Genome Context as a Predictive Tool for Identifying Regulatory Targets of the TetR Family Transcriptional Regulators

Abstract

TetR family transcriptional regulators (TFRs) are found in most bacteria and archea. Most of the family members that have been investigated to date are repressors of their target genes, and the majority of these, like the well-characterized protein TetR, regulate genes that encode transmembrane efflux pumps. In many cases repression by TFR proteins is reversed through the direct binding of a small-molecule ligand. The number of TFRs in the public database has grown rapidly as a result of genome sequencing and there are now thousands of family members; however virtually nothing is known about the biology and biochemistry they regulate. Generally applicable methods for predicting their regulatory targets would assist efforts to characterize the family. Here, we investigate chromosomal context of 372 TFRs from three Streptomyces species. We find that the majority (250 TFRs) are transcribed divergently from one neighboring gene, as is the case for TetR and its target tetA. We explore predicted target gene product identity and intergenic separation to see which either correlates with a direct regulatory relationship. While intergenic separation is a critical factor in regulatory prediction the identity of the putative target gene product is not. Our data suggest that those TFRs that are <200 bp from their divergently oriented neighbors are most likely to regulate them. These target genes include membrane proteins (26% of which 22% are probable membrane-associated pumps), enzymes (60%), other proteins such as transcriptional regulators (1%), and proteins having no predictive sequence motifs (13%). In addition to establishing a solid foundation for identifying targets for TFRs of unknown function, our analysis demonstrates a much greater diversity of TFR-regulated biochemical functions.

Transcriptional Regulation of the Daptomycin Gene Cluster in Streptomyces roseosporus by an Autoregulator, AtrA

“…7D), these sites were rich in purine, suggesting a more complex binding pattern of AtrA on its own promoter. These results, to some extent, were consistent with the previous report that in S. coelicolor, even though AtrA-atrAp interact at high affinity, no AtrA-binding sites could be determined on atrAp by DNase I footprinting assays (28).…”

The TetR Family of Regulators

“…Its well-documented role as a regulator of antibiotic efflux is shared by at most 25% of the TFR family members (23). We know that other TFRs function as both repressors and activators (e.g., DhaS), serve as local or global regulators (e.g., AmtR), and can interact with small-molecule or protein ligands (e.g., SlmA).…”

“…It would be interesting to evaluate this approach to validate potential operator sequences identified through palindrome analysis or to perhaps predict the operator DNA sequence that is recognized by a TFR. Additional information such as DNase I footprinting can aid in the prediction of TFR operator sites from DNA sequence information (23).…”

“…4), and these relationships can be used to predict the regulatory target gene(s) of the TFR (23). The majority of TFRs are classified as type I: their genes show a divergent orientation to one of the adjacent genes, as is the case for tetR and tetA.…”

Szénhidrogén bontó Rhodococcus erythropolis törzsek funkcionális genomikai analízise és biotechnológiai alkalmazása

“…RER_07500 egy feltételezhetően a TetR családba tartozó szabályozó fehérjét kódol. Az ebbe a családba tartozó fehérjék olyan negatív regulátorként ismeretesek, amelyek nemcsak a szomszédságukban található operon, hanem önmaguk expresszióját is szabályozzák [146]. A TetR szabályozó fehérje szubsztrát jelenlétében nem képes kötődni a szabályozó régióhoz, így mind az alkB gén mind pedig az őt szabályozó tetR gén kifejeződése beindul.…”