Ribosome rescue: tmRNA tagging activity and capacity inEscherichia coli

Endogenous trans-translation structure visualizes the decoding of the first tmRNA alanine codon

Ribosomes stall on truncated or otherwise damaged mRNAs. Bacteria rely on ribosome rescue mechanisms to replenish the pool of ribosomes available for translation. Trans-translation, the main ribosome-rescue pathway, uses a circular hybrid transfer-messenger RNA (tmRNA) to restart translation and label the resulting peptide for degradation. Previous studies have visualized how tmRNA and its helper protein SmpB interact with the stalled ribosome to establish a new open reading frame. As tmRNA presents the first alanine codon via a non-canonical mRNA path in the ribosome, the incoming alanyl-tRNA must rearrange the tmRNA molecule to read the codon. Here, we describe cryo-EM analyses of an endogenous Escherichia coli ribosome-tmRNA complex with tRNAAla accommodated in the A site. The flexible adenosine-rich tmRNA linker, which connects the mRNA-like domain with the codon, is stabilized by the minor groove of the canonically positioned anticodon stem of tRNAAla. This ribosome complex can also accommodate a tRNA near the E (exit) site, bringing insights into the translocation and dissociation of the tRNA that decoded the defective mRNA prior to tmRNA binding. Together, these structures uncover a key step of ribosome rescue, in which the ribosome starts translating the tmRNA reading frame.

RNA-seq reveals multifaceted gene expression response to Fab production in Escherichia coli fed-batch processes with particular focus on ribosome stalling

BACKGROUND

Escherichia coli is a cost-effective expression system for production of antibody fragments like Fabs. Various yield improvement strategies have been applied, however, Fabs remain challenging to produce. This study aimed to characterize the gene expression response of commonly used E. coli strains BL21(DE3) and HMS174(DE3) to periplasmic Fab expression using RNA sequencing (RNA-seq). Two Fabs, Fabx and FTN2, fused to a post-translational translocation signal sequence, were produced in carbon-limited fed-batch cultivations.

RESULTS

Production of Fabx impeded cell growth substantially stronger than FTN2 and yields of both Fabs differed considerably. The most noticeable, common changes in Fab-producing cells suggested by our RNA-seq data concern the cell envelope. The Cpx and Psp stress responses, both connected to inner membrane integrity, were activated, presumably by recombinant protein aggregation and impairment of the Sec translocon. The data additionally suggest changes in lipopolysaccharide synthesis, adjustment of membrane permeability, and peptidoglycan maturation and remodeling. Moreover, all Fab-producing strains showed depletion of Mg2+, indicated by activation of the PhoQP two-component signal transduction system during the early stage and sulfur and phosphate starvation during the later stage of the process. Furthermore, our data revealed ribosome stalling, caused by the Fabx amino acid sequence, as a contributor to low Fabx yields. Increased Fabx yields were obtained by a site-specific amino acid exchange replacing the stalling sequence. Contrary to expectations, cell growth was not impacted by presence or removal of the stalling sequence. Considering ribosome rescue is a conserved mechanism, the substantial differences observed in gene expression between BL21(DE3) and HMS174(DE3) in response to ribosome stalling on the recombinant mRNA were surprising.

CONCLUSIONS

Through characterization of the gene expression response to Fab production under industrially relevant cultivation conditions, we identified potential cell engineering targets. Thereby, we hope to enable rational approaches to improve cell fitness and Fab yields. Furthermore, we highlight ribosome stalling caused by the amino acid sequence of the recombinant protein as a possible challenge during recombinant protein production.

trans-translation system is important for maintaining genome integrity during DNA damage in bacteria

DNA integrity in bacteria is regulated by various factors that act on the DNA. trans-translation has previously been shown to be important for the survival of Escherichia coli cells exposed to certain DNA-damaging agents. However, the mechanisms underlying this sensitivity are poorly understood. In this study, we explored the involvement of the trans-translation system in the maintenance of genome integrity using various DNA-damaging agents and mutant backgrounds. Relative viability assays showed that SsrA-defective cells were sensitive to DNA-damaging agents, such as nalidixic acid (NA), ultraviolet radiation (UV), and methyl methanesulfonate (MMS). The viability of SsrA-defective cells was rescued by deleting sulA, although the expression of SulA was not more pronounced in SsrA-defective cells than in wild-type cells. Live cell imaging using a Gam-GFP fluorescent reporter showed increased double-strand breaks (DSBs) in SsrA-defective cells during DNA damage. We also showed that the ribosome rescue function of SsrA was sufficient for DNA damage tolerance. DNA damage sensitivity can be alleviated by partial uncoupling of transcription and translation by using sub-lethal concentrations of ribosome inhibiting antibiotic (tetracycline) or by mutating the gene coding for RNase H (rnhA). Taken together, our results highlight the importance of trans-translation system in maintaining genome integrity and bacterial survival during DNA damage.

The Long Road to a Synthetic Self-Replicating Central Dogma

The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.

Prophage excision switches the primary ribosome rescue pathway and rescue-associated gene regulations in Escherichia coli

Escherichia coli has multiple pathways to release nonproductive ribosome complexes stalled at the 3' end of nonstop mRNA: tmRNA (SsrA RNA)-mediated trans-translation and stop codon-independent termination by ArfA/RF2 or ArfB (YaeJ). The arfA mRNA lacks a stop codon and its expression is repressed by trans-translation. Therefore, ArfA is considered to complement the ribosome rescue activity of trans-translation, but the physiological situations in which ArfA is expressed have not been elucidated. Here, we found that the excision of CP4-57 prophage adjacent to E. coli ssrA leads to the inactivation of tmRNA and switches the primary rescue pathway from trans-translation to ArfA/RF2. This "rescue-switching" rearranges not only the proteome landscape in E. coli but also the phenotype such as motility. Furthermore, among the proteins with significantly increased abundance in the ArfA⁺ cells, we found ZntR, whose mRNA is transcribed together as the upstream part of nonstop arfA mRNA. Repression of ZntR and reconstituted model genes depends on the translation of the downstream nonstop ORFs that trigger the trans-translation-coupled exonucleolytic degradation by polynucleotide phosphorylase (PNPase). Namely, our studies provide a novel example of trans-translation-dependent regulation and re-define the physiological roles of prophage excision.

