Transposable elements contribute to the establishment of the glycine shuttle in Brassicaceae species.
Brassicaceae
C2 photosynthesis
C3-C4 intermediate photosynthesis
glycine decarboxylase
glycine shuttle
transposon
Journal
Plant biology (Stuttgart, Germany)
ISSN: 1438-8677
Titre abrégé: Plant Biol (Stuttg)
Pays: England
ID NLM: 101148926
Informations de publication
Date de publication:
03 Jan 2024
03 Jan 2024
Historique:
received:
08
09
2023
accepted:
15
11
2023
medline:
4
1
2024
pubmed:
4
1
2024
entrez:
3
1
2024
Statut:
aheadofprint
Résumé
C
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Deutsche Forschungsgemeinschaft (German Research Foundation)
ID : 391465903/GRK 2466
Organisme : Germany's Excellence Strategy EXC-2048/1
ID : 390686111
Organisme : ERA-CAPS (European Research Network for Coordinating Action in Plant Sciences)
ID : WE 2231/20-1
Organisme : CRC (Collaborative Research Center)
ID : 456082119
Organisme : BBSRC
ID : BB/J014427/1
Organisme : Royal Society University Research Fellowship
Informations de copyright
© 2024 The Authors. Plant Biology published by John Wiley & Sons Ltd on behalf of German Society for Plant Sciences, Royal Botanical Society of the Netherlands.
Références
Adwy W., Laxa M., Peterhansel C. (2015) A simple mechanism for the establishment of C2-specific gene expression in Brassicaceae. The Plant Journal, 84, 1231-1238.
Adwy W., Schlüter U., Papenbrock J., Peterhansel C., Offermann S. (2019) Loss of the M-box from the glycine decarboxylase P-subunit promoter in C2 Moricandia species. Plant Gene, 18, 100176.
Arias T., Beilstein M.A., Tang M., McKain M.R., Pires J.C. (2014) Diversification times among Brassica (Brassicaceae) crops suggest hybrid formation after 20 million years of divergence. American Journal of Botany, 101, 86-91.
Baena-González E., Rolland F., Thevelein J.M., Sheen J. (2007) A central integrator of transcription networks in plant stress and energy signalling. Nature, 448, 938-942.
Batista R.A., Moreno-Romero J., Qiu Y., van Boven J., Santos-González J., Figueiredo D.D., Köhler C. (2019) The MADS-box transcription factor pheres1 controls imprinting in the endosperm by binding to domesticated transposons. Elife, 8, e50541.
Behrens S., Vingron M. (2010) Studying the evolution of promoter sequences: a waiting time problem. Journal of Computational Biology, 17, 1591-1606.
Bellasio C., Farquhar G.D. (2019) A leaf-level biochemical model simulating the introduction of C2 and C4 photosynthesis in C3 rice: gains, losses and metabolite fluxes. New Phytologist, 223, 150-166.
Betti M., Bauwe H., Busch F.A., Fernie A.R., Keech O., Levey M., Ort D.R., Parry M.A., Sage R., Timm S., Walker B., Weber A.P. (2016) Manipulating photorespiration to increase plant productivity: recent advances and perspectives for crop improvement. Journal of Experimental Botany, 67, 2977-2988.
Britten R.J., Davidson E.H. (1971) Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. The Quarterly Review of Biology, 46, 111-138.
Brosius J., Gould S.J. (1992) On ‘genomenclature: a comprehensive (and respectful) taxonomy for pseudogenes and other ‘junk DNA’. Proceedings of the National Academy of Sciences of the United States of America, 89, 10706-10710.
Buchmann J.P., Matsumoto T., Stein N., Keller B., Wicker T. (2012) Inter-species sequence comparison of Brachypodium reveals how transposon activity corrodes genome colinearity. The Plant Journal, 71, 550-563.
Cai X., Cui Y., Zhang L., Wu J., Liang J., Cheng L., Wang X., Cheng F. (2018) Hotspots of Independent and multiple rounds of LTR-retrotransposon bursts in Brassica species. Horticultural Plant Journal, 4, 165-174.
