Véronique Storme

Publications (10)58.1 Total impact

• Article: Plant cell wall profiling by fast maximum likelihood reconstruction (FMLR) and region-of-interest (ROI) segmentation of solution-state 2D 1H--13C NMR spectra.

  Roger A Chylla, Rebecca Van Acker, Hoon Kim, Ali Azapira, Purba Mukerjee, John L Markley, Véronique Storme, Wout Boerjan, John Ralph
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  ABSTRACT: BACKGROUND: Interest in the detailed lignin and polysaccharide composition of plant cell walls has surged within the past decade partly as a result of biotechnology research aimed at converting biomass to biofuels. High-resolution, solution-state 2D 1H--13C HSQC NMR spectroscopy has proven to be an effective tool for rapid and reproducible fingerprinting of the numerous polysaccharides and lignin components in unfractionated plant cell wall materials, and is therefore a powerful tool for cell wall profiling based on our ability to simultaneously identify and comparatively quantify numerous components within spectra generated in a relatively short time. However, assigning peaks in new spectra, integrating them to provide relative component distributions, and producing color-assigned spectra, are all current bottlenecks to the routine use of such NMR profiling methods. RESULTS: We have assembled a high-throughput software platform for plant cell wall profiling that uses spectral deconvolution by Fast Maximum Likelihood Reconstruction (FMLR) to construct a mathematical model of the signals present in a set of related NMR spectra. Combined with a simple region of interest (ROI) table that maps spectral regions to NMR chemical shift assignments of chemical entities, the reconstructions can provide rapid and reproducible fingerprinting of numerous polysaccharide and lignin components in unfractionated cell wall material, including derivation of lignin monomer unit (S:G:H) ratios or the so-called SGH profile. Evidence is presented that ROI-based amplitudes derived from FMLR provide a robust feature set for subsequent multivariate analysis. The utility of this approach is demonstrated on a large transgenic study of Arabidopsis requiring concerted analysis of 91 ROIs (including both assigned and unassigned regions) in the lignin and polysaccharide regions of almost 100 related 2D 1H--13C HSQC spectra. CONCLUSIONS: We show that when a suitable number of replicates are obtained per sample group, the correlated patterns of enriched and depleted cell wall components can be reliably and objectively detected even prior to multivariate analysis. The analysis methodology has been implemented in a publicly-available, cross-platform (Windows/Mac/Linux), web-enabled software application that enables researchers to view and publish detailed annotated spectra in addition to summary reports in simple spreadsheet data formats. The analysis methodology is not limited to studies of plant cell walls but is amenable to any NMR study where ROI segmentation techniques generate meaningful results.Please see related article: http://www.biotechnologyforbiofuels.com/content/6/1/46/
  Biotechnology for Biofuels 04/2013; 6(1):45. · 6.09 Impact Factor
• Article: Lignin biosynthesis perturbations affect secondary cell wall composition and saccharification yield in Arabidopsis thaliana.

  Rebecca Van Acker, Ruben Vanholme, Véronique Storme, Jennifer C Mortimer, Paul Dupree, Wout Boerjan
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  ABSTRACT: BACKGROUND: Second-generation biofuels are generally produced from the polysaccharides in the lignocellulosic plant biomass, mainly cellulose. However, because cellulose is embedded in a matrix of other polysaccharides and lignin, its hydrolysis into the fermentable glucose is hampered. The senesced inflorescence stems of a set of 20 Arabidopsis thaliana mutants in 10 different genes of the lignin biosynthetic pathway were analyzed for cell wall composition and saccharification yield. Saccharification models were built to elucidate which cell wall parameters played a role in cell wall recalcitrance. RESULTS: Although lignin is a key polymer providing the strength necessary for the plant's ability to grow upward, a reduction in lignin content down to 64% of the wild-type level in Arabidopsis was tolerated without any obvious growth penalty. In contrast to common perception, we found that a reduction in lignin was not compensated for by an increase in cellulose, but rather by an increase in matrix polysaccharides. In most lignin mutants, the saccharification yield was improved by up to 88% cellulose conversion for the cinnamoyl-coenzyme A reductase1 mutants under pretreatment conditions, whereas the wild-type cellulose conversion only reached 18%. The saccharification models and Pearson correlation matrix revealed that the lignin content was the main factor determining the saccharification yield. However, also lignin composition, matrix polysaccharide content and composition, and, especially, the xylose, galactose, and arabinose contents influenced the saccharification yield. Strikingly, cellulose content did not significantly affect saccharification yield. CONCLUSIONS: Although the lignin content had the main effect on saccharification, also other cell wall factors could be engineered to potentially increase the cell wall processability, such as the galactose content. Our results contribute to a better understanding of the effect of lignin perturbations on plant cell wall composition and its influence on saccharification yield, and provide new potential targets for genetic improvement.Please see related article: http://www.biotechnologyforbiofuels.com/content/6/1/45/
  Biotechnology for Biofuels 04/2013; 6(1):46. · 6.09 Impact Factor
• Source

