Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis

One step DNA assembly for combinatorial metabolic engineering

The rapid and efficient assembly of multi-step metabolic pathways for generating microbial strains with desirable phenotypes is a critical procedure for metabolic engineering, and remains a significant challenge in synthetic biology. Although several DNA assembly methods have been developed and applied for metabolic pathway engineering, many of them are limited by their suitability for combinatorial pathway assembly. The introduction of transcriptional (promoters), translational (ribosome binding site (RBS)) and enzyme (mutant genes) variability to modulate pathway expression levels is essential for generating balanced metabolic pathways and maximizing the productivity of a strain. We report a novel, highly reliable and rapid single strand assembly (SSA) method for pathway engineering. The method was successfully optimized and applied to create constructs containing promoter, RBS and/or mutant enzyme libraries. To demonstrate its efficiency and reliability, the method was applied to fine-tune multi-gene pathways. Two promoter libraries were simultaneously introduced in front of two target genes, enabling orthogonal expression as demonstrated by principal component analysis. This shows that SSA will increase our ability to tune multi-gene pathways at all control levels for the biotechnological production of complex metabolites, achievable through the combinatorial modulation of transcription, translation and enzyme activity.

Transcript level and sequence determinants of protein abundance and noise in Escherichia coli

The range over which a protein is expressed, and its cell-to-cell variability, is often thought to be linked to the demand for its activity. Steady-state protein level is determined by multiple mechanisms controlling transcription and translation, many of which are limited by DNA- and RNA-encoded signals that affect initiation, elongation and termination of polymerases and ribosomes. We performed a comprehensive analysis of >100 sequence features to derive a predictive model composed of a minimal non-redundant set of factors explaining 66% of the total variation of protein abundance observed in >800 genes in Escherichia coli. The model suggests that protein abundance is primarily determined by the transcript level (53%) and by effectors of translation elongation (12%), whereas only a small fraction of the variation is explained by translational initiation (1%). Our analyses uncover a new sequence determinant, not previously described, affecting translation initiation and suggest that elongation rate is affected by both codon biases and specific amino acid composition. We also show that transcription and translation efficiency may have an effect on expression noise, which is more similar than previously assumed.

Design and analysis of LacI-repressed promoters and DNA-looping in a cyanobacterium

BACKGROUND

Cyanobacteria are solar-powered prokaryotes useful for sustainable production of valuable molecules, but orthogonal and regulated promoters are lacking. The Lac repressor (LacI) from Escherichia coli is a well-studied transcription factor that is orthogonal to cyanobacteria and represses transcription by binding a primary lac operator (lacO), blocking RNA-polymerase. Repression can be enhanced through DNA-looping, when a LacI-tetramer binds two spatially separated lacO and loops the DNA. Ptrc is a commonly used LacI-repressed promoter that is inefficiently repressed in the cyanobacterium Synechocystis PCC 6803. Ptrc2O, a version of Ptrc with two lacO, is more efficiently repressed, indicating DNA-looping. To investigate the inefficient repression of Ptrc and cyanobacterial DNA-looping, we designed a Ptrc-derived promoter library consisting of single lacO promoters, including a version of Ptrc with a stronger lacO (Ptrc1O-proximal), and dual lacO promoters with varying inter-lacO distances (the Ptrc2O-library).

RESULTS

We first characterized artificial constitutive promoters and used one for engineering a LacI-expressing strain of Synechocystis. Using this strain, we observed that Ptrc1O-proximal is similar to Ptrc in being inefficiently repressed. Further, the Ptrc2O-library displays a periodic repression pattern that remains for both non- and induced conditions and decreases with longer inter-lacO distances, in both E. coli and Synechocystis. Repression of Ptrc2O-library promoters with operators out of phase is less efficient in Synechocystis than in E. coli, whereas repression of promoters with lacO in phase is efficient even under induced conditions in Synechocystis. Two well-repressed Ptrc2O promoters were highly active when tested in absence of LacI in Synechocystis.

CONCLUSIONS

The artificial constitutive promoters herein characterized can be utilized for expression in cyanobacteria, as demonstrated for LacI. The inefficient repression of Ptrc and Ptrc1O-proximal in Synechocystis, as compared to E. coli, may be due to insufficient LacI expression, or differences in RNAP subunits. DNA-looping works as a transcriptional regulation mechanism similarly as in E. coli. DNA-looping contributes strongly to Ptrc2O-library repression in Synechocystis, even though they contain the weakly-repressed primary lacO of Ptrc1O-proximal and relatively low levels of LacI/cell. Hence, Synechocystis RNAP may be more sensitive to DNA-looping than E. coli RNAP, and/or the chromatin torsion resistance could be lower. Two strong and highly repressed Ptrc2O promoters could be used without induction, or together with an unstable LacI.

Predicting translation initiation rates for designing synthetic biology

In synthetic biology, precise control over protein expression is required in order to construct functional biological systems. A core principle of the synthetic biology approach is a model-guided design and based on the biological understanding of the process, models of prokaryotic protein production have been described. Translation initiation rate is a rate-limiting step in protein production from mRNA and is dependent on the sequence of the 5′-untranslated region and the start of the coding sequence. Translation rate calculators are programs that estimate protein translation rates based on the sequence of these regions of an mRNA, and as protein expression is proportional to the rate of translation initiation, such calculators have been shown to give good approximations of protein expression levels. In this review, three currently available translation rate calculators developed for synthetic biology are considered, with limitations and possible future progress discussed.

