Mining the chlamydial genome for regulatory factors

The capacity to regulate gene expression is crucial for chlamydial survival and replication within an infected host cell. By analogy to other bacteria, transcription factors are likely to play an important role in this regulation. The availability of sequence information from a number of chlamydial genomes, and in vitro functional assays developed in our lab, have made it possible to study chlamydial transcription factors. We began with a study on TrpR, a transcription factor that was predicted in the original chlamydial genome annotation. We provide functional evidence that C. trachomatis TrpR is an aporepressor that represses the tryptophan biosynthesis genes in a tryptophan-dependent manner. Our findings provide a mechanism for chlamydiae to sense changes in tryptophan levels and to respond by modulating expression of the tryptophan biosynthesis genes. It also demonstrates that the activity of a chlamydial transcription factor can be further regulated through allosteric control. We also describe the identification of a novel regulator CT069 that was not annotated as a transcription factor in the original C. trachomatis genome. We used a bioinformatics approach to mine the C. trachomatis genome for encoded proteins that are predicted to have the general structure and characteristic functional domains of a bacterial transcription factor. We demonstrate that CT069 is encoded as a fusion protein of YtgR, which is a metal-ion dependent repressor of the ytg operon, and YtgC, a transmembrane component of a predicted metal ion transporter that is encoded by this operon. We propose that CT069 allows chlamydiae to maintain the intracellular metal ion level by regulating the expression of a metal ion transporter through a negative feedback mechanism. These Studies of TrpR and CT069 demonstrate that Chlamydia has maintained the ability to homeostatically regulate essential nutrients even as it has drastically reduced the number of genes in its genome. This work has contributed to a better understanding of gene regulation in Chlamydia by describing novel mechanisms of transcriptional regulation in this human pathogen.