  Available from: Ruben Vanholme

  Dataset: vanholme2012systemsbiologylignification

  Ruben Vanholme, Véronique Storme, Bartel Vanholme, Lisa Sundin, Jørgen Holst Christensen, Geert Goeminne, Claire Halpin, Antje Rohde, Kris Morreel, Wout Boerjan
• Source

  Available from: Ruben Vanholme

  Article: A systems biology view of responses to lignin biosynthesis perturbations in Arabidopsis.

  Ruben Vanholme, Véronique Storme, Bartel Vanholme, Lisa Sundin, Jørgen Holst Christensen, Geert Goeminne, Claire Halpin, Antje Rohde, Kris Morreel, Wout Boerjan
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  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.
  The Plant Cell 09/2012; 24(9):3506-29. · 8.99 Impact Factor
• Article: Engineering traditional monolignols out of lignin by concomitant up-regulation of F5H1 and down-regulation of COMT in Arabidopsis.

  Ruben Vanholme, John Ralph, Takuya Akiyama, Fachuang Lu, Jorge Rencoret Pazo, Hoon Kim, Jørgen Holst Christensen, Brecht Van Reusel, Véronique Storme, Riet De Rycke, Antje Rohde, Kris Morreel, Wout Boerjan
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  ABSTRACT: Lignin engineering is a promising strategy to optimize lignocellulosic plant biomass for use as a renewable feedstock for agro-industrial applications. Current efforts focus on engineering lignin with monomers that are not normally incorporated into wild-type lignins. Here we describe an Arabidopsis line in which the lignin is derived to a major extent from a non-traditional monomer. The combination of mutation in the gene encoding caffeic acid O-methyltransferase (comt) with over-expression of ferulate 5-hydroxylase under the control of the cinnamate 4-hydroxylase promoter (C4H:F5H1) resulted in plants with a unique lignin comprising almost 92% benzodioxane units. In addition to biosynthesis of this particular lignin, the comt C4H:F5H1 plants revealed massive shifts in phenolic metabolism compared to the wild type. The structures of 38 metabolites that accumulated in comt C4H:F51 plants were resolved by mass spectral analyses, and were shown to derive from 5-hydroxy-substituted phenylpropanoids. These metabolites probably originate from passive metabolism via existing biochemical routes normally used for 5-methoxylated and 5-unsubstituted phenylpropanoids and from active detoxification by hexosylation. Transcripts of the phenylpropanoid biosynthesis pathway were highly up-regulated in comt C4H:F5H1 plants, indicating feedback regulation within the pathway. To investigate the role of flavonoids in the abnormal growth of comt C4H:F5H1 plants, a mutation in a gene encoding chalcone synthase (chs) was crossed in. The resulting comt C4H:F5H1 chs plants showed partial restoration of growth. However, a causal connection between flavonoid deficiency and this restoration of growth was not demonstrated; instead, genetic interactions between phenylpropanoid and flavonoid biosynthesis could explain the partial restoration. These genetic interactions must be taken into account in future cell-wall engineering strategies.
  The Plant Journal 12/2010; 64(6):885-97. · 6.16 Impact Factor
• Source

  Available from: Antje Rohde

  Article: Bud set in poplar--genetic dissection of a complex trait in natural and hybrid populations.

