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Publication Abstract from PubMed

In class II transcription activation, the transcription factor normally binds to the promoter near the -35 position and contacts the domain 4 of sigma factors (sigma4 ) to activate transcription. However, sigma4 of sigma(70) appears to be poorly folded on its own. Here, by fusing sigma4 with the RNA polymerase beta-flap-tip-helix, we constructed two sigma4 chimera proteins, one from sigma(70) sigma 4 70 c and another from sigma(S) sigma 4 S c of Klebsiella pneumoniae. The two chimera proteins well folded into a monomeric form with strong binding affinities for -35 element DNA. Determining the crystal structure of sigma 4 S c in complex with -35 element DNA revealed that sigma 4 S c adopts a similar structure as sigma4 in the Escherichia coli RNA polymerase sigma(S) holoenzyme and recognizes -35 element DNA specifically by several conserved residues from the helix-turn-helix motif. By using nuclear magnetic resonance (NMR), sigma 4 70 c was demonstrated to recognize -35 element DNA similar to sigma 4 S c . Carr-Purcell-Meiboom-Gill relaxation dispersion analyses showed that the N-terminal helix and the beta-flap-tip-helix of sigma 4 70 c have a concurrent transient alpha-helical structure and DNA binding reduced the slow dynamics on sigma 4 70 c . Finally, only sigma 4 70 c was shown to interact with the response regulator PmrA and its promoter DNA. The chimera proteins are capable of -35 element DNA recognition and can be used for study with transcription factors or other factors that interact with domain 4 of sigma factors.

Structural basis for -35 element recognition by sigma4 chimera proteins and their interactions with PmrA response regulator.,Lou YC, Chou CC, Yeh HH, Chien CY, Sadotra S, Hsu CH, Chen C Proteins. 2020 Jan;88(1):69-81. doi: 10.1002/prot.25768. Epub 2019 Jul 22. PMID:31293000^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.