Tag-Dependent Substrate Selection of ClpX Underlies Secondary Differentiation of Chlamydia trachomatis

Despite having a highly reduced genome, Chlamydia trachomatis undergoes a complex developmental cycle in which the bacteria differentiate between the following two functionally and morphologically distinct forms: the infectious, nonreplicative elementary body (EB) and the noninfectious, replicative reticulate body (RB). The transitions between EBs and RBs are not mediated by division events that redistribute intracellular proteins. Rather, both primary (EB to RB) and secondary (RB to EB) differentiation likely require bulk protein turnover. One system for targeted protein degradation is the trans-translation system for ribosomal rescue, where polypeptides stalled during translation are marked with an SsrA tag encoded by a hybrid tRNA-mRNA, tmRNA. ClpX recognizes the SsrA tag, leading to ClpXP-mediated degradation. We hypothesize that ClpX functions in chlamydial differentiation through targeted protein degradation. We found that mutation of a key residue (R230A) within the specific motif in ClpX associated with the recognition of SsrA-tagged substrates resulted in abrogated secondary differentiation while not reducing chlamydial replication or developmental cycle progression as measured by transcripts. Furthermore, inhibition of trans-translation through chemical and targeted genetic approaches also impeded chlamydial development. Knockdown of tmRNA and subsequent complementation with an allele mutated in the SsrA tag closely phenocopied the overexpression of ClpX_R230A, thus suggesting that ClpX recognition of SsrA-tagged substrates plays a critical function in secondary differentiation. Taken together, these data provide mechanistic insight into the requirements for transitions between chlamydial developmental forms. IMPORTANCE Chlamydia trachomatis is the leading cause of bacterial sexually transmitted infections and preventable infectious blindness. This unique organism undergoes developmental transitions between infectious, nondividing forms and noninfectious, dividing forms. Therefore, the chlamydial developmental cycle is an attractive target for Chlamydia-specific antibiotics, which would minimize effects of broad-spectrum antibiotics on the spread of antibiotic resistance in other organisms. However, the lack of knowledge about chlamydial development on a molecular level impedes the identification of specific, druggable targets. This work describes a mechanism through which both the fundamental processes of trans-translation and proteomic turnover by ClpXP contribute to chlamydial differentiation, a critical facet of chlamydial growth and survival. Given the almost universal presence of trans-translation and ClpX in eubacteria, this mechanism may be conserved in developmental cycles of other bacterial species. Additionally, this study expands the fields of trans-translation and Clp proteases by emphasizing the functional diversity of these systems throughout bacterial evolution.

Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria

Ribosome rescue pathways recycle stalled ribosomes and target problematic mRNAs and aborted proteins for degradation^1,2. In bacteria, it remains unclear how rescue pathways distinguish ribosomes stalled in the middle of a transcript from actively translating ribosomes^3-6. Here, using a genetic screen in Escherichia coli, we discovered a new rescue factor that has endonuclease activity. SmrB cleaves mRNAs upstream of stalled ribosomes, allowing the ribosome rescue factor tmRNA (which acts on truncated mRNAs³) to rescue upstream ribosomes. SmrB is recruited to ribosomes and is activated by collisions. Cryo-electron microscopy structures of collided disomes from E. coli and Bacillus subtilis show distinct and conserved arrangements of individual ribosomes and the composite SmrB-binding site. These findings reveal the underlying mechanisms by which ribosome collisions trigger ribosome rescue in bacteria.

Trans-Translation Is an Appealing Target for the Development of New Antimicrobial Compounds

Because of the ever-increasing multidrug resistance in microorganisms, it is crucial that we find and develop new antibiotics, especially molecules with different targets and mechanisms of action than those of the antibiotics in use today. Translation is a fundamental process that uses a large portion of the cell's energy, and the ribosome is already the target of more than half of the antibiotics in clinical use. However, this process is highly regulated, and its quality control machinery is actively studied as a possible target for new inhibitors. In bacteria, ribosomal stalling is a frequent event that jeopardizes bacterial wellness, and the most severe form occurs when ribosomes stall at the 3'-end of mRNA molecules devoid of a stop codon. Trans-translation is the principal and most sophisticated quality control mechanism for solving this problem, which would otherwise result in inefficient or even toxic protein synthesis. It is based on the complex made by tmRNA and SmpB, and because trans-translation is absent in eukaryotes, but necessary for bacterial fitness or survival, it is an exciting and realistic target for new antibiotics. Here, we describe the current and future prospects for developing what we hope will be a novel generation of trans-translation inhibitors.

Widespread ribosome stalling in a genome-reduced bacterium and the need for translational quality control

Trans-translation is a ubiquitous bacterial mechanism of ribosome rescue mediated by a transfer-messenger RNA (tmRNA) that adds a degradation tag to the truncated nascent polypeptide. Here, we characterize this quality control system in a genome-reduced bacterium, Mycoplasma pneumoniae (MPN), and perform a comparative analysis of protein quality control components in slow and fast-growing prokaryotes. We show in vivo that in MPN the sole quality control cytoplasmic protease (Lon) degrades efficiently tmRNA-tagged proteins. Analysis of tmRNA-mutants encoding a tag resistant to proteolysis reveals extensive tagging activity under normal growth. Unlike knockout strains, these mutants are viable demonstrating the requirement of tmRNA-mediated ribosome recycling. Chaperone and Lon steady-state levels maintain proteostasis in these mutants suggesting a model in which co-evolution of Lon and their substrates offer simple mechanisms of regulation without specialized degradation machineries. Finally, comparative analysis shows relative increase in Lon/Chaperone levels in slow-growing bacteria suggesting physiological adaptation to growth demand.

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Lon degrades efficiently tmRNA-tagged proteins in a genome-reduced bacterium

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tmRNA-tag mutants are viable and reveal extensive tagging activity in M. pneumoniae

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Co-evolution of Lon and their substrates offer simple mechanisms of regulation

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Chaperone and Lon relative levels correlate with bacterial growth rates

RNA Modifications in Pathogenic Bacteria: Impact on Host Adaptation and Virulence

RNA modifications are involved in numerous biological processes and are present in all RNA classes. These modifications can be constitutive or modulated in response to adaptive processes. RNA modifications play multiple functions since they can impact RNA base-pairings, recognition by proteins, decoding, as well as RNA structure and stability. However, their roles in stress, environmental adaptation and during infections caused by pathogenic bacteria have just started to be appreciated. With the development of modern technologies in mass spectrometry and deep sequencing, recent examples of modifications regulating host-pathogen interactions have been demonstrated. They show how RNA modifications can regulate immune responses, antibiotic resistance, expression of virulence genes, and bacterial persistence. Here, we illustrate some of these findings, and highlight the strategies used to characterize RNA modifications, and their potential for new therapeutic applications.

Ribosome Rescue Pathways in Bacteria

Ribosomes that become stalled on truncated or damaged mRNAs during protein synthesis must be rescued for the cell to survive. Bacteria have evolved a diverse array of rescue pathways to remove the stalled ribosomes from the aberrant mRNA and return them to the free pool of actively translating ribosomes. In addition, some of these pathways target the damaged mRNA and the incomplete nascent polypeptide chain for degradation. This review highlights the recent developments in our mechanistic understanding of bacterial ribosomal rescue systems, including drop-off, trans-translation mediated by transfer-messenger RNA and small protein B, ribosome rescue by the alternative rescue factors ArfA and ArfB, as well as Bacillus ribosome rescue factor A, an additional rescue system found in some Gram-positive bacteria, such as Bacillus subtilis. Finally, we discuss the recent findings of ribosome-associated quality control in particular bacterial lineages mediated by RqcH and RqcP. The importance of rescue pathways for bacterial survival suggests they may represent novel targets for the development of new antimicrobial agents against multi-drug resistant pathogenic bacteria.

