The DOI matches its Crossref record; 7 of the 7 references it cites were found in a registry or an index.
A Systems Biology View of Responses to Lignin Biosynthesis Perturbations in Arabidopsis
Open accessAbstract
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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Cited by
Lignin biosynthesis and its integration into metabolism
Vanholme, R., De Meester, B., Ralph, J., & Boerjan, W. (2019) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2019.02.018 · Cited by 837
Self-citationVan Acker, R., Vanholme, R., Storme, V., Mortimer, J. C., Dupree, P., & Boerjan, W. (2013) · Biotechnology for Biofuels · doi:10.1186/1754-6834-6-46 · Cited by 334
Self-citationComparative functional genomics analysis of cytochrome P450 gene superfamily in wheat and maize
Li, Y., & Wei, K. (2020) · BMC Plant Biology · doi:10.1186/s12870-020-2288-7 · Cited by 119
Indole Glucosinolate Biosynthesis Limits Phenylpropanoid Accumulation in Arabidopsis thaliana
Kim, J. I., Dolan, W. L., Anderson, N. A., & Chapple, C. (2015) · The Plant Cell · doi:10.1105/tpc.15.00127 · Cited by 117
Chen, H.-C., Song, J., Wang, J. P., Lin, Y.-C., Ducoste, J., Shuford, C. M., Liu, J., Li, Q., Shi, R., Nepomuceno, A., et al. (2014) · The Plant Cell · doi:10.1105/tpc.113.119685 · Cited by 80
Metadata
- Authors
- Vanholme, R., Storme, V., Vanholme, B., Sundin, L., Christensen, J. H., Goeminne, G., Halpin, C., Rohde, A., Morreel, K., & Boerjan, W.
- Venue
- The Plant Cell
- Publisher
- Oxford University Press (OUP)
- Published
- 2012-09-01
- Volume
- 24
- Issue
- 9
- Pages
- 3506-3529
- ISSN
- 1040-4651 (ISSN-L)
- 1532-298X
- OpenAlex
- W2036839854
- Cited by
- 365
- References
- 7
- FWCI
- 9.53
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Vanholme, R., Storme, V., Vanholme, B., Sundin, L., Christensen, J. H., Goeminne, G., Halpin, C., Rohde, A., Morreel, K., & Boerjan, W. (2012). A Systems Biology View of Responses to Lignin Biosynthesis Perturbations in Arabidopsis. The Plant Cell. https://doi.org/10.1105/tpc.112.102574
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