High-level cell-free production of membrane proteins with nanodiscs

This chapter addresses two major bottlenecks in cell-free membrane protein production. Firstly, we describe the optimization of expression templates for obtaining membrane proteins in preparative scales. We present details for a newly established tag variation screen providing high success rates in improving expression efficiencies while having only minimal impacts on the target protein structure. Secondly, we present protocols for the efficient co-translational insertion of membrane proteins into defined lipid bilayers. We describe the production of nanodiscs and their implementation into cell-free expression reactions for the co-translational reconstitution of membrane proteins. In addition we give guidelines for the loading of nanodiscs with different lipids in order to systematically analyze effects of lipids on the translocation, functional folding, and stability of cell-free expressed membrane proteins.

Enhanced production of coenzyme Q10 by self-regulating the engineered MEP pathway in Rhodobacter sphaeroides

Fine-tuning the expression level of an engineered pathway is crucial for the metabolic engineering of a host toward a desired phenotype. However, most engineered hosts suffer from nonfunctional protein expression, metabolic imbalance, cellular burden or toxicity from intermediates when an engineered pathway is first introduced, which can decrease production of the desired product. To circumvent these obstacles, we developed a self-regulation system utilizing the trc/tac promoter, LacI(q) protein and ribosomal binding sites (RBS). With the purpose of improving coenzyme Q10 (CoQ10 ) production by increasing the decaprenyl diphosphate supplement, enzymes DXS, DXR, IDI, and IspD were constitutively overexpressed under the control of the trc promoter in Rhodobacter sphaeroides. Then, a self-regulation system combining a set of RBSs for adjusting the expression of the LacI(q) protein was applied to tune the expression of the four genes, resulting in improved CoQ10 production. Finally, another copy of the tac promoter with the UbiG gene (involved in the ubiquinone pathway of CoQ10 biosynthesis) was introduced into the engineered pathway. By optimizing the expression level of both the upstream and downstream pathway, CoQ10 production in the mutants was improved up to 93.34 mg/L (7.16 mg/g DCW), about twofold of the wild-type (48.25 mg/L, 3.24 mg/g DCW).

Potential thermosensitive riboswitches in the genome of Salmonella

Currently, a number of structurally and functionally different thermosensitive elements, such as structurally and functionally different RNA thermometers, for controlling a variety of biological processes in bacteria, including virulence are known. These well-known RNA thermometers are structures, whether matched or mismatched, which are represented by either a single stretched hairpin structure or a few hairpins. Based on computer and thermodynamic analyses of 25 isolates of Salmonella enterica with complete genome, we have developed an algorithm and criteria to search for potential RNA thermometers, which will enable us to undertake a future search for potential riboswitches in the genomes of other socially significant pathogens. In addition to the well-known 4U RNA thermometer, another four hairpin-loop structures have been identified in S. enterica as new potential RNA thermometers and two of them are localized in 5'-UTR of virulence regulators gltB and yaeQ. They are highly conserved noncanonical structures and correspond to the necessary and sufficient conditions for forming RNA thermometers, since they are found in each of the 25 S. enterica genome isolates. We analyzed the thermosensitive motif in the pXO1 plasmid of Bacillus anthracis-an anthrax-causative pathogen-and visualized matched hairpins that form a cruciform structure in pUC8 supercoiled plasmid by atomic force microscopy.

The centrality of RNA for engineering gene expression

Synthetic biology holds promise as both a framework for rationally engineering biological systems and a way to revolutionize how we fundamentally understand them. Essential to realizing this promise is the development of strategies and tools to reliably and predictably control and characterize sophisticated patterns of gene expression. Here we review the role that RNA can play towards this goal and make a case for why this versatile, designable, and increasingly characterizable molecule is one of the most powerful substrates for engineering gene expression at our disposal. We discuss current natural and synthetic RNA regulators of gene expression acting at key points of control – transcription, mRNA degradation, and translation. We also consider RNA structural probing and computational RNA structure predication tools as a way to study RNA structure and ultimately function. Finally, we discuss how next-generation sequencing methods are being applied to the study of RNA and to the characterization of RNA's many properties throughout the cell.

Causes and effects of N-terminal codon bias in bacterial genes

Most amino acids are encoded by multiple codons, and codon choice has strong effects on protein expression. Rare codons are enriched at the N terminus of genes in most organisms, although the causes and effects of this bias are unclear. Here, we measure expression from >14,000 synthetic reporters in Escherichia coli and show that using N-terminal rare codons instead of common ones increases expression by ~14-fold (median 4-fold). We quantify how individual N-terminal codons affect expression and show that these effects shape the sequence of natural genes. Finally, we demonstrate that reduced RNA structure and not codon rarity itself is responsible for expression increases. Our observations resolve controversies over the roles of N-terminal codon bias and suggest a straightforward method for optimizing heterologous gene expression in bacteria.

Fluorescent proteins and in vitro genetic organization for cell-free synthetic biology

To facilitate the construction of cell-free genetic devices, we evaluated the ability of 17 different fluorescent proteins to give easily detectable fluorescence signals in real-time from in vitro transcription-translation reactions with a minimal system consisting of T7 RNA polymerase and E. coli translation machinery, i.e., the PUREsystem. The data were used to construct a ratiometric fluorescence assay to quantify the effect of genetic organization on in vitro expression levels. Synthetic operons with varied spacing and sequence composition between two genes that coded for fluorescent proteins were then assembled. The resulting data indicated which restriction sites and where the restriction sites should be placed in order to build genetic devices in a manner that does not interfere with protein expression. Other simple design rules were identified, such as the spacing and sequence composition influences of regions upstream and downstream of ribosome binding sites and the ability of non-AUG start codons to function in vitro.

