Table S5: Putative functions of genes of the large alginolyic operon of Z. galactanivorans Gene ID Zg2616 Zg2617 Putative function Cation transporter (NRAMP) Sugar permease Transcription regulator Zg2620 Uptake of oligosaccharides susD (B. thetaiotaomicron) Zg2621 Uptake of oligosaccharides susC (B. thetaiotaomicron) Zg2623 unknown kdgF (D. dadantii) Zg2612 Homologue Reference mntH (E.coli) Kehres et al, 2000 exuT (E. coli) gntR (E. coli) Nemoz et al, 1976 Izu et al., 1997 Anderson and Salyers, 1989b; Koropatlin et al, 2008 Anderson and Salyers, 1989b Condemine and RobertBaudouy, 1991; Hugouvieux-Cotte-Pattat et al., 1996 Due to their position within the large alginolytic operon and to the fact that alginate induces their transcription, we can confidently predict that the following genes also participate in alginate assimilation in Zobellia galactanivorans. Thus, the SusCD-like outer membrane proteins Zg2620 and Zg2621 are likely responsible for the uptake of alginate-oligosaccharides from the extracellular medium to the periplasm, a role similar to the homologous system characterized for starch utilization in Bacteroides thetaiotaomicron (Anderson and Salyers, 1989a, b; Koropatkin et al., 2008). The sugar permease Zg2616 is homologous to exuT which is a Major Facilitator protein responsible of the uptake of aldohexuronate in Escherichia coli (Nemoz et al., 1976). Therefore, Zg2616 probably transports alginate oligo- or monosaccharides from the periplasm to the cytoplasm. The protein Zg2617 is homologous to the transcription factor GntR which negatively regulates the gntRKU operon involved in the uptake and catabolism of gluconate in E. coli (Izu et al., 1997). Whereas most of the ARgenes had low expression values in cells growing in the glucose-supplemented medium (Table S3), zg2617 was already significantly transcribed. The transcription level of this gene further increased 4-times when cells were grown in the alginate-containing medium. This suggests that the protein Zg2617 acts as a transcription factor positively regulating the alginolytic pathway in Z. galactanivorans. Such transcription activators are already known in the GntR family (Neelakanta et al., 2009). Zg2623 is homologous to KdgF, a protein essential to the pectinolytic system of Dickeya dadantii (Condemine and Robert-Baudouy, 1991; Hugouvieux-Cotte-Pattat et al., 1996). Although the exact function of kdgF and zg2623 is unknown, it is noteworthy that these genes are both conserved in operons dedicated to the degradation of carboxylic polysaccharides (pectins and alginates) which play analogous roles in the cell walls of plants and brown algae, respectively (Popper et al., 2011). Concomitant with the induction of the catabolic pathway, the presence of alginate strongly increased the expression of a putative cation transporter from the NRAMP family (Zg2612). The emergence of such transporters was previously proposed as an adaptation to oxidative environments, including those arising during infection of animals and plants (Kehres et al., 2000; Cellier et al., 2001). Interestingly, brown algae defend themselves against pathogen aggressions by transiently emitting reactive oxygen species which can notably control the growth of epiphytic bacteria (Cosse et al., 2007). The protein Zg2612 might be part of a protection mechanism towards this oxidative burst when Z. galactanivorans is degrading an algal cell wall. References Anderson, K.L., and Salyers, A.A. (1989a) Genetic evidence that outer membrane binding of starch is required for starch utilization by Bacteroides thetaiotaomicron. J Bacteriol 171: 3199-3204. Anderson, K.L., and Salyers, A.A. (1989b) Biochemical evidence that starch breakdown by Bacteroides thetaiotaomicron involves outer membrane starch-binding sites and periplasmic starch-degrading enzymes. J Bacteriol 171: 3192-3198. Cellier, M.F., Bergevin, I., Boyer, E., and Richer, E. (2001) Polyphyletic origins of bacterial Nramp transporters. Trends Genet 17: 365-370. Condemine, G., and Robert-Baudouy, J. (1991) Analysis of an Erwinia chrysanthemi gene cluster involved in pectin degradation. Mol Microbiol 5: 2191-2202. Cosse, A., Leblanc, C., and Potin, P. (2007) Dynamic defense of marine macroalgae against pathogens: from early activated to gene-regulated responses. Adv Bot Res 46: 221-266. Hugouvieux-Cotte-Pattat, N., Condemine, G., Nasser, W., and Reverchon, S. (1996) Regulation of pectinolysis in Erwinia chrysanthemi. Annu Rev Microbiol 50: 213-257. Izu, H., Adachi, O., and Yamada, M. (1997) Gene organization and transcriptional regulation of the gntRKU operon involved in gluconate uptake and catabolism of Escherichia coli. J Mol Biol 267: 778-793. Kehres, D.G., Zaharik, M.L., Finlay, B.B., and Maguire, M.E. (2000) The NRAMP proteins of Salmonella typhimurium and Escherichia coli are selective manganese transporters involved in the response to reactive oxygen. Mol Microbiol 36: 1085-1100. Koropatkin, N.M., Martens, E.C., Gordon, J.I., and Smith, T.J. (2008) Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16: 1105-1115. Neelakanta, G., Sankar, T.S., and Schnetz, K. (2009) Characterization of a beta-glucoside operon (bgc) prevalent in septicemic and uropathogenic Escherichia coli strains. Appl Environ Microbiol 75: 2284-2293. Nemoz, G., Robert-Baudouy, J., and Stoeber, F. (1976) Physiological and genetic regulation of the aldohexuronate transport system in Escherichia coli. J Bacteriol 127: 706-718. Popper, Z.A., Michel, G., Herve, C., Domozych, D.S., Willats, W.G., Tuohy, M.G. et al. (2011) Evolution and diversity of plant cell walls: from algae to flowering plants. Annu Rev Plant Biol 62: 567-590.