1
|
Lawal RA, Arora UP, Dumont BL. Selection shapes the landscape of functional variation in wild house mice. BMC Biol 2021; 19:239. [PMID: 34794440 PMCID: PMC8603481 DOI: 10.1186/s12915-021-01165-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/14/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Through human-aided dispersal over the last ~ 10,000 years, house mice (Mus musculus) have recently colonized diverse habitats across the globe, promoting the emergence of new traits that confer adaptive advantages in distinct environments. Despite their status as the premier mammalian model system, the impact of this demographic and selective history on the global patterning of disease-relevant trait variation in wild mouse populations is poorly understood. RESULTS Here, we leveraged 154 whole-genome sequences from diverse wild house mouse populations to survey the geographic organization of functional variation and systematically identify signals of positive selection. We show that a significant proportion of wild mouse variation is private to single populations, including numerous predicted functional alleles. In addition, we report strong signals of positive selection at many genes associated with both complex and Mendelian diseases in humans. Notably, we detect a significant excess of selection signals at disease-associated genes relative to null expectations, pointing to the important role of adaptation in shaping the landscape of functional variation in wild mouse populations. We also uncover strong signals of selection at multiple genes involved in starch digestion, including Mgam and Amy1. We speculate that the successful emergence of the human-mouse commensalism may have been facilitated, in part, by dietary adaptations at these loci. Finally, our work uncovers multiple cryptic structural variants that manifest as putative signals of positive selection, highlighting an important and under-appreciated source of false-positive signals in genome-wide selection scans. CONCLUSIONS Overall, our findings highlight the role of adaptation in shaping wild mouse genetic variation at human disease-associated genes. Our work also highlights the biomedical relevance of wild mouse genetic diversity and underscores the potential for targeted sampling of mice from specific populations as a strategy for developing effective new mouse models of both rare and common human diseases.
Collapse
Affiliation(s)
| | - Uma P Arora
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA
| | - Beth L Dumont
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, 04609, USA.
- Tufts University, Graduate School of Biomedical Sciences, 136 Harrison Ave, Boston, MA, 02111, USA.
| |
Collapse
|
2
|
Li T, Pan W, Yuan Y, Liu Y, Li Y, Wu X, Wang F, Cui L. Identification, Characterization, and Expression Profile Analysis of the mTERF Gene Family and Its Role in the Response to Abiotic Stress in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2021; 12:684619. [PMID: 34335653 PMCID: PMC8319850 DOI: 10.3389/fpls.2021.684619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/23/2021] [Indexed: 05/17/2023]
Abstract
Plant mitochondrial transcription termination factor (mTERF) family regulates organellar gene expression (OGE) and is functionally characterized in diverse species. However, limited data are available about its functions in the agriculturally important cereal barley (Hordeum vulgare L.). In this study, we identified 60 mTERFs in the barley genome (HvmTERFs) through a comprehensive search against the most updated barley reference genome, Morex V2. Then, phylogenetic analysis categorized these genes into nine subfamilies, with approximately half of the HvmTERFs belonging to subfamily IX. Members within the same subfamily generally possessed conserved motif composition and exon-intron structure. Both segmental and tandem duplication contributed to the expansion of HvmTERFs, and the duplicated gene pairs were subjected to strong purifying selection. Expression analysis suggested that many HvmTERFs may play important roles in barley development (e.g., seedlings, leaves, and developing inflorescences) and abiotic stresses (e.g., cold, salt, and metal ion), and HvmTERF21 and HvmTERF23 were significant induced by various abiotic stresses and/or phytohormone treatment. Finally, the nucleotide diversity was decreased by only 4.5% for HvmTERFs during the process of barley domestication. Collectively, this is the first report to characterize HvmTERFs, which will not only provide important insights into further evolutionary studies but also contribute to a better understanding of the potential functions of HvmTERFs and ultimately will be useful in future gene functional studies.
