Genome-wide transcriptional responses of iron-starvedChlamydia trachomatisreveal prioritization of metabolic precursor synthesis over protein translation

Abstract

ABSTRACTIron is essential for growth and development ofChlamydia. Its long-term starvation in cultured mammalian cells leads to production of aberrant non-infectious chlamydial forms, also known as persistence. Immediate transcriptional responses to iron limitation have not been characterized, leaving a knowledge gap of howChlamydiaregulates its response to changes in iron availability. We used the fast-chelating agent 2,2’-Bipyridyl (BPDL) to homogeneously starveChlamydia trachomatisserovar L2 of iron, starting at 6 or 12h post-infection. Immediate transcriptional responses were monitored after only 3 or 6h of BPDL-treatment, well before formation of aberrantChlamydia.The first genome-wide transcriptional response ofC. trachomatisto iron-starvation was subsequently determined utilizing RNA-sequencing. Only 7% and 8% of the genome was differentially expressed in response to iron-starvation at early and mid-stages of development, respectively. Biological pathway analysis revealed an overarching theme. Synthesis of macromolecular precursors (deoxynucleotides, amino acids, charged tRNAs, and acetyl-coA) was up-regulated, while energy-expensive processes (ABC transport and translation) were down-regulated. A large fraction of differentially down-regulated genes are involved in translation, including ribosome assembly, initiation and termination factors, which could be analogous to the translation down-regulation triggered by stress in other prokaryotes during stringent responses. Additionally, transcriptional up-regulation of DNA repair, oxidative stress, and tryptophan salvage genes reveals a possible coordination of responses to multiple antimicrobial and immunological insults. These responses of replicative-phaseChlamydiato iron-starvation indicate a prioritization of survival over replication, enabling the pathogen to “stock the pantry” with ingredients needed for rapid growth once optimal iron levels are restored.IMPORTANCEBy utilizing an experimental approach that monitors the immediate global response ofChlamydia trachomatisto iron-starvation, clues to long-standing questions inChlamydiabiology are revealed, including howChlamydiaadapts to this stress. We determined that this pathogen initiates a transcriptional program that prioritizes replenishment of nutrient stores over replication, possibly in preparation for rapid growth once optimal iron levels are restored. Transcription of genes for biosynthesis of metabolic precursors was generally up-regulated, while those involved in multiple steps of translation were down-regulated. We also observed an increase in transcription of genes involved in DNA repair and neutralizing oxidative stress, indicating thatChlamydiaemploys an “all-or-nothing” strategy. Its small genome limits its ability to tailor a specific response to a particular stress. Therefore, the “all-or-nothing” strategy may be the most efficient way of surviving within the host, where the pathogen likely encounters multiple simultaneous immunological and nutritional insults.