Genome-wide characterization of monomeric transcriptional regulators in Mycobacterium tuberculosis

Abstract

Gene transcription catalysed by RNA polymerase is regulated by transcriptional regulators, which play central roles in the control of gene transcription in both eukaryotes and prokaryotes. In regulating gene transcription, many regulators form dimers that bind to DNA with repeated motifs. However, some regulators function as monomers, but their mechanisms of gene expression control are largely uncharacterized. Here we systematically characterized monomeric versus dimeric regulators in the tuberculosis causative agent Mycobacterium tuberculosis. Of the .160 transcriptional regulators annotated in M. tuberculosis, 154 transcriptional regulators were tested, 22 % probably act as monomers and most are annotated as hypothetical regulators. Notably, all members of the WhiB-like protein family are classified as monomers. To further investigate mechanisms of monomeric regulators, we analysed the actions of these WhiB proteins and found that the majority interact with the principal sigma factor s A , which is also a monomeric protein within the RNA polymerase holoenzyme. Taken together, our study for the first time globally classified monomeric regulators in M. tuberculosis and suggested a mechanism for monomeric regulators in controlling gene transcription through interacting with monomeric sigma factors.

Structure of a Wbl protein and implications for NO sensing by M. tuberculosis

“…A survey of the monomeric transcription regulators of M . tuberculosis showed that WhiB1 interacted with the major sigma factor, σ A 33 . Aerobic purification of an N-terminally His-tagged M .…”

The FeoC [4Fe–4S] Cluster Is Redox-Active and Rapidly Oxygen-Sensitive

“…63 However, in our hands FeoC appears to remain monomeric in the presence of its cluster, which is unusual although not unheard of for transcriptional regulators. 64, 65 Alternatively, FeoC could function as part of the larger Feo complex, which could be dynamic under changing cellular conditions in cooperation with FeoB. Support that FeoC is part of the larger complex is found in the Kp NFeoB- Kp FeoC co-crystal structure (although the [Fe-S] cluster is absent) 66 , and in studies on V. cholerae Feo system, that have shown that FeoA/B/C interact 25, 67 (although Vc FeoC is one of only a handful of FeoCs that lack the necessary cluster-binding residues).…”

“…Lowest-energy NMR conformer of Ec FeoC (PDB ID 1XN7). Labeled regions are: the helix-turn-helix (HTH) motif and the unstructured wing region that contains four Cys residues (Cys 56 , Cys 61 , Cys 64 and Cys 70 ) involved in [Fe-S] cluster binding. The labels “N” and “C” represent the amino and carboxy termini, respectively.…”

Interaction of the Streptomyces Wbl protein WhiD with the principal sigma factor σHrdB depends on the WhiD [4Fe-4S] cluster

“…A general conclusion from previous characterizations of Wbl proteins is that they are monomeric proteins ( 2 , 12 , 28 ), and so these findings for Sv WhiD were unexpected. We note that Sv WhiD has a C-terminal extension of 18 residues compared with Sc WhiD, and, although the proteins exhibit overall 78% sequence identity, only 1 of the last 33 residues of Sv WhiD is conserved in Sc WhiD (the proteins are 100% identical from residues 1–95) ( Fig.…”