Collapse
Affiliation(s)
- Tingting Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
| | - Yiyuan Yuan
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Ying Liu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Xiaoyu Wu
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Fei Wang
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, China
- *Correspondence: Licao Cui
| |
Collapse
|
3
|
Du H, Zhang H, Wei L, Li C, Duan Y, Wang H. A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.). BMC PLANT BIOLOGY 2019; 19:588. [PMID: 31881840 PMCID: PMC6935206 DOI: 10.1186/s12870-019-2172-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 11/28/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F3 progeny. RESULTS The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R2) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed. CONCLUSIONS This report presents the first QTL mapping of seed-related traits in sesame using an F2 population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.
Collapse
Affiliation(s)
- Hua Du
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Haiyang Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Libin Wei
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Chun Li
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Yinghui Duan
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| | - Huili Wang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002 People’s Republic of China
| |
Collapse
|
4
|
Han Y, Gao P, Qiu S, Zhang L, Yang L, Zuo J, Zhong C, Zhu S, Liu W. MTERF2 contributes to MPP+-induced mitochondrial dysfunction and cell damage. Biochem Biophys Res Commun 2016; 471:177-83. [DOI: 10.1016/j.bbrc.2016.01.156] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 01/24/2016] [Indexed: 02/05/2023]
|
5
|
MTERF4 regulates the mitochondrial dysfunction induced by MPP+ in SH-SY5Y cells. Biochem Biophys Res Commun 2015; 464:214-20. [DOI: 10.1016/j.bbrc.2015.06.119] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 06/17/2015] [Indexed: 11/21/2022]
|
6
|
Chen G, Dai J, Tan S, Meng S, Liu Z, Li M, Cui Q, Yu M. MTERF1 regulates the oxidative phosphorylation activity and cell proliferation in HeLa cells. Acta Biochim Biophys Sin (Shanghai) 2014; 46:512-21. [PMID: 24777141 DOI: 10.1093/abbs/gmu029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mitochondrial transcription termination factor (MTERF) family is a group of highly conserved DNA-binding proteins composed of four key members, MTERF1-4. To date, several studies have investigated the binding sites of MTERF1 on mitochondrial genome and the regulation of mitochondrial gene transcription, but the more intricate connection between mitochondrial genes transcription regulation, mitochondrial oxidative phosphorylation (OXPHOS), and cell proliferation is still poorly understood. In this study, we constructed over-expression and knockdown vectors of MTERF1 that were transfected into HeLa cells to investigate the functions of MTERF1. Results showed that although MTERF1 is a positive regulatory factor of mitochondrial genes transcription, it had no significant effect on the replication of mitochondrial DNA. Over-expression of MTERF1 increased mitochondrial oxidative phosphorylation activity and promoted ATP synthesis, cyclin D1 expression, and cell proliferation, while its knockdown inhibited ATP synthesis, decreased cyclin D1 expression, and slowed the cell growth. These results suggested that MTERF1 may promote cell proliferation by regulating oxidative phosphorylation activity in HeLa cells. Ultimately, these findings create a foundation for further and more conclusive studies on the physiological functions of MTERF family by providing novel insights into the potential mechanisms underlying cell proliferation regulation.
