User menu

Accès à distance ? S'identifier sur le proxy UCLouvain

Identification of fasciclin-like arabinogalactan proteins in textile hemp (Cannabis sativa L.): In silico analyses and gene expression patterns in different tissues

Primary tabs

download
  • Open access
  • PDF
  • 2.92 M
Guerriero, Gea [1Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg] Mangeot-Peter, Lauralie [1Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg] Legay, Sylvain [1Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg] Behr, Marc [UCL] Lutts, Stanley [UCL] Hausman, Jean-François [1Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), 5, Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg]

Background: The fasciclin-like arabinogalactan proteins (FLAs) belong to the arabinogalactan protein (AGP) superfamily and are known to play different physiological roles in plants. This class of proteins was shown to participate in plant growth, development, defense against abiotic stresses and, notably, cell wall biosynthesis. Although some studies are available on the characterization of FLA genes from different species, both woody and herbaceous, no detailed information is available on the FLA family of textile hemp (Cannabis sativa L.), an economically important fibre crop. Results: By searching the Cannabis genome and EST databases, 23 CsaFLAs have been here identified which are divided into four phylogenetic groups. A real-time qPCR analysis performed on stem tissues (isolated bast fibres and shivs sampled at three heights), hypocotyls (6-9-12-15-17-20 days-old), whole seedlings, roots, leaves and female/male flowers of the monoecious fibre variety Santhica 27, indicates that the identified FLA genes are differentially expressed. Interestingly, some hemp FLAs are expressed during early phases of fibre growth (elongation), while others are more expressed in the middle and base of the stem and thus potentially involved in secondary cell wall formation (fibre thickening). The bioinformatic analysis of the promoter regions shows that the FLAs upregulated in the younger regions of the stem share a conserved motif related to flowering control and regulation of photoperiod perception. The promoters of the FLA genes expressed at higher levels in the older stem regions, instead, share a motif putatively recognized by MYB3, a transcriptional repressor belonging to the MYB family subgroup S4. Conclusions: These results point to the existence of a transcriptional network fine-tuning the expression of FLA genes in the older and younger regions of the stem, as well as in the bast fibres/shivs of textile hemp. In summary, our study paves the way for future analyses on the biological functions of FLAs in an industrially relevant fibre crop. © 2017 The Author(s).

Document type Article de périodique (Journal article) – Article de recherche
Access type Accès libre
Publication date 2017
Language Anglais
Journal information "BMC Genomics" - Vol. 18, no.1, p. 13 (2017)
Peer reviewed yes
Publisher BioMed Central Ltd.
issn 1471-2164
e-issn 1471-2164
Publication status Publié
Affiliation UCL - SST/ELI/ELIA - Agronomy
Keywords Bast fibres ; Bioinformatics ; Cannabis sativa ; Computer model ; Controlled study ; Fiber crop ; Flower ; Gene expression ; Hypocotyl ; Nonhuman ; Phylogeny ; Cannabis sativa ; Plant gene ; Plant genome ; Plant leaf ; Plant root ; Plant tissue ; Promoter region ; Protein analysis ; Protein family ; Protein function ; Real time polymerase chain reaction ; Cell wall ; Seedling ; Fasciclin-like arabinogalactan proteins ; RT-qPCR ; Fasciclin like arabinogalactan protein ; Plant protein ; Unclassified drug ; Article
Links
  1. Tan L, Showalter A, Egelund J, Hernandez-Sanchez A, Doblin M, Bacic A. Arabinogalactan proteins and the research challenges for these enigmatic plant cell surface proteoglycans. Front Plant Sci. 2012;3:140.
