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Obudulu O, Bygdell J, Sundberg B, Moritz T, Hvidsten TR, Trygg J, Wingsle G. Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development. BMC Genomics 2016; 17:119. [PMID: 26887814 PMCID: PMC4758094 DOI: 10.1186/s12864-016-2458-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/09/2016] [Indexed: 01/08/2023] Open
Abstract
Background Wood development is of outstanding interest both to basic research and industry due to the associated cellulose and lignin biomass production. Efforts to elucidate wood formation (which is essential for numerous aspects of both pure and applied plant science) have been made using transcriptomic analyses and/or low-resolution sampling. However, transcriptomic data do not correlate perfectly with levels of expressed proteins due to effects of post-translational modifications and variations in turnover rates. In addition, high-resolution analysis is needed to characterize key transitions. In order to identify protein profiles across the developmental region of wood formation, an in-depth and tissue specific sampling was performed. Results We examined protein profiles, using an ultra-performance liquid chromatography/quadrupole time of flight mass spectrometry system, in high-resolution tangential sections spanning all wood development zones in Populus tremula from undifferentiated cambium to mature phloem and xylem, including cell expansion and cell death zones. In total, we analyzed 482 sections, 20–160 μm thick, from four 47-year-old trees growing wild in Sweden. We obtained high quality expression profiles for 3,082 proteins exhibiting consistency across the replicates, considering that the trees were growing in an uncontrolled environment. A combination of Principal Component Analysis (PCA), Orthogonal Projections to Latent Structures (OPLS) modeling and an enhanced stepwise linear modeling approach identified several major transitions in global protein expression profiles, pinpointing (for example) locations of the cambial division leading to phloem and xylem cells, and secondary cell wall formation zones. We also identified key proteins and associated pathways underlying these developmental landmarks. For example, many of the lignocellulosic related proteins were upregulated in the expansion to the early developmental xylem zone, and for laccases with a rapid decrease in early xylem zones. We observed upregulation of two forms of xylem cysteine protease (Potri.002G005700.1 and Potri.005G256000.2; Pt-XCP2.1) in early xylem and their downregulation in late maturing xylem. Our data also show that Pt-KOR1.3 (Potri.003G151700.2) exhibits an expression pattern that supports the hypothesis put forward in previous studies that this is a key xyloglucanase involved in cellulose biosynthesis in primary cell walls and reduction of cellulose crystallinity in secondary walls. Conclusion Our novel multivariate approach highlights important processes and provides confirmatory insights into the molecular foundations of wood development. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2458-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ogonna Obudulu
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden. .,Computational life science cluster (CLiC), Umeå University, Umeå, Sweden.
| | - Joakim Bygdell
- Department of Chemistry, Umeå University, SE-90187, Umeå, Sweden. .,Computational life science cluster (CLiC), Umeå University, Umeå, Sweden.
| | - Björn Sundberg
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden.
| | - Thomas Moritz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden.
| | - Torgeir R Hvidsten
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-90187, Umeå, Sweden. .,Computational life science cluster (CLiC), Umeå University, Umeå, Sweden. .,Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway.
| | - Johan Trygg
- Department of Chemistry, Umeå University, SE-90187, Umeå, Sweden. .,Computational life science cluster (CLiC), Umeå University, Umeå, Sweden.
| | - Gunnar Wingsle
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden.
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Gorshkova T, Mokshina N, Chernova T, Ibragimova N, Salnikov V, Mikshina P, Tryfona T, Banasiak A, Immerzeel P, Dupree P, Mellerowicz EJ. Aspen Tension Wood Fibers Contain β-(1---> 4)-Galactans and Acidic Arabinogalactans Retained by Cellulose Microfibrils in Gelatinous Walls. PLANT PHYSIOLOGY 2015; 169:2048-63. [PMID: 26378099 PMCID: PMC4634055 DOI: 10.1104/pp.15.00690] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 09/12/2015] [Indexed: 05/04/2023]
Abstract
Contractile cell walls are found in various plant organs and tissues such as tendrils, contractile roots, and tension wood. The tension-generating mechanism is not known but is thought to involve special cell wall architecture. We previously postulated that tension could result from the entrapment of certain matrix polymers within cellulose microfibrils. As reported here, this hypothesis was corroborated by sequential extraction and analysis of cell wall polymers that are retained by cellulose microfibrils in tension wood and normal wood of hybrid aspen (Populus tremula × Populus tremuloides). β-(1→4)-Galactan and type II arabinogalactan were the main large matrix polymers retained by cellulose microfibrils that were specifically found in tension wood. Xyloglucan was detected mostly in oligomeric form in the alkali-labile fraction and was enriched in tension wood. β-(1→4)-Galactan and rhamnogalacturonan I backbone epitopes were localized in the gelatinous cell wall layer. Type II arabinogalactans retained by cellulose microfibrils had a higher content of (methyl)glucuronic acid and galactose in tension wood than in normal wood. Thus, β-(1→4)-galactan and a specialized form of type II arabinogalactan are trapped by cellulose microfibrils specifically in tension wood and, thus, are the main candidate polymers for the generation of tensional stresses by the entrapment mechanism. We also found high β-galactosidase activity accompanying tension wood differentiation and propose a testable hypothesis that such activity might regulate galactan entrapment and, thus, mechanical properties of cell walls in tension wood.
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Affiliation(s)
- Tatyana Gorshkova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Natalia Mokshina
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Tatyana Chernova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Nadezhda Ibragimova
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Vadim Salnikov
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Polina Mikshina
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Theodora Tryfona
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Alicja Banasiak
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Peter Immerzeel
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Paul Dupree
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
| | - Ewa J Mellerowicz
- Kazan Institute of Biochemistry and Biophysics, Kazan Scientific Centre, Russian Academy of Sciences, 420111 Kazan, Russia (T.G., N.M., T.C., N.I., V.S., P.M.);Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (T.T., P.D.);Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea Plant Science Centre, 90183 Umea, Sweden (A.B., P.I., E.J.M.); andInstitute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland (A.B.)
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