Genes for transport and metabolism of spermidine in Ruegeria pomeroyi DSS-3 and other marine bacteria

Spermidine, putrescine, and other polyamines are sources of labile carbon and nitrogen in marine environments, yet a thorough analysis of the functional genes encoding their transport and metabolism by marine bacteria has not been conducted. To begin this endeavor, we first identified genes that mediate spermidine processing in the model marine bacterium Ruegeria pomeroyi and then surveyed their abundance in other cultured and uncultured marine bacteria. R. pomeroyi cells were grown on spermidine under continuous culture conditions. Microarray-based transcriptional profiling and reverse transcription-qPCR analysis were used to identify the operon responsible for spermidine transport. Homologs from 2 of 3 known pathways for bacterial polyamine degradation were also identified in the R. pomeroyi genome and shown to be upregulated by spermidine. In an analysis of genome sequences of 109 cultured marine bacteria, homologs to polyamine transport and degradation genes were found in 55% of surveyed genomes. Likewise, analysis of marine meta-genomic data indicated that up to 32% of surface ocean bacterioplankton contain homologs for transport or degradation of polyamines. The degradation pathway genes puuB (gamma-glutamyl-putrescine oxidase) and spuC (putrescine aminotransferase), which are part of the spermidine degradation pathway in R. pomeroyi, emerged as suitable targets for molecular-based studies of polyamine processing by marine bacterial communities. The frequency of genes encoding transport and catabolism of spermidine and related polyamines suggests an important role for these compounds in carbon and nitrogen budgets of marine bacterioplankton.