A stalled-ribosome rescue factor Pth3 is required for mitochondrial translation against antibiotics in Saccharomyces cerevisiae

Mitochondrial translation appears to involve two stalled-ribosome rescue factors (srRFs). One srRF is an ICT1 protein from humans that rescues a "non-stop" type of mitochondrial ribosomes (mitoribosomes) stalled on mRNA lacking a stop codon, while the other, C12orf65, reportedly has functions that overlap with those of ICT1; however, its primary role remains unclear. We herein demonstrated that the Saccharomyces cerevisiae homolog of C12orf65, Pth3 (Rso55), preferentially rescued antibiotic-dependent stalled mitoribosomes, which appear to represent a "no-go" type of ribosomes stalled on intact mRNA. On media containing a non-fermentable carbon source, which requires mitochondrial gene expression, respiratory growth was impaired significantly more by the deletion of PTH3 than that of the ICT1 homolog PTH4 in the presence of antibiotics that inhibit mitochondrial translation, such as tetracyclines and macrolides. Additionally, the in organello labeling of mitochondrial translation products and quantification of mRNA levels by quantitative RT-PCR suggested that in the presence of tetracycline, the deletion of PTH3, but not PTH4, reduced the protein expression of all eight mtDNA-encoded genes at the post-transcriptional or translational level. These results indicate that Pth3 can function as a mitochondrial srRF specific for ribosomes stalled by antibiotics and plays a role in antibiotic resistance in fungi.

Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria

Biochemical studies suggested that the antimicrobial peptide apidaecin (Api) inhibits protein synthesis by binding in the nascent peptide exit tunnel and trapping the release factor associated with a terminating ribosome. The mode of Api action in bacterial cells had remained unknown. Here genome-wide analysis reveals that in bacteria, Api arrests translating ribosomes at stop codons and causes pronounced queuing of the trailing ribosomes. By sequestering the available release factors, Api promotes pervasive stop codon bypass, leading to the expression of proteins with C-terminal extensions. Api-mediated translation arrest leads to the futile activation of the ribosome rescue systems. Understanding the unique mechanism of Api action in living cells may facilitate the development of new medicines and research tools for genome exploration.

The ClpX and ClpP2 Orthologs of Chlamydia trachomatis Perform Discrete and Essential Functions in Organism Growth and Development

Chlamydia trachomatis is the leading cause of infectious blindness globally and the most reported bacterial sexually transmitted infection both domestically and internationally. Given the economic burden, the lack of an approved vaccine, and the use of broad-spectrum antibiotics for treatment of infections, an understanding of chlamydial growth and development is critical for the advancement of novel targeted antibiotics. The Clp proteins comprise an important and conserved protease system in bacteria. Our work highlights the importance of the chlamydial Clp proteins to this clinically important bacterium. Additionally, our study implicates the Clp system playing an integral role in chlamydial developmental cycle progression, which may help establish models of how Chlamydia spp. and other bacteria progress through their respective developmental cycles. Our work also contributes to a growing body of Clp-specific research that underscores the importance and versatility of this system throughout bacterial evolution and further validates Clp proteins as drug targets.

Chlamydia trachomatis is an obligate intracellular bacterium that undergoes a complex developmental cycle in which the bacterium differentiates between two functionally and morphologically distinct forms, the elementary body (EB) and reticulate body (RB), each of which expresses its own specialized repertoire of proteins. Both primary (EB to RB) and secondary (RB to EB) differentiations require protein turnover, and we hypothesize that proteases are critical for mediating differentiation. The Clp protease system is well conserved in bacteria and important for protein turnover. Minimally, the system relies on a serine protease subunit, ClpP, and an AAA+ ATPase, such as ClpX, that recognizes and unfolds substrates for ClpP degradation. In Chlamydia, ClpX is encoded within an operon 3′ to clpP2. We present evidence that the chlamydial ClpX and ClpP2 orthologs are essential to organism viability and development. We demonstrate here that chlamydial ClpX is a functional ATPase and forms the expected homohexamer in vitro. Overexpression of a ClpX mutant lacking ATPase activity had a limited impact on DNA replication or secondary differentiation but, nonetheless, reduced EB viability with observable defects in EB morphology noted. Conversely, overexpression of a catalytically inactive ClpP2 mutant significantly impacted developmental cycle progression by reducing the overall number of organisms. Blocking clpP2X transcription using CRISPR interference led to a decrease in bacterial growth, and this effect was complemented in trans by a plasmid copy of clpP2. Taken together, our data indicate that ClpX and the associated ClpP2 serve distinct functions in chlamydial developmental cycle progression and differentiation.

Mycobacterium tuberculosis ribosomal protein S1 (RpsA) and variants with truncated C-terminal end show absence of interaction with pyrazinoic acid

Pyrazinamide (PZA) is an antibiotic used in first- and second-line tuberculosis treatment regimens. Approximately 50% of multidrug-resistant tuberculosis and over 90% of extensively drug-resistant tuberculosis strains are also PZA resistant. Despite the key role played by PZA, its mechanisms of action are not yet fully understood. It has been postulated that pyrazinoic acid (POA), the hydrolyzed product of PZA, could inhibit trans-translation by binding to Ribosomal protein S1 (RpsA) and competing with tmRNA, the natural cofactor of RpsA. Subsequent data, however, indicate that these early findings resulted from experimental artifact. Hence, in this study we assess the capacity of POA to compete with tmRNA for RpsA. We evaluated RpsA wild type (WT), RpsA ∆A438, and RpsA ∆A438 variants with truncations towards the carboxy terminal end. Interactions were measured using Nuclear Magnetic Resonance spectroscopy (NMR), Isothermal Titration Calorimetry (ITC), Microscale Thermophoresis (MST), and Electrophoretic Mobility Shift Assay (EMSA). We found no measurable binding between POA and RpsA (WT or variants). This suggests that RpsA may not be involved in the mechanism of action of PZA in Mycobacterium tuberculosis, as previously thought. Interactions observed between tmRNA and RpsA WT, RpsA ∆A438, and each of the truncated variants of RpsA ∆A438, are reported.

An overview of the bacterial SsrA system modulating intracellular protein levels and activities

In bacteria, the truncated forms of mRNAs, which usually lack a stop codon, are occasionally generated by premature termination of gene transcription and/or endo- or exonucleolytic cleavage events. Ribosomes proceeding on these molecules stall at the 3' end of the chain and are rescued by a widely distributed mechanism known as trans-translation, which includes two essential elements, ssrA RNA (a special RNA) and SmpB (a small protein). Through this mechanism, the polypeptides translated from truncated mRNAs are marked by a short peptide, known as SsrA tag, at their C-termini and directed to the specific endogenous proteases for C-terminal proteolysis. Based on the deep understanding of the SsrA tagging and degradation mechanisms, recently a series of SsrA-based genetic tools have been developed for gene regulation on the level of post-translation. They are successfully applied for controllable regulation of biological circuits in bacteria. In the present article, we systematically summarize the history, structural characteristics, and functional mechanisms of the SsrA tagging and degrading machineries, as well as their technical uses and limitations.Key Points• SsrA system plays an important role in ribosome rescue in bacteria.• SsrA-based genetic tools are useful for controlling protein levels and activities.

