Comparative analysis of plant carbohydrate active enZymes and their role in xylogenesis

Abstract

BackgroundCarbohydrate metabolism is a key feature of vascular plant architecture, and is of particular importance in large woody species, where lignocellulosic biomass is responsible for bearing the bulk of the stem and crown. Since Carbohydrate Active enZymes (CAZymes) in plants are responsible for the synthesis, modification and degradation of carbohydrate biopolymers, the differences in gene copy number and regulation between woody and herbaceous species have been highlighted previously. There are still many unanswered questions about the role of CAZymes in land plant evolution and the formation of wood, a strong carbohydrate sink.ResultsHere, twenty-two publically available plant genomes were used to characterize the frequency, diversity and complexity of CAZymes in plants. We find that a conserved suite of CAZymes is a feature of land plant evolution, with similar diversity and complexity regardless of growth habit and form. In addition, we compared the diversity and levels of CAZyme gene expression during wood formation in trees using mRNA-seq data from two distantly related angiosperm tree species Eucalyptus grandis and Populus trichocarpa, highlighting the major CAZyme classes involved in xylogenesis and lignocellulosic biomass production.ConclusionsCAZyme domain ratio across embryophytes is maintained, and the diversity of CAZyme domains is similar in all land plants, regardless of woody habit. The stoichiometric conservation of gene expression in woody and non-woody tissues of Eucalyptus and Populus are indicative of gene balance preservation.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1571-8) contains supplementary material, which is available to authorized users.

Carbohydrate-active enzymes in Trichoderma harzianum: a bioinformatic analysis bioprospecting for key enzymes for the biofuels industry

“…Several previous studies have described the contents of CAZymes in bacteria [ 37 , 38 ], fungi [ 39 – 41 ] and plants [ 42 , 43 ]. We identified a large number of CAZymes in T. harzianum , T. reesei , T. atroviride and T. virens (430, 355, 441 and 422 CAZymes, respectively), with a high diversity of families (Fig.…”

Structural and Biochemical Characterization of an Octameric Carbohydrate Acetylesterase from Sinorhizobium meliloti

“…The diversity of CE family reflects intrinsic differences in molecular structures, cellular locations, substrate specificities, and biochemical properties. In general, CEs remove ester functional groups in simple or complex carbohydrates, preparing the carbohydrates for further modification by glycoside hydrolases (GHs) . In addition to their importance in cellular functions, CEs are extensively used for biotechnological applications.…”

Poplar carbohydrate‐active enzymes: whole‐genome annotation and functional analyses based on RNA expression data

“…This increase was similar to that previously reported (Geisler‐Lee et al ., ). This observation is in line with the census of CAZyme motifs carried out in the genomes of several streptophytes, including green algae, a moss and many vascular plants, and shows that whereas the woody plants appear to have the highest absolute numbers of CAZyme motifs in their genomes, the frequencies of these domains in relation to respective genome size are stable (Pinard et al ., ). Thus, the difference in the absolute number of CAZymes between Populus and A. thaliana is related to the linage‐specific history of whole‐genome duplication and gene loss (Tuskan et al ., ).…”