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Zu Q, Deng X, Qu Y, Chen X, Cai Y, Wang C, Li Y, Chen Q, Zheng K, Liu X, Chen Q. Genetic Channelization Mechanism of Four Chalcone Isomerase Homologous Genes for Synergistic Resistance to Fusarium wilt in Gossypium barbadense L. Int J Mol Sci 2023; 24:14775. [PMID: 37834230 PMCID: PMC10572676 DOI: 10.3390/ijms241914775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Duplication events occur very frequently during plant evolution. The genes in the duplicated pathway or network can evolve new functions through neofunctionalization and subfunctionalization. Flavonoids are secondary metabolites involved in plant development and defense. Our previous transcriptomic analysis of F6 recombinant inbred lines (RILs) and the parent lines after Fusarium oxysporum f. sp. vasinfectum (Fov) infection showed that CHI genes have important functions in cotton. However, there are few reports on the possible neofunctionalization differences of CHI family paralogous genes involved in Fusarium wilt resistance in cotton. In this study, the resistance to Fusarium wilt, expression of metabolic pathway-related genes, metabolite content, endogenous hormone content, reactive oxygen species (ROS) content and subcellular localization of four paralogous CHI family genes in cotton were investigated. The results show that the four paralogous CHI family genes may play a synergistic role in Fusarium wilt resistance. These results revealed a genetic channelization mechanism that can regulate the metabolic flux homeostasis of flavonoids under the mediation of endogenous salicylic acid (SA) and methyl jasmonate (MeJA) via the four paralogous CHI genes, thereby achieving disease resistance. Our study provides a theoretical basis for studying the evolutionary patterns of homologous plant genes and using homologous genes for molecular breeding.
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Affiliation(s)
- Qianli Zu
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Xiaojuan Deng
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Yanying Qu
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Xunji Chen
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), No. 403, Nanchang Road, Urumqi 830052, China;
| | - Yongsheng Cai
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Caoyue Wang
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Ying Li
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Qin Chen
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Kai Zheng
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
| | - Xiaodong Liu
- College of Life Science, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China;
| | - Quanjia Chen
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China; (Q.Z.); (X.D.); (Y.Q.); (Y.C.); (C.W.); (Y.L.); (Q.C.); (K.Z.)
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Wei Q, Liu J, Guo F, Wang Z, Zhang X, Yuan L, Ali K, Qiang F, Wen Y, Li W, Zheng B, Bai Q, Li G, Ren H, Wu G. Kinase regulators evolved into two families by gain and loss of ability to bind plant steroid receptors. PLANT PHYSIOLOGY 2023; 191:1167-1185. [PMID: 36494097 PMCID: PMC9922406 DOI: 10.1093/plphys/kiac568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/29/2022] [Indexed: 06/17/2023]
Abstract
All biological functions evolve by fixing beneficial mutations and removing deleterious ones. Therefore, continuously fixing and removing the same essential function to separately diverge monophyletic gene families sounds improbable. Yet, here we report that brassinosteroid insensitive1 kinase inhibitor1 (BKI1)/membrane-associated kinase regulators (MAKRs) regulating a diverse function evolved into BKI1 and MAKR families from a common ancestor by respectively enhancing and losing ability to bind brassinosteroid receptor brassinosteroid insensitive1 (BRI1). The BKI1 family includes BKI1, MAKR1/BKI1-like (BKL) 1, and BKL2, while the MAKR family contains MAKR2-6. Seedless plants contain only BKL2. In seed plants, MAKR1/BKL1 and MAKR3, duplicates of BKL2, gained and lost the ability to bind BRI1, respectively. In angiosperms, BKL2 lost the ability to bind BRI1 to generate MAKR2, while BKI1 and MAKR6 were duplicates of MAKR1/BKL1 and MAKR3, respectively. In dicots, MAKR4 and MAKR5 were duplicates of MAKR3 and MAKR2, respectively. Importantly, BKI1 localized in the plasma membrane, but BKL2 localized to the nuclei while MAKR1/BKL1 localized throughout the whole cell. Importantly, BKI1 strongly and MAKR1/BKL1 weakly inhibited plant growth, but BKL2 and the MAKR family did not inhibit plant growth. Functional study of the chimeras of their N- and C-termini showed that only the BKI1 family was partially reconstructable, supporting stepwise evolution by a seesaw mechanism between their C- and N-termini to alternately gain an ability to bind and inhibit BRI1, respectively. Nevertheless, the C-terminal BRI1-interacting motif best defines the divergence of BKI1/MAKRs. Therefore, BKI1 and MAKR families evolved by gradually gaining and losing the same function, respectively, extremizing divergent evolution and adding insights into gene (BKI1/MAKR) duplication and divergence.
