title: Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development.
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.
  
  
  CONCLUSIONS
  Our novel multivariate approach highlights important processes and provides confirmatory insights into the molecular foundations of wood development.
authors.affiliation: Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden. Ogonna.Obudulu@slu.se.|Computational life science cluster (CLiC), Umeå University, Umeå, Sweden. Ogonna.Obudulu@slu.se.
authors.forename: Ogonna
authors.initials: O
authors.lastname: Obudulu
authors.affiliation: Department of Chemistry, Umeå University, SE-90187, Umeå, Sweden. Joakim.Bygdell@umu.se.|Computational life science cluster (CLiC), Umeå University, Umeå, Sweden. Joakim.Bygdell@umu.se.
authors.forename: Joakim
authors.initials: J
authors.lastname: Bygdell
authors.affiliation: Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden. Bjorn.Sundberg@slu.se.
authors.forename: Björn
authors.initials: B
authors.lastname: Sundberg
authors.affiliation: Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden. Thomas.Moritz@slu.se.
authors.forename: Thomas
authors.initials: T
authors.lastname: Moritz
authors.affiliation: Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, SE-90187, Umeå, Sweden. torgeir.r.hvidsten@nmbu.no.|Computational life science cluster (CLiC), Umeå University, Umeå, Sweden. torgeir.r.hvidsten@nmbu.no.|Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway. torgeir.r.hvidsten@nmbu.no.
authors.forename: Torgeir R
authors.initials: TR
authors.lastname: Hvidsten
authors.affiliation: Department of Chemistry, Umeå University, SE-90187, Umeå, Sweden. johan.trygg@chem.umu.se.|Computational life science cluster (CLiC), Umeå University, Umeå, Sweden. johan.trygg@chem.umu.se.
authors.forename: Johan
authors.initials: J
authors.lastname: Trygg
authors.affiliation: Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden. Gunnar.Wingsle@slu.se.
authors.forename: Gunnar
authors.initials: G
authors.lastname: Wingsle
mesh_terms: D058506:Cambium; D002482:Cellulose / Q000096:biosynthesis; D002853:Chromatography, Liquid; D013058:Mass Spectrometry; D008954:Models, Biological; D052585:Phloem / Q000254:growth & development; D010940:Plant Proteins / Q000378:metabolism*; D032107:Populus / Q000254:growth & development*; D020543:Proteome / Q000378:metabolism*; D040901:Proteomics; D013548:Sweden; D014934:Wood / Q000254:growth & development*; D052584:Xylem / Q000254:growth & development
chemical_list: D010940:Plant Proteins; D020543:Proteome; D002482:Cellulose