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Kou SH, Li J, Tam B, Lei H, Zhao B, Xiao F, Wang S. TP53 germline pathogenic variants in modern humans were likely originated during recent human history. NAR Cancer 2023; 5:zcad025. [PMID: 37304756 PMCID: PMC10251638 DOI: 10.1093/narcan/zcad025] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/05/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
TP53 is crucial for maintaining genome stability and preventing oncogenesis. Germline pathogenic variation in TP53 damages its function, causing genome instability and increased cancer risk. Despite extensive study in TP53, the evolutionary origin of the human TP53 germline pathogenic variants remains largely unclear. In this study, we applied phylogenetic and archaeological approaches to identify the evolutionary origin of TP53 germline pathogenic variants in modern humans. In the phylogenic analysis, we searched 406 human TP53 germline pathogenic variants in 99 vertebrates distributed in eight clades of Primate, Euarchontoglires, Laurasiatheria, Afrotheria, Mammal, Aves, Sarcopterygii and Fish, but we observed no direct evidence for the cross-species conservation as the origin; in the archaeological analysis, we searched the variants in 5031 ancient human genomes dated between 45045 and 100 years before present, and identified 45 pathogenic variants in 62 ancient humans dated mostly within the last 8000 years; we also identified 6 pathogenic variants in 3 Neanderthals dated 44000 to 38515 years before present and 1 Denisovan dated 158 550 years before present. Our study reveals that TP53 germline pathogenic variants in modern humans were likely originated in recent human history and partially inherited from the extinct Neanderthals and Denisovans.
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Affiliation(s)
- Si Hoi Kou
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Jiaheng Li
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Benjamin Tam
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Huijun Lei
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Bojin Zhao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - Fengxia Xiao
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
| | - San Ming Wang
- Ministry of Education Frontiers Science Center for Precision Oncology, Cancer Centre and Institute of Translational Medicine, Department of Public Health and Medical Administration, Faculty of Health Sciences, University of Macau, Macao SAR, China
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Wheeler LC, Walker JF, Ng J, Deanna R, Dunbar-Wallis A, Backes A, Pezzi PH, Palchetti MV, Robertson HM, Monaghan A, Brandão de Freitas L, Barboza GE, Moyroud E, Smith SD. Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway. Mol Biol Evol 2022; 39:6536971. [PMID: 35212724 PMCID: PMC8911815 DOI: 10.1093/molbev/msac044] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Dissecting the relationship between gene function and substitution rates is key to understanding genome-wide patterns of molecular evolution. Biochemical pathways provide powerful systems for investigating this relationship because the functional role of each gene is often well characterized. Here, we investigate the evolution of the flavonoid pigment pathway in the colorful Petunieae clade of the tomato family (Solanaceae). This pathway is broadly conserved in plants, both in terms of its structural elements and its MYB, basic helix–loop–helix, and WD40 transcriptional regulators, and its function has been extensively studied, particularly in model species of petunia. We built a phylotranscriptomic data set for 69 species of Petunieae to infer patterns of molecular evolution across pathway genes and across lineages. We found that transcription factors exhibit faster rates of molecular evolution (dN/dS) than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative data set to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions, although expression levels do predict molecular evolutionary rates. Although shifts in floral pigmentation were only weakly related to changes affecting coding regions, we found a strong relationship with the presence/absence patterns of MYB transcripts. Intensely pigmented species express all three main MYB anthocyanin activators in petals, whereas pale or white species express few or none. Our findings reinforce the notion that pathway regulators have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.