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Yoshida MA, Hirota K, Imoto J, Okuno M, Tanaka H, Kajitani R, Toyoda A, Itoh T, Ikeo K, Sasaki T, Setiamarga DHE. Gene Recruitments and Dismissals in the Argonaut Genome Provide Insights into Pelagic Lifestyle Adaptation and Shell-like Eggcase Reacquisition. Genome Biol Evol 2022; 14:evac140. [PMID: 36283693 PMCID: PMC9635652 DOI: 10.1093/gbe/evac140] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2022] [Indexed: 10/01/2023] Open
Abstract
The paper nautilus or greater argonaut, Argonauta argo, is a species of octopods which is characterized by its pelagic lifestyle and by the presence of a protective spiral-shaped shell-like eggcase in females. To reveal the genomic background of how the species adapted to the pelagic lifestyle and acquired its shell-like eggcase, we sequenced the draft genome of the species. The genome size was 1.1 Gb, which is the smallest among the cephalopods known to date, with the top 215 scaffolds (average length 5,064,479 bp) covering 81% (1.09 Gb) of the total assembly. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified nearly intact HOX, Parahox, Wnt clusters, and some gene clusters that could probably be related to the pelagic lifestyle, such as reflectin, tyrosinase, and opsin. The gene models also revealed several homologous genes related to calcified shell formation in Conchiferan mollusks, such as Pif-like, SOD, and TRX. Interestingly, comparative genomics analysis revealed that the homologous genes for such genes were also found in the genome of the shell-less octopus, as well as Nautilus, which has a true outer shell. Therefore, the draft genome sequence of Arg. argo presented here has helped us to gain further insights into the genetic background of the dynamic recruitment and dismissal of genes to form an important, converging extended phenotypic structure such as the shell and the shell-like eggcase. Additionally, it allows us to explore the evolution of from benthic to pelagic lifestyles in cephalopods and octopods.
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Affiliation(s)
- Masa-aki Yoshida
- Marine Biological Science Section, Education and Research Center for Biological Resources, Faculty of Life and Environmental Science, Shimane University, Okinoshima, Shimane 685-0024, Japan
| | - Kazuki Hirota
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN), Wakayama College, Gobo, Wakayama 644-0012, Japan
| | - Junichi Imoto
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Miki Okuno
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Hiroyuki Tanaka
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Rei Kajitani
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Kazuho Ikeo
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Takenori Sasaki
- Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan
- The University Museum, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Davin H E Setiamarga
- Department of Applied Chemistry and Biochemistry, National Institute of Technology (KOSEN), Wakayama College, Gobo, Wakayama 644-0012, Japan
- The University Museum, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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Mottes F, Villa C, Osella M, Caselle M. The impact of whole genome duplications on the human gene regulatory networks. PLoS Comput Biol 2021; 17:e1009638. [PMID: 34871317 PMCID: PMC8675932 DOI: 10.1371/journal.pcbi.1009638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/16/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
