TABLE 3.
Proteins that regulate RDTT
| Category | Protein | Main features and role(s) in RDTT |
|---|---|---|
| Transcription elongation factors | NusG | NTD binds RNAP, while CTD binds ribosome or Rho in mutually exclusive manner. Increases RNAP processivity except at RDTT terminators (Ray-Soni et al. 2016; Yakhnin et al. 2023). Stimulates RDTT in untranslated regions, notably at suboptimal Rut sites, by increasing the rate of catalytic activation of the Rho–RNA complex (Lawson et al. 2018). Constituent of λ and rrn antitermination complexes (Santangelo and Artsimovitch 2011; Huang et al. 2020). Universally conserved, NusG has idiosyncratic features in some bacteria, such as Mycobacterium tuberculosis (Kalarickal et al. 2010) or T. thermophilus (Reay et al. 2004), where it does not bind Rho. |
| NusA | NTD binds the RNA exit channel of RNAP and nascent RNA structures within it to enhance RNAP pausing or intrinsic termination (Ray-Soni et al. 2016). CTD binds Rho (Hao et al. 2021a; Said et al. 2021). Role in RDTT is debated, likely context-dependent (Burns et al. 1998; Carlomagno and Nappo 2003; Ray-Soni et al. 2016). Proposed to inhibit RDTT by binding RNA at sites overlapping with Rut sites (Qayyum et al. 2016) or to stimulate RDTT (Cardinale et al. 2008) by slowing down RNAP (Ray-Soni et al. 2016) or stabilizing the “stand-by” pretermination complex (Fig. 2D; Hao et al. 2021a; Said et al. 2021). Constituent of λ and rrn antitermination complexes (Santangelo and Artsimovitch 2011; Huang et al. 2020). A nusA deletion mutant is viable provided that Rho activity is reduced (Zheng and Friedman 1994). | |
| RfaH | NusG paralog and transcription antitermination factor operating at a subset of horizontally acquired operons in Enterobacteriaceae. Prevents Rho-dependent polarity in specific operons containing an ops sequence by excluding NusG, altering the RNAP conformation, and facilitating ribosome recruitment (Wang and Artsimovitch 2020; Molodtsov et al. 2024; Zuber et al. 2024). | |
| NusB | Constituent of λ and rrn antitermination complexes (Santangelo and Artsimovitch 2011; Huang et al. 2020). Enhances RDTT at some terminators in a boxA-dependent manner (Carlomagno and Nappo 2003; Baniulyte et al. 2017). | |
| GreA | Prevents formation of long-lived backtracked TECs by stimulating cleavage of 2–3 nt-long extruded RNA 3′end. Cooperates with Rho to remove arrested TECs and avoid genotoxic collisions with the replisome (Dutta et al. 2011). Putative Rho interaction detected by mass spectrometry (Butland et al. 2005). | |
| GreB | Reactivates backtracked TECs by stimulating cleavage of up to 18 nt-long extruded RNA 3′end. Cooperates with Rho to remove arrested TECs and avoid genotoxic collisions with the replisome (Dutta et al. 2011). Stimulates RDTT with arrested, backtracked TECs in vitro (Dutta et al. 2008). | |
| Ribosomal proteins | L3 (RplC) | 50S subunit constituents. Putative, individual interactions with Rho detected by mass spectrometry (Butland et al. 2005). Effects on RDTT are unknown. |
| L4 (RplD) | ||
| L7 (RplL) | ||
| S2 (RpsB) | ||
| S10 (NusE) | 30S subunit constituent. Binds NusG (Burmann et al. 2010) and regulates RDTT by promoting transcription–translation coupling through its interaction with NusG (Woodgate and Zenkin 2023). Constituent of λ and rrn antitermination complexes (Santangelo and Artsimovitch 2011; Huang et al. 2020). | |
| S4 | 30S subunit constituent. Constituent of the rrn antitermination complex (Santangelo and Artsimovitch 2011; Huang et al. 2020). | |