Role for cis-acting RNA sequences in the temperature-dependent expression of the multiadhesive lig proteins in Leptospira interrogans

The spirochete Leptospira interrogans causes a systemic infection that provokes a febrile illness. The putative lipoproteins LigA and LigB promote adhesion of Leptospira to host proteins, interfere with coagulation, and capture complement regulators. In this study, we demonstrate that the expression level of the LigA and LigB proteins was substantially higher when L. interrogans proliferated at 37°C instead of the standard culture temperature of 30°C. The RNA comprising the 175-nucleotide 5' untranslated region (UTR) and first six lig codons, whose sequence is identical in ligA and ligB, is predicted to fold into two distinct stem-loop structures separated by a single-stranded region. The ribosome-binding site is partially sequestered in double-stranded RNA within the second structure. Toeprint analysis revealed that in vitro formation of a 30S-tRNA(fMet)-mRNA ternary complex was inhibited unless a 5' deletion mutation disrupted the second stem-loop structure. To determine whether the lig sequence could mediate temperature-regulated gene expression in vivo, the 5' UTR and the first six codons were inserted between the Escherichia coli l-arabinose promoter and bgaB (β-galactosidase from Bacillus stearothermophilus) to create a translational fusion. The lig fragment successfully conferred thermoregulation upon the β-galactosidase reporter in E. coli. The second stem-loop structure was sufficient to confer thermoregulation on the reporter, while sequences further upstream in the 5' UTR slightly diminished expression at each temperature tested. Finally, the expression level of β-galactosidase was significantly higher when point mutations predicted to disrupt base pairs in the second structure were introduced into the stem. Compensatory mutations that maintained base pairing of the stem without restoring the wild-type sequence reinstated the inhibitory effect of the 5' UTR on expression. These results indicate that ligA and ligB expression is limited by double-stranded RNA that occludes the ribosome-binding site. At elevated temperatures, the ribosome-binding site is exposed to promote translation initiation.

Rate-limiting steps in yeast protein translation

Deep sequencing now provides detailed snapshots of ribosome occupancy on mRNAs. We leverage these data to parameterize a computational model of translation, keeping track of every ribosome, tRNA, and mRNA molecule in a yeast cell. We determine the parameter regimes in which fast initiation or high codon bias in a transgene increases protein yield and infer the initiation rates of endogenous Saccharomyces cerevisiae genes, which vary by several orders of magnitude and correlate with 5′ mRNA folding energies. Our model recapitulates the previously reported 5′-to-3′ ramp of decreasing ribosome densities, although our analysis shows that this ramp is caused by rapid initiation of short genes rather than slow codons at the start of transcripts. We conclude that protein production in healthy yeast cells is typically limited by the availability of free ribosomes, whereas protein production under periods of stress can sometimes be rescued by reducing initiation or elongation rates.

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Computational model of translation tracks all ribosomes, tRNAs, and mRNAs in a cell

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Translation is generally limited by initiation, not elongation

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Model allows inference of initiation rates for all yeast genes

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Ramp of 5′ ribosomes is caused by rapid initiation of short genes

Design and optimization of short DNA sequences that can be used as 5' fusion partners for high-level expression of heterologous genes in Escherichia coli

The 5' terminal nucleotide sequence of a gene is often a bottleneck in recombinant protein production. The ifn-α2bS gene is poorly expressed in Escherichia coli unless a translocation signal sequence (pelB) is fused to the 5' end of the gene. A combined in silico and in vivo analysis reported here further indicates that the ifn-α2bS 5' coding sequence is suboptimal for efficient gene expression. ifn-α2bS therefore presents a suitable model gene for describing properties of 5' fusions promoting expression. We show that short DNA sequences corresponding to the 5' end of the highly expressed celB gene, whose protein product is cytosolic, can functionally replace pelB as a 5' fusion partner for efficient ifn-α2bS expression. celB fusions of various lengths (corresponding to a minimum of 8 codons) led to more than 7- and 60-fold stimulation of expression at the transcript and protein levels, respectively. Moreover, the presence of a celB-based fusion partner was found to moderately reduce the decay rate of the corresponding transcript. The 5' fusions thus appear to act by enhancing translation, and bound ribosomes may accordingly contribute to increased mRNA stability and reduced mRNA decay. However, other effects, such as altered protein stability, cannot be excluded. We also developed an experimental protocol that enabled us to identify improved variants of the celB fusion, and one of these (celBD11) could be used to additionally increase ifn-α2bS expression more than 4-fold at the protein level. Interestingly, celBD11 also stimulated greater protein production of three other medically important human genes than the wild-type celB fragment.

Benchmarking various green fluorescent protein variants in Bacillus subtilis, Streptococcus pneumoniae, and Lactococcus lactis for live cell imaging

Green fluorescent protein (GFP) offers efficient ways of visualizing promoter activity and protein localization in vivo, and many different variants are currently available to study bacterial cell biology. Which of these variants is best suited for a certain bacterial strain, goal, or experimental condition is not clear. Here, we have designed and constructed two "superfolder" GFPs with codon adaptation specifically for Bacillus subtilis and Streptococcus pneumoniae and have benchmarked them against five other previously available variants of GFP in B. subtilis, S. pneumoniae, and Lactococcus lactis, using promoter-gfp fusions. Surprisingly, the best-performing GFP under our experimental conditions in B. subtilis was the one codon optimized for S. pneumoniae and vice versa. The data and tools described in this study will be useful for cell biology studies in low-GC-rich Gram-positive bacteria.