Collapse
Affiliation(s)
- Guiyuan Chen
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China Department of Biochemistry and Molecular Biology, School of Basic Medicine, Dali University, Dali 671000, China
| | - Jie Dai
- Yunnan Province Disease Prevention Control Center, Kunming 650031, China
| | - Shirui Tan
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Shengke Meng
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Zhongjian Liu
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Meizhang Li
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Qinghua Cui
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Min Yu
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming 650091, China
| |
Collapse
|
7
|
Zhang Y, Guo L, Shu Z, Sun Y, Chen Y, Liang Z, Guo H. Identification of Amplified Fragment Length Polymorphism (AFLP) Markers Tightly Associated with Drought Stress Gene in Male Sterile and Fertile Salvia miltiorrhiza Bunge. Int J Mol Sci 2013; 14:6518-28. [PMID: 23525049 PMCID: PMC3634402 DOI: 10.3390/ijms14036518] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 02/22/2013] [Accepted: 02/25/2013] [Indexed: 11/16/2022] Open
Abstract
Consistent grain yield in drought environment has attracted wide attention due to global climate change. However, the important drought-related traits/genes in crops have been rarely reported. Many near-isogenic lines (NILs) of male sterile and fertile Salvia miltiorrhiza have been obtained in our previous work through testcross and backcross in continuous field experiments conducted in 2006-2009. Both segregating sterile and fertile populations were subjected to bulked segregant analysis (BSA) and amplified fragment length polymorphism (AFLP) with 384 and 170 primer combinations, respectively. One out of 14 AFLP markers (E9/M3246) was identified in treated fertile population as tightly linked to the drought stress gene with a recombination frequency of 6.98% and at a distance of 7.02 cM. One of 15 other markers (E2/M5357) was identified in a treated sterile population that is closely associated with the drought stress gene. It had a recombination frequency of 4.65% and at a distance of 4.66 cM. Interestingly, the E9/M3246 fragment was found to be identical to another AFLP fragment E11/M4208 that was tightly linked to the male sterile gene of S. miltiorrhiza with 95% identity and e-value 4 × 10-93. Blastn analysis suggested that the drought stress gene sequence showed higher identity with nucleotides in Arabidopsis chromosome 1-5.
Collapse
Affiliation(s)
| | | | - Zhiming Shu
- Shaanxi Research Center of TCM Fingerprinting and NP Library, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (Y.Z.); (L.G.); (Z.S.); (Y.S.); (Y.C.); (Z.L.)
| | - Yiyue Sun
- Shaanxi Research Center of TCM Fingerprinting and NP Library, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (Y.Z.); (L.G.); (Z.S.); (Y.S.); (Y.C.); (Z.L.)
| | - Yuanyuan Chen
- Shaanxi Research Center of TCM Fingerprinting and NP Library, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (Y.Z.); (L.G.); (Z.S.); (Y.S.); (Y.C.); (Z.L.)
| | - Zongsuo Liang
- Shaanxi Research Center of TCM Fingerprinting and NP Library, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (Y.Z.); (L.G.); (Z.S.); (Y.S.); (Y.C.); (Z.L.)
| | - Hongbo Guo
- Shaanxi Research Center of TCM Fingerprinting and NP Library, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China; E-Mails: (Y.Z.); (L.G.); (Z.S.); (Y.S.); (Y.C.); (Z.L.)
| |
Collapse
|
8
|
Xiong W, Jiao Y, Huang W, Ma M, Yu M, Cui Q, Tan D. Regulation of the cell cycle via mitochondrial gene expression and energy metabolism in HeLa cells. Acta Biochim Biophys Sin (Shanghai) 2012; 44:347-58. [PMID: 22343378 DOI: 10.1093/abbs/gms006] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Human cervical cancer HeLa cells have functional mitochondria. Recent studies have suggested that mitochondrial metabolism plays an essential role in tumor cell proliferation. Nevertheless, how cells coordinate mitochondrial dynamics and cell cycle progression remains to be clarified. To investigate the relationship between mitochondrial function and cell cycle regulation, the mitochondrial gene expression profile and cellular ATP levels were determined by cell cycle progress analysis in the present study. HeLa cells were synchronized in the G0/G1 phase by serum starvation, and re-entered cell cycle by restoring serum culture, time course experiment was performed to analyze the expression of mitochondrial transcription regulators and mitochondrial genes, mitochondrial membrane potential (MMP), cellular ATP levels, and cell cycle progression. The results showed that when arrested G0/G1 cells were stimulated in serum-containing medium, the amount of DNA and the expression levels of both mRNA and proteins in mitochondria started to increase at 2 h time point, whereas the MMP and ATP level elevated at 4 h. Furthermore, the cyclin D1 expression began to increase at 4 h after serum triggered cell cycle. ATP synthesis inhibitor-oligomycin-treatment suppressed the cyclin D1 and cyclin B1 expression levels and blocked cell cycle progression. Taken together, our results suggested that increased mitochondrial gene expression levels, oxidative phosphorylation activation, and cellular ATP content increase are important events for triggering cell cycle. Finally, we demonstrated that mitochondrial gene expression levels and cellular ATP content are tightly regulated and might play a central role in regulating cell proliferation.
