Fig. 1: A conserved gene operon for homarine catabolism in marine bacteria.
From: Conserved pathway for homarine catabolism in environmental bacteria
a, Cobetia sp. OBi1 growth on glucose (12 mM C), glucose (12 mM C) with homarine (1 mM C) or homarine (12 mM C) for comparative transcriptomics (n = 3). Data are presented as mean ± s.d. of 2 different cultures. Grey vertical lines indicate RNA sampling times (13 h for cultures with glucose and cultures with glucose+homarine and 16.5 h for cultures with homarine). b, Differential gene expression fold change (FC) of Cobetia sp. OBi1 in homarine vs glucose. c, Differential gene expression of Cobetia sp. OBi1 in glucose+homarine vs glucose. P values were adjusted for multiple comparisons using Benjamini–Hochberg (BH) correction (two-sided Wald test). Black vertical lines indicate significantly upregulated genes; positive values represent upregulation in the homarine condition. d, Cobetia sp. OBi1 genes (arrows) upregulated in homarine relative to glucose and homologous gene clusters in R. pomeroyi DSS-3. Arrow fill colour corresponds to the type of function performed by each gene. Arrow outline colour indicates the results of growth tests with in-frame deletion mutants of Cobetia sp. OBi1 or transposon insertion KanR mutants of R. pomeroyi DSS-3. GBT, glycine betaine transporter. Grey stars (*) indicate genes upregulated in glucose+homarine compared to glucose alone; black stars (*) indicate genes upregulated in homarine compared to glucose. Full descriptions of genes found in Supplementary Table 3. e, Proposed homarine catabolic pathway inferred from omics data.
