RNA-seq analysis in simulated microgravity unveils down-regulation of the beta-rhizobial siderophore phymabactin
Exploiting the symbiotic interaction between crops and nitrogen-fixing bacteria is a simple and ecological solution to promote plants growth in prospective extraterrestrial human outposts. In this study, we investigated the adaptation of the legume symbiont Paraburkholderia phymatum to simulated microgravity (s0-g) at the transcriptome level by performing an RNA-Seq analysis. The results revealed a drastic effect on gene expression, with roughly 23 % of P. phymatum genes being differentially regulated in s0-g. Among those, 951 genes were upregulated and 858 downregulated in the cells grown in s0-g compared to terrestrial gravity (1g). Genes involved in posttranslational modification, proteins turnover and chaperones production were upregulated in s0-g, while those involved in translation, ribosomal structure and biosynthesis, motility or inorganic ions transport were downregulated. Specifically, the whole phm gene cluster, previously predicted to be involved in the production of a hypothetical siderophore, phymabactin, was approximatively 20-fold downregulated in microgravity. Accordingly, a phm-gfp reporter strain showed less expression in s0-g and iron uptake was reduced in microgravity. By constructing a mutant strain (?phmJK) we confirmed that the phm gene cluster codes for the only siderophore secreted by P. phymatum. In fact, in contrast to P. phymatum wild-type, ?phmJK did not produce any siderophores on chrome azurol S plates. These results not only provide a deeper understanding of the physiology of symbiotic organisms exposed to space-like conditions, but also increase our understanding of iron acquisition in rhizobia. Overall design: Assessing the impact of simulated microgravity in P. phymatum and identification of a beta-rhizobial siderophore