Thomas François, Bordron Philippe, Eveillard Damien, Michel Gurvan
Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, UMR 8227, Integrative Biology of Marine Models, Station Biologique de RoscoffRoscoff, France.
Sorbonne Universités, UPMC Univ Paris 06, Centre National de la Recherche Scientifique, FR2424, Analysis and Bioinformatics for Marine Science, Station Biologique de RoscoffRoscoff, France.
Front Microbiol. 2017 Sep 21;8:1808. doi: 10.3389/fmicb.2017.01808. eCollection 2017.
are recognized as key players in the marine carbon cycle, due to their ability to efficiently degrade algal polysaccharides both in the open ocean and in coastal regions. The chemical complexity of algal polysaccharides, their differences between algal groups and variations through time and space, imply that marine flavobacteria have evolved dedicated degradation mechanisms and regulation of their metabolism during interactions with algae. In the present study, we report the first transcriptome-wide gene expression analysis for an alga-associated flavobacterium during polysaccharide degradation. Dsij, originally isolated from a red alga, was grown in minimal medium with either glucose (used as a reference monosaccharide) or one selected algal polysaccharide from brown (alginate, laminarin) or red algae (agar, porphyran, ι- or κ-carrageenan) as sole carbon source. Expression profiles were determined using whole-genome microarrays. Integration of genomic knowledge with the automatic building of a co-expression network allowed the experimental validation of operon-like transcription units. Differential expression analysis revealed large transcriptomic shifts depending on the carbon source. Unexpectedly, transcriptomes shared common signatures when growing on chemically divergent polysaccharides from the same algal phylum. Together with the induction of numerous transcription factors, this hints at complex regulation events that fine-tune the cell behavior during interactions with algal biomass in the marine environment. The results further highlight genes and loci that may participate in polysaccharide utilization, notably encoding Carbohydrate Active enZymes (CAZymes) and glycan binding proteins together with a number of proteins of unknown function. This constitutes a set of candidate genes potentially representing new substrate specificities. By providing an unprecedented view of global transcriptomic responses during polysaccharide utilization in an alga-associated model flavobacterium, this study expands the current knowledge on the functional role of flavobacteria in the marine carbon cycle and on their interactions with algae.
由于能够在公海和沿海地区高效降解藻类多糖，它们被认为是海洋碳循环中的关键参与者。藻类多糖的化学复杂性、藻类群体之间的差异以及随时间和空间的变化，意味着海洋黄杆菌在与藻类相互作用的过程中已经进化出专门的降解机制和新陈代谢调节机制。在本研究中，我们报告了首例关于藻类相关黄杆菌在多糖降解过程中的全转录组基因表达分析。Dsij最初从一种红藻中分离出来，在以葡萄糖（用作参考单糖）或从褐藻（藻酸盐、海带多糖）或红藻（琼脂、紫菜聚糖、ι-或κ-卡拉胶）中选择的一种藻类多糖作为唯一碳源的基本培养基中生长。使用全基因组微阵列确定表达谱。将基因组知识与共表达网络的自动构建相结合，对操纵子样转录单元进行了实验验证。差异表达分析揭示了取决于碳源的大规模转录组变化。出乎意料的是，当在来自同一藻类门的化学性质不同的多糖上生长时，转录组具有共同特征。连同大量转录因子的诱导，这暗示了在海洋环境中与藻类生物质相互作用期间微调细胞行为的复杂调节事件。结果进一步突出了可能参与多糖利用的基因和基因座，特别是编码碳水化合物活性酶（CAZymes）和聚糖结合蛋白以及许多功能未知的蛋白质。这构成了一组可能代表新底物特异性的候选基因。通过提供前所未有的视角，观察藻类相关模式黄杆菌在多糖利用过程中的全球转录组反应，本研究扩展了目前关于黄杆菌在海洋碳循环中的功能作用及其与藻类相互作用的知识。
