ArticleThe Plant cell2012
A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis.
Article in The Plant cell, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 177 papers.
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Who cites it
177 citing papers in PubMed, 360 citations in OpenAlex.
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- Overexpression of OsCCR1, OsCOMT5, OsCAD2 and OsCCoAOMT1 Genes Enhances Lignin Accumulation and Confers Tolerance Against Rhizoctonia solani in Rice (Oryza sativa).Molecular biotechnology · 2026Article
- Integrated transcriptome and metabolome analysis reveals the molecular mechanisms of drought response in Setaria italica during the booting stage.BMC plant biology · 2026Article
- Genome-wide analysis of leucine-rich repeat-only proteins gene family revealed FaLRRop26 responding Colletotrichum Siamense infection by regulated lignin synthesis in cultivated strawberry (Fragaria × ananassa).BMC plant biology · 2026Article
- Variations in carbon flux allocation among cassava (Manihot esculenta) cultivars arise from balanced competition between starch accumulation and structural component development.Communications biology · 2026Article
- A high spatial resolution transcriptomics of tension wood reveals the genetic program of contractile G-layer formation.Frontiers in plant science · 2026Article
- Brown midrib mutants in sorghum and their applications in renewable energy production.Frontiers in plant science · 2026Review
- Metabolic engineering strategies for optimized lignan production in plants.Frontiers in plant science · 2026Review
- Loss-of-function mutation of two phenylpropanoid pathway genes PAL1 and PAL2, coupled with MYB46 upregulation, increases fermentable sugar yield and ethanol production.Journal of biological engineering · 2025Article
- Genome-wide identification and analysis of the cytochrome P450 family elucidate flavonoid biosynthesis in safflower.BMC plant biology · 2025Article
- Genome-Wide Characterization of the Phosphofructokinase Gene Family inInternational journal of molecular sciences · 2025Article
- OsLC1, a transaldolase, regulates cell patterning and leaf morphology through modulation of secondary metabolism.Plant biotechnology journal · 2025Article
- Deciphering the regulatory network of lignocellulose biosynthesis in bread wheat through genome-wide association studies.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Proteomic Dynamics in the Interaction of Susceptible and Resistant Tomato Cultivars and Potato Cyst Nematodes.International journal of molecular sciences · 2025Article
- Article
- Bio-organic fertilizer affects secondary cell wall biosynthesis of Dendrocalamus farinosus by inhibiting the phenylpropanoid metabolic pathway.BMC plant biology · 2024Article
- MENTOR: Multiplex Embedding of Networks for Team-Based Omics Research.bioRxiv : the preprint server for biology · 2024Article
- Pearl millet a promising fodder crop for changing climate: a review.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Review
- Phenolic Compounds and Antioxidant Capacity Comparison of Wild-Type and Yellow-LeafPlants (Basel, Switzerland) · 2024Article
117 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
Lignin engineering is an attractive strategy to improve lignocellulosic biomass quality for processing to biofuels and other bio-based products. However, lignin engineering also results in profound metabolic consequences in the plant. We used a systems biology approach to study the plant's response to lignin perturbations. To this end, inflorescence stems of 20 Arabidopsis thaliana mutants, each mutated in a single gene of the lignin biosynthetic pathway (phenylalanine ammonia-lyase1 [PAL1], PAL2, cinnamate 4-hydroxylase [C4H], 4-coumarate:CoA ligase1 [4CL1], 4CL2, caffeoyl-CoA O-methyltransferase1 [CCoAOMT1], cinnamoyl-CoA reductase1 [CCR1], ferulate 5-hydroxylase [F5H1], caffeic acid O-methyltransferase [COMT], and cinnamyl alcohol dehydrogenase6 [CAD6], two mutant alleles each), were analyzed by transcriptomics and metabolomics. A total of 566 compounds were detected, of which 187 could be tentatively identified based on mass spectrometry fragmentation and many were new for Arabidopsis. Up to 675 genes were differentially expressed in mutants that did not have any obvious visible phenotypes. Comparing the responses of all mutants indicated that c4h, 4cl1, ccoaomt1, and ccr1, mutants that produced less lignin, upregulated the shikimate, methyl-donor, and phenylpropanoid pathways (i.e., the pathways supplying the monolignols). By contrast, f5h1 and comt, mutants that provoked lignin compositional shifts, downregulated the very same pathways. Reductions in the flux to lignin were associated with the accumulation of various classes of 4-O- and 9-O-hexosylated phenylpropanoids. By combining metabolomic and transcriptomic data in a correlation network, system-wide consequences of the perturbations were revealed and genes with a putative role in phenolic metabolism were identified. Together, our data provide insight into lignin biosynthesis and the metabolic network it is embedded in and provide a systems view of the plant's response to pathway perturbations.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.