PXD049389

PXD049389 is an original dataset announced via ProteomeXchange.

Title	Lignin engineering in poplar via heterologous expression of dehydroshikimate dehydratase induces distinct transcriptional and metabolic changes in the shikimate and phenylpropanoid pathways
Description	Modification of lignin in crops via genetic engineering aims at reducing biomass recalcitrance to facilitate conversion processes. These improvements can be achieved via the expression of exogenous enzymes that interfere with biosynthetic pathways responsible for the production of the lignin precursors. In-planta expression of bacterial 3-dehydroshikimate dehydratase (QsuB) reduces lignin and alters its monomeric composition, which enables higher yields of fermentable sugars after cell wall polysaccharide hydrolysis. Understanding how crops respond to such genetic modifications at the transcriptional and metabolic levels is needed to facilitate further improvement and field deployment. In this work, we gathered some fundamental knowledge on lignin-modified QsuB poplar grown in a greenhouse using RNA-seq and metabolomics. The data showed that some changes in gene expression and metabolite abundance occur only in a specific tissue such as the xylem, phloem, or periderm. In the poplar line that exhibits the strongest reduction of lignin, we found that 3% of the transcripts had altered expression levels and ~19% of the detected metabolite ions had different abundances in the xylem from mature stems. Changes affect predominantly the shikimate and phenylpropanoid pathways as well as, secondary cell wall metabolism, and result in significant accumulation of hydroxybenzoates that derive from protocatechuate and salicylate.
HostingRepository	PRIDE
AnnounceDate	2024-10-17
AnnouncementXML	Submission_2024-10-17_05:06:18.944.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Christopher Petzold
SpeciesList	scientific name: Populus trichocarpa (Western balsam poplar) (Populus balsamifera subsp. trichocarpa); NCBI TaxID: 3694;
ModificationList	monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-14 12:47:09	ID requested
⏵ 1	2024-10-17 05:06:20	announced

10.1093/jxb/erae251;

Akyuz Turumtay E, Turumtay H, Tian Y, Lin CY, Chai YN, Louie KB, Chen Y, Lipzen A, Harwood T, Satish Kumar K, Bowen BP, Wang Q, Mansfield SD, Blow MJ, Petzold CJ, Northen TR, Mortimer JC, Scheller HV, Eudes A, Expression of dehydroshikimate dehydratase in poplar induces transcriptional and metabolic changes in the phenylpropanoid pathway. J Exp Bot, 75(16):4960-4977(2024) [pubmed]

submitter keyword: Aromatics, lignin, metabolomics, bioenergy, cell wall, poplar, systems biology, RNA-seq

Christopher Petzold
contact affiliation	Staff Scientist Biological Systems & Engineering Division Lawrence Berkeley National Laboratory Berkeley CA 94720
contact email	cjpetzold@lbl.gov
lab head
Christopher Petzold
contact affiliation	Lawrence Berkeley National Laboratory
contact email	cjpetzold@lbl.gov
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD049389
     1. Label: PRIDE project
     2. Name: Lignin engineering in poplar via heterologous expression of dehydroshikimate dehydratase induces distinct transcriptional and metabolic changes in the shikimate and phenylpropanoid pathways