A solid update on wood-forming enzymes.

Abstract

Wood is an important renewable source of energy, and as such, it may offer a sustainable, cost-effective alternative to fossils fuels. Wood is the primary source of building materials and many other products, and a major trade market that continues to grow steadily (FAO, 2017). Perhaps an even more significant role of woody biomass is as a carbon sink, as developing wood cells represent one of the most important traps for atmospheric CO2 (Plomion et al., 2001). Carbohydrate-Active enZymes (CAZymes) play crucial roles in the formation and modification of the carbohydrate matrix that constitutes woody biomass (Mellerowicz and Sundberg, 2008). In this issue of The Plant Journal, Kumar et al. (2019) re-annotated and re-classified CAZyme genes in the latest version of the poplar (Populus trichocarpa) genome. The work was led by Ewa Mellerowicz, a professor at the Umeå Plant Science Centre (UPSC), Sweden. Her group studies cell wall formation in woody species. Vikash Kumar, first author in the paper, joined the Mellerowicz lab as a postdoc in 2014, after graduating from the University of Delhi, India. Kumar is interested in the circadian cycle of secondary cell wall biosynthesis. Mellerowicz's group was involved in the first CAZyme annotation in poplar (Geisler-Lee et al., 2009), based on the original poplar genome assembly. Since most of the gene models changed in the current assembly (v. 3.0), the group realized that the CAZyme annotation had become outdated and set out to reannotate it. For this endeavor, they teamed up with Bernard Henrissat, from Aix-Marseille University (Marseille, France), the creator and curator of the CAZY database. They also enlisted the support of bioinformaticians Nathaniel Street and Nicolas Delhomme, the creators and curators of PopGenIE database. Alongside Chanaka Mannapperuma, they were instrumental in retrieving transcriptomic and genomic data from Populus databases. The result is one of the best annotated CAZyme databases in plants, a valuable resource for scientists investigating the function and properties of CAZymes in woody species. The database redefined all members of the many CAZyme families and closely related expansins and classified them according to their predicted function (see Figure). The authors also compared the genetic diversity of CAZyme genes in poplar and Arabidopsis. They found that poplar has 1.6× more genes and that significant differences are specific to certain enzyme families. These differences may provide hypotheses for further studies about adaptations to perennial/woody versus annual/herbaceous lifestyles. In silico analyses of gene expression during wood formation based on published datasets (Sundell et al., 2017) revealed gene clusters not only according to unique expression patterns during wood formation, but also according to different metabolites. In addition, co-expression network analyses of known CAZyme genes alongside uncharacterized ones revealed novel genes involved in wood formation. A total of 471 CAZyme genes formed a co-expression network, which included many uncharacterized genes with putative functions in cell wall biosynthesis and other cellular processes during wood formation. The association between genes with known activity with genes from partially characterized families helps predict their functions. Using this “guide genes” approach, the authors analyzed the closest network neighbors of some known cell wall-related CAZymes. For instance, within the primary wall network, cellulose, pectin, and xyloglucan-related genes were used as guides. The resulting network included several putative xyloglucan and pectin biosynthesis-related genes, providing a rich source of candidate genes for further analyses. The network also included three members of the “auxiliary activities” family of CAZymes, within a clade that had not been previously characterized in the context of wood development. These are also candidates for further investigation and may suggest a role for new gene families in wood growth. The CAZyme database will help improve the interpretation of many transcriptomics and proteomics datasets from woody tissues. Mellerowicz's group plans to use the resource to study the dynamics of cell secondary wall biosynthesis in the developing wood during the diurnal cycle. They hope this resource will support the whole plant research community working on cell wall and carbohydrates.