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Shahzad A, Fan Y, Qian M, Khan SU, Mahmood U, Wei L, Qu C, Lu K. Genome-wide characterization of Related to ABI3/VP1 transcription factors among U's triangle Brassica species reveals a negative role for BnaA06.RAV3L in seed size. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108854. [PMID: 38901228 DOI: 10.1016/j.plaphy.2024.108854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/01/2024] [Accepted: 06/16/2024] [Indexed: 06/22/2024]
Abstract
The transcription factors Related to ABI3/VP1 (RAV) are crucial for various plant processes and stress responses. Although the U's triangle Brassica species genomes have been released, the knowledge regarding the RAV family is still limited. In this study, we identified 123 putative RAV genes across the six U's triangle Brassica species (Brassica rapa, 14; Brassica oleracea, 14; Brassica nigra, 13; Brassica carinata, 27; Brassica juncea, 28; Brassica napus, 27). Phylogenetic analysis categorized them into three groups. The RAV genes exhibited diversity in both functional and structural aspects, particularly in gene structure and cis-acting elements within their promoters. The expression analysis revealed that BnaRAV genes in Group 1/2 exhibited diverse expression patterns across various tissues, while those in Group 3 did not show expression except for BnaRAV3L-2 and BnaRAV3L-6, which were exclusively expressed in seeds. Furthermore, the seed-specific expression of BnaA06. RAV3L (BnaRAV3L-2) was confirmed through promoter-GUS staining. Subcellular localization studies demonstrated that BnaA06.RAV3L is localized to the nucleus. The overexpression of BnaA06. RAV3L in Arabidopsis led to a remarkable inhibition of seed-specific traits such as seed width, seed length, seed area, and seed weight. This study provides insights into the functional evolution of the RAV gene family in U triangle Brassica species. It establishes a foundation for uncovering the molecular mechanisms underlying the negative role of RAV3L in seed development.
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Affiliation(s)
- Ali Shahzad
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Yonghai Fan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Mingchao Qian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Shahid Ullah Khan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Umer Mahmood
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Lijuan Wei
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Cunmin Qu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Kun Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Beibei, Chongqing, 400715, China.
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Parakkunnel R, K BN, Vanishree G, George A, Kv S, Yr A, K UB, Anandan A, Kumar S. Exploring selection signatures in the divergence and evolution of lipid droplet (LD) associated genes in major oilseed crops. BMC Genomics 2024; 25:653. [PMID: 38956471 PMCID: PMC11218257 DOI: 10.1186/s12864-024-10527-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Oil bodies or lipid droplets (LDs) in the cytosol are the subcellular storage compartments of seeds and the sites of lipid metabolism providing energy to the germinating seeds. Major LD-associated proteins are lipoxygenases, phospholipaseD, oleosins, TAG-lipases, steroleosins, caleosins and SEIPINs; involved in facilitating germination and enhancing peroxidation resulting in off-flavours. However, how natural selection is balancing contradictory processes in lipid-rich seeds remains evasive. The present study was aimed at the prediction of selection signatures among orthologous clades in major oilseeds and the correlation of selection effect with gene expression. RESULTS The LD-associated genes from the major oil-bearing crops were analyzed to predict natural selection signatures in phylogenetically close-knit ortholog clusters to understand adaptive evolution. Positive selection was the major force driving the evolution and diversification of orthologs in a lineage-specific manner. Significant positive selection effects were found in 94 genes particularly in oleosin and TAG-lipases, purifying with excess of non-synonymous substitution in 44 genes while 35 genes were neutral to selection effects. No significant selection impact was noticed in Brassicaceae as against LOX genes of oil palm. A heavy load of deleterious mutations affecting selection signatures was detected in T-lineage oleosins and LOX genes of Arachis hypogaea. The T-lineage oleosin genes were involved in mainly anther, tapetum and anther wall morphogenesis. In Ricinus communis and Sesamum indicum > 85% of PLD genes were under selection whereas selection pressures were low in Brassica juncea and Helianthus annuus. Steroleosin, caleosin and SEIPINs with large roles in lipid droplet organization expressed mostly in seeds and were under considerable positive selection pressures. Expression divergence was evident among paralogs and homeologs with one gene attaining functional superiority compared to the other. The LOX gene Glyma.13g347500 associated with off-flavor was not expressed during germination, rather its paralog Glyma.13g347600 showed expression in Glycine max. PLD-α genes were expressed on all the tissues except the seed,δ genes in seed and meristem while β and γ genes expressed in the leaf. CONCLUSIONS The genes involved in seed germination and lipid metabolism were under strong positive selection, although species differences were discernable. The present study identifies suitable candidate genes enhancing seed oil content and germination wherein directional selection can become more fruitful.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India.