  2. Seifert Georg J., Roberts Keith, The Biology of Arabinogalactan Proteins, 10.1146/annurev.arplant.58.032806.103801
  3. Pereira Ana Marta, Pereira Luís Gustavo, Coimbra Sílvia, Arabinogalactan proteins: rising attention from plant biologists, 10.1007/s00497-015-0254-6
  4. Schultz C. J., Using Genomic Resources to Guide Research Directions. The Arabinogalactan Protein Gene Family as a Test Case, 10.1104/pp.003459
  5. Johnson K. L., The Fasciclin-Like Arabinogalactan Proteins of Arabidopsis. A Multigene Family of Putative Cell Adhesion Molecules, 10.1104/pp.103.031237
  6. Ellis M., Egelund J., Schultz C. J., Bacic A., Arabinogalactan-Proteins: Key Regulators at the Cell Surface?, 10.1104/pp.110.156000
  7. Zang Lina, Zheng Tangchun, Chu Yanguang, Ding Changjun, Zhang Weixi, Huang Qinjun, Su Xiaohua, Genome-Wide Analysis of the Fasciclin-Like Arabinogalactan Protein Gene Family Reveals Differential Expression Patterns, Localization, and Salt Stress Response in Populus, 10.3389/fpls.2015.01140
  8. Faik Ahmed, Abouzouhair Jaouad, Sarhan Fathey, Putative fasciclin-like arabinogalactan-proteins (FLA) in wheat (Triticum aestivum) and rice (Oryza sativa): identification and bioinformatic analyses, 10.1007/s00438-006-0159-z
  9. Huang Geng-Qing, Xu Wen-Liang, Gong Si-Ying, Li Bing, Wang Xiu-Lan, Xu Dan, Li Xue-Bao, Characterization of 19 novel cottonFLAgenes and their expression profiling in fiber development and in response to phytohormones and salt stress, 10.1111/j.1399-3054.2008.01139.x
  10. Jun Li, Xiaoming Wu, Genome-wide identification, classification and expression analysis of genes encoding putative fasciclin-like arabinogalactan proteins in Chinese cabbage (Brassica rapa L.), 10.1007/s11033-012-1940-1
  11. MacMillan Colleen P., Taylor Lynette, Bi Yingdong, Southerton Simon G., Evans Rob, Spokevicius Antanas, The fasciclin-like arabinogalactan protein family ofEucalyptus grandiscontains members that impact wood biology and biomechanics, 10.1111/nph.13320
  12. MacMillan Colleen P., Mansfield Shawn D., Stachurski Zbigniew H., Evans Rob, Southerton Simon G., Fasciclin-like arabinogalactan proteins: specialization for stem biomechanics and cell wall architecture in Arabidopsis and Eucalyptus : FLAs specialized for stem biomechanics and cell walls, 10.1111/j.1365-313x.2010.04181.x
  13. Wang Haihai, Jiang Chunmei, Wang Cuiting, Yang Yang, Yang Lei, Gao Xiaoyan, Zhang Hongxia, Antisense expression of the fasciclin-like arabinogalactan protein FLA6 gene in Populus inhibits expression of its homologous genes and alters stem biomechanics and cell wall composition in transgenic trees, 10.1093/jxb/eru479
  14. Huang G.-Q., Gong S.-Y., Xu W.-L., Li W., Li P., Zhang C.-J., Li D.-D., Zheng Y., Li F.-G., Li X.-B., A Fasciclin-Like Arabinogalactan Protein, GhFLA1, Is Involved in Fiber Initiation and Elongation of Cotton, 10.1104/pp.112.203760
  15. Roach Melissa J., Deyholos Michael K., Microarray analysis of flax (Linum usitatissimum L.) stems identifies transcripts enriched in fibre-bearing phloem tissues, 10.1007/s00438-007-0241-1
