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Deng D, Guo Y, Guo L, Li C, Nie Y, Wang S, Wu W. Functional Divergence in Orthologous Transcription Factors: Insights from AtCBF2/3/1 and OsDREB1C. Mol Biol Evol 2024; 41:msae089. [PMID: 38723179 PMCID: PMC11119335 DOI: 10.1093/molbev/msae089] [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: 01/13/2024] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Despite traditional beliefs of orthologous genes maintaining similar functions across species, growing evidence points to their potential for functional divergence. C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) are critical in cold acclimation, with their overexpression enhancing stress tolerance but often constraining plant growth. In contrast, a recent study unveiled a distinctive role of rice OsDREB1C in elevating nitrogen use efficiency (NUE), photosynthesis, and grain yield, implying functional divergence within the CBF/DREB1 orthologs across species. Here, we delve into divergent molecular mechanisms of OsDREB1C and AtCBF2/3/1 by exploring their evolutionary trajectories across rice and Arabidopsis genomes, regulatomes, and transcriptomes. Evolutionary scrutiny shows discrete clades for OsDREB1C and AtCBF2/3/1, with the Poaceae-specific DREB1C clade mediated by a transposon event. Genome-wide binding profiles highlight OsDREB1C's preference for GCCGAC compared to AtCBF2/3/1's preference for A/GCCGAC, a distinction determined by R12 in the OsDREB1C AP2/ERF domain. Cross-species multiomic analyses reveal shared gene orthogroups (OGs) and underscore numerous specific OGs uniquely bound and regulated by OsDREB1C, implicated in NUE, photosynthesis, and early flowering, or by AtCBF2/3/1, engaged in hormone and stress responses. This divergence arises from gene gains/losses (∼16.7% to 25.6%) and expression reprogramming (∼62.3% to 66.2%) of OsDREB1C- and AtCBF2/3/1-regulated OGs during the extensive evolution following the rice-Arabidopsis split. Our findings illustrate the regulatory evolution of OsDREB1C and AtCBF2/3/1 at a genomic scale, providing insights on the functional divergence of orthologous transcription factors following gene duplications across species.
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Affiliation(s)
- Deyin Deng
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Yixin Guo
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Chengyang Li
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Yuqi Nie
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
- Zhejiang International Science and Technology Cooperation Base for Plant Germplasm Resources Conservation and Utilization, Zhejiang A&F University, Hangzhou 311300, China
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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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3
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Evans-Yamamoto D, Dubé AK, Saha G, Plante S, Bradley D, Gagnon-Arsenault I, Landry CR. Parallel Nonfunctionalization of CK1δ/ε Kinase Ohnologs Following a Whole-Genome Duplication Event. Mol Biol Evol 2023; 40:msad246. [PMID: 37979156 PMCID: PMC10699747 DOI: 10.1093/molbev/msad246] [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: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
Whole-genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast family Saccharomycetaceae, HRR25 is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy in Saccharomyces cerevisiae where it is now essential, but has been maintained as pairs in at least 7 species post-WGD. In S. cerevisiae, HRR25 encodes the casein kinase 1δ/ε and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicated HRR25 ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay in S. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post-WGD and non-WGD species, and have nonconserved cellular localization, consistent with their ongoing loss of function. The analysis in Naumovozyma castellii shows that the noncomplementing ohnolog is expressed at a lower level and has become nonessential. Taken together, our results indicate that HRR25 orthologs are undergoing gradual nonfunctionalization.
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Affiliation(s)
- Daniel Evans-Yamamoto
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Gourav Saha
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani K K Birla Goa Campus, South Goa, India
| | - Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, Québec, QC, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, Québec, QC, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, Québec, QC, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Kanagawa, 252-0882, Japan
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Rossio V, Liu X, Paulo JA. Comparative Proteomic Analysis of Two Commonly Used Laboratory Yeast Strains: W303 and BY4742. Proteomes 2023; 11:30. [PMID: 37873872 PMCID: PMC10594481 DOI: 10.3390/proteomes11040030] [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: 08/06/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023] Open
Abstract
The yeast Saccharomyces cerevisiae is a powerful model system that is often used to expand our understanding of cellular processes and biological functions. Although many genetically well-characterized laboratory strains of S. cerevisiae are available, they may have different genetic backgrounds which can confound data interpretation. Here, we report a comparative whole-proteome analysis of two common laboratory yeast background strains, W303 and BY4742, in both exponential and stationary growth phases using isobaric-tag-based mass spectrometry to highlight differences in proteome complexity. We quantified over 4400 proteins, hundreds of which showed differences in abundance between strains and/or growth phases. Moreover, we used proteome-wide protein abundance to profile the mating type of the strains used in the experiment, the auxotrophic markers, and associated metabolic pathways, as well as to investigate differences in particular classes of proteins, such as the pleiotropic drug resistance (PDR) proteins. This study is a valuable resource that offers insight into mechanistic differences between two common yeast background strains and can be used as a guide to select a background that is best suited for addressing a particular biological question.