Large-scale identification of trans-translation substrates targeted by tmRNA in Aeromonas veronii

Transfer-messenger RNA (tmRNA) is ubiquitous in bacteria, acting as the core component for the trans-translation system that contributes to label the aberrantly synthesized peptides for degradation and to release the stalled ribosomes. Deletion of tmRNA causes a variety of phenotypes related to important physiological processes in bacteria. To illustrate the molecular mechanism of the versatility of tmRNA in aquatic pathogen Aeromonas veronii, we mutated the C-terminal nucleotides of tmRNA (MutmRNA) for encoding a tag containing six histidine residues (His₆tag), so as to capture and enrich the trans-translation substrates from the cell lysates through a Ni²⁺-NTA affinity chromatograph. The results showed that the concentrated substrates were detected as distinct and specific bands in western blotting using anti-His antibody, demonstrating that specific defective mRNAs were frequently and intensively rescued by trans-translation during the translation process in A. veronii. The substrates were analyzed by LC-MS/MS and further identified by searching a theoretically constructed database specific for A. veronii. Total of 24 potential substrates were identified, with various functions involved in metabolism, as well as structure and signal-based cellular events. Among the identified substrates, PspA and AsmA were labeled by Flag, and expressed in the presence of the modified trans-translation system in E. coli. Their labelings with MutmRNA were validated by purification through Ni²⁺-NTA column followed by western blotting using anti-Flag antibody. This study provided the most abundant set of endogenous targets for tmRNA in A. veronii, and facilitated further investigations about the molecular mechanism and signal pathway of tmRNA-mediated trans-translation.

Aggregation of CAT tails blocks their degradation and causes proteotoxicity in S. cerevisiae

The Ribosome-associated Quality Control (RQC) pathway co-translationally marks incomplete polypeptides from stalled translation with two signals that trigger their proteasome-mediated degradation. The E3 ligase Ltn1 adds ubiquitin and Rqc2 directs the large ribosomal subunit to append carboxy-terminal alanine and threonine residues (CAT tails). When excessive amounts of incomplete polypeptides evade Ltn1, CAT-tailed proteins accumulate and can self-associate into aggregates. CAT tail aggregation has been hypothesized to either protect cells by sequestering potentially toxic incomplete polypeptides or harm cells by disrupting protein homeostasis. To distinguish between these possibilities, we modulated CAT tail aggregation in Saccharomyces cerevisiae with genetic and chemical tools to analyze CAT tails in aggregated and un-aggregated states. We found that enhancing CAT tail aggregation induces proteotoxic stress and antagonizes degradation of CAT-tailed proteins, while inhibiting aggregation reverses these effects. Our findings suggest that CAT tail aggregation harms RQC-compromised cells and that preventing aggregation can mitigate this toxicity.

Alkylative damage of mRNA leads to ribosome stalling and rescue by trans translation in bacteria

Similar to DNA replication, translation of the genetic code by the ribosome is hypothesized to be exceptionally sensitive to small chemical changes to its template mRNA. Here we show that the addition of common alkylating agents to growing cultures of Escherichia coli leads to the accumulation of several adducts within RNA, including N(1)-methyladenosine (m¹A). As expected, the introduction of m¹A to model mRNAs was found to reduce the rate of peptide bond formation by three orders of magnitude in a well-defined in vitro system. These observations suggest that alkylative stress is likely to stall translation in vivo and necessitates the activation of ribosome-rescue pathways. Indeed, the addition of alkylation agents was found to robustly activate the transfer-messenger RNA system, even when transcription was inhibited. Our findings suggest that bacteria carefully monitor the chemical integrity of their mRNA and they evolved rescue pathways to cope with its effect on translation.

How a circularized tmRNA moves through the ribosome

During trans-translation, transfer-messenger RNA (tmRNA) and small protein B (SmpB) together rescue ribosomes stalled on a truncated mRNA and tag the nascent polypeptide for degradation. We used cryo-electron microscopy to determine the structures of three key states of the tmRNA-SmpB-ribosome complex during trans translation at resolutions of 3.7 to 4.4 angstroms. The results show how tmRNA and SmpB act specifically on stalled ribosomes and how the circularized complex moves through the ribosome, enabling translation to switch from the old defective message to the reading frame on tmRNA.

When transfer-messenger RNA scars reveal its ancient origins

In bacteria, trans-translation is the primary quality control mechanism for rescuing ribosomes arrested during translation. This key process is universally conserved and plays a crucial role in the viability and virulence of all bacteria. It is performed by transfer-messenger RNA (tmRNA) and its protein partner small protein B (SmpB). Here, we show that tmRNA is a key molecule that could have given birth to modern protein synthesis. The traces of an ancient RNA world persist in the structure of modern tmRNA, suggesting its old origins. Therefore, since it has both tRNA and mRNA functions, tmRNA could be the missing link that allowed modern genetic code to be read by the ribosome.

Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue

Organisms possessing genetic codes with unassigned codons raise the question of how cellular machinery resolves such codons and how this could impact horizontal gene transfer. Here, we use a genomically recoded Escherichia coli to examine how organisms address translation at unassigned UAG codons, which obstruct propagation of UAG-containing viruses and plasmids. Using mass spectrometry, we show that recoded organisms resolve translation at unassigned UAG codons via near-cognate suppression, dramatic frameshifting from at least −3 to +19 nucleotides, and rescue by ssrA-encoded tmRNA, ArfA, and ArfB. We then demonstrate that deleting tmRNA restores expression of UAG-ending proteins and propagation of UAG-containing viruses and plasmids in the recoded strain, indicating that tmRNA rescue and nascent peptide degradation is the cause of impaired virus and plasmid propagation. The ubiquity of tmRNA homologs suggests that genomic recoding is a promising path for impairing horizontal gene transfer and conferring genetic isolation in diverse organisms.

Usually, DNA passes from parent to offspring, vertically down the generations. But not always. In some cases, it can move directly from one organism to another by a process called horizontal gene transfer. In bacteria, this happens when DNA segments pass through a bacterium’s cell wall, which can then be picked up by another bacterium. Because the vast majority of organisms share the same genetic code, the bacteria can read this DNA with ease, as it is in the same biological language.

Horizontal gene transfer helps bacteria adapt and evolve to their surroundings, letting them swap and share genetic information that could be useful. The process also poses a threat to human health because the DNA that bacteria share can help spread antibiotic resistance. However, some organisms use an alternative genetic code, which obstructs horizontal gene transfer. They cannot read the DNA transmitted to them, because it is in a different ‘biological language’. The mechanism of how this language barrier works has been poorly understood until now.

Ma, Hemez, Barber et al. investigated this using Escherichia coli bacteria with an artificially alternated genetic code. In this E. coli, one of the three-letter DNA ‘words’ in the sequence is a blank – it does not exist in the bacterium’s biological language. This three-letter DNA word normally corresponds to a particular protein building block. Using a technique called mass spectrometry, Ma et al. analyzed the proteins this E. coli forms. The results showed that it has several strategies to deal with DNA transmitted horizontally into the bacterium. One method is destroying the proteins that are half-created from the DNA, using molecules called tmRNAs. These are part of a rescue system that intervenes when protein translation stalls on the blank word. The tmRNAs help to add a tag to half-formed proteins, marking them for destruction.