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Anjitha George
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Sripathy Kv
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Aruna Yr
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - A Anandan
- ICAR- Indian Institute of Seed Science, Regional Station, GKVK Campus, Bengaluru, 560065, Karnataka, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, 275103, Uttar Pradesh, India
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Searle PC, Shiozawa DK, Evans RP, Hill JT, Suli A, Stark MR, Belk MC. Heterochronic shift in gene expression leads to ontogenetic morphological divergence between two closely related polyploid species. iScience 2024; 27:109566. [PMID: 38632992 PMCID: PMC11022054 DOI: 10.1016/j.isci.2024.109566] [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: 05/24/2023] [Revised: 11/04/2023] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
Heterochrony-alteration to the rate or timing of development-is an important mechanism of trait differentiation associated with speciation. Heterochrony may explain the morphological divergence between two polyploid species, June sucker (Chasmistes liorus) and Utah sucker (Catostomus ardens). The larvae of both species have terminal mouths; however, as adults, June sucker and Utah sucker develop subterminal and ventral mouths, respectively. We document a difference in the timing of shape development and a corresponding change in the timing of gene expression, suggesting the distinctive mouth morphology in June suckers may result from paedomorphosis. Specifically, adult June suckers exhibit an intermediate mouth morphology between the larval (terminal) and ancestral (ventral) states. Endemic and sympatric Chasmistes/Catostomus pairs in two other lakes also are morphologically divergent, but genetically similar. These species pairs could have resulted from the differential expression of genes and corresponding divergence in trait development. Paedomorphosis may lead to adaptive diversification in Catostomids.
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Affiliation(s)
- Peter C. Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
| | | | - R. Paul Evans
- Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA
| | - Jonathon T. Hill
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Arminda Suli
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Michael R. Stark
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Mark C. Belk
- Department of Biology, Brigham Young University, Provo, UT 84602, USA
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Zhang LY, Yang C, Wu ZC, Zhang XJ, Fan SJ. Comprehensive Time-Course Transcriptome Reveals the Crucial Biological Pathways Involved in the Seasonal Branch Growth in Siberian Elm ( Ulmus pumila). Int J Mol Sci 2023; 24:14976. [PMID: 37834427 PMCID: PMC10573607 DOI: 10.3390/ijms241914976] [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: 08/30/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Timber, the most prevalent organic material on this planet, is the result of a secondary xylem emerging from vascular cambium. Yet, the intricate processes governing its seasonal generation are largely a mystery. To better understand the cyclic growth of vascular tissues in elm, we undertook an extensive study examining the anatomy, physiology, and genetic expressions in Ulmus pumila. We chose three robust 15-year-old elm trees for our study. The cultivars used in this study were collected from the Inner Mongolia Autonomous Region in China and nurtured in the tree farm of Shandong Normal University. Monthly samples of 2-year-old elm branches were taken from the tree from February to September. Marked seasonal shifts in elm branch vascular tissues were observed by phenotypic observation: In February, the cambium of the branch emerged from dormancy, spurring growth. By May, elms began generating secondary xylem, or latewood, recognized by its tiny pores and dense cell structure. From June to August, there was a marked increase in the thickness of the secondary xylem. Transcriptome sequencing provides a potential molecular mechanism for the thickening of elm branches and their response to stress. In February, the tree enhanced its genetic responses to cold and drought stress. The amplified expression of CDKB, CYCB, WOX4, and ARF5 in the months of February and March reinforced their essential role in the development of the vascular cambium in elm. Starting in May, the elm deployed carbohydrates as a carbon resource to synthesize the abundant cellulose and lignin necessary for the formation of the secondary wall. Major genes participating in cellulose (SUC and CESA homologs), xylan (UGD, UXS, IRX9, IRX10, and IRX14), and lignin (PAL, C4H, 4CL, HCT, C3H, COMT, and CAD) biosynthetic pathways for secondary wall formation were up-regulated by May or/and June. In conclusion, our findings provided a foundation for an in-depth exploration of the molecular processes dictating the seasonal growth of elm timber.