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Affiliation(s)
- Valentina Rossio
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA;
| | | | - Joao A. Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA;
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5
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Evans-Yamamoto D, Dubé AK, Saha G, Plante S, Bradley D, Gagnon-Arsenault I, Landry CR. Parallel nonfunctionalization of CK1δ/ε kinase ohnologs following a whole-genome duplication event. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560513. [PMID: 37873368 PMCID: PMC10592909 DOI: 10.1101/2023.10.02.560513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Whole genome duplication (WGD) followed by speciation allows us to examine the parallel evolution of ohnolog pairs. In the yeast family Saccharomycetaceae, HRR25 is a rare case of repeated ohnolog maintenance. This gene has reverted to a single copy in S. cerevisiae where it is now essential, but has been maintained as pairs in at least 7 species post WGD. In S. cerevisiae, HRR25 encodes the casein kinase (CK) 1δ/ε and plays a role in a variety of functions through its kinase activity and protein-protein interactions (PPIs). We hypothesized that the maintenance of duplicated HRR25 ohnologs could be a result of repeated subfunctionalization. We tested this hypothesis through a functional complementation assay in S. cerevisiae, testing all pairwise combinations of 25 orthologs (including 7 ohnolog pairs). Contrary to our expectations, we observed no cases of pair-dependent complementation, which would have supported the subfunctionalization hypothesis. Instead, most post-WGD species have one ohnolog that failed to complement, suggesting their nonfunctionalization or neofunctionalization. The ohnologs incapable of complementation have undergone more rapid protein evolution, lost most PPIs that were observed for their functional counterparts and singletons from post and non-WGD species, and have non-conserved cellular localization, consistent with their ongoing loss of function. The analysis in N. castelli shows that the non-complementing ohnolog is expressed at a lower level and has become non-essential. Taken together, our results indicate that HRR25 orthologs are undergoing gradual nonfunctionalization.
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Affiliation(s)
- Daniel Evans-Yamamoto
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
- Institute for Advanced Biosciences, Keio University, Fujisawa, 252-0882, Japan
| | - Alexandre K Dubé
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Gourav Saha
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani K K Birla Goa campus, Zuarinagar, South Goa, Goa, India
- Current address: Department of Bioengineering, University of California, CA 90095, United States
| | - Samuel Plante
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
- Current address: Département de Biochimie, Université de Sherbrooke, Québec, J1K 0A5, Canada
| | - David Bradley
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Isabelle Gagnon-Arsenault
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
| | - Christian R Landry
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- Département de Biologie, Faculté des Sciences et de Génie, Université Laval, G1V 0A6, Canada
- PROTEO, Le regroupement québécois de recherche sur la fonction, l’ingénierie et les applications des protéines, Université Laval, G1V 0A6, Canada
- Centre de Recherche sur les Données Massives (CRDM), Université Laval, G1V 0A6, Canada
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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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Grosjean N, Le Jean M, Ory J, Blaudez D. Yeast Deletomics to Uncover Gadolinium Toxicity Targets and Resistance Mechanisms. Microorganisms 2023; 11:2113. [PMID: 37630673 PMCID: PMC10459663 DOI: 10.3390/microorganisms11082113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Among the rare earth elements (REEs), a crucial group of metals for high-technologies. Gadolinium (Gd) is the only REE intentionally injected to human patients. The use of Gd-based contrasting agents for magnetic resonance imaging (MRI) is the primary route for Gd direct exposure and accumulation in humans. Consequently, aquatic environments are increasingly exposed to Gd due to its excretion through the urinary tract of patients following an MRI examination. The increasing number of reports mentioning Gd toxicity, notably originating from medical applications of Gd, necessitates an improved risk-benefit assessment of Gd utilizations. To go beyond toxicological studies, unravelling the mechanistic impact of Gd on humans and the ecosystem requires the use of genome-wide approaches. We used functional deletomics, a robust method relying on the screening of a knock-out mutant library of Saccharomyces cerevisiae exposed to toxic concentrations of Gd. The analysis of Gd-resistant and -sensitive mutants highlighted the cell wall, endosomes and the vacuolar compartment as cellular hotspots involved in the Gd response. Furthermore, we identified endocytosis and vesicular trafficking pathways (ESCRT) as well as sphingolipids homeostasis as playing pivotal roles mediating Gd toxicity. Finally, tens of yeast genes with human orthologs linked to renal dysfunction were identified as Gd-responsive. Therefore, the molecular and cellular pathways involved in Gd toxicity and detoxification uncovered in this study underline the pleotropic consequences of the increasing exposure to this strategic metal.