This work studies the effects of the two rounds of Whole Genome Duplication (WGD) at the origin of the vertebrate lineage on the architecture of the human gene regulatory networks. We integrate information on transcriptional regulation, miRNA regulation, and protein-protein interactions to comparatively analyse the role of WGD and Small Scale Duplications (SSD) in the structural properties of the resulting multilayer network. We show that complex network motifs, such as combinations of feed-forward loops and bifan arrays, deriving from WGD events are specifically enriched in the network. Pairs of WGD-derived proteins display a strong tendency to interact both with each other and with common partners and WGD-derived transcription factors play a prominent role in the retention of a strong regulatory redundancy. Combinatorial regulation and synergy between different regulatory layers are in general enhanced by duplication events, but the two types of duplications contribute in different ways. Overall, our findings suggest that the two WGD events played a substantial role in increasing the multi-layer complexity of the vertebrate regulatory network by enhancing its combinatorial organization, with potential consequences on its overall robustness and ability to perform high-level functions like signal integration and noise control. Lastly, we discuss in detail the RAR/RXR pathway as an illustrative example of the evolutionary impact of WGD duplications in human. Gene duplication is one of the main mechanisms driving genome evolution. The duplication of a genomic segment can be the result of a local event, involving only a small portion of the genome, or of a dramatic duplication of the whole genome, which is however only rarely retained. All vertebrates descend from two rounds of Whole-Genome Duplication (WGD) that occurred approximately 500 Mya. We show that these events influenced in unique ways the evolution of different human gene regulatory networks, with sizeable effects on their current structure. We find that WGDs statistically increased the presence of specific classes of simple genetic circuits, considered to be fundamental building blocks of more sophisticated circuitry and commonly associated to complex functions. Our findings support the hypothesis that these rare, large-scale events have played a substantial role in the emergence of complex traits in vertebrates.
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Affiliation(s)
| | - Chiara Villa
- School of Mathematics and Statistics, University of St Andrews, Mathematical Institute, North Haugh, St Andrews, United Kingdom
| | - Matteo Osella
- Department of Physics, University of Turin & INFN, Turin, Italy
| | - Michele Caselle
- Department of Physics, University of Turin & INFN, Turin, Italy
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Wu Y, Wu J, Deng M, Lin Y. Yeast cell fate control by temporal redundancy modulation of transcription factor paralogs. Nat Commun 2021; 12:3145. [PMID: 34035307 PMCID: PMC8149833 DOI: 10.1038/s41467-021-23425-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 04/28/2021] [Indexed: 11/19/2022] Open
Abstract
Recent single-cell studies have revealed that yeast stress response involves transcription factors that are activated in pulses. However, it remains unclear whether and how these dynamic transcription factors temporally interact to regulate stress survival. Here we show that budding yeast cells can exploit the temporal relationship between paralogous general stress regulators, Msn2 and Msn4, during stress response. We find that individual pulses of Msn2 and Msn4 are largely redundant, and cells can enhance the expression of their shared targets by increasing their temporal divergence. Thus, functional redundancy between these two paralogs is modulated in a dynamic manner to confer fitness advantages for yeast cells, which might feed back to promote the preservation of their redundancy. This evolutionary implication is supported by evidence from Msn2/Msn4 orthologs and analyses of other transcription factor paralogs. Together, we show a cell fate control mechanism through temporal redundancy modulation in yeast, which may represent an evolutionarily important strategy for maintaining functional redundancy between gene duplicates.
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Affiliation(s)
- Yan Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Jiaqi Wu
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Minghua Deng
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- School of Mathematical Sciences, Peking University, Beijing, China
- Center for Statistical Science, Peking University, Beijing, China
| | - Yihan Lin
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.