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Affiliation(s)
| | | | | | - Xue-Jie Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, No. 88 Wenhuadong Road, Ji’nan 250014, China; (L.-Y.Z.); (C.Y.); (Z.-C.W.)
| | - Shou-Jin Fan
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, No. 88 Wenhuadong Road, Ji’nan 250014, China; (L.-Y.Z.); (C.Y.); (Z.-C.W.)
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Fleitas AL, Castro A, Blumwald E, Vidal S. Functional specialization of chloroplast vesiculation ( CV) duplicated genes from soybean shows partial overlapping roles during stress-induced or natural senescence. FRONTIERS IN PLANT SCIENCE 2023; 14:1184020. [PMID: 37346131 PMCID: PMC10280078 DOI: 10.3389/fpls.2023.1184020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/12/2023] [Indexed: 06/23/2023]
Abstract
Soybean is a globally important legume crop which is highly sensitive to drought. The identification of genes of particular relevance for drought responses provides an important basis to improve tolerance to environmental stress. Chloroplast Vesiculation (CV) genes have been characterized in Arabidopsis and rice as proteins participating in a specific chloroplast-degradation vesicular pathway (CVV) during natural or stress-induced leaf senescence. Soybean genome contains two paralogous genes encoding highly similar CV proteins, CV1 and CV2. In this study, we found that expression of CV1 was differentially upregulated by drought stress in soybean contrasting genotypes exhibiting slow-wilting (tolerant) or fast-wilting (sensitive) phenotypes. CV1 reached higher induction levels in fast-wilting plants, suggesting a negative correlation between CV1 gene expression and drought tolerance. In contrast, autophagy (ATG8) and ATI-PS (ATI1) genes were induced to higher levels in slow-wilting plants, supporting a pro-survival role for these genes in soybean drought tolerance responses. The biological function of soybean CVs in chloroplast degradation was confirmed by analyzing the effect of conditional overexpression of CV2-FLAG fusions on the accumulation of specific chloroplast proteins. Functional specificity of CV1 and CV2 genes was assessed by analyzing their specific promoter activities in transgenic Arabidopsis expressing GUS reporter gene driven by CV1 or CV2 promoters. CV1 promoter responded primarily to abiotic stimuli (hyperosmolarity, salinity and oxidative stress), while the promoter of CV2 was predominantly active during natural senescence. Both promoters were highly responsive to auxin but only CV1 responded to other stress-related hormones, such as ABA, salicylic acid and methyl jasmonate. Moreover, the dark-induced expression of CV2, but not of CV1, was strongly inhibited by cytokinin, indicating similarities in the regulation of CV2 to the reported expression of Arabidopsis and rice CV genes. Finally, we report the expression of both CV1 and CV2 genes in roots of soybean and transgenic Arabidopsis, suggesting a role for the encoded proteins in root plastids. Together, the results indicate differential roles for CV1 and CV2 in development and in responses to environmental stress, and point to CV1 as a potential target for gene editing to improve crop performance under stress without compromising natural development.
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Affiliation(s)
- Andrea Luciana Fleitas
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Alexandra Castro
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Sabina Vidal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Yu X, Wei P, Zhao S, Chen Z, Li X, Zhang W, Liu C, Yang Y, Li X, Liu X. Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai-Tibetan plateau. PLANT CELL REPORTS 2023; 42:879-893. [PMID: 36973418 DOI: 10.1007/s00299-023-03005-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 03/14/2023] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes. Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.
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Affiliation(s)
- Xiaolei Yu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Shuqi Zhao
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Zhuyifu Chen
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xinzhong Li
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China
| | - Wencai Zhang
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Yujiao Yang
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan, 430072, Hubei, China.
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, Laboratory of Plant Systematics and Evolutionary Biology, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
- Laboratory of Extreme Environmental Biological Resources and Adaptive Evolution, Research Center for Ecology, School of Sciences, Tibet University, Lhasa, 850000, Tibet, China.