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Affiliation(s)
- Nicolas Grosjean
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
| | - Marie Le Jean
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France;
| | - Jordan Ory
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France;
| | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France;
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8
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Ding K, Wang S, Luo Y. Supervised biological network alignment with graph neural networks. Bioinformatics 2023; 39:i465-i474. [PMID: 37387160 DOI: 10.1093/bioinformatics/btad241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023] Open
Abstract
MOTIVATION Despite the advances in sequencing technology, massive proteins with known sequences remain functionally unannotated. Biological network alignment (NA), which aims to find the node correspondence between species' protein-protein interaction (PPI) networks, has been a popular strategy to uncover missing annotations by transferring functional knowledge across species. Traditional NA methods assumed that topologically similar proteins in PPIs are functionally similar. However, it was recently reported that functionally unrelated proteins can be as topologically similar as functionally related pairs, and a new data-driven or supervised NA paradigm has been proposed, which uses protein function data to discern which topological features correspond to functional relatedness. RESULTS Here, we propose GraNA, a deep learning framework for the supervised NA paradigm for the pairwise NA problem. Employing graph neural networks, GraNA utilizes within-network interactions and across-network anchor links for learning protein representations and predicting functional correspondence between across-species proteins. A major strength of GraNA is its flexibility to integrate multi-faceted non-functional relationship data, such as sequence similarity and ortholog relationships, as anchor links to guide the mapping of functionally related proteins across species. Evaluating GraNA on a benchmark dataset composed of several NA tasks between different pairs of species, we observed that GraNA accurately predicted the functional relatedness of proteins and robustly transferred functional annotations across species, outperforming a number of existing NA methods. When applied to a case study on a humanized yeast network, GraNA also successfully discovered functionally replaceable human-yeast protein pairs that were documented in previous studies. AVAILABILITY AND IMPLEMENTATION The code of GraNA is available at https://github.com/luo-group/GraNA.
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Affiliation(s)
- Kerr Ding
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Sheng Wang
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, United States
| | - Yunan Luo
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, United States
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9
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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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10
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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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11
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Yap WS, Thibault G. A new combinatorial megaplasmid library assembly method designed to screen for minimal pathways by using SCRaMbLE. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000657. [PMID: 36389121 PMCID: PMC9647409 DOI: 10.17912/micropub.biology.000657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/10/2022] [Accepted: 10/20/2022] [Indexed: 11/23/2022]
Abstract
Human proteins expressed in yeast are common to enhance protein production while the expression of functional human pathways remain challenging. Here, we propose a simple and economical high-throughput gene assembly method to create a yeast megaplasmid library from human cDNA to screen for minimal human functional pathways. We introduced artificial promoters followed by symmetric loxP sites into the megaplasmids using Golden Gate assembly coupled with streptavidin-bead-based purification. The isolated high molecular weight, randomly assembled cDNA megaplasmid library may be useful for high-throughput directed evolution experiments and may be adapted for use in other model organisms.
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Affiliation(s)
- Wei Sheng Yap
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551
,
Current address: Department of Biochemistry, University of Toronto, Toronto, Canada
| | - Guillaume Thibault
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551
,
Mechanobiology Institute, National University of Singapore, Singapore, 117411
,
Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673
,
Correspondence to: Guillaume Thibault (
)
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12
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Epremyan KK, Goleva TN, Rogov AG, Lavrushkina SV, Zinovkin RA, Zvyagilskaya RA. The First Yarrowia lipolytica Yeast Models Expressing Hepatitis B Virus X Protein: Changes in Mitochondrial Morphology and Functions. Microorganisms 2022; 10:microorganisms10091817. [PMID: 36144419 PMCID: PMC9501646 DOI: 10.3390/microorganisms10091817] [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: 07/17/2022] [Revised: 09/04/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Chronic hepatitis B virus infection is the dominant cause of hepatocellular carcinoma, the main cause of cancer death. HBx protein, a multifunctional protein, is essential for pathogenesis development; however, the underlying mechanisms are not fully understood. The complexity of the system itself, and the intricate interplay of many factors make it difficult to advance in understanding the mechanisms underlying these processes. The most obvious solution is to use simpler systems by reducing the number of interacting factors. Yeast cells are particularly suitable for studying the relationships between oxidative stress, mitochondrial dynamics (mitochondrial fusion and fragmentation), and mitochondrial dysfunction involved in HBx-mediated pathogenesis. For the first time, genetically modified yeast, Y. lipolytica, was created, expressing the hepatitis B virus core protein HBx, as well as a variant fused with eGFP at the C-end. It was found that cells expressing HBx experienced stronger oxidative stress than the control cells. Oxidative stress was alleviated by preincubation with the mitochondria-targeted antioxidant SkQThy. Consistent with these data, in contrast to the control cells (pZ-0) containing numerous mitochondrial forming a mitochondrial reticulum, in cells expressing HBx protein, mitochondria were fragmented, and preincubation with SkQThy partially restored the mitochondrial reticulum. Expression of HBx had a significant influence on the bioenergetic function of mitochondria, making them loosely coupled with decreased respiratory rate and reduced ATP formation. In sum, the first highly promising yeast model for studying the impact of HBx on bioenergy, redox-state, and dynamics of mitochondria in the cell and cross-talk between these parameters was offered. This fairly simple model can be used as a platform for rapid screening of potential therapeutic agents, mitigating the harmful effects of HBx.
