NMR structure note: N-terminal domain of Thermus thermophilus CdnL

Abstract

The CarD_CdnL_TRCF protein family (PF02559 in the protein family database; http://pfam.sanger.ac.uk) consists of members that are widely (and exclusively) distributed in bacteria, and for many of these proteins the functions remain to be fully characterized. The family is defined by the *180-residue N-terminal domain of CarD, a global transcriptional regulator in the Gram-negative soil bacterium Myxococcus xanthus required in the activation of lightand starvation-induced genes as well as in other processes (Padmanabhan et al. 2001; Cayuela et al. 2003; Garcia-Moreno et al. 2010). This domain in CarD interacts with CarG, a zinc-associated factor essential in every CarDdependent process (Penalver-Mellado et al. 2006), and with a specific domain in the RNA polymerase (RNAP) b-subunit (Garcia-Moreno et al. 2010). CarD can also bind to DNA via an intrinsically unfolded, *140-residue C-terminal domain resembling eukaryotic high mobility group A (HMGA) proteins (Padmanabhan et al. 2001). Besides CarD and its orthologs (found so far only in myxobacteria; Elias-Arnanz et al. 2010), the CarD_CdnL_TRCF family consists of two other classes of proteins. One class corresponds to that formed by the RNAP-interacting domain, RID, that spans an *70-residue segment of the much larger ([1,000 residues) transcription-repair coupling factor or TRCF, a widely conserved multidomain protein that mediates transcription-coupled repair of DNA lesions encountered by the transcribing complex in bacteria (Selby and Sancar 1995; Deaconescu et al. 2006). The other class within the CarD_CdnL_TRCF family includes several proteins that are typically 150–200 residues long (and so considerably smaller than CarD or TRCF orthologs) and have been denoted as CdnL (for CarD N-terminus-Like) to distinguish them from CarD (Cayuela et al. 2003; GarciaMoreno et al. 2010). CdnL has been found to be essential for cell viability and growth in nearly all of the few bacterial species where it has been examined (Garcia-Moreno et al. 2010; Stallings et al. 2009). However, the functions of CdnL and its mode of action remain enigmatic. In M. xanthus, CdnL has been shown to be functionally distinct from CarD, and to interact with the same domain of RNAP-b as CarD but not with CarG. Despite lacking the ability to directly bind DNA, CdnL localizes to the nucleoid in vivo and directly or indirectly affects cell division (Garcia-Moreno et al. 2010). Mycobacterial CdnL has been reported to also interact with RNAP-b and has been implicated in regulating ribosomal RNA transcription (Stallings et al. 2009). In bacteria where it is present, CdnL often coexists with TRCF and, in myxobacteria, with CarD as well. Since all three proteins interact with the same RNAP-b domain, understanding the molecular details for these interactions would provide significant insights into the interplay among them and their functional differences. Electronic supplementary material The online version of this article (doi:10.1007/s10858-012-9648-z) contains supplementary material, which is available to authorized users.