Tryptophan Codon-Dependent Transcription in Chlamydia pneumoniae during Gamma Interferon-Mediated Tryptophan Limitation

Abstract

In evolving to an obligate intracellular niche, Chlamydia has streamlined its genome by eliminating superfluous genes as it relies on the host cell for a variety of nutritional needs like amino acids. However, Chlamydia can experience amino acid starvation when the human host cell in which the bacteria reside is exposed to interferon gamma (IFN-␥), which leads to a tryptophan (Trp)-limiting environment via induction of the enzyme indoleamine-2,3-dioxygenase (IDO). The stringent response is used to respond to amino acid starvation in most bacteria but is missing from Chlamydia. Thus, how Chlamydia, a Trp auxotroph, responds to Trp starvation in the absence of a stringent response is an intriguing question. We previously observed that C. pneumoniae responds to this stress by globally increasing transcription while globally decreasing translation, an unusual response. Here, we sought to understand this and hypothesized that the Trp codon content of a given gene would determine its transcription level. We quantified transcripts from C. pneumoniae genes that were either rich or poor in Trp codons and found that Trp codon-rich transcripts were increased, whereas those that lacked Trp codons were unchanged or even decreased. There were exceptions, and these involved operons or large genes with multiple Trp codons: downstream transcripts were less abundant after Trp codon-rich sequences. These data suggest that ribosome stalling on Trp codons causes a negative polar effect on downstream sequences. Finally, reassessing previous C. pneumoniae microarray data based on codon content, we found that upregulated transcripts were enriched in Trp codons, thus supporting our hypothesis. Chlamydia is an obligate intracellular bacterial pathogen that causes a range of illnesses in humans and animals (1-4). It alternates between functionally and morphologically distinct forms during its developmental cycle (see reference 5 for review). The elementary body (EB) mediates attachment and internalization into a susceptible host cell, whereas the reticulate body (RB) grows and divides within a membrane-bound pathogen-specified parasitic organelle termed an inclusion (6). In evolving to obligate intracellular parasitism, Chlamydia has streamlined its genome by eliminating superfluous pathways and genes (7). Conversely, if Chlamydia has maintained a set of genes, then it is likely important for the bacterium.There are two primary species of Chlamydia that cause significant disease in humans: C. pneumoniae and C. trachomatis. Many chlamydial infections are often unrecognized and asymptomatic, and failure to treat these infections can lead to chronic sequelae. For C. trachomatis, these sequelae can include pelvic inflammatory disease, tubal factor infertility, and reactive arthritis (8, 9). C. pneumoniae has been associated with a number of chronic conditions, including atherosclerosis and adult-onset asthma among others (10, 11). One possible explanation for asymptomatic chlamydial infections may be due to the ability of the organism to ente...

Inhibition of tRNA Synthetases Induces Persistence inChlamydia

“…Firstly, groEL_1 transcripts generally increased during the analysis in C. trachomatis . This is consistent with what we previously characterized as codon-dependent transcriptional changes during amino acid starvation as Hsp60_1 contains 45 L residues (26). Secondly, trpB transcripts were not increased 4h after treatment, as expected since leu starvation should not activate expression of the trpRBA operon.…”

“…To determine whether indolmycin and AN3365 could mimic a more nuanced characteristic of IFNγ-induced persistence, we looked to the ytgABCD operon (26). As previously described by Ouellette et al (32), IFNγ treatment results in Rho-dependent polarization of the ytg operon.…”

“…We recently demonstrated differences in transcript levels between the 5’ and 3’ ends of large monocistronic and polycistronic transcripts (26). We further connected this to Rho-dependent polarity prematurely terminating transcription in trp-codon rich transcripts during IFNγ-mediated trp starvation (32).…”

“…Nevertheless, persistence models are characterized by bacteria (i) remaining viable yet non-infectious, (ii) being non-replicative, (iii) exhibiting an aberrant morphology, (iv) and reactivating to resume the development cycle after the stress is removed (18, 25). Importantly, and as it relates to IFNγ-induced persistence, transcriptomic and proteomic changes also occur, and these changes are predictable based on the trp content of the transcript or protein (26).…”

The iron-dependent repressor YtgR regulates the tryptophan salvage pathway through a bipartite mechanism of transcriptional control inChlamydia trachomatis

“…Ouellette, Rueden, & Rucks, 2016). In sum, this set of experiments provides evidence 806 that iron-depletion specifically alters the representation of particular mRNA species 807 across the trpRBA operon.…”