Oxidation of Monolignols by Members of the Berberine Bridge Enzyme Family Suggests a Role in Plant Cell Wall Metabolism

Daniel, Bastian; Pavkov‐Keller, Tea; Steiner, Barbara; Đordić, Anđela; Gutmann, Alexander; Nidetzky, Bernd; Sensen, Christoph Wilhelm; Graaff, Eric van der; Wallner, Silvia; Gruber, Karl; Macheroux, Peter

doi:10.1074/jbc.m115.659631

Cited by 88 publications

(92 citation statements)

References 49 publications

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“…Further, we found a related GO term, GO:0055114 (oxidation-reduction process), enriched among genes induced at 6-, 12- and 24-HAI; this group includes aldehyde dehydrogenases, FAD-binding Berberine family proteins, lipoxygenases, peroxidases, Sks cell wall oxidoreductases and rhamnose synthases. Although structurally distinct, several of these families have been linked with cell wall metabolism and homeostasis242526.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome analysis uncovers key regulatory and metabolic aspects of soybean embryonic axes during germination

Bellieny-Rabelo

Oliveira

Ribeiro

et al. 2016

Sci Rep

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Soybean (Glycine max) is a major legume crop worldwide, providing a critical source of protein and oil. The release of the soybean genome fuelled several transcriptome projects comprising multiple developmental stages and environmental conditions. Nevertheless, the global transcriptional patterns of embryonic axes during germination remain unknown. Here we report the analysis of ~1.58 billion RNA-Seq reads from soybean embryonic axes at five germination stages. Our results support the early activation of processes that are critical for germination, such as glycolysis, Krebs cycle and cell wall remodelling. Strikingly, only 3 hours after imbibition there is a preferential up-regulation of protein kinases and transcription factors, particularly from the LOB domain family, implying that transcriptional and post-transcriptional regulation play major roles early after imbibition. Lipid mobilization and glyoxylate pathways are also transcriptionally active in the embryonic axes, indicating that the local catabolism of oil reserves in the embryonic axes contributes to energy production during germination. We also present evidence supporting abscisic acid inactivation and the up-regulation of gibberellin, ethylene and brassinosteroid pathways. Further, there is a remarkable differential activation of paralogous genes in these hormone signalling pathways. Taken together, our results provide insights on the regulation and biochemistry of soybean germination.

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Section: Resultsmentioning

confidence: 99%

Transcriptome analysis uncovers key regulatory and metabolic aspects of soybean embryonic axes during germination

Bellieny-Rabelo

Oliveira

Ribeiro

et al. 2016

Sci Rep

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“…The number of BBE genes in different plant species varies significantly from one in moss ( Physcomitrella patens ) to 64 in western poplar ( Populus trichocarpa ) ( Daniel et al , 2015). A. thaliana has 27 TAIR IDs assigned to BBE enzymes, with two splice variants ( Supplementary Table 1) ( Daniel et al , 2015).…”

Section: Resultsmentioning

confidence: 99%

“…A. thaliana has 27 TAIR IDs assigned to BBE enzymes, with two splice variants ( Supplementary Table 1) ( Daniel et al , 2015). Based on the current transcriptome, there are four full length BBE genes ( Jr BBE1 to 4) that map to different scaffolds in the WGS, in addition to other fragmented transcripts ( Table 2 and Table 3).…”

Section: Resultsmentioning

confidence: 99%

YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools

2016

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Background: The transcriptome, a treasure trove of gene space information, remains severely under-used by current genome annotation methods. Methods: Here, we present an annotation method in the YeATS suite (YeATSAM), based on information encoded by the transcriptome, that demonstrates artifacts of the assembler, which must be addressed to achieve proper annotation. Results and Discussion: YeATSAM was applied to the transcriptome obtained from twenty walnut tissues and compared to MAKER-P annotation of the recently published walnut genome sequence (WGS). MAKER-P and YeATSAM both failed to annotate several hundred proteins found by the other. Although many of these unannotated proteins have repetitive sequences (possibly transposable elements), other crucial proteins were excluded by each method. An egg cell-secreted protein and a homer protein were undetected by YeATSAM, although these did not produce any transcripts. Importantly, MAKER-P failed to classify key photosynthesis-related proteins, which we show emanated from Trinity assembly artifacts potentially not handled by MAKER-P. Also, no proteins from the large berberine bridge enzyme (BBE) family were annotated by MAKER-P. BBE is implicated in biosynthesis of several alkaloids metabolites, like anti-microbial berberine. As further validation, YeATSAM identified ~1000 genes that are not annotated in the NCBI database by Gnomon. YeATSAM used a RNA-seq derived chickpea ( Cicer arietinum L.) transcriptome assembled using Newbler v2.3. Conclusions: Since the current version of YeATSAM does not have an ab initio module, we suggest a combined annotation scheme using both MAKER-P and YeATSAM to comprehensively and accurately annotate the WGS.

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“…The most abundant ones were the reticuline-like oxidases (berberine bridge enzyme-like and reticuline oxidase) and cinnamyl-alcohol dehydrogenase. Reticuline-like oxidases (FAD-family) are monolignol oxidoreductases that play a role in monolignol metabolism and lignin formation [73,107]. These enzymes may participate in the mobilization and oxidation of monolignols (aromatic allylic alcohols, such as coumaryl-, sinapyl-, and coniferyl alcohol), to the corresponding aldehydes.…”

Section: The Biological Processes Detected In the Ecsmentioning

confidence: 99%

Protein Dynamics in the Plant Extracellular Space

et al. 2016

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The extracellular space (ECS or apoplast) is the plant cell compartment external to the plasma membrane, which includes the cell walls, the intercellular space and the apoplastic fluid (APF). The present review is focused on APF proteomics papers and intends to draw information on the metabolic processes occurring in the ECS under abiotic and biotic stresses, as well as under non-challenged conditions. The large majority of the proteins detected are involved in “cell wall organization and biogenesis”, “response to stimulus” and “protein metabolism”. It becomes apparent that some proteins are always detected, irrespective of the experimental conditions, although with different relative contribution. This fact suggests that non-challenged plants have intrinsic constitutive metabolic processes of stress/defense in the ECS. In addition to the multiple functions ascribed to the ECS proteins, should be considered the interactions established between themselves and with the plasma membrane and its components. These interactions are crucial in connecting exterior and interior of the cell, and even simple protein actions in the ECS can have profound effects on plant performance. The proteins of the ECS are permanently contributing to the high dynamic nature of this plant compartment, which seems fundamental to plant development and adaptation to the environmental conditions.

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Oxidation of Monolignols by Members of the Berberine Bridge Enzyme Family Suggests a Role in Plant Cell Wall Metabolism

Cited by 88 publications

References 49 publications

Transcriptome analysis uncovers key regulatory and metabolic aspects of soybean embryonic axes during germination

Transcriptome analysis uncovers key regulatory and metabolic aspects of soybean embryonic axes during germination

YeATSAM analysis of the walnut and chickpea transcriptome reveals key genes undetected by current annotation tools

Protein Dynamics in the Plant Extracellular Space

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