title: The structural basis for promoter -35 element recognition by the group IV sigma factors.
abstract: The control of bacterial transcription initiation depends on a primary sigma factor for housekeeping functions, as well as alternative sigma factors that control regulons in response to environmental stresses. The largest and most diverse subgroup of alternative sigma factors, the group IV extracytoplasmic function sigma factors, directs the transcription of genes that regulate a wide variety of responses, including envelope stress and pathogenesis. We determined the 2.3-A resolution crystal structure of the -35 element recognition domain of a group IV sigma factor, Escherichia coli sigma(E)4, bound to its consensus -35 element, GGAACTT. Despite similar function and secondary structure, the primary and group IV sigma factors recognize their -35 elements using distinct mechanisms. Conserved sequence elements of the sigma(E) -35 element induce a DNA geometry characteristic of AA/TT-tract DNA, including a rigid, straight double-helical axis and a narrow minor groove. For this reason, the highly conserved AA in the middle of the GGAACTT motif is essential for -35 element recognition by sigma(E)4, despite the absence of direct protein-DNA interactions with these DNA bases. These principles of sigma(E)4/-35 element recognition can be applied to a wide range of other group IV sigma factors.
authors.affiliation: The Rockefeller University, New York, New York, United States of America.
authors.forename: William J
authors.initials: WJ
authors.lastname: Lane
authors.forename: Seth A
authors.initials: SA
authors.lastname: Darst
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites; D003460:Crystallization; D004268:DNA-Binding Proteins / Q000737:chemistry; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry; D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000737:chemistry; D015964:Gene Expression Regulation, Bacterial; D008954:Models, Biological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D011487:Protein Conformation; D050436:Regulatory Elements, Transcriptional / Q000502:physiology*; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D012808:Sigma Factor / Q000737:chemistry*
chemical_list: D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D012808:Sigma Factor; D012321:DNA-Directed RNA Polymerases