This mechanism creates a ‘genetic firewall’ that prevents horizontal gene transfer. In organisms engineered to work from an altered genetic code, this helps to isolate them from outside interference. The findings could have applications in creating engineered bacteria that are safer for use in fields such as medicine and biofuel production.

Multiple domains of bacterial and human Lon proteases define substrate selectivity

The Lon protease selectively degrades abnormal proteins or certain normal proteins in response to environmental and cellular conditions in many prokaryotic and eukaryotic organisms. However, the mechanism(s) behind the substrate selection of normal proteins remains largely unknown. In this study, we identified 10 new substrates of F. tularensis Lon from a total of 21 candidate substrates identified in our previous work, the largest number of novel Lon substrates from a single study. Cross-species degradation of these and other known Lon substrates revealed that human Lon is unable to degrade many bacterial Lon substrates, suggestive of a “organism-adapted” substrate selection mechanism for the natural Lon variants. However, individually replacing the N, A, and P domains of human Lon with the counterparts of bacterial Lon did not enable the human protease to degrade the same bacterial Lon substrates. This result showed that the “organism-adapted” substrate selection depends on multiple domains of the Lon proteases. Further in vitro proteolysis and mass spectrometry analysis revealed a similar substrate cleavage pattern between the bacterial and human Lon variants, which was exemplified by predominant representation of leucine, alanine, and other hydrophobic amino acids at the P(−1) site within the substrates. These observations suggest that the Lon proteases select their substrates at least in part by fine structural matching with the proteins in the same organisms.

Ribosome pausing, arrest and rescue in bacteria and eukaryotes

Ribosomes translate genetic information into polypeptides in several basic steps: initiation, elongation, termination and recycling. When ribosomes are arrested during elongation or termination, the cell's capacity for protein synthesis is reduced. There are numerous quality control systems in place to distinguish between paused ribosomes that need some extra input to proceed and terminally stalled ribosomes that need to be rescued. Here, we discuss similarities and differences in the systems for resolution of pauses and rescue of arrested ribosomes in bacteria and eukaryotes, and how ribosome profiling has transformed our ability to decipher these molecular events.This article is part of the themed issue 'Perspectives on the ribosome'.

Structural Basis for Ribosome Rescue in Bacteria

Ribosomes that translate mRNAs lacking stop codons become stalled at the 3' end of the mRNA. Recycling of these stalled ribosomes is essential for cell viability. In bacteria three ribosome rescue systems have been identified so far, with the most ubiquitous and best characterized being the trans-translation system mediated by transfer-messenger RNA (tmRNA) and small protein B (SmpB). The two additional rescue systems present in some bacteria employ alternative rescue factor (Arf) A and release factor (RF) 2 or ArfB. Recent structures have revealed how ArfA mediates ribosome rescue by recruiting the canonical termination factor RF2 to ribosomes stalled on truncated mRNAs. This now provides us with the opportunity to compare and contrast the available structures of all three bacterial ribosome rescue systems.

Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria

Ribosome stalling on mRNAs can decrease protein expression. To decipher ribosome kinetics at stall sites, we induced ribosome stalling at specific codons by starving the bacterium Escherichia coli for the cognate amino acid. We measured protein synthesis rates from a reporter library of over 100 variants that encoded systematic perturbations of translation initiation rate, the number of stall sites, and the distance between stall sites. Our measurements are quantitatively inconsistent with two widely-used kinetic models for stalled ribosomes: ribosome traffic jams that block initiation, and abortive (premature) termination of stalled ribosomes. Rather, our measurements support a model in which collision with a trailing ribosome causes abortive termination of the stalled ribosome. In our computational analysis, ribosome collisions selectively stimulate abortive termination without fine-tuning of kinetic rate parameters at ribosome stall sites. We propose that ribosome collisions serve as a robust timer for translational quality control pathways to recognize stalled ribosomes.

Occlusion of the Ribosome Binding Site Connects the Translational Initiation Frequency, mRNA Stability and Premature Transcription Termination

Protein production is controlled by ribosome binding to the messenger RNA (mRNA), quantified in part by the binding affinity between the ribosome and the ribosome binding sequence on the mRNA. Using the E. coli lac operon as model, Ringquist et al. (1992) found a more than 1,000-fold difference in protein yield when varying the Shine-Dalgarno sequence and its distance to the translation start site. Their proposed model accounted for this large variation by only a variation in the binding affinity and the subsequent initiation rate. Here we demonstrate that the decrease in protein yield with weaker ribosome binding sites in addition is caused by a decreased mRNA stability, and by an increased rate of premature transcription termination. Using different ribosome binding site sequences of the E. coli lacZ gene, we found that an approximately 100-fold span in protein expression could be subdivided into three mechanisms that each affected expression 3- to 6-fold. Our experiments is consistent with a two-step ribosome initiation model, in which occlusion of the initial part of the mRNA by a ribosome simultaneously protects the mRNA from both premature transcription termination and degradation: The premature termination we suggest is coupled to the absence of occlusion that allows binding of transcription termination factor, possibly Rho. The mRNA stability is explained by occlusion that prevents binding of the degrading enzymes. In our proposed scenario, a mRNA with lower translation initiation rate would at the same time be “hit” by an increased premature termination and a shorter life-time. Our model further suggests that the transcription from most if not all natural promoters is substantially influenced by premature termination.

Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth

Bacteria growing under different conditions experience a broad range of demand on the rate of protein synthesis, which profoundly affects cellular resource allocation. During fast growth, protein synthesis has long been known to be modulated by adjusting the ribosome content, with the vast majority of ribosomes engaged at a near-maximal rate of elongation. Here, we systematically characterize protein synthesis by Escherichia coli, focusing on slow-growth conditions. We establish that the translational elongation rate decreases as growth slows, exhibiting a Michaelis-Menten dependence on the abundance of the cellular translational apparatus. However, an appreciable elongation rate is maintained even towards zero growth, including the stationary phase. This maintenance, critical for timely protein synthesis in harsh environments, is accompanied by a drastic reduction in the fraction of active ribosomes. Interestingly, well-known antibiotics such as chloramphenicol also cause a substantial reduction in the pool of active ribosomes, instead of slowing down translational elongation as commonly thought.

Trans-translation is essential in the human pathogen Legionella pneumophila

Trans-translation is a ubiquitous bacterial mechanism for ribosome rescue in the event of translation stalling. Although trans-translation is not essential in several bacterial species, it has been found essential for viability or virulence in a wide range of pathogens. We describe here that trans-translation is essential in the human pathogen Legionella pneumophila, the etiologic agent of Legionnaire's disease (LD), a severe form of nosocomial and community-acquired pneumonia. The ssrA gene coding for tmRNA, the key component of trans-translation, could not be deleted in L. pneumophila. To circumvent this and analyse the consequences of impaired trans-translation, we placed ssrA under the control of a chemical inducer. Phenotypes associated with the inhibition of ssrA expression include growth arrest in rich medium, hampered cell division, and hindered ability to infect eukaryotic cells (amoebae and human macrophages). LD is often associated with failure of antibiotic treatment and death (>10% of clinical cases). Decreasing tmRNA levels led to significantly higher sensitivity to ribosome-targeting antibiotics, including to erythromycin. We also detected a higher sensitivity to the transcription inhibitor rifampicin. Both antibiotics are recommended treatments for LD. Thus, interfering with trans-translation may not only halt the infection, but could also potentiate the recommended therapeutic treatments of LD.