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Affiliation(s)
- Khoren K. Epremyan
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
- Correspondence: (K.K.E.); (R.A.Z.); Tel.: +7-(917)-575-3560 (K.K.E.)
| | - Tatyana N. Goleva
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
| | - Anton G. Rogov
- National Research Center “Kurchatov Institute”, Akademika Kurchatova pl. 1, 123182 Moscow, Russia
| | - Svetlana V. Lavrushkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1/40, 119992 Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1/73, 119234 Moscow, Russia
| | - Roman A. Zinovkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1/40, 119992 Moscow, Russia
| | - Renata A. Zvyagilskaya
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Leninsky Ave. 33/2, 119071 Moscow, Russia
- Correspondence: (K.K.E.); (R.A.Z.); Tel.: +7-(917)-575-3560 (K.K.E.)
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13
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Oz N, Vayndorf EM, Tsuchiya M, McLean S, Turcios-Hernandez L, Pitt JN, Blue BW, Muir M, Kiflezghi MG, Tyshkovskiy A, Mendenhall A, Kaeberlein M, Kaya A. Evidence that conserved essential genes are enriched for pro-longevity factors. GeroScience 2022; 44:1995-2006. [PMID: 35695982 PMCID: PMC9616985 DOI: 10.1007/s11357-022-00604-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/03/2022] [Indexed: 02/02/2023] Open
Abstract
At the cellular level, many aspects of aging are conserved across species. This has been demonstrated by numerous studies in simple model organisms like Saccharomyces cerevisiae, Caenorhabdits elegans, and Drosophila melanogaster. Because most genetic screens examine loss of function mutations or decreased expression of genes through reverse genetics, essential genes have often been overlooked as potential modulators of the aging process. By taking the approach of increasing the expression level of a subset of conserved essential genes, we found that 21% of these genes resulted in increased replicative lifespan in S. cerevisiae. This is greater than the ~ 3.5% of genes found to affect lifespan upon deletion, suggesting that activation of essential genes may have a relatively disproportionate effect on increasing lifespan. The results of our experiments demonstrate that essential gene overexpression is a rich, relatively unexplored means of increasing eukaryotic lifespan.
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Affiliation(s)
- Naci Oz
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Elena M Vayndorf
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Mitsuhiro Tsuchiya
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Samantha McLean
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | | | - Jason N Pitt
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin W Blue
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael Muir
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Michael G Kiflezghi
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Alexander Mendenhall
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, 98195, USA.
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA.
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, 23298, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA, 23284, USA.
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14
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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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15
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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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16
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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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17
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Crow M, Suresh H, Lee J, Gillis J. Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. Nucleic Acids Res 2022; 50:4302-4314. [PMID: 35451481 PMCID: PMC9071420 DOI: 10.1093/nar/gkac276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 03/30/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
What makes a mouse a mouse, and not a hamster? Differences in gene regulation between the two organisms play a critical role. Comparative analysis of gene coexpression networks provides a general framework for investigating the evolution of gene regulation across species. Here, we compare coexpression networks from 37 species and quantify the conservation of gene activity 1) as a function of evolutionary time, 2) across orthology prediction algorithms, and 3) with reference to cell- and tissue-specificity. We find that ancient genes are expressed in multiple cell types and have well conserved coexpression patterns, however they are expressed at different levels across cell types. Thus, differential regulation of ancient gene programs contributes to transcriptional cell identity. We propose that this differential regulation may play a role in cell diversification in both the animal and plant kingdoms.
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Affiliation(s)
- Megan Crow
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
| | - Hamsini Suresh
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
| | - John Lee
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
| | - Jesse Gillis
- Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor NY, USA
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18
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Logviniuk D, Jaber QZ, Dobrovetsky R, Kozer N, Ksiezopolska E, Gabaldón T, Carmeli S, Fridman M. Benzylic Dehydroxylation of Echinocandin Antifungal Drugs Restores Efficacy against Resistance Conferred by Mutated Glucan Synthase. J Am Chem Soc 2022; 144:5965-5975. [PMID: 35347986 PMCID: PMC8991007 DOI: 10.1021/jacs.2c00269] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Each year, infections caused by fungal pathogens claim the lives of about 1.6 million people and affect the health of over a billion people worldwide. Among the most recently developed antifungal drugs are the echinocandins, which noncompetitively inhibit β-glucan synthase, a membrane-bound protein complex that catalyzes the formation of the main polysaccharide component of the fungal cell wall. Resistance to echinocandins is conferred by mutations in FKS genes, which encode the catalytic subunit of the β-glucan synthase complex. Here, we report that selective removal of the benzylic alcohol of the nonproteinogenic amino acid 3S,4S-dihydroxy-l-homotyrosine of the echinocandins anidulafungin and rezafungin, restored their efficacy against a large panel of echinocandin-resistant Candida strains. The dehydroxylated compounds did not significantly affect the viability of human-derived cell culture lines. An analysis of the efficacy of the dehydroxylated echinocandins against resistant Candida strains, which contain mutations in the FKS1 and/or FKS2 genes of the parental strains, identified amino acids of the Fks proteins that are likely to reside in proximity to the l-homotyrosine residue of the bound drug. This study describes the first example of a chemical modification strategy to restore the efficacy of echinocandin drugs, which have a critical place in the arsenal of antifungal drugs, against resistant fungal pathogens.