| Inositol monophosphatase | SuhB | May contribute to rRNA and ribosome maturation independently from its monophosphatase activity (Singh et al. 2016). Constituent of the rrn antitermination complex (Singh et al. 2016; Huang et al. 2020). May be more important for ribosome maturation than for antitermination per se (Singh et al. 2016). |
| RNA binding and processing proteins | Hfq | Ring-shaped RNA chaperone, involved in gene silencing where it stabilizes sRNA–mRNA duplexes (Katsuya-Gaviria et al. 2022). Hfq can stably bind Rho and trigger antitermination in vitro and in E. coli cells with a model system (Rabhi et al. 2011a). Interaction with RNA is required for antitermination. Physiological targets of Hfq-dependent antitermination are unidentified but may include the general stress regulator rpoS gene (Sedlyarova et al. 2016). |
| CsrA | Regulates RDTT in the 5′UTR of the pgaABCD operon of E. coli by preventing formation of a hairpin-like structure blocking the Rut site (Figueroa-Bossi et al. 2014). | |
| CspA | Major cold shock protein. Regulates RDTT-dependent expression of cold shock proteins (Fig. 5; Delaleau et al. 2024). | |
| RNase E | Major component of RNA degradosome. Rho associates with RNase E in Rhodobacter capsulatus (Jager et al. 2001, 2004) and under specific growth conditions in E. coli (Tuckerman et al. 2011). | |
| YgjH | Putative tRNA binding protein. Reduces RDTT in in vivo reporter screen based on sgrS terminator (Morita et al. 2022). | |
| DNA-binding proteins | H-NS | Filament-forming NAP. Binds A/T-rich DNA and works synergistically with Rho to silence specific loci, including xenogeneic regions of E. coli and Salmonella genomes (Peters et al. 2012; Bossi et al. 2019). |
| UvrABD complex | Involved in SOS-mediated transcription antitermination during TCR, possibly because of overlapping, mutually exclusive Rho/NusG and UvrABD binding sites on RNAP (Martinez et al. 2022). | |
| Direct, endogenous Rho inhibitors | Rof (YaeO) | Direct Rho interactor and inhibitor (Pichoff et al. 1998). Protects E. coli from oxidative stress (Kawamura et al. 2005) and is required for virulence gene expression and host cell invasion in Salmonella (Zhang et al. 2024). Cryo-EM structures of Rof–Rho complexes show Rof molecules bound at Rho protomer interfaces where they partly occlude the PBS and lock Rho in an inactive, open-ring conformation (Said et al. 2024; Zhang et al. 2024). YaeO from V. cholerae may operate by a distinct mechanism disrupting the oligomeric state of V. cholerae Rho (Pal et al. 2019). |
| YihE | Stress response kinase. Direct Rho interactor and antagonist in the cell envelope stress response (Wang et al. 2022). | |
| Phage proteins | λN | Allows expression of phage λ early genes. Intrinsically unstructured (Krupp et al. 2019). Constituent of λ antitermination complex (Santangelo and Artsimovitch 2011; Wang and Artsimovitch 2020). Invades RNAP hybrid channel in cryo-EM structure of the antitermination complex (Krupp et al. 2019). |
| Qλ, Q21, Q82 | Allow expression of phage λ late genes. Qλ, Q21, and Q82 are functional (but not sequence) antitermination homologs from lambdoid phages. Q protein loads onto promoter-proximal, σ-dependent paused TEC using a Q-binding element (aka qut) in the DNA template (Roberts et al. 2008). Loaded Q extends and narrows the RNA exit channel of RNAP, making it highly processive and less prone to pausing or termination (Shi et al. 2019; Yin et al. 2019, 2022). Qλ is a proven polarity suppressor (Forbes and Herskowitz 1982). NusA stabilizes Qλ and Q82 antitermination complexes and helps protect the Q82 complex against Rho in vitro (Yang and Roberts 1989; Shankar et al. 2007). | |
