1
|
Makhokh H, Lafite P, Larcher M, Lamblin F, Chefdor F, Depierreux C, Tanigawa M, Maeda T, Carpin S, Héricourt F. Searching for Osmosensing Determinants in Poplar Histidine-Aspartate Kinases. Int J Mol Sci 2023; 24:ijms24076318. [PMID: 37047295 PMCID: PMC10093795 DOI: 10.3390/ijms24076318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/20/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Previous works have shown the existence of protein partnership, belonging to a MultiStep Phosphorelay (MSP), potentially involved in osmosensing in Populus. The first actor of this signalling pathway belongs to the histidine-aspartate kinase (HK) family, which also includes the yeast osmosensor Sln1, as well as the Arabidopsis putative osmosensor AHK1. In poplar, the homologous AHK1 protein corresponds to a pair of paralogous proteins, HK1a and HK1b, exhibiting an extracellular domain (ECD), as in Sln1 and AHK1. An ECD alignment of AHK1-like proteins, from different plant species, showed a particularly well conserved ECD and revealed the presence of a cache domain. This level of conservation suggested a functional role of this domain in osmosensing. Thus, we tested this possibility by modelling assisted mutational analysis of the cache domain of the Populus HK1 proteins. The mutants were assessed for their ability to respond to different osmotic stress and the results point to an involvement of this domain in HK1 functionality. Furthermore, since HK1b was shown to respond better to stress than HK1a, these two receptors constituted a good system to search for osmosensing determinants responsible for this difference in efficiency. With domain swapping experiments, we finally demonstrated that the cache domain, as well as the second transmembrane domain, are involved in the osmosensing efficiency of these receptors.
Collapse
Affiliation(s)
- Hanae Makhokh
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d’Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
| | - Pierre Lafite
- Institut de Chimie Organique et Analytique (ICOA), UMR CNRS-Université d’Orléans 7311, Université d’Orléans, BP 6759, 45067 Orléans Cedex 2, France
| | - Mélanie Larcher
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d’Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
| | - Frédéric Lamblin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d’Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
| | - Françoise Chefdor
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d’Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
| | - Christiane Depierreux
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d’Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
| | - Mirai Tanigawa
- Department of Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Shizuoka 431-3192, Japan
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Shizuoka 431-3192, Japan
| | - Sabine Carpin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d’Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
- Correspondence: authors: (S.C.); (F.H.); Tel.: +33-2-3849-4804 (S.C.); +33-2-38-49-4806 (F.H.)
| | - François Héricourt
- Laboratoire de Biologie des Ligneux et des Grandes Cultures (LBLGC), Université d’Orléans, INRAE USC1328, 45067 Orléans Cedex 2, France
- Correspondence: authors: (S.C.); (F.H.); Tel.: +33-2-3849-4804 (S.C.); +33-2-38-49-4806 (F.H.)
| |
Collapse
|
2
|
Cytokinins: Wide-Spread Signaling Hormones from Plants to Humans with High Medical Potential. Nutrients 2022; 14:nu14071495. [PMID: 35406107 PMCID: PMC9003334 DOI: 10.3390/nu14071495] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/29/2022] [Accepted: 03/31/2022] [Indexed: 02/04/2023] Open
Abstract
Nature is a rich source of biologically active novel compounds. Sixty years ago, the plant hormones cytokinins were first discovered. These play a major role in cell division and cell differentiation. They affect organogenesis in plant tissue cultures and contribute to many other physiological and developmental processes in plants. Consequently, the effect of cytokinins on mammalian cells has caught the attention of researchers. Many reports on the contribution and potential of cytokinins in the therapy of different human diseases and pathophysiological conditions have been published and are reviewed here. We compare cytokinin effects and pathways in plants and mammalian systems and highlight the most important biological activities. We present the strong profile of the biological actions of cytokinins and their possible therapeutic applications.