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Affiliation(s)
- Dana Logviniuk
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Qais Z Jaber
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roman Dobrovetsky
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Noga Kozer
- The Wohl Drug Discovery institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ewa Ksiezopolska
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, Barcelona 08034, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, Barcelona 08034, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona 08010, Spain.,Centro Investigación Biomédica En Red de Enfermedades Infecciosas, Madrid 28029, Spain
| | - Shmuel Carmeli
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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19
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Elias R, Basu P, Fridman M. Fluconazole-COX Inhibitor Hybrids: A Dual-Acting Class of Antifungal Azoles. J Med Chem 2022; 65:2361-2373. [PMID: 35084852 PMCID: PMC8842223 DOI: 10.1021/acs.jmedchem.1c01807] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
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When used in combination
with azole antifungal drugs, cyclooxygenase
(COX) inhibitors such as ibuprofen improve antifungal efficacy. We
report the conjugation of a chiral antifungal azole pharmacophore
to COX inhibitors and the evaluation of activity of 24 hybrids. Hybrids
derived from ibuprofen and flurbiprofen were considerably more potent
than fluconazole and comparable to voriconazole against a panel of Candida species. The potencies of hybrids composed
of an S-configured azole pharmacophore were higher
than those with an R-configured pharmacophore. Tolerance,
defined as the ability of a subpopulation of cells to grow in the
presence of the drug, to the hybrids was lower than to fluconazole
and voriconazole. The hybrids were active against a mutant lacking
CYP51, the target of azole drugs, indicating that these agents act
via a dual mode of action. This study established that azole-COX inhibitor
hybrids are a novel class of potent antifungals with clinical potential.
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Affiliation(s)
- Rebecca Elias
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Pallabita Basu
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Micha Fridman
- School of Chemistry, Raymond & Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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20
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Kuzmin E, Taylor JS, Boone C. Retention of duplicated genes in evolution. Trends Genet 2022; 38:59-72. [PMID: 34294428 PMCID: PMC8678172 DOI: 10.1016/j.tig.2021.06.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/03/2023]
Abstract
Gene duplication is a prevalent phenomenon across the tree of life. The processes that lead to the retention of duplicated genes are not well understood. Functional genomics approaches in model organisms, such as yeast, provide useful tools to test the mechanisms underlying retention with functional redundancy and divergence of duplicated genes, including fates associated with neofunctionalization, subfunctionalization, back-up compensation, and dosage amplification. Duplicated genes may also be retained as a consequence of structural and functional entanglement. Advances in human gene editing have enabled the interrogation of duplicated genes in the human genome, providing new tools to evaluate the relative contributions of each of these factors to duplicate gene retention and the evolution of genome structure.
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Affiliation(s)
- Elena Kuzmin
- Department of Biochemistry, Rosalind and Morris Goodman Cancer Research Centre, McGill University, 1160 Ave des Pins Ouest, Montreal, Quebec, H3A 1A3, Canada.,Correspondence to: (E.K.)
| | - John S. Taylor
- Department of Biology, University of Victoria, PO Box 1700, Station CSC, Victoria, BC, V8W 2Y2, Canada
| | - Charles Boone
- Department of Molecular Genetics, Donnelly Centre, University of Toronto, 160 College Street, Toronto ON, M5S 3E1, Canada.,RIKEN Centre for Sustainable Resource Science, Waiko, Saitama, Japan
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21
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Sequence, structural and functional conservation among the human and fission yeast ELL and EAF transcription elongation factors. Mol Biol Rep 2021; 49:1303-1320. [PMID: 34807377 DOI: 10.1007/s11033-021-06958-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/11/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Transcription elongation is a dynamic and tightly regulated step of gene expression in eukaryotic cells. Eleven nineteen Lysine rich Leukemia (ELL) and ELL Associated Factors (EAF) family of conserved proteins are required for efficient RNA polymerase II-mediated transcription elongation. Orthologs of these proteins have been identified in different organisms, including fission yeast and humans. METHODS AND RESULTS In the present study, we have examined the sequence, structural and functional conservation between the fission yeast and human ELL and EAF orthologs. Our computational analysis revealed that these proteins share some sequence characteristics, and were predominantly disordered in both organisms. Our functional complementation assays revealed that both human ELL and EAF proteins could complement the lack of ell1+ or eaf1+ in Schizosaccharomyces pombe respectively. Furthermore, our domain mapping experiments demonstrated that both the amino and carboxyl terminal domains of human EAF proteins could functionally complement the S. pombe eaf1 deletion phenotypes. However, only the carboxyl-terminus domain of human ELL was able to partially rescue the phenotypes associated with lack of ell1+ in S. pombe. CONCLUSIONS Collectively, our work adds ELL-EAF to the increasing list of human-yeast complementation gene pairs, wherein the simpler fission yeast can be used to further enhance our understanding of the role of these proteins in transcription elongation and human disease.