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Verta JP, Barton HJ, Pritchard V, Primmer CR. Genetic Drift Dominates Genome-Wide Regulatory Evolution Following an Ancient Whole-Genome Duplication in Atlantic Salmon. Genome Biol Evol 2021; 13:evab059. [PMID: 33749748 PMCID: PMC8140206 DOI: 10.1093/gbe/evab059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2021] [Indexed: 11/23/2022] Open
Abstract
Whole-genome duplications (WGD) have been considered as springboards that potentiate lineage diversification through increasing functional redundancy. Divergence in gene regulatory elements is a central mechanism for evolutionary diversification, yet the patterns and processes governing regulatory divergence following events that lead to massive functional redundancy, such as WGD, remain largely unknown. We studied the patterns of divergence and strength of natural selection on regulatory elements in the Atlantic salmon (Salmo salar) genome, which has undergone WGD 100-80 Ma. Using ChIPmentation, we first show that H3K27ac, a histone modification typical to enhancers and promoters, is associated with genic regions, tissue-specific transcription factor binding motifs, and with gene transcription levels in immature testes. Divergence in transcription between duplicated genes from WGD (ohnologs) correlated with difference in the number of proximal regulatory elements, but not with promoter elements, suggesting that functional divergence between ohnologs after WGD is mainly driven by enhancers. By comparing H3K27ac regions between duplicated genome blocks, we further show that a longer polyploid state post-WGD has constrained regulatory divergence. Patterns of genetic diversity across natural populations inferred from resequencing indicate that recent evolutionary pressures on H3K27ac regions are dominated by largely neutral evolution. In sum, our results suggest that post-WGD functional redundancy in regulatory elements continues to have an impact on the evolution of the salmon genome, promoting largely neutral evolution of regulatory elements despite their association with transcription levels. These results highlight a case where genome-wide regulatory evolution following an ancient WGD is dominated by genetic drift.
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Affiliation(s)
- Jukka-Pekka Verta
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
| | - Henry J Barton
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
| | - Victoria Pritchard
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
| | - Craig R Primmer
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
- Institute of Biotechnology, HiLIFE, University of Helsinki, Finland
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Gillard GB, Grønvold L, Røsæg LL, Holen MM, Monsen Ø, Koop BF, Rondeau EB, Gundappa MK, Mendoza J, Macqueen DJ, Rohlfs RV, Sandve SR, Hvidsten TR. Comparative regulomics supports pervasive selection on gene dosage following whole genome duplication. Genome Biol 2021; 22:103. [PMID: 33849620 PMCID: PMC8042706 DOI: 10.1186/s13059-021-02323-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Whole genome duplication (WGD) events have played a major role in eukaryotic genome evolution, but the consequence of these extreme events in adaptive genome evolution is still not well understood. To address this knowledge gap, we used a comparative phylogenetic model and transcriptomic data from seven species to infer selection on gene expression in duplicated genes (ohnologs) following the salmonid WGD 80-100 million years ago. RESULTS We find rare cases of tissue-specific expression evolution but pervasive expression evolution affecting many tissues, reflecting strong selection on maintenance of genome stability following genome doubling. Ohnolog expression levels have evolved mostly asymmetrically, by diverting one ohnolog copy down a path towards lower expression and possible pseudogenization. Loss of expression in one ohnolog is significantly associated with transposable element insertions in promoters and likely driven by selection on gene dosage including selection on stoichiometric balance. We also find symmetric expression shifts, and these are associated with genes under strong evolutionary constraints such as ribosome subunit genes. This possibly reflects selection operating to achieve a gene dose reduction while avoiding accumulation of "toxic mutations". Mechanistically, ohnolog regulatory divergence is dictated by the number of bound transcription factors in promoters, with transposable elements being one likely source of novel binding sites driving tissue-specific gains in expression. CONCLUSIONS Our results imply pervasive adaptive expression evolution following WGD to overcome the immediate challenges posed by genome doubling and to exploit the long-term genetic opportunities for novel phenotype evolution.