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Affiliation(s)
- Lucas C Wheeler
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
| | - Joseph F Walker
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, 60607 U.S.A
| | - Julienne Ng
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
| | - Rocío Deanna
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334.,Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina
| | - Amy Dunbar-Wallis
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
| | - Alice Backes
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Pedro H Pezzi
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - M Virginia Palchetti
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina
| | - Holly M Robertson
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Andrew Monaghan
- Research Computing,University of Colorado, 3100 Marine Street, 597 UCB Boulder, CO 80303
| | - Loreta Brandão de Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, 91501-970, Porto Alegre, RS, Brazil
| | - Gloria E Barboza
- Instituto Multidisciplinario de Biología Vegetal (IMBIV), CONICET and Universidad Nacional de Córdoba, CC 495, CP 5000, Córdoba, Argentina.,Facultad de Ciencias Químicas, Universidad Nacional de Córdoba,Haya de la Torre y Medina Allende, Córdoba, Argentina
| | - Edwige Moyroud
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, 1900 Pleasant Street 334 UCB, Boulder, CO, USA, 80309-0334
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Bronikowski AM, Meisel RP, Biga PR, Walters J, Mank JE, Larschan E, Wilkinson GS, Valenzuela N, Conard AM, de Magalhães JP, Duan J, Elias AE, Gamble T, Graze R, Gribble KE, Kreiling JA, Riddle NC. Sex-specific aging in animals: Perspective and future directions. Aging Cell 2022; 21:e13542. [PMID: 35072344 PMCID: PMC8844111 DOI: 10.1111/acel.13542] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/15/2021] [Accepted: 12/11/2021] [Indexed: 12/14/2022] Open
Abstract
Sex differences in aging occur in many animal species, and they include sex differences in lifespan, in the onset and progression of age-associated decline, and in physiological and molecular markers of aging. Sex differences in aging vary greatly across the animal kingdom. For example, there are species with longer-lived females, species where males live longer, and species lacking sex differences in lifespan. The underlying causes of sex differences in aging remain mostly unknown. Currently, we do not understand the molecular drivers of sex differences in aging, or whether they are related to the accepted hallmarks or pillars of aging or linked to other well-characterized processes. In particular, understanding the role of sex-determination mechanisms and sex differences in aging is relatively understudied. Here, we take a comparative, interdisciplinary approach to explore various hypotheses about how sex differences in aging arise. We discuss genomic, morphological, and environmental differences between the sexes and how these relate to sex differences in aging. Finally, we present some suggestions for future research in this area and provide recommendations for promising experimental designs.
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Affiliation(s)
- Anne M. Bronikowski
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | - Richard P. Meisel
- Department of Biology and BiochemistryUniversity of HoustonHoustonTexasUSA
| | - Peggy R. Biga
- Department of BiologyThe University of Alabama at BirminghamBirminghamAlabamaUSA
| | - James R. Walters
- Department of Ecology and Evolutionary BiologyThe University of KansasLawrenceKansasUSA
| | - Judith E. Mank
- Department of ZoologyUniversity of British ColumbiaVancouverBritish ColumbiaCanada
- Department of BioscienceUniversity of ExeterPenrynUK
| | - Erica Larschan
- Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode IslandUSA
| | | | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | - Ashley Mae Conard
- Department of Computer ScienceCenter for Computational and Molecular BiologyBrown UniversityProvidenceRhode IslandUSA
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing GroupInstitute of Ageing and Chronic DiseaseUniversity of LiverpoolLiverpoolUK
| | | | - Amy E. Elias
- Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode IslandUSA
| | - Tony Gamble
- Department of Biological SciencesMarquette UniversityMilwaukeeWisconsinUSA
- Milwaukee Public MuseumMilwaukeeWisconsinUSA
- Bell Museum of Natural HistoryUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Rita M. Graze
- Department of Biological SciencesAuburn UniversityAuburnAlabamaUSA
| | - Kristin E. Gribble
- Josephine Bay Paul Center for Comparative Molecular Biology and EvolutionMarine Biological LaboratoryWoods HoleMassachusettsUSA
| | - Jill A. Kreiling
- Department of Molecular Biology, Cell Biology and BiochemistryBrown UniversityProvidenceRhode IslandUSA
| | - Nicole C. Riddle
- Department of BiologyThe University of Alabama at BirminghamBirminghamAlabamaUSA
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The Changes in the p53 Protein across the Animal Kingdom Point to Its Involvement in Longevity. Int J Mol Sci 2021; 22:ijms22168512. [PMID: 34445220 PMCID: PMC8395165 DOI: 10.3390/ijms22168512] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 12/14/2022] Open
Abstract
Recently, the quest for the mythical fountain of youth has produced extensive research programs that aim to extend the healthy lifespan of humans. Despite advances in our understanding of the aging process, the surprisingly extended lifespan and cancer resistance of some animal species remain unexplained. The p53 protein plays a crucial role in tumor suppression, tissue homeostasis, and aging. Long-lived, cancer-free African elephants have 20 copies of the TP53 gene, including 19 retrogenes (38 alleles), which are partially active, whereas humans possess only one copy of TP53 and have an estimated cancer mortality rate of 11–25%. The mechanism through which p53 contributes to the resolution of the Peto’s paradox in Animalia remains vague. Thus, in this work, we took advantage of the available datasets and inspected the p53 amino acid sequence of phylogenetically related organisms that show variations in their lifespans. We discovered new correlations between specific amino acid deviations in p53 and the lifespans across different animal species. We found that species with extended lifespans have certain characteristic amino acid substitutions in the p53 DNA-binding domain that alter its function, as depicted from the Phenotypic Annotation of p53 Mutations, using the PROVEAN tool or SWISS-MODEL workflow. In addition, the loop 2 region of the human p53 DNA-binding domain was identified as the longest region that was associated with longevity. The 3D model revealed variations in the loop 2 structure in long-lived species when compared with human p53. Our findings show a direct association between specific amino acid residues in p53 protein, changes in p53 functionality, and the extended animal lifespan, and further highlight the importance of p53 protein in aging.
