Considering the depletion of natural fossil fuels and the great environmental pollution of air, soil and groundwater, together with massive release of greenhouse gases, the world is in great need for innovations in the field of green energy production that can satisfy the growing demand. Cellulose, a linear polysaccharide, is the most abundant carbon source on earth, yet its recalcitrant nature renders it unavailable for bio-degradation. Among several cellulolytic microorganisms is Ruminococcus flavefaciens FD-1 that is prominent in the rumen of herbivores. Recently its full genome was sequenced, revealing an elaborate cellulosome system with a unique set of small scaffoldins and as many as 222 dockerin-bearing proteins. Bio-informatics analysis of these dockerin sequences resulted in their classification into six major groups and eleven subgroups. Since these modules are directly engaged in constructing cellulosome architecture, it was important to search for their cohesin partners and test if the observed sequence variation translates into functional discrepancies. In this study, a network of 462 possible interactions between 14 chosen cohesins and 33 dockerins, chosen to represent the distinct groups, were experimentally put to test, while improving a previously established cellulose-based microarray method for work with crude cell extracts. A total of 41 previously unknown positive interactions were found, and a clear preference of cohesin recognition by the six major dockerin groups was observed. The second-order classification was found to be functionally redundant. Three novel putative adaptor scaffoldins emerged: ScaJ, ScaM and ScaO. The novel pairs found herein provide a snapshot into the intricate cellulosome organization of R. flavefaciens FD-1, and an updated model is proposed. This knowledge may be applicable in future conversion of lignocellulosic biomass into fermentable monosaccharides for biofuel production and cellulosic waste management.
