The role of E. coli Nus-factors in transcription regulation and transcription:translation coupling: From structure to mechanism

Structural basis of RfaH-mediated transcription-translation coupling

The NusG paralog RfaH mediates bacterial transcription-translation coupling in genes that contain a DNA sequence element, termed an ops site, required for pausing RNA polymerase (RNAP) and for loading RfaH onto the paused RNAP. Here, we report cryo-electron microscopy structures of transcription-translation complexes (TTCs) containing Escherichia coli RfaH. The results show that RfaH bridges RNAP and the ribosome, with the RfaH N-terminal domain interacting with RNAP and the RfaH C-terminal domain interacting with the ribosome. The results show that the distribution of translational and orientational positions of RNAP relative to the ribosome in RfaH-coupled TTCs is more restricted than in NusG-coupled TTCs because of the more restricted flexibility of the RfaH interdomain linker. The results further suggest that the structural organization of RfaH-coupled TTCs in the 'loading state', in which RNAP and RfaH are located at the ops site during formation of the TTC, is the same as the structural organization of RfaH-coupled TTCs in the 'loaded state', in which RNAP and RfaH are located at positions downstream of the ops site during function of the TTC. The results define the structural organization of RfaH-containing TTCs and set the stage for analysis of functions of RfaH during translation initiation and transcription-translation coupling.

Discovery of Inhibitors Targeting Protein-Protein Interaction between Bacterial RNA Polymerase and NusG as Novel Antimicrobials

Bacterial RNA polymerase (RNAP), the core enzyme responsible for bacterial transcription, requires the NusG factor for efficient transcription elongation and termination. As the primary binding site for NusG, the RNAP clamp-helix (CH) domain represents a potential protein-protein interaction (PPI) target for novel antimicrobial agent design and discovery. In this study, we designed a pharmacophore model based on the essential amino acids of the CH for binding to NusG, such as R270, R278, and R281 (Escherichia coli numbering), and identified a hit compound with mild antimicrobial activity. Subsequent rational design and synthesis of this hit compound led to improved antimicrobial activity against Streptococcus pneumoniae, with the minimum inhibitory concentration (MIC) reduced from 128 to 1 μg/mL. Additional characterization of the antimicrobial activity, inhibitory activity against RNAP-NusG interaction, and cell-based transcription and fluorescent assays of the optimized compounds demonstrated their potential for further lead optimization.

Allosteric couplings upon binding of RfaH to transcription elongation complexes

In every domain of life, NusG-like proteins bind to the elongating RNA polymerase (RNAP) to support processive RNA synthesis and to couple transcription to ongoing cellular processes. Structures of factor-bound transcription elongation complexes (TECs) reveal similar contacts to RNAP, consistent with a shared mechanism of action. However, NusG homologs differ in their regulatory roles, modes of recruitment, and effects on RNA synthesis. Some of these differences could be due to conformational changes in RNAP and NusG-like proteins, which cannot be captured in static structures. Here, we employed hydrogen-deuterium exchange mass spectrometry to investigate changes in local and non-local structural dynamics of Escherichia coli NusG and its paralog RfaH, which have opposite effects on expression of xenogenes, upon binding to TEC. We found that NusG and RfaH regions that bind RNAP became solvent-protected in factor-bound TECs, whereas RNAP regions that interact with both factors showed opposite deuterium uptake changes when bound to NusG or RfaH. Additional changes far from the factor-binding site were observed only with RfaH. Our results provide insights into differences in structural dynamics exerted by NusG and RfaH during binding to TEC, which may explain their different functional outcomes and allosteric regulation of transcriptional pausing by RfaH.

RNA Polymerase's Relationship with the Ribosome: Not So Physical, Most of the Time

In bacteria, the rates of transcription elongation and translation elongation are coordinated, changing together in response to growth conditions. It has been proposed that this is due to physical coupling of RNA polymerase and the lead ribosome on nascent mRNA, an interaction important for preventing premature transcription termination by Rho factor. Recent studies challenge this view and provide evidence that coordination is indirect, mediated in Escherichia coli by the alarmone (p)ppGpp. Here, we discuss these new findings and how they shape our understanding of the functional relationship between RNA polymerase and the ribosome as well as the basis of transcriptional polarity.