Substrate-translocating loops regulate mechanochemical coupling and power production in AAA+ protease ClpXP

ATP-dependent proteases of the AAA+ family, including Escherichia coli ClpXP and the eukaryotic proteasome, contribute to maintenance of cellular proteostasis. ClpXP unfolds and translocates substrates into an internal degradation chamber, using cycles of alternating dwell and burst phases. The ClpX motor performs chemical transformations during the dwell and translocates the substrate in increments of 1-4 nm during the burst, but the processes occurring during these phases remain unknown. Here we characterized the complete mechanochemical cycle of ClpXP, showing that ADP release and ATP binding occur nonsequentially during the dwell, whereas ATP hydrolysis and phosphate release occur during the burst. The highly conserved translocating loops within the ClpX pore are optimized to maximize motor power generation, the coupling between chemical and mechanical tasks, and the efficiency of protein processing. Conformational resetting of these loops between consecutive bursts appears to determine ADP release from individual ATPase subunits and the overall duration of the motor's cycle.

The ssrA-Tag Facilitated Degradation of an Integral Membrane Protein

ATP-dependent degradation plays a critical role in the quality control and recycling of proteins in cells. However, complete degradation of membrane proteins by ATP-dependent proteases in bacteria is not well-studied. We discovered that the degradation of a multidomain and multispan integral membrane protein AcrB could be facilitated by the introduction of a ssrA-tag at the C-terminus of the protein sequence and demonstrated that the cytoplasmic unfoldase-protease complex ClpXP was involved in the degradation. This is the first report to our knowledge to reveal that the ClpXP complex is capable of degrading integral membrane proteins. The chaperone SspB also played a role in the degradation. Using purified proteins, we demonstrated that the addition of the ssrA-tag did not drastically affect the structure of AcrB, and the degradation of detergent solubilized AcrB by purified ClpXP could be observed in vitro.

Human Cells Require Non-stop Ribosome Rescue Activity in Mitochondria

Bacteria use trans-translation and the alternative rescue factors ArfA (P36675) and ArfB (Q9A8Y3) to hydrolyze peptidyl-tRNA on ribosomes that stall near the 3' end of an mRNA during protein synthesis. The eukaryotic protein ICT1 (Q14197) is homologous to ArfB. In vitro ribosome rescue assays of human ICT1 and Caulobacter crescentus ArfB showed that these proteins have the same activity and substrate specificity. Both ArfB and ICT1 hydrolyze peptidyl-tRNA on nonstop ribosomes or ribosomes stalled with ≤6 nucleotides extending past the A site, but are unable to hydrolyze peptidyl-tRNA when the mRNA extends ≥14 nucleotides past the A site. ICT1 provided sufficient ribosome rescue activity to support viability in C. crescentus cells that lacked both trans-translation and ArfB. Likewise, expression of ArfB protected human cells from death when ICT1 was silenced with siRNA. These data indicate that ArfB and ICT1 are functionally interchangeable, and demonstrate that ICT1 is a ribosome rescue factor. Because ICT1 is essential in human cells, these results suggest that ribosome rescue activity in mitochondria is required in humans.

Ribosomes can stall during protein synthesis on truncated or damaged mRNAs that lack a stop codon. In bacteria, these “non-stop” ribosomes are rescued by trans-translation or by an alternative rescue factor, ArfA or ArfB. Most eukaryotes do not have trans-translation, but mammals have a homolog of ArfB named ICT1. ICT1 is targeted to mitochondria, and is essential in human cells. Here, we show that human ICT1 and ArfB from the bacterium Caulobacter crescentus have the same biochemical activity and specificity. We also demonstrate that ICT1 and ArfB are functionally interchangeable in both bacteria and human cells. Collectively, this work demonstrates a new essential function in human cells—rescue of mitochondrial non-stop translation complexes.

La synthèse des protéines par le ribosome

La synthèse des protéines, également appelée traduction, est assurée dans chaque cellule par des machines moléculaires très sophistiquées : les ribosomes. Compte tenu de l’immense quantité de données biologiques à traiter, il arrive régulièrement que ces machines se bloquent et mettent en péril la survie de la cellule. Chez les bactéries, le principal processus de sauvetage des ribosomes bloqués est la trans-traduction. Il est assuré par un acide ribonucléique (ARN) hybride, l’ARN transfert-messager (ARNtm), associé à une petite protéine basique, SmpB (small protein B). Plusieurs autres systèmes de contrôle qualité ont récemment été mis en évidence, révélant un réseau de maintien de la survie cellulaire très sophistiqué. Cette machinerie du contrôle qualité de la synthèse protéique est une cible très prometteuse pour le développement de futurs antibiotiques.

An integrated approach reveals regulatory controls on bacterial translation elongation

Ribosomes elongate at a nonuniform rate during translation. Theoretical models and experiments disagree on the in vivo determinants of elongation rate and the mechanism by which elongation rate affects protein levels. To resolve this conflict, we measured transcriptome-wide ribosome occupancy under multiple conditions and used it to formulate a whole-cell model of translation in E. coli. Our model predicts that elongation rates at most codons during nutrient-rich growth are not limited by the intracellular concentrations of aminoacyl-tRNAs. However, elongation pausing during starvation for single amino acids is highly sensitive to the kinetics of tRNA aminoacylation. We further show that translation abortion upon pausing accounts for the observed ribosome occupancy along mRNAs during starvation. Abortion reduces global protein synthesis, but it enhances the translation of a subset of mRNAs. These results suggest a regulatory role for aminoacylation and abortion during stress, and our study provides an experimentally constrained framework for modeling translation.

Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate

Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.

The bacterial translation stress response

Throughout their life, bacteria need to sense and respond to environmental stress. Thus, such stress responses can require dramatic cellular reprogramming, both at the transcriptional as well as the translational level. This review focuses on the protein factors that interact with the bacterial translational apparatus to respond to and cope with different types of environmental stress. For example, the stringent factor RelA interacts with the ribosome to generate ppGpp under nutrient deprivation, whereas a variety of factors have been identified that bind to the ribosome under unfavorable growth conditions to shut-down (RelE, pY, RMF, HPF and EttA) or re-program (MazF, EF4 and BipA) translation. Additional factors have been identified that rescue ribosomes stalled due to stress-induced mRNA truncation (tmRNA, ArfA, ArfB), translation of unfavorable protein sequences (EF-P), heat shock-induced subunit dissociation (Hsp15), or antibiotic inhibition (TetM, FusB). Understanding the mechanism of how the bacterial cell responds to stress will not only provide fundamental insight into translation regulation, but will also be an important step to identifying new targets for the development of novel antimicrobial agents.