Reconstitution of active mycobacterial binuclear iron monooxygenase complex in Escherichia coli

Bacterial binuclear iron monooxygenases play numerous physiological roles in oxidative metabolism. Monooxygenases of this type found in actinomycetes also catalyze various useful reactions and have attracted much attention as oxidation biocatalysts. However, difficulties in expressing these multicomponent monooxygenases in heterologous hosts, particularly in Escherichia coli, have hampered the development of engineered oxidation biocatalysts. Here, we describe a strategy to functionally express the mycobacterial binuclear iron monooxygenase MimABCD in Escherichia coli. Sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis of the mimABCD gene expression in E. coli revealed that the oxygenase components MimA and MimC were insoluble. Furthermore, although the reductase MimB was expressed at a low level in the soluble fraction of E. coli cells, a band corresponding to the coupling protein MimD was not evident. This situation rendered the transformed E. coli cells inactive. We found that the following factors are important for functional expression of MimABCD in E. coli: coexpression of the specific chaperonin MimG, which caused MimA and MimC to be soluble in E. coli cells, and the optimization of the mimD nucleotide sequence, which led to efficient expression of this gene product. These two remedies enabled this multicomponent monooxygenase to be actively expressed in E. coli. The strategy described here should be generally applicable to the E. coli expression of other actinomycetous binuclear iron monooxygenases and related enzymes and will accelerate the development of engineered oxidation biocatalysts for industrial processes.

Efficient translation initiation dictates codon usage at gene start

Rare codons are enriched at gene start in many genomes. Genome analysis and experimental testing show that this enrichment evolved to keep the ribosome binding site free from stable mRNA structures, in order to facilitate efficient translation initiation.

The use of rare codons coincides with suppression of mRNA structures at the ribosome binding site across genomes.

There is preferential selection for synonymous codons that reduce GC-content at the beginning of genes and a stronger pressure for rare codon usage in GC-rich organisms.

Amino acids encoded by AU-rich codons are preferred at gene start.

Experimental results show that mRNA structure at translation start strongly influences protein yield.

The genetic code is degenerate; thus, protein evolution does not uniquely determine the coding sequence. One of the puzzles in evolutionary genetics is therefore to uncover evolutionary driving forces that result in specific codon choice. In many bacteria, the first 5–10 codons of protein-coding genes are often codons that are less frequently used in the rest of the genome, an effect that has been argued to arise from selection for slowed early elongation to reduce ribosome traffic jams. However, genome analysis across many species has demonstrated that the region shows reduced mRNA folding consistent with pressure for efficient translation initiation. This raises the possibility that unusual codon usage is a side effect of selection for reduced mRNA structure. Here we discriminate between these two competing hypotheses, and show that in bacteria selection favours codons that reduce mRNA folding around the translation start, regardless of whether these codons are frequent or rare. Experiments confirm that primarily mRNA structure, and not codon usage, at the beginning of genes determines the translation rate.

Short ROSE-like RNA thermometers control IbpA synthesis in Pseudomonas species

The bacterial small heat shock protein IbpA protects client proteins from aggregation. Due to redundancy in the cellular chaperone network, deletion of the ibpA gene often leads to only a mild or no phenotypic defect. In this study, we show that a Pseudomonas putida ibpA deletion mutant has a severe growth defect under heat stress conditions and reduced survival during recovery revealing a critical role of IbpA in heat tolerance. Transcription of the ibpA gene depends on the alternative heat shock sigma factor σ³². Production of IbpA protein only at heat shock temperatures suggested additional translational control. We conducted a comprehensive structural and functional analysis of the 5′ untranslated regions of the ibpA genes from P. putida and Pseudomonas aeruginosa. Both contain a ROSE-type RNA thermometer that is substantially shorter and simpler than previously reported ROSE elements. Comprised of two hairpin structures only, they inhibit translation at low temperature and permit translation initiation after a temperature upshift. Both elements regulate reporter gene expression in Escherichia coli and ribosome binding in vitro in a temperature-dependent manner. Structure probing revealed local melting of the second hairpin whereas the first hairpin remained unaffected. High sequence and structure conservation of pseudomonal ibpA untranslated regions and their ability to confer thermoregulation in vivo suggest that short ROSE-like thermometers are commonly used to control IbpA synthesis in Pseudomonas species.

Quantitative and simultaneous translational control of distinct mammalian mRNAs

The introduction of multiple genes into cells is increasingly required for understanding and engineering biological systems. Small-molecule–responsive transcriptional regulation has been widely used to control transgene expression. In contrast, methods for specific and simultaneous regulation of multiple genes with a single regulatory protein remain undeveloped. In this report, we describe a method for quantitatively tuning the expression of multiple transgenes with a translational regulatory protein. A protein that binds a specific RNA motif inserted in the 5′-untranslated region (UTR) of an mRNA modulates the translation of that message in mammalian cells. We provide two independent mechanisms by which to rationally fine-tune the output: the efficiency of translation correlates well with the distance between the inserted motif and the 5′ terminus of the mRNA and is further modulated by the tandem insertion of multiple RNA motifs. The combination of these two approaches allowed us to fine-tune the translational efficiency of target mRNAs over a wide dynamic range. Moreover, we controlled the expression of two transgenes simultaneously and specifically by engineering each cis-regulatory 5′-UTR. The approach provides a useful alternative regulatory layer for controlling gene expression in biological research and engineering.

Sequence and structure-specific elements of HERG mRNA determine channel synthesis and trafficking efficiency

Human ether-á-gogo-related gene (HERG) encodes a potassium channel that is highly susceptible to deleterious mutations resulting in susceptibility to fatal cardiac arrhythmias. Most mutations adversely affect HERG channel assembly and trafficking. Why the channel is so vulnerable to missense mutations is not well understood. Since nothing is known of how mRNA structural elements factor in channel processing, we synthesized a codon-modified HERG cDNA (HERG-CM) where the codons were synonymously changed to reduce GC content, secondary structure, and rare codon usage. HERG-CM produced typical IKr-like currents; however, channel synthesis and processing were markedly different. Translation efficiency was reduced for HERG-CM, as determined by heterologous expression, in vitro translation, and polysomal profiling. Trafficking efficiency to the cell surface was greatly enhanced, as assayed by immunofluorescence, subcellular fractionation, and surface labeling. Chimeras of HERG-NT/CM indicated that trafficking efficiency was largely dependent on 5' sequences, while translation efficiency involved multiple areas. These results suggest that HERG translation and trafficking rates are independently governed by noncoding information in various regions of the mRNA molecule. Noncoding information embedded within the mRNA may play a role in the pathogenesis of hereditary arrhythmia syndromes and could provide an avenue for targeted therapeutics.