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Affiliation(s)
- Gareth B. Gillard
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Lars Grønvold
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Line L. Røsæg
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Matilde Mengkrog Holen
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Øystein Monsen
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Ben F. Koop
- Department of Biology, University of Victoria, Victoria, Canada
| | - Eric B. Rondeau
- Department of Biology, University of Victoria, Victoria, Canada
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - John Mendoza
- Department of Computer Science, San Francisco State University, San Francisco, USA
| | - Daniel J. Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Rori V. Rohlfs
- Department of Biology, San Francisco State University, San Francisco, USA
| | - Simen R. Sandve
- Center for Integrative Genetics, Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Torgeir R. Hvidsten
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
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Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep. Sci Rep 2021; 11:2466. [PMID: 33510350 PMCID: PMC7844035 DOI: 10.1038/s41598-021-81932-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/11/2021] [Indexed: 12/14/2022] Open
Abstract
The identification of genome-wide selection signatures can provide insights on the mechanisms of natural and/or artificial selection and uncover genes related to biological functions and/or phenotypes. Tibetan sheep are an important livestock in Tibet, providing meat and wool for Tibetans who are renown for breeding livestock that adapt well to high altitudes. Using whole-genome sequences with an effective sequencing depth of 5×, we investigated the genomic diversity and structure and, identified selection signatures of White Tibetan, Oula and Poll Dorset sheep. We obtained 30,163,679 Single Nucleotide Polymorphisms (SNPs) and 5,388,372 indels benchmarked against the ovine Oar_v4.0 genome assembly. Next, using FST, ZHp and XP-EHH approaches, we identified selection signatures spanning a set of candidate genes, including HIF1A, CAPN3, PRKAA1, RXFP2, TRHR and HOXA10 that are associated with pathways and GO categories putatively related to hypoxia responses, meat traits and disease resistance. Candidate genes and GO terms associated with coat color were also identified. Finally, quantification of blood physiological parameters, revealed higher levels of mean corpuscular hemoglobin measurement and mean corpuscular hemoglobin concentration in Tibetan sheep compared with Poll Dorset, suggesting a greater oxygen-carrying capacity in the Tibetan sheep and thus better adaptation to high-altitude hypoxia. In conclusion, this study provides a greater understanding of genome diversity and variations associated with adaptive and production traits in sheep.
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Basu S, Mallik S, Hait S, Kundu S. Genome-scale molecular principles of mRNA half-life regulation in yeast. FEBS J 2020; 288:3428-3447. [PMID: 33319437 DOI: 10.1111/febs.15670] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 11/07/2020] [Accepted: 12/11/2020] [Indexed: 12/22/2022]
Abstract
Precise control of protein and messenger RNA (mRNA) degradation is essential for cellular metabolism and homeostasis. Controlled and specific degradation of both molecular species necessitates their engagements with the respective degradation machineries; this engagement involves a disordered/unstructured segment of the substrate traversing the degradation tunnel of the machinery and accessing the catalytic sites. However, while molecular factors influencing protein degradation have been extensively explored on a genome scale, and in multiple organisms, such a comprehensive understanding remains missing for mRNAs. Here, we analyzed multiple genome-scale experimental yeast mRNA half-life data in light of experimentally derived mRNA secondary structures and protein binding data, along with high-resolution X-ray crystallographic structures of the RNase machines. Results unraveled a consistent genome-scale trend that mRNAs comprising longer terminal and/or internal unstructured segments have significantly shorter half-lives; the lengths of the 5'-terminal, 3'-terminal, and internal unstructured segments that affect mRNA half-life are compatible with molecular structures of the 5' exo-, 3' exo-, and endoribonuclease machineries. Sequestration into ribonucleoprotein complexes elongates mRNA half-life, presumably by burying ribonuclease engagement sites under oligomeric interfaces. After gene duplication, differences in terminal unstructured lengths, proportions of internal unstructured segments, and oligomerization modes result in significantly altered half-lives of paralogous mRNAs. Side-by-side comparison of molecular principles underlying controlled protein and mRNA degradation in yeast unravels their remarkable mechanistic similarities and suggests how the intrinsic structural features of the two molecular species, at two different levels of the central dogma, regulate their half-lives on genome scale.
