title: Structural insights into RNA polymerase recognition and essential function of Myxococcus xanthus CdnL.
abstract: CdnL and CarD are two functionally distinct members of the CarD_CdnL_TRCF family of bacterial RNA polymerase (RNAP)-interacting proteins, which co-exist in Myxococcus xanthus. While CarD, found exclusively in myxobacteria, has been implicated in the activity of various extracytoplasmic function (ECF) σ-factors, the function and mode of action of the essential CdnL, whose homologs are widespread among bacteria, remain to be elucidated in M. xanthus. Here, we report the NMR solution structure of CdnL and present a structure-based mutational analysis of its function. An N-terminal five-stranded β-sheet Tudor-like module in the two-domain CdnL mediates binding to RNAP-β, and mutations that disrupt this interaction impair cell growth. The compact CdnL C-terminal domain consists of five α-helices folded as in some tetratricopeptide repeat-like protein-protein interaction domains, and contains a patch of solvent-exposed nonpolar and basic residues, among which a set of basic residues is shown to be crucial for CdnL function. We show that CdnL, but not its loss-of-function mutants, stabilizes formation of transcriptionally competent, open complexes by the primary σA-RNAP holoenzyme at an rRNA promoter in vitro. Consistent with this, CdnL is present at rRNA promoters in vivo. Implication of CdnL in RNAP-σA activity and of CarD in ECF-σ function in M. xanthus exemplifies how two related members within a widespread bacterial protein family have evolved to enable distinct σ-dependent promoter activity.
authors.affiliation: Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain.
authors.forename: Aránzazu
authors.initials: A
authors.lastname: Gallego-García
authors.affiliation: Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Madrid, Spain.
authors.forename: Yasmina
authors.initials: Y
authors.lastname: Mirassou
authors.affiliation: Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain.
authors.forename: Diana
authors.initials: D
authors.lastname: García-Moreno
authors.affiliation: Departamento de Genética y Microbiología, Área de Genética (Unidad Asociada al IQFR-CSIC), Facultad de Biología, Universidad de Murcia, Murcia, Spain.
authors.forename: Montserrat
authors.initials: M
authors.lastname: Elías-Arnanz
authors.affiliation: Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Madrid, Spain.
authors.forename: María Angeles
authors.initials: MA
authors.lastname: Jiménez
authors.affiliation: Instituto de Química Física 'Rocasolano', Consejo Superior de Investigaciones Científicas (IQFR-CSIC), Madrid, Spain.
authors.forename: S
authors.initials: S
authors.lastname: Padmanabhan
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism / Q000502:physiology*; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009154:Mutation; D016941:Myxococcus xanthus / Q000201:enzymology* / Q000378:metabolism; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D012321:DNA-Directed RNA Polymerases