Overview of regulatory strategies and molecular elements in metabolic engineering of bacteria

From a viewpoint of biotechnology, metabolic engineering mainly aims to change the natural status of a pathway in a microorganism towards the overproduction of certain bioproducts. The biochemical nature of a pathway implies us that changed pathway is often the collective results of altered behavior of the metabolic enzymes encoded by corresponding genes. By finely modulating the expression of these genes or the properties of the enzyme, we can gain efficient control on the pathway. In this article, we reviewed the typical methods that have been applied to regulate the expression of genes in metabolic engineering. These methods are grouped according to the operation targets in a typical gene. The transcription of a gene is controlled by an indispensable promoter. By utilizing promoters with different strengths, expected levels of expression can be easily achieved, and screening a promoter library may find suitable mutant promoters that can provide tunable expression of a gene. Auto-responsive promoter (quorum sensing (QS)-based or oxygen-inducible) simplifies the induction process by driving the expression of a gene in an automated manner. Light responsive promoter enables reversible and noninvasive control on gene activity, providing a promising method in controlling gene expression with time and space resolution in metabolic engineering involving complicated genetic circuits. Through directed evolution and/or rational design, the encoding sequences of a gene can be altered, leading to the possibly most profound changes in properties of a metabolic enzyme. Introducing an engineered riboswitch in mRNA can make it a regulatory molecule at the same time; ribosomal binding site is commonly engineered to be more attractive for a ribosome through design. Terminator of a gene will affect the stability of an mRNA, and intergenic region will influence the expression of many related genes. Improving the performance of these elements are generally the main activities in metabolic engineering.

Weak 5'-mRNA secondary structures in short eukaryotic genes

Experimental studies of translation have found that short genes tend to exhibit greater densities of ribosomes than long genes in eukaryotic species. It remains an open question whether the elevated ribosome density on short genes is due to faster initiation or slower elongation dynamics. Here, we address this question computationally using 5′-mRNA folding energy as a proxy for translation initiation rates and codon bias as a proxy for elongation rates. We report a significant trend toward reduced 5′-secondary structure in shorter coding sequences, suggesting that short genes initiate faster during translation. We also find a trend toward higher 5′-codon bias in short genes, suggesting that short genes elongate faster than long genes. Both of these trends hold across a diverse set of eukaryotic taxa. Thus, the elevated ribosome density on short eukaryotic genes is likely caused by differential rates of initiation, rather than differential rates of elongation.

Translational efficiency of rpoS mRNA from Borrelia burgdorferi: effects of the length and sequence of the mRNA leader region

Regulation of the enzootic cycle in Borrelia burgdorferi requires a shift to the RNA polymerase alternative sigma factor, RpoS. We used in vitro and in vivo assays to assess the relative importance of the putative Shine-Dalgarno sequence and its sequestration for the translational efficiency of rpoS. We created mutant leader regions in which we either removed the Shine-Dalgarno sequence, disrupted the secondary structure or both. Binding assays and toeprint assays demonstrated that both the presence and the availability of the Shine-Dalgarno sequence are important to the efficiency and specificity of ribosome binding. Adding a DsrABb mimic in the form of a single-stranded DNA oligonucleotide increased the level and specificity of binding ribosomes to the transcript with an extended leader, presumably by making the Shine-Dalgarno sequence available for binding. In in vivo assays we confirmed that the Shine-Dalgarno sequence must be both present and un-sequestered in order for translation to proceed efficiently. The longer transcript was significantly better translated in B. burgdorferi at 37 °C than at 26 °C, lending support to the hypothesis that DsrABb acts as a temperature-dependent stimulator of translation. These studies demonstrate that translational regulation of gene expression in B. burgdorferi may be an important mechanism for responding to environmental signals important in the enzootic cycle.

Search for the new potential RNA thermometers in the genome of Salmonella enterica

Currently, a number of structurally and functionally different temperature-sensitive elements such as RNA thermometers which control a variety of biological processes in bacteria, including virulence, are known. Based on computer and thermodynamic analysis of completely sequenced genomes of 25 Salmonella enterica isolates, the algorithm and criteria for the search of potential RNA thermometers were developed. It will make it possible to carry out the search for potential riboswitches in the genome of other socially important pathogens. For S. enterica, apart from the known 4U RNA thermometer, four hairpin-loop structures were identified which may probably act as additional RNA thermometers. They satisfy the necessary and sufficient conditions for formation of RNA thermometers and are highly conservative uncanonical structures, since these highly conservative structures were found in the genome of all 25 isolates of S. enterica. The hairpins forming a cruciform structure in the supercoiled pUC8 DNA were visualized by atomic force microscopy.