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Beatty AE, Schwartz TS. Gene expression of the IGF hormones and IGF binding proteins across time and tissues in a model reptile. Physiol Genomics 2020; 52:423-434. [PMID: 32776803 PMCID: PMC7509249 DOI: 10.1152/physiolgenomics.00059.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/16/2022] Open
Abstract
The insulin and insulin-like signaling (IIS) network regulates cellular processes including pre- and postnatal growth, cellular development, wound healing, reproduction, and longevity. Despite their importance in the physiology of vertebrates, the study of the specific functions of the top regulators of the IIS network, insulin-like growth factors (IGFs) and IGF binding proteins (IGFBPs), has been mostly limited to a few model organisms. To expand our understanding of this network, we performed quantitative gene expression of IGF hormones in liver and qualitative expression of IGFBPs across tissues and developmental stages in a model reptile, the brown anole lizard (Anolis sagrei). We found that lizards express IGF2 across all life stages (preoviposition embryos to adulthood) and at a higher level than IGF1, which is opposite to patterns seen in laboratory rodents but similar to those seen in humans and other vertebrate models. IGFBP expression was ubiquitous across tissues (brain, gonad, heart, liver, skeletal muscle, tail, and regenerating tail) in adults, apart from IGFBP5, which was variable. These findings provide an essential foundation for further developing the anole lizard as a physiological and biomedical reptile model, as well as expanding our understanding of the function of the IIS network across species.
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Affiliation(s)
- Abby E Beatty
- Department of Biological Sciences, Auburn University, Auburn, Alabama
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, Alabama
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Hoekstra LA, Schwartz TS, Sparkman AM, Miller DAW, Bronikowski AM. The untapped potential of reptile biodiversity for understanding how and why animals age. Funct Ecol 2020; 34:38-54. [PMID: 32921868 PMCID: PMC7480806 DOI: 10.1111/1365-2435.13450] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022]
Abstract
1. The field of comparative aging biology has greatly expanded in the past 20 years. Longitudinal studies of populations of reptiles with a range of maximum lifespans have accumulated and been analyzed for evidence of mortality senescence and reproductive decline. While not as well represented in studies of amniote senescence, reptiles have been the subjects of many recent demographic and mechanistic studies of the biology of aging. 2. We review recent literature on reptile demographic senescence, mechanisms of senescence, and identify unanswered questions. Given the ecophysiological and demographic diversity of reptiles, what is the expected range of reptile senescence rates? Are known mechanisms of aging in reptiles consistent with canonical hallmarks of aging in model systems? What are the knowledge gaps in our understanding of reptile aging? 3. We find ample evidence of increasing mortality with advancing age in many reptiles. Testudines stand out as slower aging than other orders, but data on crocodilians and tuatara are sparse. Sex-specific analyses are generally not available. Studies of female reproduction suggest that reptiles are less likely to have reproductive decline with advancing age than mammals. 4. Reptiles share many physiological and molecular pathways of aging with mammals, birds, and laboratory model organisms. Adaptations related to stress physiology coupled with reptilian ectothermy suggest novel comparisons and contrasts that can be made with canonical aging phenotypes in mammals. These include stem cell and regeneration biology, homeostatic mechanisms, IIS/TOR signaling, and DNA repair. 5. To overcome challenges to the study of reptile aging, we recommend extending and expanding long-term monitoring of reptile populations, developing reptile cell lines to aid cellular biology, conducting more comparative studies of reptile morphology and physiology sampled along relevant life-history axes, and sequencing more reptile genomes for comparative genomics. Given the diversity of reptile life histories and adaptations, achieving these directives will likely greatly benefit all aging biology.
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Affiliation(s)
- Luke A Hoekstra
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50010, USA
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
| | - Amanda M Sparkman
- Department of Biology, Westmont College, Santa Barbara, California, 93108, USA
| | - David A W Miller
- Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802, USA
| | - Anne M Bronikowski
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, 50010, USA
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