Dataset Information

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

ABSTRACT: Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32–38 kDa proteins that are involved in membrane trafficking. A proteomics approach was taken to elucidate function of the SCAMPs in wood formation of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3; Potri.019G104000). Secondary xylem tissues were run on a SynaptTM G2 HDMS mass spectrometer equipped with a nanoflow electrospray ionization interface. Multivariate OnPLS (orthogonal projections to latent structures) modeling was applied to identify consistent changes in the proteomes of the transgenic lines compared to the wild type trees. The woody tissues of the transgenic trees displayed increased amounts of both polysaccharides and lignin oligomers, indicating increased deposition of both the carbohydrate and lignin components of the secondary cell walls. This coincided with slightly increased wood density as well as significantly increased thickness of the suberized cork in the transgenic lines. The OnPLS model identified a rather large number of proteins that were more abundant in the transgenic lines than in the wild type. Several of these were related to secretion and/or endocytosis as well as both primary and secondary cell wall biosynthesis, suggesting function of the Populus SCAMP proteins in membrane trafficking to fine-tune the abundance of cell wall precursors and/or proteins involved in cell wall biosynthesis and transport. The data provides a multi-level source of information for future studies on the function of the SCAMP proteins in plant stem tissues.

OTHER RELATED OMICS DATASETS IN: MTBLS628MTBLS478

INSTRUMENT(S): Synapt G2 HDMS

ORGANISM(S): Populus Tremula X Populus Tremuloides

TISSUE(S): Xylem

SUBMITTER: Joakim Bygdell

LAB HEAD: Hannele Tuominen

PROVIDER: PXD008266 | Pride | 2018-01-10

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	2013-05-20_BIO_G911-1.raw.tgz	Raw
	2013-05-20_BIO_G911-1_IA_final_peptide.csv	Csv
	2013-05-20_BIO_G911-2.raw.tgz	Raw
	2013-05-20_BIO_G911-2_IA_final_peptide.csv	Csv
	2013-05-20_BIO_G912-1.raw.tgz	Raw

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

Obudulu Ogonna O Mähler Niklas N Skotare Tomas T Bygdell Joakim J Abreu Ilka N IN Ahnlund Maria M Latha Gandla Madhavi M Petterle Anna A Moritz Thomas T Hvidsten Torgeir R TR Jönsson Leif J LJ Wingsle Gunnar G Trygg Johan J Tuominen Hannele H

BMC genomics 20180103 1

<h4>Background</h4>Secretory Carrier-Associated Membrane Proteins (SCAMPs) are highly conserved 32-38 kDa proteins that are involved in membrane trafficking. A systems approach was taken to elucidate function of SCAMPs in wood formation of Populus trees. Phenotypic and multi-omics analyses were performed in woody tissues of transgenic Populus trees carrying an RNAi construct for Populus tremula x tremuloides SCAMP3 (PttSCAMP3; Potri.019G104000).<h4>Results</h4>The woody tissues of the transgenic ...[more]