Collapse
|
3
|
Zhou R, Macaya-Sanz D, Schmutz J, Jenkins JW, Tuskan GA, DiFazio SP. Sequencing and Analysis of the Sex Determination Region of Populus trichocarpa. Genes (Basel) 2020; 11:E843. [PMID: 32722098 PMCID: PMC7465354 DOI: 10.3390/genes11080843] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/19/2022] Open
Abstract
The ages and sizes of a sex-determination region (SDR) are difficult to determine in non-model species. Due to the lack of recombination and enrichment of repetitive elements in SDRs, the quality of assembly with short sequencing reads is universally low. Unique features present in the SDRs help provide clues about how SDRs are established and how they evolve in the absence of recombination. Several Populus species have been reported with a male heterogametic configuration of sex (XX/XY system) mapped on chromosome 19, but the exact location of the SDR has been inconsistent among species, and thus far, none of these SDRs has been fully assembled in a genomic context. Here we identify the Y-SDR from a Y-linked contig directly from a long-read PacBio assembly of a Populus trichocarpa male individual. We also identified homologous gene sequences in the SDR of P. trichocarpa and the SDR of the W chromosome in Salix purpurea. We show that inverted repeats (IRs) found in the Y-SDR and the W-SDR are lineage-specific. We hypothesize that, although the two IRs are derived from the same orthologous gene within each species, they likely have independent evolutionary histories. Furthermore, the truncated inverted repeats in P. trichocarpa may code for small RNAs that target the homologous gene for RNA-directed DNA methylation. These findings support the hypothesis that diverse sex-determining systems may be achieved through similar evolutionary pathways, thereby providing a possible mechanism to explain the lability of sex-determination systems in plants in general.
Collapse
Affiliation(s)
- Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA; (R.Z.); (D.M.-S.)
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA; (R.Z.); (D.M.-S.)
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA; (J.S.); (J.W.J.)
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA;
| | - Jerry W. Jenkins
- HudsonAlpha Institute of Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA; (J.S.); (J.W.J.)
| | - Gerald A. Tuskan
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA;
- Center for Bioenergy Innovation, Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37830, USA
| | - Stephen P. DiFazio
- Department of Biology, West Virginia University, Morgantown, WV 26506-6057, USA; (R.Z.); (D.M.-S.)
| |
Collapse
|
4
|
Ahmad B, Azeem F, Ali MA, Nawaz MA, Nadeem H, Abbas A, Batool R, Atif RM, Ijaz U, Nieves-Cordones M, Chung G. Genome-wide identification and expression analysis of two component system genes in Cicer arietinum. Genomics 2020; 112:1371-1383. [DOI: 10.1016/j.ygeno.2019.08.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/19/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
|
5
|
Zhou R, Macaya-Sanz D, Carlson CH, Schmutz J, Jenkins JW, Kudrna D, Sharma A, Sandor L, Shu S, Barry K, Tuskan GA, Ma T, Liu J, Olson M, Smart LB, DiFazio SP. A willow sex chromosome reveals convergent evolution of complex palindromic repeats. Genome Biol 2020; 21:38. [PMID: 32059685 PMCID: PMC7023750 DOI: 10.1186/s13059-020-1952-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/03/2020] [Indexed: 12/19/2022] Open
Abstract
Background Sex chromosomes have arisen independently in a wide variety of species, yet they share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that show sequence conservation through gene conversion and contain genes that are crucial for sexual reproduction. In plants, it is not clear if palindromic repeats play a role in maintaining sequence conservation in the absence of homologous recombination. Results Here we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrub Salix purpurea. The W chromosome has an expanded number of genes due to transpositions from autosomes. It also contains two consecutive palindromes that span a region of 200 kb, with conspicuous 20-kb stretches of highly conserved sequences among the four arms that show evidence of gene conversion. Four genes in the palindrome are homologous to genes in the sex determination regions of the closely related genus Populus, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes. Conclusion The presence of palindromes in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.
