Expression profiling of Cellvibrio japonicus using either glucose or xylan

Lignocellulose degradation by microbes plays a central role in global carbon cycling, human gut metabolism, and renewable energy technologies While considerable effort has been put into understanding the biochemical aspects of lignocellulose degradation, much less work has been done to understand how these enzymes work in an in vivo context Here, we report a systems level study of xylan degradation in the saprophytic bacterium Cellvibrio japonicus Transcriptome analysis indicated seven genes that encode carbohydrate active enzymes were up-regulated during growth with xylan containing media In-frame deletion analysis of these genes found that only gly43F is critical for utilization of xylo-oligosaccharides, xylan, and arabinoxylan Heterologous expression of gly43F was sufficient for the utilization of xylo-oligosaccharides in Escherichia coli Additional analysis found that the xyn11A, xyn11B, abf43L, abf43K, and abf51A gene products were critical for utilization of arabinoxylan Furthermore, a predicted transporter (CJA_1315) was required for effective utilization of xylan substrates, and we propose this unannotated gene be called xntA (xylan transporter A) Our major findings are 1) C japonicus employs both secreted and surface associated enzymes for xylan degradation, which differs from the strategy used for cellulose degradation, and 2) a single cytoplasmic ß-xylosidase is essential for the utilization of xylo-oligosaccharides Overall design: One carbon condition (xylan); Two sample points (exponential phase, stationary phase); Data collected in biological triplicate; Total of 6 samples Please note that glucose-grown sample data is published and thus, available in the previous GEO records [GSE90955; GSM2418311-GSM2418316].