The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection

Bacterial transcription is initiated after RNA polymerase (RNAP) binds to promoter DNA, melts ~14 bp around the transcription start site and forms a single-stranded "transcription bubble" within a catalytically active RNAP-DNA open complex (RP(o)). There is significant flexibility in the transcription start site, which causes variable spacing between the promoter elements and the start site; this in turn causes differences in the length and sequence at the 5' end of RNA transcripts and can be important for gene regulation. The start-site variability also implies the presence of some flexibility in the positioning of the DNA relative to the RNAP active site in RP(o). The flexibility may occur in the positioning of the transcription bubble prior to RNA synthesis and may reflect bubble expansion ("scrunching") or bubble contraction ("unscrunching"). Here, we assess the presence of dynamic flexibility in RP(o) with single-molecule FRET (Förster resonance energy transfer). We obtain experimental evidence for dynamic flexibility in RP(o) using different FRET rulers and labeling positions. An analysis of FRET distributions of RP(o) using burst variance analysis reveals conformational fluctuations in RP(o) in the millisecond timescale. Further experiments using subsets of nucleotides and DNA mutations allowed us to reprogram the transcription start sites, in a way that can be described by repositioning of the single-stranded transcription bubble relative to the RNAP active site within RP(o). Our study marks the first experimental observation of conformational dynamics in the transcription bubble of RP(o) and indicates that DNA dynamics within the bubble affect the search for transcription start sites.

Reannotation of translational start sites in the genome of Mycobacterium tuberculosis

Identification and correction of incorrect ORF start sites is important for a variety of experimental and analytical purposes, ranging from cloning to inference of operon structure. The genome of the H37Rv reference strain of Mycobacterium tuberculosis (Mtb) was originally annotated when it was first sequenced nearly 15 years ago. While this annotation has served the TB research community well as a standard of reference for over a decade, it has been demonstrated experimentally that the actual start sites for an estimated 5-10% of open reading frames differ from the annotation. In this paper, we present a comprehensive bioinformatic analysis of all 3989 ORFs (open reading frames) in the M. tuberculosis H37Rv genome. Our method combines information from comparative analysis (alignment to start sites of orthologs in other Actinobacteria), sequence conservation, "protein likeness", putative ribosome binding sites, and other data to identify translational start sites. The features are combined in a linear model that is trained on dataset of known start sites verified by mass spectrometry, with a cross-validated accuracy of 94%. The method can be viewed as an augmentation of Hidden Markov Model-based tools such as Glimmer and GeneMark by incorporating more information than just the raw genomic sequence to decide which position is the legitimate translational start site for each ORF. Using this analysis, we identify 269 genes that most likely need to be re-annotated, and identify the best alterative translational start site for each. These revised ORF definitions could be used in the reannotation of the H37Rv genome, as well as to prioritize genes for experimental start-site validation.

Modelling translation initiation under the influence of sRNA

Bacterial small non-coding RNA (sRNA) plays an important role in post-transcriptional gene regulation. Although the number of annotated sRNA is steadily increasing, their functional characterization is still lagging behind. Various computational strategies for finding sRNA−mRNA interactions, and thus putative sRNA targets, were developed. Most of them suffer from a high false positive rate. Here, we present a qualitative model to simulate the effect of an sRNA on the translation initiation of a potential target. Information about the ribosome−mRNA interaction, sRNA−mRNA interaction and expression information from deep sequencing experiments is integrated to calculate the change in translation initiation complex formation, as a proxy for translational activity. This model can be used to post-evaluate predicted targets, hence condensing the list of potential targets. We show that our translation initiation model, under the influence of an sRNA, can successfully simulate thirteen out of fifteen tested sRNA−mRNA interactions in a qualitative manner. To show the gain in specificity, we applied our method to a target search for the Escherichia coli sRNA RyhB. Compared with simple target prediction without post-evaluation, we reduce the number of targets to less than one fourth potential targets, considerably reducing the burden of experimental validation.

Diversity of pili-specific bacteriophages: genome sequence of IncM plasmid-dependent RNA phage M

Background

Bacteriophages of the Leviviridae family are small RNA viruses with linear, positive-sense, single-stranded RNA genomes that encode only four proteins. All phages of this family require bacterial pili to attach to and infect cells. Leviviridae phages utilizing F-pili for this purpose have been extensively studied. RNA phages specific for conjugative plasmid-encoded pili other than that of plasmid F have been isolated, but are much less understood and their relation to the F-pili-specific phages in many cases is not known.

Results

Phage M has the smallest known Leviviridae genome to date and has the typical genome organization with maturation, coat and replicase genes in the 5′ to 3′ direction. The lysis gene is located in a different position than in other known Leviviridae phages and completely overlaps with the replicase gene in a different reading frame. It encodes a 37 residue long polypeptide that contains a transmembrane helix like the other known lysis proteins of leviviruses. Sequence identities of M proteins to those of other phages do not exceed 25% for maturation protein, 51% for coat protein and 41% for replicase. Similarities in protein sequences and RNA secondary structures at the 3′ untranslated region place phage M together with phages specific for IncP, IncC and IncH, but not IncF plasmid-encoded pili. Phylogenetic analysis using the complete genome sequences and replicase proteins suggests that phage M represents a lineage that branched off early in the course of RNA phage specialization on different conjugative plasmids.

Conclusions

The genome sequence of phage M shows that it is clearly related to other conjugative pili-specific leviviruses but has an atypical location of the lysis gene. It provides a better view on the remarkable diversification of the plasmid-specific RNA phages.

Sensitive measurement of single-nucleotide polymorphism-induced changes of RNA conformation: application to disease studies

Single-nucleotide polymorphisms (SNPs) are often linked to critical phenotypes such as diseases or responses to vaccines, medications and environmental factors. However, the specific molecular mechanisms by which a causal SNP acts is usually not obvious. Changes in RNA secondary structure emerge as a possible explanation necessitating the development of methods to measure the impact of single-nucleotide variation on RNA structure. Despite the recognition of the importance of considering the changes in Boltzmann ensemble of RNA conformers in this context, a formal method to perform directly such comparison was lacking. Here, we solved this problem and designed an efficient method to compute the relative entropy between the Boltzmann ensembles of the native and a mutant structure. On the basis of this theoretical progress, we developed a software tool, remuRNA, and investigated examples of its application. Comparing the impact of common SNPs naturally occurring in populations with the impact of random point mutations, we found that structural changes introduced by common SNPs are smaller than those introduced by random point mutations. This suggests a natural selection against mutations that significantly change RNA structure and demonstrates, surprisingly, that randomly inserted point mutations provide inadequate estimation of random mutations effects. Subsequently, we applied remuRNA to determine which of the disease-associated non-coding SNPs are potentially related to RNA structural changes.