  Antje Rohde, Véronique Storme, Véronique Jorge, Muriel Gaudet, Nicola Vitacolonna, Francesco Fabbrini, Tom Ruttink, Giusi Zaina, Nicolas Marron, Sophie Dillen, Marijke Steenackers, Maurizio Sabatti, Michele Morgante, Wout Boerjan, Catherine Bastien
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  ABSTRACT: • The seasonal timing of growth events is crucial to tree distribution and conservation. The seasonal growth cycle is strongly adapted to the local climate that is changing because of global warming. We studied bud set as one cornerstone of the seasonal growth cycle in an integrative approach. • Bud set was dissected at the phenotypic level into several components, and phenotypic components with most genetic variation were identified. While phenotypic variation resided in the timing of growth cessation, and even so more in the duration from growth cessation to bud set, the timing of growth cessation had a stronger genetic component in both natural and hybrid populations. • Quantitative trait loci (QTL) were identified for the most discriminative phenotypic bud-set components across four poplar pedigrees. The QTL from different pedigrees were recurrently detected in six regions of the poplar genome. • These regions of 1.83-4.25 Mbp in size, containing between 202 and 394 genes, form the basis for further molecular-genetic dissection of bud set.
  New Phytologist 10/2010; 189(1):106-21. · 6.64 Impact Factor
• Source

  Available from: Lapierre Catherine

  Article: Downregulation of cinnamoyl-coenzyme A reductase in poplar: multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure.

  Jean-Charles Leplé, Rebecca Dauwe, Kris Morreel, Véronique Storme, Catherine Lapierre, Brigitte Pollet, Annette Naumann, Kyu-Young Kang, Hoon Kim, Katia Ruel, [......], Ines Fehrle, Michel Petit-Conil, Joachim Kopka, Andrea Polle, Eric Messens, Björn Sundberg, Shawn D Mansfield, John Ralph, Gilles Pilate, Wout Boerjan
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  ABSTRACT: Cinnamoyl-CoA reductase (CCR) catalyzes the penultimate step in monolignol biosynthesis. We show that downregulation of CCR in transgenic poplar (Populus tremula x Populus alba) was associated with up to 50% reduced lignin content and an orange-brown, often patchy, coloration of the outer xylem. Thioacidolysis, nuclear magnetic resonance (NMR), immunocytochemistry of lignin epitopes, and oligolignol profiling indicated that lignin was relatively more reduced in syringyl than in guaiacyl units. The cohesion of the walls was affected, particularly at sites that are generally richer in syringyl units in wild-type poplar. Ferulic acid was incorporated into the lignin via ether bonds, as evidenced independently by thioacidolysis and by NMR. A synthetic lignin incorporating ferulic acid had a red-brown coloration, suggesting that the xylem coloration was due to the presence of ferulic acid during lignification. Elevated ferulic acid levels were also observed in the form of esters. Transcript and metabolite profiling were used as comprehensive phenotyping tools to investigate how CCR downregulation impacted metabolism and the biosynthesis of other cell wall polymers. Both methods suggested reduced biosynthesis and increased breakdown or remodeling of noncellulosic cell wall polymers, which was further supported by Fourier transform infrared spectroscopy and wet chemistry analysis. The reduced levels of lignin and hemicellulose were associated with an increased proportion of cellulose. Furthermore, the transcript and metabolite profiling data pointed toward a stress response induced by the altered cell wall structure. Finally, chemical pulping of wood derived from 5-year-old, field-grown transgenic lines revealed improved pulping characteristics, but growth was affected in all transgenic lines tested.
  The Plant Cell 12/2007; 19(11):3669-91. · 8.99 Impact Factor
• Article: A molecular timetable for apical bud formation and dormancy induction in poplar.

  Tom Ruttink, Matthias Arend, Kris Morreel, Véronique Storme, Stephane Rombauts, Jörg Fromm, Rishikesh P Bhalerao, Wout Boerjan, Antje Rohde
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  ABSTRACT: The growth of perennial plants in the temperate zone alternates with periods of dormancy that are typically initiated during bud development in autumn. In a systems biology approach to unravel the underlying molecular program of apical bud development in poplar (Populus tremula x Populus alba), combined transcript and metabolite profiling were applied to a high-resolution time course from short-day induction to complete dormancy. Metabolite and gene expression dynamics were used to reconstruct the temporal sequence of events during bud development. Importantly, bud development could be dissected into bud formation, acclimation to dehydration and cold, and dormancy. To each of these processes, specific sets of regulatory and marker genes and metabolites are associated and provide a reference frame for future functional studies. Light, ethylene, and abscisic acid signal transduction pathways consecutively control bud development by setting, modifying, or terminating these processes. Ethylene signal transduction is positioned temporally between light and abscisic acid signals and is putatively activated by transiently low hexose pools. The timing and place of cell proliferation arrest (related to dormancy) and of the accumulation of storage compounds (related to acclimation processes) were established within the bud by electron microscopy. Finally, the identification of a large set of genes commonly expressed during the growth-to-dormancy transitions in poplar apical buds, cambium, or Arabidopsis thaliana seeds suggests parallels in the underlying molecular mechanisms in different plant organs.
  The Plant Cell 09/2007; 19(8):2370-90. · 8.99 Impact Factor
• Article: Genetical metabolomics of flavonoid biosynthesis in Populus: a case study.