Measures of single- versus multiple-round translation argue against a mechanism to ensure coupling of transcription and translation

In prokaryotes, the synthesis of RNA and protein occurs simultaneously in the cytoplasm. A number of studies indicate that translation can strongly impact transcription, a phenomenon often attributed to physical coupling between RNA polymerase (RNAP) and the lead ribosome on the nascent mRNA. Whether there generally exists a mechanism to ensure or promote RNAP-ribosome coupling remains unclear. Here, we used an efficient hammerhead ribozyme and developed a reporter system to measure single- versus multiple-round translation in Escherichia coli Six pairs of cotranscribed and differentially translated genes were analyzed. For five of them, the stoichiometry of the two protein products came no closer to unity (1:1) when the rounds of translation were severely reduced in wild-type cells. Introduction of mutation rpoB(I572N), which slows RNAP elongation, could promote coupling, as indicated by stoichiometric SspA and SspB products in the single-round assay. These data are consistent with models of stochastic coupling in which the probability of coupling depends on the relative rates of transcription and translation and suggest that RNAP often transcribes without a linked ribosome.

NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble

Universally conserved factors from NusG family bind at the upstream fork junction of transcription elongation complexes and modulate RNA synthesis in response to translation, processing, and folding of the nascent RNA. Escherichia coli NusG enhances transcription elongation in vitro by a poorly understood mechanism. Here we report that E. coli NusG slows Gre factor-stimulated cleavage of the nascent RNA, but does not measurably change the rates of single nucleotide addition and translocation by a non-paused RNA polymerase. We demonstrate that NusG slows RNA cleavage by inhibiting backtracking. This activity is abolished by mismatches in the upstream DNA and is independent of the gate and rudder loops, but is partially dependent on the lid loop. Our comprehensive mapping of the upstream fork junction by base analogue fluorescence and nucleic acids crosslinking suggests that NusG inhibits backtracking by stabilizing the minimal transcription bubble.

DOI:http://dx.doi.org/10.7554/eLife.18096.001

Cells decode genes in two steps. First, they synthesize a molecule similar to DNA, called RNA, which is a complementary copy of the gene. This process, known as transcription, creates an intermediate RNA molecule that is turned into protein in the second step. RNA polymerase is an enzyme that carries out transcription; it separates the two strands of the DNA helix so that the RNA can be synthesized from the DNA template. By opening up the DNA downstream of where active copying is taking place, and re-annealing it upstream, RNA polymerase maintains a structure called a "transcription bubble". RNA polymerases do not copy continuously but oscillate back and forth along the DNA. Sometimes larger backwards oscillations, known as backtracking, temporarily block the production of the RNA molecule and slow down the transcription process.

A protein called NusG helps to couple transcription to the other related processes that happen at the same time. One end of the protein, the N-terminal domain, anchors it to RNA polymerase and stimulates transcription elongation. The other end, the C-terminal domain, interacts with other proteins involved in the related processes and can positively or negatively control transcription elongation. Nevertheless it was poorly understood how NusG carries out these roles.

Turtola and Belogurov investigated how NusG from the bacterium Escherichia coli affects the individual steps of transcription elongation. A simple experimental system was used, consisting of short pieces of DNA and RNA, an RNA polymerase and NusG. A transcription bubble resembles an opening in a zipper with two sliders; and rather than affecting the synthesis of RNA, NusG affected the part that corresponds to the “slider” located at the rear edge of the bubble. NusG helped this slider-like element to bring the DNA strands at this edge of the bubble back together and modified it so that it behaved as a ratchet that inhibited RNA polymerase from backtracking. This did not affect the smaller backwards and forwards oscillations of RNA polymerase.

Turtola and Belogurov suggest that these newly discovered effects play a key role in regulating transcription; NusG’s N-terminal domain makes the RNA polymerase more efficient, whilst the C-terminal domain makes it amenable to control by other proteins. Future studies will investigate whether these effects are seen in more complex experimental systems, which include proteins that interact with NusG.