Collapse
Affiliation(s)
- Wei Xiong
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, Kunming, China
| | | | | | | | | | | | | |
Collapse
|
9
|
Guja KE, Garcia-Diaz M. Hitting the brakes: termination of mitochondrial transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:939-47. [PMID: 22137970 DOI: 10.1016/j.bbagrm.2011.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 11/07/2011] [Accepted: 11/15/2011] [Indexed: 10/15/2022]
Abstract
Deficiencies in mitochondrial protein production are associated with human disease and aging. Given the central role of transcription in gene expression, recent years have seen a renewed interest in understanding the molecular mechanisms controlling this process. In this review, we have focused on the mostly uncharacterized process of transcriptional termination. We review how several recent breakthroughs have provided insight into our understanding of the termination mechanism, the protein factors that mediate termination, and the functional relevance of different termination events. Furthermore, the identification of termination defects resulting from a number of mtDNA mutations has led to the suggestion that this could be a common mechanism influencing pathogenesis in a number of mitochondrial diseases, highlighting the importance of understanding the processes that regulate transcription in human mitochondria. We discuss how these recent findings set the stage for future studies on this important regulatory mechanism. This article is part of a Special Issue entitled: Mitochondrial Gene Expression.
Collapse
Affiliation(s)
- Kip E Guja
- Medical Scientist Training Program, Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, NY 11794, USA.
| | | |
Collapse
|
10
|
Xiong W, Huang W, Jiao Y, Ma J, Yu M, Ma M, Wu H, Tan D. Production, purification and characterization of mouse monoclonal antibodies against human mitochondrial transcription termination factor 2 (MTERF2). Protein Expr Purif 2011; 82:11-9. [PMID: 22094411 DOI: 10.1016/j.pep.2011.10.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 10/28/2011] [Accepted: 10/31/2011] [Indexed: 10/15/2022]
Abstract
Human mitochondrial transcription termination factor 2 (MTERF2) is a member of the mitochondrial transcription termination factors (MTERFs) family and a cell growth inhibitor. To create a specific mouse monoclonal antibody against human MTERF2, the full-length His-tag MTERF2 protein (1-385 aa) was expressed in Escherichia coli, and purified recombinant protein was injected into three BALB/c mice to perform an immunization procedure. Eight stable positive monoclonal cell lines were screened and established. ELISA results demonstrated that all antibody light chains were kappa, while the heavy chains displayed three subtypes IgG1, IgG2a, and IgG2b respectively. The sensitivity and specificity of the monoclonal antibodies against human MTERF2 were determined using immunoblotting, immunoprecipitation and immunofluorescence analyses. Furthermore, serum regulation of human MTERF2 protein expression levels in human glioma U251 cells was examined with these monoclonal antibodies and the results demonstrated that the expression level of MTERF2 protein was dramatically inhibited by the addition of serum to serum-starved cells. Taken together, our results demonstrate the functionality of these mouse anti-human MTERF2 monoclonal antibodies, which may provide a useful tool to elucidate the role of MTERF2 in human mitochondrial transcription as well as other potential activities. To our knowledge, this is the first report on the preparation and characterization of mouse monoclonal antibodies against human MTERF2.
Collapse
Affiliation(s)
- Wei Xiong
- Laboratory of Biochemistry and Molecular Biology, School of Life Sciences, Yunnan University, 002 Cuihu Road, Kunming 650091, PR China
| | | | | | | | | | | | | | | |
Collapse
|