  Kris Morreel, Geert Goeminne, Véronique Storme, Lieven Sterck, John Ralph, Wouter Coppieters, Peter Breyne, Marijke Steenackers, Michel Georges, Eric Messens, Wout Boerjan
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  ABSTRACT: Genetical metabolomics [metabolite profiling combined with quantitative trait locus (QTL) analysis] has been proposed as a new tool to identify loci that control metabolite abundances. This concept was evaluated in a case study with the model tree Populus. Using HPLC, the peak abundances were analyzed of 15 closely related flavonoids present in apical tissues of two full-sib poplar families, Populus deltoides cv. S9-2 x P. nigra cv. Ghoy and P. deltoides cv. S9-2 x P. trichocarpa cv. V24, and correlation and QTL analysis were used to detect flux control points in flavonoid biosynthesis. Four robust metabolite quantitative trait loci (mQTL), associated with rate-limiting steps in flavonoid biosynthesis, were mapped. Each mQTL was involved in the flux control to one or two flavonoids. Based on the identities of the affected metabolites and the flavonoid pathway structure, a tentative function was assigned to three of these mQTL, and the corresponding candidate genes were mapped. The data indicate that the combination of metabolite profiling with QTL analysis is a valuable tool to identify control points in a complex metabolic pathway of closely related compounds.
  The Plant Journal 08/2006; 47(2):224-37. · 6.16 Impact Factor
• Article: Paternity analysis of Populus nigra L. offspring in a Belgian plantation of native and exotic poplars

  An Vanden Broeck, Joan Cottrell, Paul Quataert, Peter Breyne, Véronique Storme, Wout Boerjan, Jos Van Slycken
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  ABSTRACT: Gene flow from cultivated poplar plantations into wild populations of Populus nigra L. is considered to represent a potential threat to the survival of P. nigra. In this study we investigated if pollen competition of Populus nigra L. and Populus $\times$ canadensis Moench in fertilising P. nigra ovules detected in a greenhouse experiment also occurs under field conditions. The results confirm non-random mating between males of $P.$ $\times$ canadensis and P. nigra in fertilizing P. nigra females in the artificial species-mixed Belgian poplar stand. A paternity analysis also revealed non-random intra-specific mating patterns within P. nigra in the stand. No paternities were assigned to the male cultivar P. nigra cv. Italica. Practical implications for the conservation of wild P. nigra populations are discussed. Analyse de paternité dans des descendances de Populus nigra L. issues d'une plantation belge de peupliers indigènes et exotiques. Les flux de gènes à partir des plantations de peupliers cultivés vers les populations sauvages de Populus nigra L. peut représenter une menace potentielle pour la survie de P. nigra. Dans cette étude, nous avons voulu vérifier si la compétition pollinique entre pollen de P. nigra et de $P.$ $\times$ canadensis Moench. observée en croisements artificiels sur P. nigra se produit également au sein d'une plantation in situ. Les résultats de cette étude confirment qu'une fertilisation non aléatoire entre les parents mâles de $P.$ $\times$ canadensis et P. nigra d'une part et les parents femelles de P. nigra d'autre part a bien lieu sur le terrain. Une analyse de paternité indique également la présence d'une fertilisation intraspécifique non aléatoire au sein des P. nigra. Aucun lien de paternité n'a pu être attribué au cultivar mâle P. nigra cv. Italica. Les implications pratiques pour la conservation de populations sauvages de P. nigra sont discutées.
  http://dx.doi.org/10.1051/forest:2006060.