DOI:http://dx.doi.org/10.7554/eLife.18096.002

Nascent RNA length dictates opposing effects of NusA on antitermination

The NusA protein is a universally conserved bacterial transcription elongation factor that binds RNA polymerase (RNAP). When functioning independently, NusA enhances intrinsic termination. Paradoxically, NusA stimulates the function of the N and Q antiterminator proteins of bacteriophage λ. The mechanistic basis for NusA's functional plasticity is poorly understood. Here we uncover an effect of nascent RNA length on the ability of NusA to collaborate with Q. Ordinarily, Q engages RNAP during early elongation when it is paused at a specific site just downstream of the phage late-gene promoter. NusA facilitates this engagement process and both proteins remain associated with the transcription elongation complex (TEC) as it escapes the pause and transcribes the late genes. We show that the λ-related phage 82 Q protein (82Q) can also engage RNAP that is paused at a promoter-distal position and thus contains a nascent RNA longer than that associated with the natively positioned TEC. However, the effect of NusA in this context is antagonistic rather than stimulatory. Moreover, cleaving the long RNA associated with the promoter-distal TEC restores NusA's stimulatory effect. Our findings reveal a critical role for nascent RNA in modulating NusA's effect on 82Q-mediated antitermination, with implications for understanding NusA's functional plasticity.

Quantitative and predictive model of kinetic regulation by E. coli TPP riboswitches

Riboswitches are non-coding elements upstream or downstream of mRNAs that, upon binding of a specific ligand, regulate transcription and/or translation initiation in bacteria, or alternative splicing in plants and fungi. We have studied thiamine pyrophosphate (TPP) riboswitches regulating translation of thiM operon and transcription and translation of thiC operon in E. coli, and that of THIC in the plant A. thaliana. For all, we ascertained an induced-fit mechanism involving initial binding of the TPP followed by a conformational change leading to a higher-affinity complex. The experimental values obtained for all kinetic and thermodynamic parameters of TPP binding imply that the regulation by A. thaliana riboswitch is governed by mass-action law, whereas it is of kinetic nature for the two bacterial riboswitches. Kinetic regulation requires that the RNA polymerase pauses after synthesis of each riboswitch aptamer to leave time for TPP binding, but only when its concentration is sufficient. A quantitative model of regulation highlighted how the pausing time has to be linked to the kinetic rates of initial TPP binding to obtain an ON/OFF switch in the correct concentration range of TPP. We verified the existence of these pauses and the model prediction on their duration. Our analysis also led to quantitative estimates of the respective efficiency of kinetic and thermodynamic regulations, which shows that kinetically regulated riboswitches react more sharply to concentration variation of their ligand than thermodynamically regulated riboswitches. This rationalizes the interest of kinetic regulation and confirms empirical observations that were obtained by numerical simulations.

Effects of cooperation between translating ribosome and RNA polymerase on termination efficiency of the Rho-independent terminator

An experimental system was designed to measure in vivo termination efficiency (TE) of the Rho-independent terminator and position–function relations were quantified for the terminator tR2 in Escherichia coli. The terminator function was almost completely repressed when tR2 was located several base pairs downstream from the gene, and TE gradually increased to maximum values with the increasing distance between the gene and terminator. This TE–distance relation reflected a stochastic coupling of the ribosome and RNA polymerase (RNAP). Terminators located in the first 100 bp of the coding region can function efficiently. However, functional repression was observed when the terminator was located in the latter part of the coding region, and the degree of repression was determined by transcriptional and translational dynamics. These results may help to elucidate mechanisms of Rho-independent termination and reveal genomic locations of terminators and functions of the sequence that precedes terminators. These observations may have important applications in synthetic biology.

