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The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa

Bergkessel, Megan and Babin, Brett M. and VanderVelde, David and Sweredoski, Michael J. and Moradian, Annie and Eggleston-Rangel, Roxana and Hess, Sonja and Tirrell, David and Artsimovitch, Irina and Newman, Dianne K. (2019) The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa. Molecular Microbiology, 112 (3). pp. 992-1009. ISSN 0950-382X. PMCID PMC6736744 . doi:10.1111/mmi.14337.

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Though most bacteria in nature are nutritionally limited and grow slowly, our understanding of core processes like transcription comes largely from studies in model organisms doubling rapidly. We previously identified a small protein of unknown function, SutA, in a screen of proteins synthesized in Pseudomonas aeruginosa during dormancy. SutA binds RNA polymerase (RNAP), causing widespread changes in gene expression, including upregulation of the ribosomal RNA genes. Here, using biochemical and structural methods, we examine how SutA interacts with RNAP and the functional consequences of these interactions. We show that SutA comprises a central α‐helix with unstructured N‐ and C‐terminal tails, and binds to the β1 domain of RNAP. It activates transcription from the rrn promoter by both the housekeeping sigma factor holoenzyme (Eσ^(70)) and the stress sigma factor holoenzyme (Eσ^S) in vitro, but has a greater impact on Eσ^S. In both cases, SutA appears to affect intermediates in the open complex formation and its N‐terminal tail is required for activation. The small magnitudes of in vitro effects are consistent with a role in maintaining activity required for homeostasis during dormancy. Our results add SutA to a growing list of transcription regulators that use their intrinsically disordered regions to remodel transcription complexes.

Item Type:Article
Related URLs:
URLURL TypeDescription Paper CentralArticle
Bergkessel, Megan0000-0002-4530-1224
Babin, Brett M.0000-0002-4133-6665
VanderVelde, David0000-0002-2907-0366
Sweredoski, Michael J.0000-0003-0878-3831
Moradian, Annie0000-0002-0407-2031
Hess, Sonja0000-0002-5904-9816
Tirrell, David0000-0003-3175-4596
Newman, Dianne K.0000-0003-1647-1918
Additional Information:© 2019 John Wiley & Sons Ltd. Issue Online: 10 September 2019; Version of Record online: 10 July 2019; Accepted manuscript online: 28 June 2019; Manuscript accepted: 25 June 2019. We thank Ben Ramirez (University of Illinois at Chicago) for helping us with preliminary NMR studies of SutA, Jacqueline Barton (Caltech) for giving us access to her lab to perform experiments involving radioactivity, Nate Glasser for help with HPLC measurements to quantify SutA, Hsiau‐Wei (Jack) Lee and Aimee Marceau (University of California, Santa Cruz) for help with the NMR binding experiment using the Bruker AVIII HD 800 MHz NMR, Weidong Hu (City of Hope) for help with NMR experiments using the Bruker AV III 700 MHz spectrometer, and Julia Kardon and Niels Bradshaw (Brandeis University) and members of the Newman lab for feedback on the project at different stages. MB was supported by a postdoctoral fellowship from the Cystic Fibrosis Foundation (BERGKE16F0). Grants from the NIH (GM067153) to IA and grants from the NIH (R01HL117328 and 1R01AI127850‐01A1) to DKN supported this work. The Proteome Exploration Laboratory is supported by the Beckman Institute and NIH 1S10OD02001301. This work was also supported by the Institute for Collaborative Biotechnologies through grant W911NF‐09‐0001 from the U.S. Army Research Office. The content of the information does not necessarily reflect the position or the policy of the Government and no official endorsement should be inferred. The authors have no conflicts of interest to disclose.
Group:Division of Geological and Planetary Sciences
Funding AgencyGrant Number
Cystic Fibrosis FoundationBERGKE16F0
Caltech Beckman InstituteUNSPECIFIED
Army Research Office (ARO)W911NF‐09‐0001
Subject Keywords:Pseudomonas aeruginosa; Bacterial gene expression regulation; RNA polymerase beta subunit; Sigma factor; Intrinsically disordered proteins; Bacterial physiological phenomena
Issue or Number:3
PubMed Central ID:PMC6736744
Record Number:CaltechAUTHORS:20181029-102517113
Persistent URL:
Official Citation:Bergkessel, M. , Babin, B. M., VanderVelde, D. , Sweredoski, M. J., Moradian, A. , Eggleston‐Rangel, R. , Hess, S. , Tirrell, D. A., Artsimovitch, I. and Newman, D. K. (2019), The dormancy‐specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa. Mol Microbiol, 112: 992-1009. doi:10.1111/mmi.14337
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:90464
Deposited By: Tony Diaz
Deposited On:29 Oct 2018 17:52
Last Modified:01 Jun 2023 23:30

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