Cao C., Xu J., Zheng G., Zhu X.G. (2016) Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis. BMC Genomics, 17, 201.
Christin P.A., Sage T.L., Edwards E.J., Ogburn R.M., Khoshravesh R., Sage R.F. (2011) Complex evolutionary transitions and the significance of C3-C4 intermediate forms of photosynthesis in Molluginaceae. Evolution, 65, 643-660.
Dengler N.G., Dengler R.E., Donnelly P.M., Hattersley P.W. (1994) Quantitative leaf anatomy of C3 and C4 grasses (Poaceae): bundle sheath and mesophyll surface area relationships. Annals of Botany, 73, 241-255.
Dickinson P.J., Knerovà J., Szecowka M., Stevenson S.R., Burgess S.J., Mulvey H., Bagman A.M., Gaudinier A., Brady S.M., Hibberd J.M. (2020) A bipartite transcription factor module controlling expression in the bundle sheath of Arabidopsis thaliana. Nature Plants, 6, 1468-1479.
Dickinson P.J., Triesch S., Schlüter U., Weber A.P., Hibberd J.M. (2023) A transcription factor module mediating C2 photosynthesis bioRxiv, 2023-09.
Feschotte C. (2008) Transposable elements and the evolution of regulatory networks. Nature Reviews Genetics, 9, 397-405.
Gowik U., Schulze S., Saladi'e M., Rolland V., Tanz S.K., Westhoff P., Ludwig M. (2017) A MEM1-like motif directs mesophyll cell-specific expression of the gene encoding the C4 carbonic anhydrase in Flaveria. Journal of Experimental Botany, 68, 311-320.
Guerreiro R., Bonthala V.S., Schlüter U., Hoang N.V., Triesch S., Schranz M.E., Weber A.P.M., Stich B. (2023) A genomic panel for studying C3-C4 intermediate photosynthesis in the Brassiceae tribe. Plant, Cell & Environment, 46, 3611-3627. https://doi.org/10.1111/pce.14662
Hibberd J.M., Covshoff S. (2010) The regulation of gene expression required for C4 photosynthesis. Annual Review of Plant Biology, 61, 181-207. https://doi.org/10.1146/annurev-arplant-042809-112238
Hirsch C.D., Springer N.M. (2017) Transposable element influences on gene expression in plants. Biochimica et Biophysica Acta Gene Regulatory Mechanisms, 1860, 157-165.
Hoang N.V., Sogbohossou E.O.D., Xiong W., Simpson C.J.C., Singh P., van den Bergh E., Zhu X.-G., Brautigam A., Weber A.P.M., van Haarst J.C., Schijlen E.G.W.M., Hendre P.S., Deynze A.V., Achigan-Dako E.G., Hibberd J.M., Schranz M.E. (2022) The genome of Gynandropsis gynandra provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae bioRxiv. 2022.07.09.499295.
Holst F., Bolger A., Günther C., Maß J., Triesch S., Kindel F., Kiel N., Saadat N., Ebenhöh O., Usadel B., Schwacke R., Bolger M., Weber A.P., Denton A.K. (2023) Helixer - de novo prediction of primary eukaryotic gene models conbining deep learning and a Hidden Marcov Model https://doi.org/10.1101/2023.02.06.527280.bioRxiv
Hylton C.M., Rawsthorne S., Smith A.M., Jones D.A., Woolhouse H.W. (1988) Glycine decarboxylase is confined to the bundle-sheath cells of leaves of C3-C4 intermediate species. Planta, 175, 452-459.
Jiao W.B., Accinelli G.G., Hartwig B., Kiefer C., Baker D., Severing E., Willing E.M., Piednoel M., Woetzel S., Madrid-Herrero E., Huettel B., Hümann U., Reinhard R., Koch M.A., Swan D., Clavijo B., Coupland G., Schneeberger K. (2017) Improving and correcting the contiguity of long-read genome assemblies of three plant species using optical mapping and chromosome conformation capture data. Genome Research, 27, 778-786.