Sm-like protein Hfq: Composition of the native complex, modifications, and interactions

The bacterial Sm-like protein Hfq has been linked functionally to reactions that involve RNA; however, its explicit role and primary cellular localization remain elusive. We carried out a detailed biochemical characterization of native Escherichia coli Hfq obtained through methods that preserve its posttranslational modifications. ESI-MS analyses indicate modifications in 2-3 subunits/hexamer with a molecular mass matching that of an oxidized C:18 lipid. We show that the majority of cellular Hfq cannot be extracted without detergents and that purified Hfq can be retained on hydrophobic matrices. Analyses of purified Hfq and the native Hfq complexes observed in whole-cell E. coli extracts indicate the existence of dodecameric assemblies likely stabilized by interlocking C-terminal polypeptides originating from separate Hfq hexamers and/or accessory nucleic acid. We demonstrate that cellular Hfq is redistributed between transcription complexes and an insoluble fraction that includes protein complexes harboring polynucleotide phosphorylase (PNP). This distribution pattern is consistent with a function at the interface of the apparatuses responsible for synthesis and degradation of RNA. Taken together with the results of prior studies, these results suggest that Hfq could function as an anchor/coupling factor responsible for de-solubilization of RNA and its tethering to the degradosome complex.

Ubiquitous transcription factors display structural plasticity and diverse functions: NusG proteins - Shifting shapes and paradigms

Numerous accessory factors modulate RNA polymerase response to regulatory signals and cellular cues and establish communications with co-transcriptional RNA processing. Transcription regulators are astonishingly diverse, with similar mechanisms arising via convergent evolution. NusG/Spt5 elongation factors comprise the only universally conserved and ancient family of regulators. They bind to the conserved clamp helices domain of RNA polymerase, which also interacts with non-homologous initiation factors in all domains of life, and reach across the DNA channel to form processivity clamps that enable uninterrupted RNA chain synthesis. In addition to this ubiquitous function, NusG homologs exert diverse, and sometimes opposite, effects on gene expression by competing with each other and other regulators for binding to the clamp helices and by recruiting auxiliary factors that facilitate termination, antitermination, splicing, translation, etc. This surprisingly diverse range of activities and the underlying unprecedented structural changes make studies of these "transformer" proteins both challenging and rewarding.

Redundancy of primary RNA-binding functions of the bacterial transcription terminator Rho

The bacterial transcription terminator, Rho, terminates transcription at half of the operons. According to the classical model derived from in vitro assays on a few terminators, Rho is recruited to the transcription elongation complex (EC) by recognizing specific sites (rut) on the nascent RNA. Here, we explored the mode of in vivo recruitment process of Rho. We show that sequence specific recognition of the rut site, in majority of the Rho-dependent terminators, can be compromised to a great extent without seriously affecting the genome-wide termination function as well as the viability of Escherichia coli. These terminators function optimally only through a NusG-assisted recruitment and activation of Rho. Our data also indicate that at these terminators, Rho-EC-bound NusG interaction facilitates the isomerization of Rho into a translocase-competent form by stabilizing the interactions of mRNA with the secondary RNA binding site, thereby overcoming the defects of the primary RNA binding functions.

Spatially segregated transcription and translation in cells of the endomembrane-containing bacterium Gemmata obscuriglobus

The dogma of coupled transcription and translation in bacteria has been challenged by recent reports of spatial segregation of these processes within the relatively simple cellular organization of the model organisms Escherichia coli and Bacillus subtilis. The bacterial species Gemmata obscuriglobus possesses an extensive endomembrane system. The membranes generate a very convoluted intracellular architecture in which some of the cell's ribosomes appear to have less direct access to the cell's nucleoid(s) than others. This observation prompted us to test the hypothesis that a substantial proportion of G. obscuriglobus translation may be spatially segregated from transcription. Using immunofluorescence and immunoelectron microscopy, we showed that translating ribosomes are localized throughout the cell, with a quantitatively greater proportion found in regions distal to nucleoid(s). Our results extend information about the phylogenetic and morphological diversity of bacteria in which the spatial organization of transcription and translation has been studied. These findings also suggest that endomembranes may provide an obstacle to colocated transcription and translation, a role for endomembranes that has not been reported previously for a prokaryotic organism. Our studies of G. obscuriglobus may provide a useful background for consideration of the evolutionary development of eukaryotic cellular complexity and how it led to decoupled processes of gene expression in eukaryotes.

