Dataset Information

Lignin engineering in poplar via heterologous expression of dehydroshikimate dehydratase induces distinct transcriptional and metabolic changes in the shikimate and phenylpropanoid pathways

ABSTRACT: 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.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Populus Trichocarpa (western Balsam Poplar) (populus Balsamifera Subsp. Trichocarpa)

TISSUE(S): Xylem

SUBMITTER: Christopher Petzold

LAB HEAD: Christopher Petzold

PROVIDER: PXD049389 | Pride | 2024-10-17

REPOSITORIES: Pride

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Expression of dehydroshikimate dehydratase in poplar induces transcriptional and metabolic changes in the phenylpropanoid pathway.

Akyuz Turumtay Emine E Turumtay Halbay H Tian Yang Y Lin Chien-Yuan CY Chai Yen Ning YN Louie Katherine B KB Chen Yan Y Lipzen Anna A Harwood Thomas T Satish Kumar Kavitha K Bowen Benjamin P BP Wang Qian Q Mansfield Shawn D SD Blow Matthew J MJ Petzold Christopher J CJ Northen Trent R TR Mortimer Jenny C JC Scheller Henrik V HV Eudes Aymerick A

Journal of experimental botany 20240801 16

Modification of lignin in feedstocks via genetic engineering aims to reduce biomass recalcitrance to facilitate efficient conversion processes. These improvements can be achieved by expressing exogenous enzymes that interfere with native biosynthetic pathways responsible for the production of the lignin precursors. In planta expression of a bacterial 3-dehydroshikimate dehydratase in poplar trees reduced lignin content and altered the monomer composition, which enabled higher yields of sugars af ...[more]

PMID: 38809816

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Project description:Microarrays have become established tools for describing microbial systems, however the assessment of expression profiles for environmental microbial communities still presents unique challenges. Notably, the concentration of particular transcripts are likely very dilute relative to the pool of total RNA, and PCR-based amplification strategies are vulnerable to amplification biases and the appropriate primer selection. Thus, we apply a signal amplification approach, rather than template amplification, to analyze the expression of selected lignin-degrading enzymes in soil. Controls in the form of known amplicons and cDNA from Phanerochaete chrysosporium were included and mixed with the soil cDNA both before and after the signal amplification in order to assess the dynamic range of the microarray. We demonstrate that restored prairie soil expresses a diverse range of lignin-degrading enzymes following incubation with lignin substrate, while farmed agricultural soil does not. The mixed additions of control cDNA with soil cDNA indicate that the mixed biomass in the soil does interfere with low abundance transcript changes, nevertheless our microarray approach consistently reports the most robust signals. Keywords: comparative analysis, microbial ecology, soil microbial communities We used lignin degradation as a model process to demonstrate the use of an oligonucleotide microarray for directly detecting gene expression in soil communities using signal amplification instead of template amplification to avoid the introduction of PCR bias. In the current study, we analyzed mRNA isolated from two distinct soil microbial communities and demonstrate our ability to detect the expression of a small subset of lignin degrading genes following exposure to a lignitic substrate. We also included purified control amplicons and mixed target experiments with pure P. chrysosporium genomic cDNA to determine the level of interference from soil biomass on target hybridization.

Project description:Hybrid poplar (Populus alba?×?grandidentata; p39) wild type (WT) and QsuB transgenic low-lignin lines were previously described (Unda et al., 2022). WT and lines QsuB1, QsuB5, and QsuB15 were grown in a greenhouse as described in Lin et al., 2022. Samples for metabolomic analyses were collected after a growth period of six months. Stems were cut 5 cm above the root collar and segments of 5 cm were collected above the 1st (bottom), 20th (middle), and 40th (top) internodes. The bark was peeled and developing xylem tissue was collected by scraping the surface of the debarked segments using a razor blade. This approach generated developing xylem samples from the mature (bottom segment), intermediate (middle segment), and immature (top segment) parts of the stem. All the samples were immediately placed in liquid nitrogen, and stored at ?80 °C until time of use. Frozen samples were pulverized with a ball mill (Retsch) using stainless steel jars and grinding balls. Four biological replicates from each transgenic poplar line and WT control were used for metabolomic analyses. The data showed that some changes in 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 ~19% of the detected metabolite ions had different abundances in the xylem from mature stems. Changes affect predominantly the shikimate and phenylpropanoid pathways, secondary cell wall metabolism, and result in significant accumulation of hydroxybenzoates that derive from protocatechuate and salicylate. Unda et al., 2022: https://doi.org/10.1111/nph.18136 Lin et al., 2022: https://doi.org/10.1186/s13068-022-02245-4. The work (proposal:https://doi.org/10.46936/10.25585/60000514) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.

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	QsuB-1-R1.raw	Raw
	QsuB-1-R2.raw	Raw
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	QsuB-1-R4.raw	Raw
	QsuB-15-R1.raw	Raw