Kennedy R.A., Laetsch W.M. (1974) Plant species intermediate for C3, C4 photosynthesis. Science, 184, 1087-1089.
Kohany O., Gentles A.J., Hankus L., Jurka J. (2006) Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor. BMC Bioinformatics, 7, 474.
Lamesch P., Berardini T.Z., Li D., Swarbreck D., Wilks C., Sasidharan R., Muller R., Dreher K., Alexander D.L., Garcia-Hernandez M., Karthikeyan A.S., Lee C.H., Nelson W.D., Ploetz L., Singh S., Wensel A., Huala E. (2012) The Arabidopsis information resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research, 40(D1), D1202-D1210.
Lee S.-I., Kim N.-S. (2014) Transposable elements and genome size variations in plants. Genomics & Informatics, 12, 87-97.
Lin M.-Y., Koppers N., Denton A., Schlüter U., Weber A.P. (2021) Whole genome sequencing and assembly data of Moricandia moricandioides and M. arvensis. Data in Brief, 35, 106922.
Liu Z., Fan M., Yue E.K., Li Y., Tao R.F., Xu H.M., Duan M.H., Xu J.H. (2020) Natural variation and evolutionary dynamics of transposable elements in Brassica oleracea based on next-generation sequencing data. Horticulture Research, 7, 145.
Lundgren M.R. (2020) C2 photosynthesis: a promising route towards crop improvement? New Phytologist, 228, 1734-1740.
Lysak M.A., Koch M.A., Beaulieu J.M., Meister A., Leitch I.J. (2009) The dynamic ups and downs of genome size evolution in Brassicaceae. Molecular Biology and Evolution, 26, 85-98.
Mirouze M., Vitte C. (2014) Transposable elements, a treasure trove to decipher epigenetic variation: insights from Arabidopsis and crop epigenomes. Journal of Experimental Botany, 65, 2801-2812.
Monson R.K., Edwards G.E. (1984) C3-C4 intermediate photosynthesis in plants. Bioscience, 34, 563-574.
Morgan C.L., Turner S.R., Rawsthorne S. (1993) Coordination of the cell-specific distribution of the four subunits of glycine decarboxylase and of serine hydroxymethyltransferase in leaves of C3-C4 intermediate species from different genera. Planta, 190, 468-473.
Nagata H., Ono A., Tonosaki K., Kawakatsu T., Sato Y., Yano K., Kishima Y., Kinoshita T. (2022) Temporal changes in transcripts of miniature inverted-repeat transposable elements during rice endosperm development. The Plant Journal, 109, 1035-1047.
Naito K., Zhang F., Tsukiyama T., Saito H., Hancock C.N., Richardson A.O., Okumoto Y., Tanisaka T., Wessler S.R. (2009) Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature, 461, 1130-1134.
Oono J., Hatakeyama Y., Yabiku T., Ueno O. (2022) Effects of growth temperature and nitrogen nutrition on expression of C3-C4 intermediate traits in Chenopodium album. Journal of Plant Research, 135, 15-27.
Ou S., Su W., Liao Y., Chougule K., Agda J.R., Hellinga A.J., Lugo C.S.B., Elliott T.A., Ware D., Peterson T., Jiang N., Hirsch C.N., Hufford M.B. (2019) Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology, 20, 275.
Parkin I.A., Koh C., Tang H., Robinson S.J., Kagale S., Clarke W.E., Town C.D., Nixon J., Krishnakumar V., Bidwell S.L., Denoeud F., Belcram H., Links M.G., Just J., Clarke C., Bender T., Huebert T., Mason A.S., Chris Pires J., Barker G., Moore J., Walley P.G., Manoli S., Batley J., Edwards D., Nelson M.N., Wang X., Paterson A.H., King G., Bancroft I., Chalhoub B., Sharpe A.G. (2014) Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology, 15, R77.
Pietzenuk B., Markus C., Gaubert H., Bagwan N., Merotto A., Bucher E., Pecinka A. (2016) Recurrent evolution of heat-responsiveness in Brassicaceae COPIA elements. Genome Biology, 17, 209.
