Domain Architecture of a High Mobility Group A-type Bacterial Transcriptional Factor

Abstract

Myxococcus xanthus transcriptional factor CarD participates in carotenogenesis and fruiting body formation. It is the only reported prokaryotic protein having adjacent "AT-hook" DNA-binding and acidic regions characteristic of eukaryotic high mobility group A (HMGA) proteins. The latter are small, unstructured, nonhistone nuclear proteins that function as architectural factors to remodel DNA and chromatin structure and modulate various DNA binding activities. We find CarD to be predominantly dimeric with two stable domains: (a) an N-terminal domain of defined secondary and tertiary structure which is absent in eukaryotic HMGA proteins; (b) a C-terminal domain formed by the acidic and AT-hook segments and lacking defined structure. CarD, like HMGA proteins, binds specifically to the minor-groove of AT-rich DNA present in two appropriately spaced tracts. As in HMGA proteins, casein kinase II can phosphorylate the CarD acidic region, and this dramatically decreases the DNA binding affinity of CarD. The acidic region, in addition to modulating DNA binding, confers structural stability to CarD. We discuss how the structural and functional plasticity arising from domain organization in CarD could be linked to its role as a general transcriptional factor in M. xanthus.

Operator Design and Mechanism for CarA Repressor-mediated Down-regulation of the Photoinducible carB Operon in Myxococcus xanthus

“…Once liberated, CarQ up-regulates expression of car-QRS and crtI (18). In this, CarQ is aided by the high mobility group A-type protein CarD (23)(24)(25)(26) and the histone-like protein IhfA (integration host factor ␣ subunit) (27). The photo-induced expression of the carB operon is regulated by CarA, which is produced independently of light from an adjacent operon, and by CarS (28,29).…”

High-Mobility-Group A-Like CarD Binds to a DNA Site Optimized for Affinity and Position and to RNA Polymerase To Regulate a Light-Inducible Promoter in Myxococcus xanthus

“…1A) (13)(14)(15). In contrast to mammalian HMGA, CarD also has a structurally well-defined Nterminal domain of ϳ180 residues which is essential for function and defines the widely distributed CarD_CdnL_TRCF family of bacterial proteins or protein modules that have been implicated in interactions with RNA polymerase (RNAP) (5,(13)(14)(15)(16)(17). Through this domain CarD forms a stable complex with CarG, which is indispensable in every known CarD-dependent process (13,15).…”

“…We addressed this in the present study by carrying out a detailed analysis of a site upstream of the light-inducible promoter of the carQRS operon (P QRS ), (Fig. 1B), the only one that has thus far been experimentally demonstrated to be important for both CarD binding and function (6,(13)(14)(15). Expression from P QRS is driven by the RNAP holoenzyme containing CarQ, an alternative factor of the extracytoplasmic function (ECF) family (20).…”

“…Expression from P QRS is driven by the RNAP holoenzyme containing CarQ, an alternative factor of the extracytoplasmic function (ECF) family (20). It also absolutely requires the CarD-CarG complex and a site that spans position Ϫ65 to Ϫ77 relative to the P QRS transcription start site that is important for CarD function in vivo and to which CarD binds in vitro (6,(13)(14)(15). This CarD binding site contains two optimally phased 3-bp-long AT tracts (Fig.…”

“…M. xanthus CarD has a C-terminal domain with four AT hooks that resembles human HMGA1a (with three AT hooks) in its physical, structural, and DNA binding properties (Fig. 1A) (13)(14)(15). In contrast to mammalian HMGA, CarD also has a structurally well-defined Nterminal domain of ϳ180 residues which is essential for function and defines the widely distributed CarD_CdnL_TRCF family of bacterial proteins or protein modules that have been implicated in interactions with RNA polymerase (RNAP) (5,(13)(14)(15)(16)(17).…”