response to mtDNA stress, as well as the physiological implications of such adaptations.
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Affiliation(s)
- Ahmed A A Amine
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei 11529, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Wei Liao
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Po-Chen Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Florica J G Opoc
- Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Jun-Yi Leu
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei 11529, Taiwan; Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan.
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Hsu PC, Lu TC, Hung PH, Jhou YT, Amine AAA, Liao CW, Leu JY. Plastic rewiring of Sef1 transcriptional networks and the potential of non-functional transcription factor binding in facilitating adaptive evolution. Mol Biol Evol 2021; 38:4732-4747. [PMID: 34175931 PMCID: PMC8557406 DOI: 10.1093/molbev/msab192] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Prior and extensive plastic rewiring of a transcriptional network, followed by a functional switch of the conserved transcriptional regulator, can shape the evolution of a new network with diverged functions. The presence of three distinct iron regulatory systems in fungi that use orthologous transcriptional regulators suggests that these systems evolved in that manner. Orthologs of the transcriptional activator Sef1 are believed to be central to how iron regulatory systems developed in fungi, involving gene gain, plastic network rewiring, and switches in regulatory function. We show that, in the protoploid yeast Lachancea kluyveri, plastic rewiring of the L. kluyveri Sef1 (Lk-Sef1) network, together with a functional switch, enabled Lk-Sef1 to regulate TCA cycle genes, unlike Candida albicans Sef1 that mainly regulates iron-uptake genes. Moreover, we observed pervasive nonfunctional binding of Sef1 to its target genes. Enhancing Lk-Sef1 activity resuscitated the corresponding transcriptional network, providing immediate adaptive benefits in changing environments. Our study not only sheds light on the evolution of Sef1-centered transcriptional networks but also shows the adaptive potential of nonfunctional transcription factor binding for evolving phenotypic novelty and diversity.
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Affiliation(s)
- Po-Chen Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Tzu-Chiao Lu
- Research Center for Healthy Aging and Institute of New Drug Development, China Medical University, Taichung, Taiwan, ROC.,Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan, ROC
| | - Po-Hsiang Hung
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan, ROC
| | - Yu-Ting Jhou
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Ahmed A A Amine
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC.,Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chia-Wei Liao
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC
| | - Jun-Yi Leu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, ROC.,Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan, ROC.,Molecular and Cell Biology Program, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan, ROC
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Noor AM, ElMardi KA, Abdelgader TM, Patil AP, Amine AAA, Bakhiet S, Mukhtar MM, Snow RW. Malaria risk mapping for control in the republic of Sudan. Am J Trop Med Hyg 2012; 87:1012-1021. [PMID: 23033400 PMCID: PMC3516068 DOI: 10.4269/ajtmh.2012.12-0390] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 08/09/2012] [Indexed: 11/19/2022] Open
Abstract
Evidence shows that malaria risk maps are rarely tailored to address national control program ambitions. Here, we generate a malaria risk map adapted for malaria control in Sudan. Community Plasmodium falciparum parasite rate (PfPR) data from 2000 to 2010 were assembled and were standardized to 2-10 years of age (PfPR(2-10)). Space-time Bayesian geostatistical methods were used to generate a map of malaria risk for 2010. Surfaces of aridity, urbanization, irrigation schemes, and refugee camps were combined with the PfPR(2-10) map to tailor the epidemiological stratification for appropriate intervention design. In 2010, a majority of the geographical area of the Sudan had risk of < 1% PfPR(2-10). Areas of meso- and hyperendemic risk were located in the south. About 80% of Sudan's population in 2011 was in the areas in the desert, urban centers, or where risk was < 1% PfPR(2-10). Aggregated data suggest reducing risks in some high transmission areas since the 1960s.
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Affiliation(s)
- Abdisalan M. Noor
- Malaria Public Health Theme, Centre for Geographic Medicine Research, Coast, Kenya Medical Research Institute/Wellcome Trust Research Programme, Nairobi, Kenya; Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom; National Malaria Control Programme, Federal Ministry of Health, Republic of Sudan; Sense Inc., Detroit, Michigan; Institute of Endemic Diseases, Department of Parasitology, University of Khartoum, Khartoum, Sudan
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