M. Zuhaib Qayyum's research while affiliated with St. Jude Children's Research Hospital and other places

... 43,44 In cyanobacterial RNAP, SI3 is much larger and consists of eight SBHM motifs. 45 Recent structural data show that it adopts an elongated, archlike architecture, which spans across the polymerase surface and contacts s factor during transcription initiation. 19,45 In the PEP, SI3 is even larger and adopts a unique structure. ...

... In Bacteria, NusG suppresses pausing and backtracking of the RNAP and interacts with effector proteins such as the termination factor Rho via its KOW domain 26,27 .Furthermore, it was shown that NusG mediates the coupling between RNAP and the ribosome contacting the RNAP clamp and the ribosomal subunit S10 [28][29][30][31] . In contrast to NusG in E. coli, a gene-specific homologue called RfaH and B. subtilis 'NusG-like' homologues interact with the nontemplate strand of the transcription bubble and thereby enhance transcriptional pausing [32][33][34][35] . ...

... However, other studies suggest that ASH-Ski2 might be involved in transcription termination ( 39 ,73 ). ASH-Ski2 from Thermococcus kodakarensis (denoted as Eta) has been shown to have a translocase activity in vitro ( 73 ). The interaction be-tween ASH-Ski2 / Eta and RNA polymerase is suggested to be mediated by the ratchet domain residues, rather than the Nterminal domain that is unique to the ASH-Ski2 group. ...

... In bulk transcription reactions with purified RNAP and σ 70 , the addition of RapA strongly stimulates multiround transcription cycling and transcript production, raising the possibility that it acts following termination (18,(23)(24)(25)(26). However, multiple other activities for RapA have been proposed, including stabilizing open-promoter complexes during transcription initiation (27), promoting nascent transcript release from elongation complexes (25), preventing binding of RNAP on nonpromoter DNA (28), and removing stalled elongation complexes via backtracking (29). ...

... Time-resolved singlemolecule FRET measurements of the RNAP apo enzymes from E. coli moreover revealed that the clamp is conformationally flexible and populates three distinct states 62 . In bacterial transcription elongation complexes 35,63 , the clamp adopts a closed state and apparently reopens during transcription termination 64 . These clamp movements are of functional importance for bacterial but also archaeal transcription as an opening of the clamp promotes for example transcription initiation 19,65 most likely by supporting the separation of the DNA strands. ...

... However, the relative positions of RapA to RNAP are slightly different in two structures, and the RapA-RNAP complex is more compact in the crystal structure than that in our cryo-EM structure (Supplementary Figure S3). Besides, the overall structure of our RapA-RNAP elongation complex is similar to that of the RapA-RNAP elongation complex (PDB ID: 7MKN) reported in a recent preprint manuscript (35), with a root-meansquare deviation (RMSD) of 2.3Å (C␣ aligned). In the preprint, the clamp in RapA-RNAP binary complex adopts a 'closed' state compared to that in the RNAP core enzyme (open clamp). ...

... The MerR family TF crystals used for structural comparison were BmrR (PDB: 7CKQ) [40], CadR (PDB: 6JGX) [39], CueR (PDB: 1Q05 [70] and 6XH7 [42]), EcmrR (PDB: 6XL6) [43], MerR (PDB: 5CRL) [16], MtaN (PDB: 1R8D) [37], and PbrR (PDB: 5GPE) [71]. The crystals used to analyze the structure and interactions of the sigma factor were PDB: 5TW1 (Mtb AP3 promoter from Mycolicibacterium smegmatis MC2 155) [72], 6M7J (6M7J (PDB No.) was the rRNA P3 promoter and RNA polymerase from Mycolicibacterium tuberculosis) [73], the 7KHB (rrnBP1 promoter and RNA polymerase from E. coli K-12) [74], and 8GZH (from Synechocystis sp. PCC 6803.). ...

... The evaluation of protein-ligand complex compactness and its associated stability commonly relies on monitoring the Radius of Gyration (Rg) during a simulation (Muteeb et al., 2020). In our study, we analyzed the Rg of Mpro in isolated and complexed forms with compounds 4, 5, 10, and 14 over a 100 ns simulation period (Fig. 8A) 4-25.4 ...

... NTPs enter the RNAP via a secondary channel, and many auxiliary transcription factors interact with RNAP via this channel. Binding of (p)ppGpp to the RNAP-DksA complex changes the 3D structures of both RNAP and DksA allowing reduction of transcription of the rRNA operon and enhancement of transcription of amino acid synthesis enzymes(Molodtsov et al., 2018;Shin et al., 2020).In Gram-positive bacteria, most (p)ppGpp binding amino acids are not conserved in RNAP, the DksA protein is missing, and an ω deletion strain does not influence stringent response(Ross et al., 2013;Weiss et al., 2017). Instead, (p)ppGpp reduces the amount of GTP in cells by inhibiting GTP synthesizing enzymes including guanylate kinase(Kriel et al., 2012;Liu et al., 2015). ...

... Protein-protein interactions between σ 70 and the conserved β 0 coiled coil domain and the β flap tip helix also simultaneously strengthen these contacts. Then, through stepwise isomerization, the promoter DNA duplex is driven open by RNAP to form a catalytical RNAPpromoter open complex (RPo), which can efficiently initiate transcription with addition of nucleotides (Zuo and Steitz, 2015;Narayanan et al., 2018;Chen et al., 2020Chen et al., , 2021. While as to promoters without the above consensus elements, the interactions between RNAP and promoter DNA are not so powerful enough to promote formation of a stable RPo. ...