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22
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Buchholz PCF, van Loo B, Eenink BDG, Bornberg-Bauer E, Pleiss J. Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation. J R Soc Interface 2021; 18:20210389. [PMID: 34727710 DOI: 10.1098/rsif.2021.0389] [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: 11/12/2022] Open
Abstract
Evolutionary relationships of protein families can be characterized either by networks or by trees. Whereas trees allow for hierarchical grouping and reconstruction of the most likely ancestral sequences, networks lack a time axis but allow for thresholds of pairwise sequence identity to be chosen and, therefore, the clustering of family members with presumably more similar functions. Here, we use the large family of arylsulfatases and phosphonate monoester hydrolases to investigate similarities, strengths and weaknesses in tree and network representations. For varying thresholds of pairwise sequence identity, values of betweenness centrality and clustering coefficients were derived for nodes of the reconstructed ancestors to measure the propensity to act as a bridge in a network. Based on these properties, ancestral protein sequences emerge as bridges in protein sequence networks. Interestingly, many ancestral protein sequences appear close to extant sequences. Therefore, reconstructed ancestor sequences might also be interpreted as yet-to-be-identified homologues. The concept of ancestor reconstruction is compared to consensus sequences, too. It was found that hub sequences in a network, e.g. reconstructed ancestral sequences that are connected to many neighbouring sequences, share closer similarity with derived consensus sequences. Therefore, some reconstructed ancestor sequences can also be interpreted as consensus sequences.
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Affiliation(s)
- Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart 70569, Germany
| | - Bert van Loo
- Department of Applied Sciences, Northumbria University, Newcastle-upon-Tyne NE1 8ST, UK.,Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
| | - Bernard D G Eenink
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, Hüfferstraße 1, Münster 48149, Germany.,Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen 72076, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart 70569, Germany
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23
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Brzáčová Z, Peťková M, Veljačiková K, Zajičková T, Tomáška Ľ. Reconstruction of human genome evolution in yeast: an educational primer for use with "systematic humanization of the yeast cytoskeleton discerns functionally replaceable from divergent human genes". Genetics 2021; 219:6380399. [PMID: 34849890 DOI: 10.1093/genetics/iyab118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 07/14/2021] [Indexed: 01/01/2023] Open
Abstract
The evolution of eukaryotic organisms starting with the last eukaryotic common ancestor was accompanied by lineage-specific expansion of gene families. A paper by Garge et al. provides an excellent opportunity to have students explore how expansion of gene families via gene duplication results in protein specialization, in this case in the context of eukaryotic cytoskeletal organization . The authors tested hypotheses about conserved protein function by systematic "humanization" of the yeast cytoskeletal components while employing a wide variety of methodological approaches. We outline several exercises to promote students' ability to explore the genomic databases, perform bioinformatic analyses, design experiments for functional analysis of human genes in yeast and critically interpret results to address both specific and general questions.
