We study the mechanism and regulation of RNA chain synthesis in bacteria using a combination of genetic, biochemical and biophysical techniques to elucidate the fine details of diverse catalytic reactions carried out by RNA polymerase and the molecular mechanisms by which accessory protein factors and small molecules, including antibiotics, modulate RNA polymerase progression through the transcription cycle. We also investigate crosstalk between transcription and concurrent processes, such as translation, the nascent RNA folding, and DNA repair.

Bacterial virulence factor RfaH is the focal point of our current projects. RfaH belongs to the only universally conserved family of transcription factors. We showed that RfaH acts as a processivity clamp that locks around the DNA to enable RNA polymerase to transcribe long mRNAs. Unexpectedly, we found that RfaH has an additional, and much larger, effect on gene expression mediated by direct recruitment of the ribosome to the nascent mRNAs that are devoid of canonical ribosome binding sites.

We showed that RfaH undergoes dramatic conformational rearrangements during its life cycle. RfaH in a closed, autoinhibited state is recruited to a transcription elongation complex paused at a specific ops site (ops-TEC) via contacts to the non-template DNA strand. Recruitment triggers domain dissociation, allowing the N-terminal domain binding to RNA polymerase. The released C-terminal domain transforms into a β-barrel and recruits the ribosome. RfaH remains bound to RNAP until termination, when it is released and recycled into the autoinhibited state. This conformational switch is similar to those that underlie transformation from harmless into disease-causing proteins, as in the case of prion diseases.

RfaH is also an attractive target for novel antibiotics and vaccines ‒ its target genes encode toxins, diverse virulence determinants, and conjugation functions. Inactivation of RfaH abrogates virulence in Klebsiella pneumoniae, Escherichia coli, and Salmonella species. Many antibiotic-resistance determinants isolated from clinical strains are carried on conjugative plasmids that also encode RfaH paralogs as part of their pilus synthesis operons.

We are actively working on

• The mechanism of RfaH recruitment to the transcription complex;
• The mechanism by which RfaH increases translation processivity;
• The mechanism of RfaH-mediated ribosome recruitment;
• Identification of small molecules that target E. coli and K. pneumoniae RfaH;
• The evolution of RfaH family of regulators.

Recent relevant publications:

Zuber PK, Schgweimer K, Rösch P, Artsimovitch I, Knauer SH (2019). Reversible fold-switching of the antitermination factor RfaH. Nat Commun., doi: 10.1038/s41467-019-08567-6.

Widom JR, Nedialkov YA, Rai V, Hayes RL, Brooks CL III, Artsimovitch I, Walter NG (2018) Ligand modulates cross-coupling between riboswitch folding and transcriptional pausing. Mol Cell, doi: 10.1016/j.molcel.2018.08.046

Svetlov D, Shi D, Twentyman J, Nedialkov Y, Rosen DA, Abagyan R, Artsimovitch I (2018) In silico discovery of small molecules that inhibit RfaH recruitment to RNA polymerase. Mol Microbiol. doi: 10.1111/mmi.14093.

Kang JY, Mooney RA, Nedialkov Y, Saba J, Mishanina TV, Artsimovitch I, Landick R, Darst SA* (2018) Structural basis for transcript elongation control by NusG family universal regulators. Cell. doi.org/10.1016/j.cell.2018.05.017.

Zuber PK, Artsimovitch I, NandyMazumdar M, Liu Z, Nedialkov Y, Schweimer K, Rösch P, Knauer SH (2018) The universally-conserved transcription factor RfaH is recruited to a hairpin structure of the non-template DNA strand. eLife. doi: 10.7554/eLife.36349.

Nedialkov Y, Svetlov D, Belogurov GA, Artsimovitch I (2018) Locking the non-template DNA to control transcription. Mol Microbiol. doi: 10.1111/mmi.13983.

Shi D, Svetlov D, Abagyan R, Artsimovitch I (2017) Flipping states: a few key residues decide the winning conformation of the only universally conserved transcription factor. Nucleic Acids Res. doi: 10.1093/nar/gkx523.

Hu K, Artsimovitch I (2017) Screen for rfaH suppressors reveals a key role for a connector region of the termination factor Rho. MBio 8(3): e00753-17. doi: 10.1128/mBio.00753-17.

Other relevant publications:

NandyMazumdar M, Nedialkov Y, Svetlov D, Sevostyanova A, Belogurov GA, Artsimovitch I (2016) RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes. Proc Natl Acad Sci U S A. 113, 14994-14999.

Burmann BM, Knauer SH, Sevostyanova A, Schweimer K, Mooney RA, Landick R, Artsimovitch I & Rösch P (2012) An α-helix to β-barrel domain switch transforms the transcription factor RfaH into a translation factor. Cell, 150, 291-303.

Sevostyanova A, Belogurov GA, Mooney RA, Landick R & Artsimovitch I (2011) The beta subunit gate loop is required for RNA polymerase modification by RfaH and NusG. Mol Cell. 43, 253-62.

Belogurov GA, Vassylyeva MN, Sevostyanova A, Appleman JR, Xiang AX, Lira R, Webber SE, Klyuyev S, Nudler E, Artsimovitch I & Vassylyev DG (2009) Transcription inactivation through local refolding of the RNA polymerase structure. Nature. 457, 332-5.

Belogurov GA, Mooney RA, Svetlov V, Landick R & Artsimovitch I (2009) Functional specialization of transcription elongation factors. EMBO J. 28, 112-22.

Sevostyanova A, Svetlov V, Vassylyev DG & Artsimovitch I (2008) The elongation factor RfaH and the initiation factor sigma bind to the same site on the transcription elongation complex. Proc Natl Acad Sci U S A. 105, 865-70.

Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH & Artsimovitch I (2007) Structural basis for transcription elongation by bacterial RNA polymerase. Nature. 448, 157-62.

Belogurov GA, Vassylyeva MN, Svetlov V, Klyuyev S, Grishin NV, Vassylyev DG & Artsimovitch I (2007) Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol Cell. 26, 117-29.

Vassylyev DG, Svetlov V, Vassylyeva MN, Perederina A, Igarashi N, Matsugaki N, Wakatsuki S & Artsimovitch I (2005) Structural basis for transcription inhibition by tagetitoxin. Nat Struct Mol Biol. 12, 1086-93.

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