Engineering signal peptides for enhanced protein secretion from Lactococcus lactis

Lactococcus lactis is an attractive vehicle for biotechnological production of proteins and clinical delivery of therapeutics. In many such applications using this host, it is desirable to maximize secretion of recombinant proteins into the extracellular space, which is typically achieved by using the native signal peptide from a major secreted lactococcal protein, Usp45. In order to further increase protein secretion from L. lactis, inherent limitations of the Usp45 signal peptide (Usp45sp) must be elucidated. Here, we performed extensive mutagenesis on Usp45sp to probe the effects of both the mRNA sequence (silent mutations) and the peptide sequence (amino acid substitutions) on secretion. We screened signal peptides based on their resulting secretion levels of Staphylococcus aureus nuclease and further evaluated them for secretion of Bacillus subtilis α-amylase. Silent mutations alone gave an increase of up to 16% in the secretion of α-amylase through a mechanism consistent with relaxed mRNA folding around the ribosome binding site and enhanced translation. Targeted amino acid mutagenesis in Usp45sp, combined with additional silent mutations from the best clone in the initial screen, yielded an increase of up to 51% in maximum secretion of α-amylase while maintaining secretion at lower induction levels. The best sequence from our screen preserves the tripartite structure of the native signal peptide but increases the positive charge of the n-region. Our study presents the first example of an engineered L. lactis signal peptide with a higher secretion yield than Usp45sp and, more generally, provides strategies for further enhancing protein secretion in bacterial hosts.

The toxin-antitoxin system tisB-istR1: Expression, regulation, and biological role in persister phenotypes

Chromosomally encoded toxin-antitoxin (TA) systems are abundantly present in bacteria and archaea. They have become a hot topic in recent years, because-after many frustrating years of searching for biological functions-some are now known to play roles in persister formation. Persister cells represent a subset of a bacterial population that enters a dormant state and thus becomes refractory to the action of antibiotics. TA modules come in several different flavors, regarding the nature of their gene products, their molecular mechanisms of regulation, their cellular targets, and probably their role in physiology. This review will primarily focus on the SOS-associated tisB/istR1 system in Escherichia coli and discuss its nuts and bolts as well as its effect in promoting a subpopulation phenotype that likely benefits long-term survival of a stressed population.

Bacterial translational regulations: high diversity between all mRNAs and major role in gene expression

BACKGROUND

In bacteria, the weak correlations at the genome scale between mRNA and protein levels suggest that not all mRNAs are translated with the same efficiency. To experimentally explore mRNA translational level regulation at the systemic level, the detailed translational status (translatome) of all mRNAs was measured in the model bacterium Lactococcus lactis in exponential phase growth.

RESULTS

Results demonstrated that only part of the entire population of each mRNA species was engaged in translation. For transcripts involved in translation, the polysome size reached a maximum of 18 ribosomes. The fraction of mRNA engaged in translation (ribosome occupancy) and ribosome density were not constant for all genes. This high degree of variability was analyzed by bioinformatics and statistical modeling in order to identify general rules of translational regulation. For most of the genes, the ribosome density was lower than the maximum value revealing major control of translation by initiation. Gene function was a major translational regulatory determinant. Both ribosome occupancy and ribosome density were particularly high for transcriptional regulators, demonstrating the positive role of translational regulation in the coordination of transcriptional networks. mRNA stability was a negative regulatory factor of ribosome occupancy and ribosome density, suggesting antagonistic regulation of translation and mRNA stability. Furthermore, ribosome occupancy was identified as a key component of intracellular protein levels underlining the importance of translational regulation.

CONCLUSIONS

We have determined, for the first time in a bacterium, the detailed translational status for all mRNAs present in the cell. We have demonstrated experimentally the high diversity of translational states allowing individual gene differentiation and the importance of translation-level regulation in the complex process linking gene expression to protein synthesis.

Single mutation in Shine-Dalgarno-like sequence present in the amino terminal of lactate dehydrogenase of Plasmodium effects the production of an eukaryotic protein expressed in a prokaryotic system

One of the most important step in structure-based drug design studies is obtaining the protein in active form after cloning the target gene. In one of our previous study, it was determined that an internal Shine-Dalgarno-like sequence present just before the third methionine at N-terminus of wild type lactate dehydrogenase enzyme of Plasmodium falciparum prevent the translation of full length protein. Inspection of the same region in P. vivax LDH, which was overproduced as an active enzyme, indicated that the codon preference in the same region was slightly different than the codon preference of wild type PfLDH. In this study, 5'-GGAGGC-3' sequence of P. vivax that codes for two glycine residues just before the third methionine was exchanged to 5'-GGAGGA-3', by mimicking P. falciparum LDH, to prove the possible effects of having an internal SD-like sequence when expressing an eukaryotic protein in a prokaryotic system. Exchange was made by site-directed mutagenesis. Results indicated that having two glycine residues with an internal SD-like sequence (GGAGGA) just before the third methionine abolishes the enzyme activity due to the preference of the prokaryotic system used for the expression. This study emphasizes the awareness of use of a prokaryotic system to overproduce an eukaryotic protein.