Qiu Y., Köhler C. (2020) Mobility connects: transposable elements wire new transcriptional networks by transferring transcription factor binding motifs. Biochemical Society Transactions, 48, 1005-1017.
Rawsthorne S., Hylton C.M., Smith A.M., Woolhouse H.W. (1988) Photorespiratory metabolism and immunogold localization of photorespiratory enzymes in leaves of C3 and C3-C4 intermediate species of Moricandia. Planta, 173, 298-308.
Reeves G., Grangè-Guermente M.J., Hibberd J.M. (2017) Regulatory gateways for cell-specific gene expression in C4 leaves with Kranz anatomy. Journal of Experimental Botany, 68, 107-116.
Revell L.J. (2012) phytools: an R package for phylogenetic comparative biology (and other things). Methods in Ecology and Evolution, 3, 217-223.
Sage R.F., Sage T.L., Kocacinar F. (2012) Photorespiration and the evolution of C4 photosynthesis. Annual Review of Plant Biology, 63, 19-47.
Schlüter U., Bouvier J.W., Guerreiro R., Malisic M., Kontny C., Westhoff P., Stich B., Weber A.P.M. (2022) Brassicaceae display diverse photorespiratory carbon recapturing mechanisms bioRxiv.
Schlüter U., Bräutigam A., Gowik U., Melzer M., Christin P.A., Kurz S., Mettler-Altmann T., Weber A.P. (2017) Photosynthesis in C3-C4 intermediate Moricandia species. Journal of Experimental Botany, 68, 191-206.
Schlüter U., Weber A.P. (2016) The road to C4 photosynthesis: evolution of a complex trait via intermediary states. Plant and Cell Physiology, 57, 881-889.
Schulze S., Mallmann J., Burscheidt J., Koczor M., Streubel M., Bauwe H., Gowik U., Westhoff P. (2013) Evolution of C4 photosynthesis in the genus Flaveria: establishment of a photorespiratory CO2 pump. The Plant Cell, 25, 2522-2535.
Schulze S., Westhoff P., Gowik U. (2016) Glycine decarboxylase in C3, C4 and C3-C4 intermediate species. Current Opinion in Plant Biology, 31, 29-35.
Schwacke R., Ponce-Soto G.Y., Krause K., Bolger A.M., Arsova B., Hallab A., Gruden K., Stitt M., Bolger M.E., Usadel B. (2019) MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis. Molecular Plant, 12, 879-892.
Walden N., German D.A., Wolf E.M., Kiefer M., Rigault P., Huang X.C., Kiefer C., Schmickl R., Franzke A., Neuffer B., Mummenhoff K., Koch M.A. (2020) Nested whole-genome duplications coincide with diversification and high morphological disparity in Brassicaceae. Nature Communications, 11, 3795.
Wicker T., Sabot F., Hua-Van A., Bennetzen J.L., Capy P., Chalhoub B., Flavell A., Leroy P., Morgante M., Panaud O., Paux E., SanMiguel P., Schulman A.H. (2007) A unified classification system for eukaryotic transposable elements. Nature Reviews Genetics, 8, 973-982.
Williams B.P., Burgess S.J., Reyna-Llorens I., Knerova J., Aubry S., Stanley S., Hibberd J.M. (2015) An untranslated cis-element regulates the accumulation of multiple C4 enzymes in Gynandropsis gynandra mesophyll cells. The Plant Cell, 28, 454-465.
Wiludda C., Schulze S., Gowik U., Engelmann S., Koczor M., Streubel M., Bauwe H., Westhoff P. (2012) Regulation of the photorespiratory GLDPA gene in C4 Flaveria: an intricate interplay of transcriptional and posttranscriptional processes. The Plant Cell, 24, 137-151.
Wurzinger B., Nukarinen E., Nägele T., Weckwerth W., Teige M. (2018) The SnRK1 kinase as central mediator of energy signaling between different organelles. Plant Physiology, 176, 1085-1094.