Spatial organization of transcription in bacterial cells

Prokaryotic transcription has been extensively studied over the past half a century. However, there often exists a gap between the structural, mechanistic description of transcription obtained from in vitro biochemical studies, and the cellular, phenomenological observations from in vivo genetic studies. It is now accepted that a living bacterial cell is a complex entity; the heterogeneous cellular environment is drastically different from the homogenous, well-mixed situation in vitro. Where molecules are inside a cell may be important for their function; hence, the spatial organization of different molecular components may provide a new means of transcription regulation in vivo, possibly bridging this gap. In this review, we survey current evidence for the spatial organization of four major components of transcription [genes, transcription factors, RNA polymerase (RNAP) and RNAs] and critically analyze their biological significance.

Escherichia coli transcription termination factor NusA: heat-induced oligomerization and chaperone activity

Escherichia coli NusA, an essential component of the RNA polymerase elongation complex, is involved in transcriptional elongation, termination, anti-termination, cold shock and stress-induced mutagenesis. In this study, we demonstrated that NusA can self-assemble into oligomers under heat shock conditions and that this property is largely determined by the C-terminal domain. In parallel with the self-assembly process, NusA also acquires chaperone activity. Furthermore, NusA overexpression results in the enhanced heat shock resistance of host cells, which may be due to the chaperone activity of NusA. Our results suggest that E. coli NusA can act as a protector to prevent protein aggregation under heat stress conditions in vitro and in the NusA-overexpressing strain. We propose a new hypothesis that NusA could serve as a molecular chaperone in addition to its functions as a transcription factor. However, it remains to be further investigated whether NusA has the same function under normal physiological conditions.

RNA polymerase and the ribosome: the close relationship

In bacteria transcription and translation are linked in time and space. When coupled to RNA polymerase (RNAP), the translating ribosome ensures transcriptional processivity by preventing RNAP backtracking. Recent advances in the field have characterized important linker proteins that bridge the gap between transcription and translation: In particular, the NusE(S10):NusG complex and the NusG homolog, RfaH. The direct link between the moving ribosome and RNAP provides a basis for maintaining genomic integrity while enabling efficient transcription and timely translation of various genes within the bacterial cell.

Transcription start site associated RNAs in bacteria

A new class of small RNA (~45 bases long) is identified in gram positive and negative bacteria. These tssRNAs are associated with RNA polymerase pausing some 45 bases downstream of the transcription start site and show global changes in expression during the growth cycle.

A new class of bacterial small RNAs have been identified. They are related to eukaryotic tiRNAs in their localization (transcription start sites, TSS) but not in their biogenesis.

tssRNAs are generated at the same positions as long transcripts, as well as at independent positions, but both seem to have promoter-like characteristics (Pribnow box).

We provide compelling evidence that tssRNAs are not mRNA degradation products and neither abortive transcripts; rather, they are newly synthesized transcripts and require more factors than the basal transcription machinery (i.e., RNA polymerase subunits)

tssRNAs show dynamic behavior dependent on the growth phase.

We show that RNA polymerase is halted at tssRNAs positions, both in bona fide genes and in positions where no long transcript is produced. This indicates that tssRNAs could be generated by RNA polymerase pausing to ensure that no spurious long RNA is generated by random appearance of Pribnow sequences in the genome.

Here, we report the genome-wide identification of small RNAs associated with transcription start sites (TSSs), termed tssRNAs, in Mycoplasma pneumoniae. tssRNAs were also found to be present in a different bacterial phyla, Escherichia coli. Similar to the recently identified promoter-associated tiny RNAs (tiRNAs) in eukaryotes, tssRNAs are associated with active promoters. Evidence suggests that these tssRNAs are distinct from previously described abortive transcription RNAs. ssRNAs have an average size of 45 bases and map exactly to the beginning of cognate full-length transcripts and to cryptic TSSs. Expression of bacterial tssRNAs requires factors other than the standard RNA polymerase holoenzyme. We have found that the RNA polymerase is halted at tssRNA positions in vivo, which may indicate that a pausing mechanism exists to prevent transcription in the absence of genes. These results suggest that small RNAs associated with TSSs could be a universal feature of bacterial transcription.