The SmpB C-terminal tail helps tmRNA to recognize and enter stalled ribosomes

In bacteria, transfer-messenger RNA (tmRNA) and SmpB comprise the most common and effective system for rescuing stalled ribosomes. Ribosomes stall on mRNA transcripts lacking stop codons and are rescued as the defective mRNA is swapped for the tmRNA template in a process known as trans-translation. The tmRNA–SmpB complex is recruited to the ribosome independent of a codon–anticodon interaction. Given that the ribosome uses robust discriminatory mechanisms to select against non-cognate tRNAs during canonical decoding, it has been hard to explain how this can happen. Recent structural and biochemical studies show that SmpB licenses tmRNA entry through its interactions with the decoding center and mRNA channel. In particular, the C-terminal tail of SmpB promotes both EFTu activation and accommodation of tmRNA, the former through interactions with 16S rRNA nucleotide G530 and the latter through interactions with the mRNA channel downstream of the A site. Here we present a detailed model of the earliest steps in trans-translation, and in light of these mechanistic considerations, revisit the question of how tmRNA preferentially reacts with stalled, non-translating ribosomes.

RNA function. Ribosome stalling induced by mutation of a CNS-specific tRNA causes neurodegeneration

In higher eukaryotes, transfer RNAs (tRNAs) with the same anticodon are encoded by multiple nuclear genes, and little is known about how mutations in these genes affect translation and cellular homeostasis. Similarly, the surveillance systems that respond to such defects in higher eukaryotes are not clear. Here, we discover that loss of GTPBP2, a novel binding partner of the ribosome recycling protein Pelota, in mice with a mutation in a tRNA gene that is specifically expressed in the central nervous system causes ribosome stalling and widespread neurodegeneration. Our results not only define GTPBP2 as a ribosome rescue factor but also unmask the disease potential of mutations in nuclear-encoded tRNA genes.

Resolving nonstop translation complexes is a matter of life or death

Problems during gene expression can result in a ribosome that has translated to the 3' end of an mRNA without terminating at a stop codon, forming a nonstop translation complex. The nonstop translation complex contains a ribosome with the mRNA and peptidyl-tRNA engaged, but because there is no codon in the A site, the ribosome cannot elongate or terminate the nascent chain. Recent work has illuminated the importance of resolving these nonstop complexes in bacteria. Transfer-messenger RNA (tmRNA)-SmpB specifically recognizes and resolves nonstop translation complexes in a reaction known as trans-translation. trans-Translation releases the ribosome and promotes degradation of the incomplete nascent polypeptide and problematic mRNA. tmRNA and SmpB have been found in all bacteria and are essential in some species. However, other bacteria can live without trans-translation because they have one of the alternative release factors, ArfA or ArfB. ArfA recruits RF2 to nonstop translation complexes to promote hydrolysis of the peptidyl-tRNAs. ArfB recognizes nonstop translation complexes in a manner similar to tmRNA-SmpB recognition and directly hydrolyzes the peptidyl-tRNAs to release the stalled ribosomes. Genetic studies indicate that most or all species require at least one mechanism to resolve nonstop translation complexes. Consistent with such a requirement, small molecules that inhibit resolution of nonstop translation complexes have broad-spectrum antibacterial activity. These results suggest that resolving nonstop translation complexes is a matter of life or death for bacteria.

An unusual mechanism for EF-Tu activation during tmRNA-mediated ribosome rescue

In bacteria, ribosomes stalled on truncated mRNAs are rescued by transfer-messenger RNA (tmRNA) and its protein partner SmpB. Acting like tRNA, the aminoacyl-tmRNA/SmpB complex is delivered to the ribosomal A site by EF-Tu and accepts the transfer of the nascent polypeptide. Although SmpB binding within the decoding center is clearly critical for licensing tmRNA entry into the ribosome, it is not known how activation of EF-Tu occurs in the absence of a codon-anticodon interaction. A recent crystal structure revealed that SmpB residue His136 stacks on 16S rRNA nucleotide G530, a critical player in the canonical decoding mechanism. Here we use pre-steady-state kinetic methods to probe the role of this interaction in ribosome rescue. We find that although mutation of His136 does not reduce SmpB's affinity for the ribosomal A-site, it dramatically reduces the rate of GTP hydrolysis by EF-Tu. Surprisingly, the same mutation has little effect on the apparent rate of peptide-bond formation, suggesting that release of EF-Tu from the tmRNA/SmpB complex on the ribosome may occur prior to GTP hydrolysis. Consistent with this idea, we find that peptidyl transfer to tmRNA is relatively insensitive to the antibiotic kirromycin. Taken together, our studies provide a model for the initial stages of ribosomal rescue by tmRNA.

Ribosomes regulate the stability and action of the exoribonuclease RNase R

Ribonucleases play an important role in RNA metabolism. Yet, they are also potentially destructive enzymes whose activity must be controlled. Here we describe a novel regulatory mechanism affecting RNase R, a 3' to 5' exoribonuclease able to act on essentially all RNAs including those with extensive secondary structure. Most RNase R is sequestered on ribosomes in growing cells where it is stable and participates in trans-translation. In contrast, the free form of the enzyme, which is deleterious to cells, is extremely unstable, turning over with a half-life of 2 min. RNase R binding to ribosomes is dependent on transfer-messenger RNA (tmRNA)-SmpB, nonstop mRNA, and the modified form of ribosomal protein S12. Degradation of the free form of RNase R also requires tmRNA-SmpB, but this process is independent of ribosomes, indicating two distinct roles for tmRNA-SmpB. Inhibition of RNase R binding to ribosomes leads to slower growth and a massive increase in RNA degradation. These studies indicate a previously unknown role for ribosomes in cellular homeostasis.

Mycobacterium tuberculosis possesses an unusual tmRNA rescue system

Trans-translation is a key process in bacteria which recycles stalled ribosomes and tags incomplete nascent proteins for degradation. This ensures the availability of ribosomes for protein synthesis and prevents the accumulation of dysfunctional proteins. The tmRNA, ssrA, is responsible for both recovering stalled ribosomes and encodes the degradation tag; ssrA associates and functions with accessory proteins such as SmpB. Although ssrA and smpB are ubiquitous in bacteria, they are not essential for the viability of many species. The Mycobacterium tuberculosis genome has homologues of both ssrA and smpB. We demonstrated that ssrA is essential in M. tuberculosis, since the chromosomal copy of the gene could only be deleted in the presence of a functional copy integrated elsewhere. However, we were able to delete the proteolytic tagging function by constructing strains carrying a mutant allele (ssrADD). This demonstrates that ribosome rescue by ssrA is the essential function in M. tuberculosis, SmpB was not required for aerobic growth, since we were able to construct a deletion strain. However, the smpBΔ strain was more sensitive to antibiotics targeting the ribosome. Strains with deletion of smpB or mutations in ssrA did not show increased sensitivity (or resistance) to pyrazinamide suggesting that this antibiotic does not directly target these components of the tmRNA tagging system.