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Affiliation(s)
- Zuzana Brzáčová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava 842 15, Slovakia
| | - Mária Peťková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava 842 15, Slovakia
| | - Katarína Veljačiková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava 842 15, Slovakia
| | - Terézia Zajičková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava 842 15, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava 842 15, Slovakia
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24
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Geck RC, Boyle G, Amorosi CJ, Fowler DM, Dunham MJ. Measuring Pharmacogene Variant Function at Scale Using Multiplexed Assays. Annu Rev Pharmacol Toxicol 2021; 62:531-550. [PMID: 34516287 DOI: 10.1146/annurev-pharmtox-032221-085807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As costs of next-generation sequencing decrease, identification of genetic variants has far outpaced our ability to understand their functional consequences. This lack of understanding is a central challenge to a key promise of pharmacogenomics: using genetic information to guide drug selection and dosing. Recently developed multiplexed assays of variant effect enable experimental measurement of the function of thousands of variants simultaneously. Here, we describe multiplexed assays that have been performed on nearly 25,000 variants in eight key pharmacogenes (ADRB2, CYP2C9, CYP2C19, NUDT15, SLCO1B1, TMPT, VKORC1, and the LDLR promoter), discuss advances in experimental design, and explore key challenges that must be overcome to maximize the utility of multiplexed functional data. Expected final online publication date for the Annual Review of Pharmacology and Toxicology, Volume 62 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Renee C Geck
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Gabriel Boyle
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Clara J Amorosi
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; , .,Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
| | - Maitreya J Dunham
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; ,
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25
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Garge RK, Cha HJ, Lee C, Gollihar JD, Kachroo AH, Wallingford JB, Marcotte EM. Discovery of new vascular disrupting agents based on evolutionarily conserved drug action, pesticide resistance mutations, and humanized yeast. Genetics 2021; 219:6317676. [PMID: 34849907 DOI: 10.1093/genetics/iyab101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 06/15/2021] [Indexed: 12/20/2022] Open
Abstract
Thiabendazole (TBZ) is an FDA-approved benzimidazole widely used for its antifungal and antihelminthic properties. We showed previously that TBZ is also a potent vascular disrupting agent and inhibits angiogenesis at the tissue level by dissociating vascular endothelial cells in newly formed blood vessels. Here, we uncover TBZ's molecular target and mechanism of action. Using human cell culture, molecular modeling, and humanized yeast, we find that TBZ selectively targets only 1 of 9 human β-tubulin isotypes (TUBB8) to specifically disrupt endothelial cell microtubules. By leveraging epidemiological pesticide resistance data and mining chemical features of commercially used benzimidazoles, we discover that a broader class of benzimidazole compounds, in extensive use for 50 years, also potently disrupt immature blood vessels and inhibit angiogenesis. Thus, besides identifying the molecular mechanism of benzimidazole-mediated vascular disruption, this study presents evidence relevant to the widespread use of these compounds while offering potential new clinical applications.
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Affiliation(s)
- Riddhiman K Garge
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hye Ji Cha
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.,US Army Research Laboratory-South, Austin, TX 78758, USA
| | - Aashiq H Kachroo
- The Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montreal, QC H4B 1R6, Canada
| | - John B Wallingford
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA
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26
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Begum T, Robinson-Rechavi M. Special Care Is Needed in Applying Phylogenetic Comparative Methods to Gene Trees with Speciation and Duplication Nodes. Mol Biol Evol 2021; 38:1614-1626. [PMID: 33169790 PMCID: PMC8042747 DOI: 10.1093/molbev/msaa288] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
How gene function evolves is a central question of evolutionary biology. It can be investigated by comparing functional genomics results between species and between genes. Most comparative studies of functional genomics have used pairwise comparisons. Yet it has been shown that this can provide biased results, as genes, like species, are phylogenetically related. Phylogenetic comparative methods should be used to correct for this, but they depend on strong assumptions, including unbiased tree estimates relative to the hypothesis being tested. Such methods have recently been used to test the “ortholog conjecture,” the hypothesis that functional evolution is faster in paralogs than in orthologs. Although pairwise comparisons of tissue specificity (τ) provided support for the ortholog conjecture, phylogenetic independent contrasts did not. Our reanalysis on the same gene trees identified problems with the time calibration of duplication nodes. We find that the gene trees used suffer from important biases, due to the inclusion of trees with no duplication nodes, to the relative age of speciations and duplications, to systematic differences in branch lengths, and to non-Brownian motion of tissue specificity on many trees. We find that incorrect implementation of phylogenetic method in empirical gene trees with duplications can be problematic. Controlling for biases allows successful use of phylogenetic methods to study the evolution of gene function and provides some support for the ortholog conjecture using three different phylogenetic approaches.
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Affiliation(s)
- Tina Begum
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
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27
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Genome-wide toxicogenomic study of the lanthanides sheds light on the selective toxicity mechanisms associated with critical materials. Proc Natl Acad Sci U S A 2021; 118:2025952118. [PMID: 33903247 DOI: 10.1073/pnas.2025952118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Lanthanides are a series of critical elements widely used in multiple industries, such as optoelectronics and healthcare. Although initially considered to be of low toxicity, concerns have emerged during the last few decades over their impact on human health. The toxicological profile of these metals, however, has been incompletely characterized, with most studies to date solely focusing on one or two elements within the group. In the current study, we assessed potential toxicity mechanisms in the lanthanide series using a functional toxicogenomics approach in baker's yeast, which shares many cellular pathways and functions with humans. We screened the homozygous deletion pool of 4,291 Saccharomyces cerevisiae strains with the lanthanides and identified both common and unique functional effects of these metals. Three very different trends were observed within the lanthanide series, where deletions of certain proteins on membranes and organelles had no effect on the cellular response to early lanthanides while inducing yeast sensitivity and resistance to middle and late lanthanides, respectively. Vesicle-mediated transport (primarily endocytosis) was highlighted by both gene ontology and pathway enrichment analyses as one of the main functions disturbed by the majority of the metals. Protein-protein network analysis indicated that yeast response to lanthanides relied on proteins that participate in regulatory paths used for calcium (and other biologically relevant cations), and lanthanide toxicity included disruption of biosynthetic pathways by enzyme inhibition. Last, multiple genes and proteins identified in the network analysis have human orthologs, suggesting that those may also be targeted by lanthanides in humans.