  16. Roach Melissa J., Deyholos Michael K., Microarray Analysis of Developing Flax Hypocotyls Identifies Novel Transcripts Correlated with Specific Stages of Phloem Fibre Differentiation, 10.1093/aob/mcn110
  17. Guerriero Gea, Hausman Jean-Francois, Strauss Joseph, Ertan Haluk, Siddiqui Khawar Sohail, Lignocellulosic biomass: Biosynthesis, degradation, and industrial utilization, 10.1002/elsc.201400196
  18. Behr Marc, Legay Sylvain, Žižková Eva, Motyka Václav, Dobrev Petre I., Hausman Jean-Francois, Lutts Stanley, Guerriero Gea, Studying Secondary Growth and Bast Fiber Development: The Hemp Hypocotyl Peeks behind the Wall, 10.3389/fpls.2016.01733
  19. Andre Christelle M., Hausman Jean-Francois, Guerriero Gea, Cannabis sativa: The Plant of the Thousand and One Molecules, 10.3389/fpls.2016.00019
  20. Mangeot-Peter Lauralie, Legay Sylvain, Hausman Jean-Francois, Esposito Sergio, Guerriero Gea, Identification of Reference Genes for RT-qPCR Data Normalization in Cannabis sativa Stem Tissues, 10.3390/ijms17091556
  21. Guerriero Gea, Sergeant Kjell, Hausman Jean-François, Integrated -Omics: A Powerful Approach to Understanding the Heterogeneous Lignification of Fibre Crops, 10.3390/ijms140610958
  22. Mokshina Natalia, Gorshkova Tatyana, Deyholos Michael K., Chitinase-Like (CTL) and Cellulose Synthase (CESA) Gene Expression in Gelatinous-Type Cellulosic Walls of Flax (Linum usitatissimum L.) Bast Fibers, 10.1371/journal.pone.0097949
  23. Guerriero Gea, Mangeot-Peter Lauralie, Hausman Jean-Francois, Legay Sylvain, Extraction of High Quality RNA from Cannabis sativa Bast Fibres: A Vademecum for Molecular Biologists, 10.3390/fib4030023
  24. Lev-Yadun Simcha, Plant fibers: Initiation, growth, model plants, and open questions, 10.1134/s1021443710030015
  25. Snegireva Anastasia, Chernova Tatyana, Ageeva Marina, Lev-Yadun Simcha, Gorshkova Tatyana, Intrusive growth of primary and secondary phloem fibres in hemp stem determines fibre-bundle formation and structure, 10.1093/aobpla/plv061
  26. Guerriero Gea, Hausman Jean-Francois, Cai Giampiero, No Stress! Relax! Mechanisms Governing Growth and Shape in Plant Cells, 10.3390/ijms15035094
  27. Gorshkova Tatyana A., Sal'nikov Vadim V., Chemikosova Svetlana B., Ageeva Marina V., Pavlencheva Natalia V., van Dam Jan E.G., The snap point: a transition point in Linum usitatissimum bast fiber development, 10.1016/s0926-6690(03)00043-8
  28. van Bakel Harm, Stout Jake M, Cote Atina G, Tallon Carling M, Sharpe Andrew G, Hughes Timothy R, Page Jonathan E, The draft genome and transcriptome of Cannabis sativa, 10.1186/gb-2011-12-10-r102
  29. Eisenhaber B., Glycosylphosphatidylinositol Lipid Anchoring of Plant Proteins. Sensitive Prediction from Sequence- and Genome-Wide Studies for Arabidopsis and Rice, 10.1104/pp.103.023580
  30. Yang Jianyi, Yan Renxiang, Roy Ambrish, Xu Dong, Poisson Jonathan, Zhang Yang, The I-TASSER Suite: protein structure and function prediction, 10.1038/nmeth.3213
  31. Guex Nicolas, Peitsch Manuel C., SWISS-MODEL and the Swiss-Pdb Viewer: An environment for comparative protein modeling, 10.1002/elps.1150181505
