Fig. 4
a Malonate utilization operon annotated from ST64 C. sakazakii strain GK1025B. The schematic representation of the nine gene malonate utilization operon. b Comparison of the malonate utilization operon from different strains of ST64 isolates: The reference strain GK1025B was previous reported in Chase et al. [18] and Cro2819A3 was reported by Zheng et al. [27]. Only the partial sequence of topoisomerase was included for illustration. BAA-894 fragments in the last two tracks are contiguous in its genome separated by a 325 bp intergenic region; the operon is inserted in this spacer region in other species. Comparative genomic analysis of the malonate operon allele sequences from eight ST64 malonate-positive C. sakazakii strains compared to that of malonate-negative C. sakazakii strain BAA-894. A similar operon structure was found for all 23 strains. The ST64 C. sakazakii malonate utilization operon is flanked upstream by gyrB which encodes a topoisomerase IV subunit B gene (EC 5.99.1), and downstream by katG, encoding a catalase/peroxidase gene (EC 1.11.1.6; EC 1.11.1.7). The malonate utilization gene cluster-flanking regions were found to be conserved among all Cronobacter species even malonate-negative C. sakazakii strains; however, instead of the 7.7 kbp malonate utilization gene cluster, there is a 323–325 bp nucleotide region. The operon contains genes encoding enzymes and proteins involved in the decarboxylation of malonate and includes a malonate utilization transcriptional regulator mdcR, malonate decarboxylase consists of the oligomerization of alpha, delta, beta, and gamma protein subunits and is encoded by four genes, mdcADBC. Finally, this gene cluster also contains genes encoding for a 2-(5′-triphosphoribosyl)-3′-dephosphocoenzyme-A synthase (ybdT), malonyl CoA acyl carrier protein transacylase (fabD) and a phosphoribosyl-dephospho-CoA transferase (mdcG) which are thought to stabilize the coenzyme-A complex, and may allow the proper conformation of malonate decarboxylase to be maintained in a high substrate affinity configuration