PMID: 29298676

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Project description:Using whole genome microarrays based on the annotated genomes of Postia placenta, we monitored the changes in its transcriptomes relevant to cell wall degradation during growth on three chemically distinct Populus trichocarpa (poplar) wood substrates. The research goal is to identtify genes essential for cellulose depolymerization. From a data set of 12438 unique gene models, each NimbleGen (Madison, WI) array targeted 9959 genes and featured 10 unique 60mers per gene, all in triplicate. RNA and protein were obtained from P. placenta strain MAD-698-R (USDA Forest Mycology Center, Forest Products Laboratory, Madison WI) grown in malt extract agar for 10 days prior to inoculation with wood wafers. Three poplar wood substrates with distinct cell wall chemical properties were selected from several hundred 4-year old poplar (Populus trichocarpa) trees grown in a common garden field trial at the University of British Columbia (Canada). We selected three poplar genotypes based on cell wall chemical traits. Substrate A corresponds to a genotype with a higher than average lignin content and lower that average glucose content; Substrate B, a lower than average lignin content and higher that average glucose content; Substrate C lignin and glucose contents are near the population average. Poplar wood stems were cut into 0.5 mm wafers on a microtome, sterilized for 20 min at 121°C, dried at 50°C overnight, and cooled to room temperature. The specimens were then inoculated in Petri dishes with actively growing mycelia. Approximately 5 g of wood wafers were placed in each Petri dish (exact weights were recorded), sealed and incubated at 22°C and 70 ± 5% relative humidity for 10, 20 or 30 days. For RNA, the degraded wafers were removed from the Petri dishes, immediately snap-frozen in liquid nitrogen and stored at -80°C for later use. Total RNA was converted to Cy3 labelled cDNA, hybridized to microarrays and scanned as previously described by Vanden Wymelenberg et al 2010 (Appl Enviro Microbiol 76:3599-3610).The 24 arrays per fungal species were scanned and data extracted using NimbleScan v.2.4. The raw data was loaded into GeneSpring, where the intensities were converted to log2 and quantile normalized, and all probes per gene averaged. This data was then exported and further analyzed in R. For substrates “A” and “B”, three replicates were used for each wood substrate/fungus and incubation period combination. For substrate “C” only 2 biological replicates were employed.

Project description:Using whole genome microarrays based on the annotated genomes of Phanerochaete chrysosporium, we monitored the changes in its transcriptomes relevant to cell wall degradation during growth on three chemically distinct Populus trichocarpa (poplar) wood substrates. Results of this study are sumbitted for review in Biotechnology for Biofuels From a data set of 10004 unique gene models, each NimbleGen (Madison, WI) array targeted 9959 genes and featured 12 unique 60mers per gene, all in triplicate. RNA and protein were obtained from P. chrysosporium strain RP-78 (USDA Forest Mycology Center, Forest Products Laboratory, Madison WI) grown in malt extract agar for 10 days prior to inoculation with wood wafers. Three poplar wood substrates with distinct cell wall chemical properties were selected from several hundred 4-year old Populus trichocarpa trees grown in a common garden field trial at the University of British Columbia (Canada). We selected three poplar genotypes based on cell wall chemical traits. Substrate A corresponds to a genotype with a higher than average lignin content and lower that average glucose content; Substrate B, a lower than average lignin content and higher that average glucose content; Substrate C lignin and glucose contents are near the population average. Poplar wood stems were cut into 0.5 mm wafers on a microtome, sterilized for 20 min at 121°C, dried at 50°C overnight, and cooled to room temperature. The specimens were then inoculated in Petri dishes with actively growing mycelia. Approximately 5 g of wood wafers were placed in each Petri dish (exact weights were recorded), sealed and incubated at 22°C and 70 ± 5% relative humidity for 10, 20 or 30 days. For RNA, the degraded wafers were removed from the Petri dishes, immediately snap-frozen in liquid nitrogen and stored at -80°C for later use. Total RNA was converted to Cy3 labelled cDNA, hybridized to microarrays and scanned as previously described by Vanden Wymelenberg et al 2010 (Appl Enviro Microbiol 76:3599-3610).The 24 arrays per fungal species were scanned and data extracted using NimbleScan v.2.4. The raw data was loaded into GeneSpring, where the intensities were converted to log2 and quantile normalized, and all probes per gene averaged. This data was then exported and further analyzed in R. For substrates “A” and “B”, three replicates were used for each wood substrate/fungus and incubation period combination. For substrate “C” only 2 biological replicates were employed.