| Psu | Bacteriophage P4 capsid decorating protein. Binds and inactivates Rho (Linderoth et al. 1997) as a dimer (Ranjan et al. 2013; Gjorgjevikj et al. 2025). Rho's ATPase activity is affected, while its RNA binding capacity is not (Pani et al. 2006). Recent cryo-EM structures of the Psu–Rho complex supports that Psu constrains the Rho ring into an open, inactive conformation allowing its hyper-oligomerization (Gjorgjevikj et al. 2025). | |
| Putative Rho interactors detected by mass spectrometry (Butland et al. 2005) | Hda | AAA + ATPase. Inhibits reinitiation of DNA replication. Effect on RDTT is unknown. |
| ClpA | AAA + ATPase. Component of the ClpAP and ClpAXP protease complexes. Effect on RDTT is unknown. | |
| ClpP | Serine protease. Component of ClpAP, ClpAPX, and ClpXP protease complexes. Effect on RDTT is unknown. | |
| SspB | ClpXP protease specificity-enhancing factor. Effect on RDTT is unknown. | |
| CspC | Cold shock protein. Promotes transcriptional readthrough at the sgrS locus, which is regulated by Rho inhibitors Rof and bicyclomycin (Morita et al. 2022) and contains a candidate Rut site (Delaleau et al. 2022). Effect of CspC on RDTT has not been investigated. | |
| CspD | Cold shock protein. Promotes transcriptional readthrough at the sgrS locus, which is regulated by Rho inhibitors Rof and bicyclomycin (Morita et al. 2022) and contains a candidate Rut site (Delaleau et al. 2022). Effect of CspD on RDTT has not been investigated. | |
| CspE | Cold shock protein. Effect on RDTT is unknown. | |
| DnaJ | Cochaperone of Hsp70 chaperone; binds σ32 factor. Effect on RDTT is unknown. | |
| DxS | 1-Deoxy-d-xylulose-5-phosphate synthase. Effect on RDTT is unknown. | |
| FabI | Enoyl-[acyl-carrier-protein] reductase. Effect on RDTT is unknown. | |
| FtsA | Essential cell division protein. Overexpression of Rho inhibitor protein Rof suppresses temperature-sensitive mutations in ftsA (Pichoff et al. 1998). Effect on RDTT is unknown. | |
| GcpE | (E)-4-hydroxy-3-methylbut-2-enyl-diphosphate synthase. Effect on RDTT is unknown. | |
| GyrA | DNA gyrase subunit A. Effect on RDTT is unknown. | |
| LpxD | UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase. Effect on RDTT is unknown. | |
| MalT | DNA-binding transcriptional activator. Effect on RDTT is unknown. | |
| MreB | Cytoskeletal protein. Effect on RDTT is unknown. | |
| PlsB | Glycerol-3-phosphate 1-O-acyltransferase. Effect on RDTT is unknown. | |
| PrsA | Ribose-phosphate diphosphokinase. Effect on RDTT is unknown. | |
| PyrH | UMP kinase. Effect on RDTT is unknown. | |
| GsP | Glutathionylspermidine amidase/synthetase. Effect on RDTT is unknown. | |
| MenF | Isochorismate synthase. Effect on RDTT is unknown. | |
| Tu | Translation elongation factor. Regulates its own expression in Salmonella by an attenuation-by-RDTT mechanism (Brandis et al. 2016). Effect on RDTT is otherwise unknown. | |
| YhbY | Ribosome assembly factor. Effect on RDTT is unknown. | |
| RnpA | RNase P subunit. Effect on RDTT is unknown. | |
| RuvB | Holliday junction branch migration protein. Effect on RDTT is unknown. | |
| SecA | Protein translocation ATPase. Effect on RDTT is unknown. | |
| SelB | Specialized translation factor. Effect on RDTT is unknown. |