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7
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Bellec A, Sow MD, Pont C, Civan P, Mardoc E, Duchemin W, Armisen D, Huneau C, Thévenin J, Vernoud V, Depège-Fargeix N, Maunas L, Escale B, Dubreucq B, Rogowsky P, Bergès H, Salse J. Tracing 100 million years of grass genome evolutionary plasticity. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36919199 DOI: 10.1111/tpj.16185] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/29/2023] [Accepted: 02/24/2023] [Indexed: 05/17/2023]
Abstract
Grasses derive from a family of monocotyledonous plants that includes crops of major economic importance such as wheat, rice, sorghum and barley, sharing a common ancestor some 100 million years ago. The genomic attributes of plant adaptation remain obscure and the consequences of recurrent whole genome duplications (WGD) or polyploidization events, a major force in plant evolution, remain largely speculative. We conducted a comparative analysis of omics data from ten grass species to unveil structural (inversions, fusions, fissions, duplications, substitutions) and regulatory (expression and methylation) basis of genome plasticity, as possible attributes of plant long lasting evolution and adaptation. The present study demonstrates that diverged polyploid lineages sharing a common WGD event often present the same patterns of structural changes and evolutionary dynamics, but these patterns are difficult to generalize across independent WGD events as a result of non-WGD factors such as selection and domestication of crops. Polyploidy is unequivocally linked to the evolutionary success of grasses during the past 100 million years, although it remains difficult to attribute this success to particular genomic consequences of polyploidization, suggesting that polyploids harness the potential of genome duplication, at least partially, in lineage-specific ways. Overall, the present study clearly demonstrates that post-polyploidization reprogramming is more complex than traditionally reported in investigating single species and calls for a critical and comprehensive comparison across independently polyploidized lineages.
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Affiliation(s)
- Arnaud Bellec
- INRAE/CNRGV US 1258, 24 Chemin de Borde Rouge, 31320, Auzeville-Tolosane, France
| | - Mamadou Dia Sow
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Caroline Pont
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Peter Civan
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Emile Mardoc
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | | | - David Armisen
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Cécile Huneau
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
| | - Johanne Thévenin
- INRAE/AgroParisTech-UMR 1318. Bat 2. Centre INRA de Versailles, route de Saint Cyr, 78026, Versailles CEDEX, France
| | - Vanessa Vernoud
- INRAE/CNRS/ENS/Univ. Lyon-UMR 879, 46 allée d'Italie, 69364, Lyon Cedex 07, France
| | | | - Laurent Maunas
- Arvalis-Institut du végétal, 21 chemin de Pau, 64121 Montardon, France
| | - Brigitte Escale
- Arvalis-Institut du végétal, 21 chemin de Pau, 64121 Montardon, France
- Direction de l'agriculture de Polynésie française, Route de l'Hippodrome, 98713, Papeete, France
| | - Bertrand Dubreucq
- INRAE/AgroParisTech-UMR 1318. Bat 2. Centre INRA de Versailles, route de Saint Cyr, 78026, Versailles CEDEX, France
| | - Peter Rogowsky
- INRAE/CNRS/ENS/Univ. Lyon-UMR 879, 46 allée d'Italie, 69364, Lyon Cedex 07, France
| | - Hélène Bergès
- INRAE/CNRGV US 1258, 24 Chemin de Borde Rouge, 31320, Auzeville-Tolosane, France
| | - Jerome Salse
- UCA, INRAE, GDEC, 5 Chemin de Beaulieu, 63000, Clermont-Ferrand, France
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8
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Kakarla M, ChallaSivaKanaka S, Dufficy MF, Gil V, Filipovich Y, Vickman R, Crawford SE, Hayward SW, Franco OE. Ephrin B Activate Src Family Kinases in Fibroblasts Inducing Stromal Remodeling in Prostate Cancer. Cancers (Basel) 2022; 14:2336. [PMID: 35565468 PMCID: PMC9102363 DOI: 10.3390/cancers14092336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/29/2022] [Accepted: 05/06/2022] [Indexed: 12/14/2022] Open
Abstract
