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Codon-dependent transcriptional changes in response to tryptophan limitation in the tryptophan auxotrophic pathogens Chlamydia trachomatis and Streptococcus pyogenes

ABSTRACT: Codon-dependent transcriptional changes in response to tryptophan limitation in the tryptophan auxotrophic pathogens Chlamydia trachomatis and Streptococcus pyogenes

PROVIDER: PRJNA728014 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14464900_1.fastq.gz	Fastqsanger.gz
	SRR14464900_2.fastq.gz	Fastqsanger.gz
	SRR14464901_1.fastq.gz	Fastqsanger.gz
	SRR14464901_2.fastq.gz	Fastqsanger.gz
	SRR14464833_1.fastq.gz	Fastqsanger.gz

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Codon-dependent transcriptional changes in response to tryptophan limitation in the tryptophan auxotrophic pathogens Chlamydia trachomatis and Streptococcus pyogenes

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Project description: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-γ), 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.

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Project description:Limitation for amino acids is thought to regulate translation in mammalian cells primarily by signaling through the kinases mTORC1 and GCN2. We find that limitation for the amino acid arginine causes a selective loss of tRNA charging, which regulates translation through ribosome pausing at two of six arginine codons. Interestingly, limitation for leucine, an essential and abundant amino acid in protein, results in little or no ribosome pausing. Chemical and genetic perturbation of mTORC1 and GCN2 signaling revealed that their robust response to leucine limitation prevents ribosome pausing, while an insufficient response to arginine limitation led to loss of arginine tRNA charging and ribosome pausing. Codon-specific ribosome pausing decreased protein production and triggered premature ribosome termination without significantly reducing mRNA levels. Together, our results suggest that amino acids which are not optimally sensed by the mTORC1 and GCN2 pathways still regulate translation through an evolutionarily conserved mechanism based on synonymous codon usage.

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