Metaproteomics identifies key cell wall degrading enzymes and proteins potentially related to inter-field variability in fiber quality during flax dew retting

In this study, metaproteomics and biochemical analyses were used to identify for the first time specific proteins and associated micro-organisms responsible for cell wall degrading enzyme activity during dew retting of flax in two adjacent fields in northern France. This approach identified 6032 non-redundant proteins present at 4 key retting stages (R0/day 1, R2/day 6, R4/day 13, and R7/day 25), of which 75 contained CAZy (Carbohydrate Active Enzyme) motifs belonging to 31 different families from all 5 CAZy classes. 19 families were putatively related to the degradation of different plant cell wall polymers including lignin (AA1), pectins (CE13, CE8, PL1, PL3, GH28, GH35), hemicellulose (GH2, GH10, GH26, GH35, GH55, GH3, GH5, GH17) and cellulose (GH5, GH7, GH3, GH94, AA3). Taxonomy of identified proteins indicated that 85 % come from bacteria, 13 % from fungi, and 2 % from plants; however, ∼60 % of CAZymes involved in the degradation of plant wall polymers are of fungal origin. Although 88 % of total proteins and almost 65 % of cell wall degrading CAZymes were similar between the two investigated fields, certain differences in the abundance and dynamics of certain CAZymes might be related to observed inter-field variability in cell wall degrading enzyme activities, stem/fiber yield and industrial qualities of fibers harvested from the two fields. Overall, these results highlight the interest of using metaproteomics for improving our biological understanding of how retting impacts fiber quality. In addition, the identification of several new bacterial and fungal species in this study demonstrates that such an approach is also extremely powerful for generating novel taxonomic data.