Collapse
Affiliation(s)
- Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA
| | - David Macaya-Sanz
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA
| | - Craig H Carlson
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA.,Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | | | - David Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Aditi Sharma
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Laura Sandor
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Walnut Creek, California, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.,State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & College of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Box 43131, Lubbock, TX, 79409-3131, USA
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY, 14456, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, 26506-6057, USA.
| |
Collapse
|
6
|
Abstract
Signal transduction systems configured around a core phosphotransfer step between a histidine kinase and a cognate response regulator protein occur in organisms from all domains of life. These systems, termed two-component systems, constitute the majority of multi-component signaling pathways in Bacteria but are less prevalent in Archaea and Eukarya. The core signaling domains are modular, allowing versatility in configuration of components into single-step phosphotransfer and multi-step phosphorelay pathways, the former being predominant in bacteria and the latter in eukaryotes. Two-component systems regulate key cellular regulatory processes that provide adaptive responses to environmental stimuli and are of interest for the development of antimicrobial therapeutics, biotechnology applications, and biosensor engineering. In bacteria, two-component systems have been found to mediate responses to an extremely broad array of extracellular and intracellular chemical and physical stimuli, whereas in archaea and eukaryotes, the use of two-component systems is more limited. This review summarizes recent advances in exploring the repertoire of sensor histidine kinases in the Archaea and Eukarya domains of life.
Collapse
Affiliation(s)
- Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène (GEIHP, EA 3142), SFR ICAT 4208, UNIV Angers, UNIV Brest, Angers, France
| | - Ann M Stock
- Department of Biochemistry and Molecular Biology, Center for Advanced Biotechnology and Medicine, Rutgers-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| |
Collapse
|
7
|
Héricourt F, Larcher M, Chefdor F, Koudounas K, Carqueijeiro I, Lemos Cruz P, Courdavault V, Tanigawa M, Maeda T, Depierreux C, Lamblin F, Glévarec G, Carpin S. New Insight into HPts as Hubs in Poplar Cytokinin and Osmosensing Multistep Phosphorelays: Cytokinin Pathway Uses Specific HPts. PLANTS 2019; 8:plants8120591. [PMID: 31835814 PMCID: PMC6963366 DOI: 10.3390/plants8120591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/04/2019] [Accepted: 12/09/2019] [Indexed: 02/02/2023]
Abstract
We have previously identified proteins in poplar which belong to an osmosensing (OS) signaling pathway, called a multistep phosphorelay (MSP). The MSP comprises histidine-aspartate kinases (HK), which act as membrane receptors; histidine phosphotransfer (HPt) proteins, which act as phosphorelay proteins; and response regulators (RR), some of which act as transcription factors. In this study, we identified the HK proteins homologous to the Arabidopsis cytokinin (CK) receptors, which are first partners in the poplar cytokinin MSP, and focused on specificity of these two MSPs (CK and OS), which seem to share the same pool of HPt proteins. Firstly, we isolated five CK HKs from poplar which are homologous to Arabidopsis AHK2, AHK3, and AHK4, namely, HK2, HK3a, HK3b, HK4a, HK4b. These HKs were shown to be functional kinases, as observed in a functional complementation of a yeast HK deleted strain. Moreover, one of these HKs, HK4a, was shown to have kinase activity dependent on the presence of CK. Exhaustive interaction tests between these five CK HKs and the 10 HPts characterized in poplar were performed using two-hybrid and BiFC experiments. The resulting partnership was compared to that previously identified between putative osmosensors HK1a/1b and HPt proteins. Finally, in planta coexpression analysis of genes encoding these potential partners revealed that almost all HPts are coexpressed with CK HKs in four different poplar organs. Overall, these results allowed us to unravel the common and specific partnerships existing between OS and CK MSP in Populus.
Collapse
Affiliation(s)
- François Héricourt
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Mélanie Larcher
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Françoise Chefdor
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Konstantinos Koudounas
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Inês Carqueijeiro
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Pamela Lemos Cruz
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Vincent Courdavault
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Mirai Tanigawa
- Department of Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (M.T.); (T.M.)
| | - Tatsuya Maeda
- Department of Biology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan; (M.T.); (T.M.)
| | - Christiane Depierreux
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Frédéric Lamblin
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
| | - Gaëlle Glévarec
- BBV, University of Tours, EA 2106, 31 Avenue Monge, 37200 Tours, France; (K.K.); (I.C.); (P.L.C.); (V.C.); (G.G.)
| | - Sabine Carpin
- LBLGC, University of Orléans, EA1207, INRA, USC1328, rue de Chartres, CEDEX 2, 45067 Orléans, France; (F.H.); (M.L.); (F.C.); (C.D.); (F.L.)
- Correspondence: ; Tel.: +33-2-3849-4804
| |
Collapse
|