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Affiliation(s)
- Sudipto Basu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
| | - Saurav Mallik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Suman Hait
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India
| | - Sudip Kundu
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata, India.,Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, Kolkata, India
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Pechmann S. Programmed Trade-offs in Protein Folding Networks. Structure 2020; 28:1361-1375.e4. [PMID: 33053320 DOI: 10.1016/j.str.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/25/2020] [Accepted: 09/23/2020] [Indexed: 12/14/2022]
Abstract
Molecular chaperones as specialized protein quality control enzymes form the core of cellular protein homeostasis. How chaperones selectively interact with their substrate proteins thus allocate their overall limited capacity remains poorly understood. Here, I present an integrated analysis of sequence and structural determinants that define interactions of protein domains as the basic protein folding unit with the Saccharomyces cerevisiae Hsp70 Ssb. Structural homologs of single-domain proteins that differentially interact with Ssb for de novo folding were found to systematically differ in complexity of their folding landscapes, selective use of nonoptimal codons, and presence of short discriminative sequences, thus highlighting pervasive trade-offs in chaperone-assisted protein folding landscapes. However, short discriminative sequences were found to contribute by far the strongest signal toward explaining Ssb interactions. This observation suggested that some chaperone interactions may be directly programmed in the amino acid sequences rather than responding to folding challenges, possibly for regulatory advantages.
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Affiliation(s)
- Sebastian Pechmann
- Département de biochimie, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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11
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Transcriptional Rewiring, Adaptation, and the Role of Gene Duplication in the Metabolism of Ethanol of Saccharomyces cerevisiae. mSystems 2020; 5:5/4/e00416-20. [PMID: 32788405 PMCID: PMC7426151 DOI: 10.1128/msystems.00416-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ethanol is the main by-product of yeast sugar fermentation that affects microbial growth parameters, being considered a dual molecule, a nutrient and a stressor. Previous works demonstrated that the budding yeast arose after an ancient hybridization process resulted in a tier of duplicated genes within its genome, many of them with implications in this ethanol "produce-accumulate-consume" strategy. The evolutionary link between ethanol production, consumption, and tolerance versus ploidy and stability of the hybrids is an ongoing debatable issue. The implication of ancestral duplicates in this metabolic rewiring, and how these duplicates differ transcriptionally, remains unsolved. Here, we study the transcriptomic adaptive signatures to ethanol as a nonfermentative carbon source to sustain clonal yeast growth by experimental evolution, emphasizing the role of duplicated genes in the adaptive process. As expected, ethanol was able to sustain growth but at a lower rate than glucose. Our results demonstrate that in asexual populations a complete transcriptomic rewiring was produced, strikingly by downregulation of duplicated genes, mainly whole-genome duplicates, whereas small-scale duplicates exhibited significant transcriptional divergence between copies. Overall, this study contributes to the understanding of evolution after gene duplication, linking transcriptional divergence with duplicates' fate in a multigene trait as ethanol tolerance.IMPORTANCE Gene duplication events have been related with increasing biological complexity through the tree of life, but also with illnesses, including cancer. Early evolutionary theories indicated that duplicated genes could explore alternative functions due to relaxation of selective constraints in one of the copies, as the other remains as ancestral-function backup. In unicellular eukaryotes like yeasts, it has been demonstrated that the fate and persistence of duplicates depend on duplication mechanism (whole-genome or small-scale events), shaping their actual genomes. Although it has been shown that small-scale duplicates tend to innovate and whole-genome duplicates specialize in ancestral functions, the implication of duplicates' transcriptional plasticity and transcriptional divergence on environmental and metabolic responses remains largely obscure. Here, by experimental adaptive evolution, we show that Saccharomyces cerevisiae is able to respond to metabolic stress (ethanol as nonfermentative carbon source) due to the persistence of duplicated genes. These duplicates respond by transcriptional rewiring, depending on their transcriptional background. Our results shed light on the mechanisms that determine the role of duplicates, and on their evolvability.
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