Through stromal-epithelial interactions, carcinoma associated fibroblasts (CAF) play a critical role in tumor growth and progression. Activation of erythrophoyetin-producing human hepatocellular (Eph) receptors has been implicated in cancer. Eph receptor interactions with Ephrin ligands lead to bidirectional signals in the recipient and effector cells. The consequences of continuous reverse Ephrin signaling activation in fibroblasts on prostate cancer (PCa) is unknown. When compared to benign prostate fibroblast, CAF displayed higher expression of Ephrin B1, B2, and B3 ligands (EFNB1, EFNB2, and EFNB3). In this study, we found that continuous activation of EFNB1 and EFNB3 in a benign human prostate stromal cell line (BHPrS1) increased the expression of CAF markers and induced a CAF phenotype. BHPrS1EFNB1 and BHPrS1EFNB3 displayed a pro-tumorigenic secretome with multiple effects on neovascularization, collagen deposition, and cancer cell proliferation, overall increasing tumorigenicity of a premalignant prostate epithelial cell line BPH1 and PCa cell line LNCaP, both in vitro and in vivo. Inhibition of Src family kinases (SFK) in BHPrS1EFNB1 and BHPrS1EFNB3 suppressed EFNB-induced ɑ-SMA (Alpha-smooth muscle actin) and TN-C (Tenascin-C) in vitro. Our study suggests that acquisition of CAF characteristics via SFK activation in response to increased EFNB ligands could promote carcinogenesis via modulation of TME in PCa.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Omar E. Franco
- Department of Surgery, NorthShore University HealthSystem, Research Institute, 1001 University Place, Chicago, IL 60201, USA; (M.K.); (S.C.); (M.F.D.); (V.G.); (Y.F.); (R.V.); (S.E.C.); (S.W.H.)
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Gómez-Martínez H, Gil-Muñoz F, Bermejo A, Zuriaga E, Badenes ML. Insights of Phenolic Pathway in Fruits: Transcriptional and Metabolic Profiling in Apricot ( Prunus armeniaca). Int J Mol Sci 2021; 22:ijms22073411. [PMID: 33810284 PMCID: PMC8037730 DOI: 10.3390/ijms22073411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/17/2021] [Accepted: 03/24/2021] [Indexed: 11/16/2022] Open
Abstract
There is an increasing interest in polyphenols, plant secondary metabolites, in terms of fruit quality and diet, mainly due to their antioxidant effect. However, the identification of key gene enzymes and their roles in the phenylpropanoid pathway in temperate fruits species remains uncertain. Apricot (Prunus armeniaca) is a Mediterranean fruit with high diversity and fruit quality properties, being an excellent source of polyphenol compounds. For a better understanding of the phenolic pathway in these fruits, we selected a set of accessions with genetic-based differences in phenolic compounds accumulation. HPLC analysis of the main phenolic compounds and transcriptional analysis of the genes involved in key steps of the polyphenol network were carried out. Phenylalanine ammonia-lyase (PAL), dihydroflavonol-4-reductase (DFR) and flavonol synthase (FLS) were the key enzymes selected. Orthologous of the genes involved in transcription of these enzymes were identified in apricot: ParPAL1, ParPAL2, ParDFR, ParFLS1 and ParFLS2. Transcriptional data of the genes involved in those critical points and their relationships with the polyphenol compounds were analyzed. Higher expression of ParDFR and ParPAL2 has been associated with red-blushed accessions. Differences in expression between paralogues could be related to the presence of a BOXCOREDCPAL cis-acting element related to the genes involved in anthocyanin synthesis ParFLS2, ParDFR and ParPAL2.
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Van de Peer Y, Ashman TL, Soltis PS, Soltis DE. Polyploidy: an evolutionary and ecological force in stressful times. THE PLANT CELL 2021; 33:11-26. [PMID: 33751096 PMCID: PMC8136868 DOI: 10.1093/plcell/koaa015] [Citation(s) in RCA: 263] [Impact Index Per Article: 87.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/07/2020] [Indexed: 05/10/2023]
Abstract
Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.
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Affiliation(s)
| | - Tia-Lynn Ashman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611
- Department of Biology, University of Florida, Gainesville, Florida 32611
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