  32. Bailey TL, Elkan C. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Edited by Edited by AAAI press 1994:28–36.
  33. Gupta Shobhit, Stamatoyannopoulos John A, Bailey Timothy L, Noble William, Quantifying similarity between motifs, 10.1186/gb-2007-8-2-r24
  34. Mathelier Anthony, Fornes Oriol, Arenillas David J., Chen Chih-yu, Denay Grégoire, Lee Jessica, Shi Wenqiang, Shyr Casper, Tan Ge, Worsley-Hunt Rebecca, Zhang Allen W., Parcy François, Lenhard Boris, Sandelin Albin, Wasserman Wyeth W., JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles, 10.1093/nar/gkv1176
  35. Hu Bo, Jin Jinpu, Guo An-Yuan, Zhang He, Luo Jingchu, Gao Ge, GSDS 2.0: an upgraded gene feature visualization server, 10.1093/bioinformatics/btu817
  36. Bustin S. A., Benes V., Garson J. A., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T., Pfaffl M. W., Shipley G. L., Vandesompele J., Wittwer C. T., The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments, 10.1373/clinchem.2008.112797
  37. ITO Shinsaku, SUZUKI Yoshihito, MIYAMOTO Kensuke, UEDA Junichi, YAMAGUCHI Isomaro, AtFLA11, a Fasciclin-Like Arabinogalactan-Protein, Specifically Localized in Screlenchyma Cells, 10.1271/bbb.69.1963
  38. Shi H., The Arabidopsis SOS5 Locus Encodes a Putative Cell Surface Adhesion Protein and Is Required for Normal Cell Expansion, 10.1105/tpc.007872
  39. Johnson Kim L., Kibble Natalie A. J., Bacic Antony, Schultz Carolyn J., A Fasciclin-Like Arabinogalactan-Protein (FLA) Mutant of Arabidopsis thaliana, fla1, Shows Defects in Shoot Regeneration, 10.1371/journal.pone.0025154
  40. Crônier David, Monties Bernard, Chabbert Brigitte, Structure and Chemical Composition of Bast Fibers Isolated from Developing Hemp Stem, 10.1021/jf051253k
  41. Lafarguette Florian, Leplé Jean-Charles, Déjardin Annabelle, Laurans Françoise, Costa Guy, Lesage-Descauses Marie-Claude, Pilate Gilles, Poplar genes encoding fasciclin-like arabinogalactan proteins are highly expressed in tension wood, 10.1111/j.1469-8137.2004.01175.x
  42. Gritsch Cristina, Wan Yongfang, Mitchell Rowan A. C., Shewry Peter R., Hanley Steven J., Karp Angela, G-fibre cell wall development in willow stems during tension wood induction, 10.1093/jxb/erv358
  43. Melzer Siegbert, Lens Frederic, Gennen Jerôme, Vanneste Steffen, Rohde Antje, Beeckman Tom, Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana, 10.1038/ng.253
  44. Jin H., Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis, 10.1093/emboj/19.22.6150
  45. Day Arnaud, Ruel Katia, Neutelings Godfrey, Crônier David, David Hélène, Hawkins Simon, Chabbert Brigitte, Lignification in the flax stem: evidence for an unusual lignin in bast fibers, 10.1007/s00425-005-1537-1
  46. Huis R., Morreel K., Fliniaux O., Lucau-Danila A., Fenart S., Grec S., Neutelings G., Chabbert B., Mesnard F., Boerjan W., Hawkins S., Natural Hypolignification Is Associated with Extensive Oligolignol Accumulation in Flax Stems, 10.1104/pp.111.192328
  47. Guerriero Gea, Behr Marc, Legay Sylvain, Mangeot-Peter Lauralie, Zorzan Simone, Ghoniem Mohammad, Hausman Jean-Francois, Transcriptomic profiling of hemp bast fibres at different developmental stages, 10.1038/s41598-017-05200-8
Bibliographic reference Guerriero, Gea ; Mangeot-Peter, Lauralie ; Legay, Sylvain ; Behr, Marc ; Lutts, Stanley ; et. al. Identification of fasciclin-like arabinogalactan proteins in textile hemp (Cannabis sativa L.): In silico analyses and gene expression patterns in different tissues. In: BMC Genomics, Vol. 18, no.1, p. 13 (2017)
Permanent URL http://hdl.handle.net/2078.1/189218