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28
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Rogov AG, Goleva TN, Epremyan KK, Kireev II, Zvyagilskaya RA. Propagation of Mitochondria-Derived Reactive Oxygen Species within the Dipodascus magnusii Cells. Antioxidants (Basel) 2021; 10:antiox10010120. [PMID: 33467672 PMCID: PMC7830518 DOI: 10.3390/antiox10010120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 01/12/2021] [Indexed: 12/04/2022] Open
Abstract
Mitochondria are considered to be the main source of reactive oxygen species (ROS) in the cell. It was shown that in cardiac myocytes exposed to excessive oxidative stress, ROS-induced ROS release is triggered. However, cardiac myocytes have a network of densely packed organelles that do not move, which is not typical for the majority of eukaryotic cells. The purpose of this study was to trace the spatiotemporal development (propagation) of prooxidant-induced oxidative stress and its interplay with mitochondrial dynamics. We used Dipodascus magnusii yeast cells as a model, as they have advantages over other models, including a uniquely large size, mitochondria that are easy to visualize and freely moving, an ability to vigorously grow on well-defined low-cost substrates, and high responsibility. It was shown that prooxidant-induced oxidative stress was initiated in mitochondria, far preceding the appearance of generalized oxidative stress in the whole cell. For yeasts, these findings were obtained for the first time. Preincubation of yeast cells with SkQ1, a mitochondria-addressed antioxidant, substantially diminished production of mitochondrial ROS, while only slightly alleviating the generalized oxidative stress. This was expected, but had not yet been shown. Importantly, mitochondrial fragmentation was found to be primarily induced by mitochondrial ROS preceding the generalized oxidative stress development.
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Affiliation(s)
- Anton G. Rogov
- Bach Institute of Biochemistry, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences 33, bld. 2 Leninsky Ave., Moscow 119071, Russia; (A.G.R.); (T.N.G.); (K.K.E.)
| | - Tatiana N. Goleva
- Bach Institute of Biochemistry, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences 33, bld. 2 Leninsky Ave., Moscow 119071, Russia; (A.G.R.); (T.N.G.); (K.K.E.)
| | - Khoren K. Epremyan
- Bach Institute of Biochemistry, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences 33, bld. 2 Leninsky Ave., Moscow 119071, Russia; (A.G.R.); (T.N.G.); (K.K.E.)
| | - Igor I. Kireev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobyevy Gory 1, Moscow 119992, Russia;
| | - Renata A. Zvyagilskaya
- Bach Institute of Biochemistry, Federal Research Center “Fundamentals of Biotechnology” of the Russian Academy of Sciences 33, bld. 2 Leninsky Ave., Moscow 119071, Russia; (A.G.R.); (T.N.G.); (K.K.E.)
- Correspondence:
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29
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Stamboulian M, Guerrero RF, Hahn MW, Radivojac P. The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. Bioinformatics 2020; 36:i219-i226. [PMID: 32657391 PMCID: PMC7355290 DOI: 10.1093/bioinformatics/btaa468] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
MOTIVATION The computational prediction of gene function is a key step in making full use of newly sequenced genomes. Function is generally predicted by transferring annotations from homologous genes or proteins for which experimental evidence exists. The 'ortholog conjecture' proposes that orthologous genes should be preferred when making such predictions, as they evolve functions more slowly than paralogous genes. Previous research has provided little support for the ortholog conjecture, though the incomplete nature of the data cast doubt on the conclusions. RESULTS We use experimental annotations from over 40 000 proteins, drawn from over 80 000 publications, to revisit the ortholog conjecture in two pairs of species: (i) Homo sapiens and Mus musculus and (ii) Saccharomyces cerevisiae and Schizosaccharomyces pombe. By making a distinction between questions about the evolution of function versus questions about the prediction of function, we find strong evidence against the ortholog conjecture in the context of function prediction, though questions about the evolution of function remain difficult to address. In both pairs of species, we quantify the amount of information that would be ignored if paralogs are discarded, as well as the resulting loss in prediction accuracy. Taken as a whole, our results support the view that the types of homologs used for function transfer are largely irrelevant to the task of function prediction. Maximizing the amount of data used for this task, regardless of whether it comes from orthologs or paralogs, is most likely to lead to higher prediction accuracy. AVAILABILITY AND IMPLEMENTATION https://github.com/predragradivojac/oc. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Moses Stamboulian
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Rafael F Guerrero
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Matthew W Hahn
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA
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