Mutagenic dissection of the sequence determinants of protein folding, recognition, and machine function

Understanding the relationship between the amino-acid sequence of a protein and its ability to fold and to function is one of the major challenges of protein science. Here, cases are reviewed in which mutagenesis, biochemistry, structure determination, protein engineering, and single-molecule biophysics have illuminated the sequence determinants of folding, binding specificity, and biological function for DNA-binding proteins and ATP-fueled machines that forcibly unfold native proteins as a prelude to degradation. In addition to structure-function relationships, these studies provide information about folding intermediates, mutations that accelerate folding, slow unfolding, and stabilize proteins against denaturation, show how new binding specificities and folds can evolve, and reveal strategies that proteolytic machines use to recognize, unfold, and degrade thousands of distinct substrates.

The transfer-messenger RNA-small protein B system plays a role in avian pathogenic Escherichia coli pathogenicity

Extraintestinal pathogenic Escherichia coli (ExPEC) is capable of colonizing outside of the intestinal tract and evolving into a systemic infection. Avian pathogenic E. coli (APEC) is a member of the ExPEC group and causes avian colibacillosis. Transfer-mRNA-small protein B (tmRNA-SmpB)-mediated trans-translation is a bacterial translational control system that directs the modification and degradation of proteins, the biosynthesis of which has stalled or has been interrupted, facilitating the rescue of ribosomes stalled at the 3' ends of defective mRNAs that lack a stop codon. We found that disruption of one, or both, of the smpB or ssrA genes significantly decreased the virulence of the APEC strain E058, as assessed by chicken infection assays. Furthermore, the mutants were obviously attenuated in colonization and persistence assays. The results of quantitative real-time reverse transcription-PCR analysis indicated that the transcription levels of the transcriptional regulation gene rfaH and the virulence genes kpsM, chuA, and iss were significantly decreased compared to those of the wild-type strain. Macrophage infection assays showed that the mutant strains reduced the replication and/or survival ability in the macrophage HD11 cell line compared to that of the parent strain, E058. However, no significant differences were observed in ingestion by macrophages and in chicken serum resistance between the mutant and the wild-type strains. These data indicate that the tmRNA-SmpB system is important in the pathogenesis of APEC O2 strain E058.

The task force that rescues stalled ribosomes in bacteria

In bacteria, the main quality control mechanism for rescuing ribosomes that have arrested during translation is trans-translation, performed by transfer-mRNA (tmRNA) associated with small protein B (SmpB). Intriguingly, this very elegant mechanism is not always necessary to maintain cell viability, suggesting the existence of alternatives. Other rescue systems have recently been discovered, revealing a far more complicated story than expected. These include the alternative ribosome rescue factors ArfA and ArfB, the elongation factors EF4 and EF-P, the peptidyl-tRNA hydrolase Pth, and several protein synthesis factors. These discoveries make it possible to describe a large network of factors dedicated to ribosome rescue, thus ensuring cell survival during stresses that induce ribosome stalling.

Machines of destruction - AAA+ proteases and the adaptors that control them

Bacteria are frequently exposed to changes in environmental conditions, such as fluctuations in temperature, pH or the availability of nutrients. These assaults can be detrimental to cell as they often result in a proteotoxic stress, which can cause the accumulation of unfolded proteins. In order to restore a productive folding environment in the cell, bacteria have evolved a network of proteins, known as the protein quality control (PQC) network, which is composed of both chaperones and AAA+ proteases. These AAA+ proteases form a major part of this PQC network, as they are responsible for the removal of unwanted and damaged proteins. They also play an important role in the turnover of specific regulatory or tagged proteins. In this review, we describe the general features of an AAA+ protease, and using two of the best-characterised AAA+ proteases in Escherichia coli (ClpAP and ClpXP) as a model for all AAA+ proteases, we provide a detailed mechanistic description of how these machines work. Specifically, the review examines the physiological role of these machines, as well as the substrates and the adaptor proteins that modulate their substrate specificity.

Effects of gene length on the dynamics of gene expression

In Escherichia coli, the nucleotide length of a gene is bound to affect its expression dynamics. From simulations of a stochastic model of gene expression at the nucleotide and codon levels we show that, within realistic parameter values, the nucleotide length affects RNA and protein mean levels, as well as the expected transient time for RNA and protein numbers to change, following a signal. Fluctuations in RNA and protein numbers are found to be minimized for a small range of lengths, which matches the means of the distributions of lengths found in E. coli of both essential and non-essential genes. The variance of the length distribution for essential genes is found to be smaller than for non-essential genes, implying that these distributions are far from random. Finally, gene lengths are shown to affect the kinetics of a genetic switch, namely, the correlation between temporal proteins numbers, the stability of the two noisy attractors of the switch, and how biased is the choice of noisy attractor. The stability increases with gene length due to increased 'memory' about the previous states of the switch. We argue that, by affecting the dynamics of gene expression and of genetic circuits, gene lengths are subject to selection.

Effects of codon sequence on the dynamics of genetic networks

In prokaryotes, the rate at which codons are translated varies from one codon to the next. Using a stochastic model of transcription and translation at the nucleotide and codon levels, we investigate the effects of the codon sequence on the dynamics of protein numbers. For sequences generated according to the codon frequencies in Escherichia coli, we find that mean protein numbers at near equilibrium differ with the codon sequence, due to the mean codon translation efficiencies, in particular of the codons at the ribosome binding site region. We find close agreement between these predictions and measurements of protein expression levels as a function of the codon sequence. Next, we investigate the effects of short codon sequences at the start/end of the RNA sequence with linearly increasing/decreasing translation efficiencies, known as slow ramps. The ramps affect the mean, but not the fluctuations, in proteins numbers by affecting the rate of translation initiation. Finally, we show that slow ramps affect the dynamics of small genetic circuits, namely, switches and clocks. In switches, ramps affect the frequency of switching and bias the robustness of the noisy attractors. In repressilators, ramps alter the robustness of periodicity. We conclude that codon sequences affect the dynamics of gene expression and genetic circuits and, thus, are likely to be under selection regarding both mean codon frequency as well as spatial arrangement along the sequence.

Detecting sequence dependent transcriptional pauses from RNA and protein number time series

BACKGROUND

Evidence suggests that in prokaryotes sequence-dependent transcriptional pauses affect the dynamics of transcription and translation, as well as of small genetic circuits. So far, a few pause-prone sequences have been identified from in vitro measurements of transcription elongation kinetics.

RESULTS

Using a stochastic model of gene expression at the nucleotide and codon levels with realistic parameter values, we investigate three different but related questions and present statistical methods for their analysis. First, we show that information from in vivo RNA and protein temporal numbers is sufficient to discriminate between models with and without a pause site in their coding sequence. Second, we demonstrate that it is possible to separate a large variety of models from each other with pauses of various durations and locations in the template by means of a hierarchical clustering and a random forest classifier. Third, we introduce an approximate likelihood function that allows to estimate the location of a pause site.

CONCLUSIONS

This method can aid in detecting unknown pause-prone sequences from temporal measurements of RNA and protein numbers at a genome-wide scale and thus elucidate possible roles that these sequences play in the dynamics of genetic networks and phenotype.