Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development

Abstract

BackgroundWood 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.ResultsWe 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.ConclusionOur novel multivariate approach highlights important processes and provides confirmatory insights into the molecular foundations of wood development.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2458-z) contains supplementary material, which is available to authorized users.

The function of two type II metacaspases in woody tissues of Populus trees

“…(a) Location of three peptides within the Populus RD21 protein sequence that were retrieved from Obudulu et al . () as being highly expressed in the xylem tissues of hybrid aspen trees. Protein domains as in Fig.…”

“…Further indication for processing of RD21 by PttMC13/14 was obtained by data-mining a proteomic dataset from the different tissue types of hybrid aspen stem (Obudulu et al, 2016). Three peptides corresponding to RD21 were highly abundant throughout the phloem, cambial and xylem tissues of the stem (Fig.…”

“…High-resolution quantification of RD21 peptides in the xylem tissues of wild-type hybrid aspen trees. (a) Location of three peptides within the Populus RD21 protein sequence that were retrieved fromObudulu et al (2016) as being highly expressed in the xylem tissues of hybrid aspen trees. Protein domains as in…”

Protein expression in tension wood formation monitored at high tissue resolution in Populus

“…The proteins identified from the soluble and pellet fractions were combined for each sample prior to final analysis. Proteome analysis and protein identification and quantification were performed using mass spectrometry as described by Obudulu et al (2016) . In essence, the peptides were separated using a nanoACQUITYTM ultra-performance liquid chromatography system (Waters, Milford, MA).…”

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of​ ​​Populus​​ ​trees

“…Total proteins were extracted from 20 mg of frozen stem tissue powder as described earlier [ 32 ]. The samples were run on a Synapt™ G2 HDMS mass spectrometer (Waters, UK) equipped with a nanoflow electrospray ionization interface according to [ 33 ]. Protein identification and peptide quantification was described earlier [ 14 ].…”