Project description:rs04-03_myb - myb - Xylogenesis is a fundamental developmental process that is specific of vascular plants. It allows the formation of xylem, also called wood in trees, a complex tridimensional tissue composed of different cell types. This process occurs through the control of fundamental cell mechanisms like cell division and differentiation, secondary cell wall synthesis, lignin deposition and programmed cell death. Xylogenesis is controlled spatially and temporally by specific genetic programs that involve hundreds of genes. For instance, lignin biosynthetic genes, CAD and CCR, are specifically expressed during xylogenesis through MYB transcription factor binding sites, a process that seems to be common to all vascular plants. We have cloned two xylem specific MYB transcription factors, EgMYB1 et EgMYB2, in Eucalyptus. Interestingly, they are able to bind MYB consensus sequences of CAD and CCR promoters in vitro and to modulate CAD and CCR expression in vivo. When overexpressed in Arabidopsis or tobacco, they affect xylem structure by changing cell wall structure and quality. To follow expression changes of Arabidopsis genes in transgenic plants overexpressing Eg MYB1 and EgMYB2 should help us to find out which genes might be target of those transcription factors. This should help us to decipher the actual role of those two MYBs in xylogenesis, two new members of a large family of transcription factors in plants. - Xylogenesis is a fundamental developmental process that is specific of vascular plants. It allows the formation of xylem, also called wood in trees, a complex tridimensional tissue composed of different cell types. This process occurs through the control of fundamental cell mechanisms like cell division and differentiation, secondary cell wall synthesis, lignin deposition and programmed cell death. Xylogenesis is controlled spatially and temporally by specific genetic programs that involve hundreds of genes. For instance, lignin biosynthetic genes, CAD and CCR, are specifically expressed during xylogenesis through MYB transcription factor binding sites, a process that seems to be common to all vascular plants. We have cloned two xylem specific MYB transcription factors, EgMYB1 et EgMYB2, in Eucalyptus. Interestingly, they are able to bind MYB consensus sequences of CAD and CCR promoters in vitro and to modulate CAD and CCR expression in vivo. When overexpressed in Arabidopsis or tobacco, they affect xylem structure by changing cell wall structure and quality. To follow expression changes of Arabidopsis genes in transgenic plants overexpressing Eg MYB1 and EgMYB2 should help us to find out which genes might be target of those transcription factors. This should help us to decipher the actual role of those two MYBs in xylogenesis, two new members of a large family of transcription factors in plants. Keywords: gene knock in (transgenic)

Project description:The within-tree variation in wood properties constitutes an exceptional model to study the mechanisms that adjust the different biosynthetic pathways providing substrates with the massive and variable demands of different biosynthetic reactions of cell wall polymers. Although a few genes have been reported as differentially expressed in differentiating compression wood compared to normal or opposite wood, the expression of a larger set of genes is expected to change due the broad range of features that distinguish this reaction wood. By combining the construction of different cDNA libraries with microarray analyses, using samples from different Pinus pinaster provenances collected in different years and geographic locations, we have identified a total of 496 genes that change their expression during differentiation of compression wood (331 up-regulated and 165 down-regulated compared to opposite wood). Consistent with the well-known structural and chemical characteristics of compression wood, a large number of genes involved in the biosynthesis of cell wall components were shown to be up-regulated during compression wood differentiation, including genes involved in synthesis of cellulose, hemicellulose, lignin and lignans. In particular, further analysis of a set of these genes involved in providing S-adenosylmethionine, ammonium recycling, lignin and lignans biosynthesis showed parallel expression profiles to levels of lignin accumulation in cells undergoing xylogenesis in vivo and in vitro. The comparative transcriptomic analysis of compression and opposite wood formation in this work have revealed a broad spectrum of coordinated transcriptional modulation of biosynthetic reactions for different cell wall polymers associated to within-tree variations in softwood structure and composition. In particular, it suggest the occurrence of a mechanism that modulates at transcriptional level genes encoding enzymes involved in S-adenosylmethionine synthesis and ammonium assimilation with coniferyl alcohol demand for lignin and lignan synthesis, as a key metabolic requirement in cells undergoing lignification. Two-condition experiment including dye-swap experiments, Compression Differentiating Xylem vs. Opposite Differentiating Xylem. Biological replicates: 4 compression xylem, 4 opposite xylew, harvested from four different individual pine trees. Two replicates per array.

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

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

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

Dataset's files

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets

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