Glucose-dependent, CcpA-dependent genes All genes found to be subject to regulation by glucose in a CcpA-dependent way are depicted in the Additional files 3: CcpA dependent down-regulation by glucose, and 4: CcpA-dependent up-regulation by glucose. For consistency reasons, a few genes which were not meeting the arbitrary threshold, such as SA0605 or SA0299 (indicated by a paragraph), were included, since these genes are part of putative operons and showed a tendency towards regulation. As before, only a minor part of the affected genes/operons (48 out of 155) contained putative Vactosertib cre-sites in their promoter regions, indicating a

direct control by CcpA, while the majority of genes seemed to be controlled by CcpA in a way that did not involve the interaction PLX-4720 datasheet with an apparent cre-site. Grouping the regulated genes into functional categories according to the selleck screening library DOGAN annotation [26] and/or KEGG database [27] showed that unknown proteins represented again the largest regulated category (39 genes), followed by transport/binding

proteins and lipoproteins (22 genes), metabolism of amino acids (19 genes), and metabolism of carbohydrates (17 genes) (Fig. 3B). CcpA-independent regulation by glucose We found a small group of genes, encoding the 6-phospho-betaglucosidase, the putative ascorbate transport- and the lactose-operon, to be regulated by glucose in an apparently CcpA-independent way (Table 2). The lactose operon, reported to be controlled by catabolite repression [28] requires intracellular galactose-6-phosphate for induction [29]. The lack of specific inducer

under the conditions used here may have obscured the CcpA-dependent regulatory effects on the lac- and other operons, or mechanisms accounting for CcpA-independent catabolite control may be active [9]. Again, the table includes a few genes not meeting the arbitrary threshold (indicated by a paragraph), which were nevertheless listed, since they are likely to form part of putative operons and showed a tendency towards regulation DOK2 that was consistent with the other member(s) of these operons. Table 2 Genes/operons with CcpA-independent regulation by glucose ID   Producta wt mut N315 Newman common   +/- b +/- b Down-regulated by glucose SA0256 NWMN_0200 bglA 6-phospho-beta-glucosidase 0.5 0.5 SA0318 NWMN_0322   ascorbate-specific PTS system enzyme IIC 0.1 0.3 SA0319 NWMN_0323   similar to PTS system component 0.2 0.2 SA0320 NWMN_0324   similar to PTS transport system IIA component 0.2 0.2 SA0321 NWMN_0325   similar to PTS multidomain regulator 0.3 0.2 SA1991 NWMN_2093 lacG 6-phospho-beta-galactosidase 0.5 0.5 SA1992 NWMN_2094 lacE PTS system, lactose-specific IIBC component 0.5 0.4 SA1993 NWMN_2095 lacF PTS system, lactose-specific IIA component 0.4 0.