Application of synthetic biology in cyanobacteria and algae

Cyanobacteria and algae are becoming increasingly attractive cell factories for producing renewable biofuels and chemicals due to their ability to capture solar energy and CO₂ and their relatively simple genetic background for genetic manipulation. Increasing research efforts from the synthetic biology approach have been made in recent years to modify cyanobacteria and algae for various biotechnological applications. In this article, we critically review recent progresses in developing genetic tools for characterizing or manipulating cyanobacteria and algae, the applications of genetically modified strains for synthesizing renewable products such as biofuels and chemicals. In addition, the emergent challenges in the development and application of synthetic biology for cyanobacteria and algae are also discussed.

Teasing apart translational and transcriptional components of stochastic variations in eukaryotic gene expression

The intrinsic stochasticity of gene expression leads to cell-to-cell variations, noise, in protein abundance. Several processes, including transcription, translation, and degradation of mRNA and proteins, can contribute to these variations. Recent single cell analyses of gene expression in yeast have uncovered a general trend where expression noise scales with protein abundance. This trend is consistent with a stochastic model of gene expression where mRNA copy number follows the random birth and death process. However, some deviations from this basic trend have also been observed, prompting questions about the contribution of gene-specific features to such deviations. For example, recent studies have pointed to the TATA box as a sequence feature that can influence expression noise by facilitating expression bursts. Transcription-originated noise can be potentially further amplified in translation. Therefore, we asked the question of to what extent sequence features known or postulated to accompany translation efficiency can also be associated with increase in noise strength and, on average, how such increase compares to the amplification associated with the TATA box. Untangling different components of expression noise is highly nontrivial, as they may be gene or gene-module specific. In particular, focusing on codon usage as one of the sequence features associated with efficient translation, we found that ribosomal genes display a different relationship between expression noise and codon usage as compared to other genes. Within nonribosomal genes we found that sequence high codon usage is correlated with increased noise relative to the average noise of proteins with the same abundance. Interestingly, by projecting the data on a theoretical model of gene expression, we found that the amplification of noise strength associated with codon usage is comparable to that of the TATA box, suggesting that the effect of translation on noise in eukaryotic gene expression might be more prominent than previously appreciated.

The stochastic nature of gene expression leads to cell-to-cell differences in protein level referred to as noise. Expression noise can be disadvantageous, by affecting the precision of biological functions, but it may also be advantageous by enabling heterogeneous stress-response programs to environmental changes. Therefore various genes and gene groups might display various levels of expression noise. Importantly, gene expression is a multi-step process and the stochasticity of its individual steps, including transcription and translation, contributes to the resulting variability. Recent single cell analyses of gene expression in yeast have confirmed the theoretically predicted general trend where expression noise scales with protein abundance. However, some deviations from this basic trend have also been observed, prompting questions about the contribution of gene-specific features to such deviations. Accounting for noise heterogeneity in different gene groups, we revealed a clear relationship between noise and translation-related genomic features, specifically codon usage and 5′ UTR secondary structure. Our results suggest that the effect of translation on these deviations might be more prominent than previously appreciated, and provide important clues towards understanding expression stochasticity in yeast.

Probing translation initiation through ligand binding to the 5' mRNA coding region

Secondary structure matters: We have constructed artificial intragenic riboswitches to probe ribosome accessibility to the 5' mRNA coding region at three-base resolution in Escherichia coli. We show that only mRNA folding stability in the +1 to +15 nt region affects the translation process.

G, Shapiro A, Okunji C, Kosti I, Shomron N, Grigoryan V, Przytycka TM, Sauna ZE, Salari R, Mandel-Gutfreund Y, Komar AA, Kimchi-Sarfaty C. Characterization of coding synonymous and non-synonymous variants in ADAMTS13 using ex vivo and in silico approaches

Synonymous variations, which are defined as codon substitutions that do not change the encoded amino acid, were previously thought to have no effect on the properties of the synthesized protein(s). However, mounting evidence shows that these “silent” variations can have a significant impact on protein expression and function and should no longer be considered “silent”. Here, the effects of six synonymous and six non-synonymous variations, previously found in the gene of ADAMTS13, the von Willebrand Factor (VWF) cleaving hemostatic protease, have been investigated using a variety of approaches. The ADAMTS13 mRNA and protein expression levels, as well as the conformation and activity of the variants have been compared to that of wild-type ADAMTS13. Interestingly, not only the non-synonymous variants but also the synonymous variants have been found to change the protein expression levels, conformation and function. Bioinformatic analysis of ADAMTS13 mRNA structure, amino acid conservation and codon usage allowed us to establish correlations between mRNA stability, RSCU, and intracellular protein expression. This study demonstrates that variants and more specifically, synonymous variants can have a substantial and definite effect on ADAMTS13 function and that bioinformatic analysis may allow development of predictive tools to identify variants that will have significant effects on the encoded protein.

In silico design of functional DNA constructs

The promise of synthetic biology lies in the creation of novel function from the proper combination of genetic elements. De novo gene synthesis has become a cost-effective method for building virtually any conceptualized genetic construct, removing the constraints of extant sequences, and greatly facilitating study of the relationships between gene sequence and function. With the rapid increase in the number and variety of characterized and cataloged genetic elements, tools that facilitate assembly of such parts into functional constructs (genes, vectors, circuits, etc.) are essential. The Gene Designer software allows scientists and engineers to readily manage and recombine genetic elements into novel assemblies. It also provides tools for the simulation of molecular cloning schemes as well as the engineering and optimization of protein-coding sequences. Together, the functions in Gene Designer provide a complete capability to design functional genetic constructs.

Differential transcription of bacteriophage φX174 genes at 37 °C and 42 °C

To investigate how high temperature affects viral transcription, the absolute amounts of mRNA for six bacteriophage φX174 genes were compared at 37°C and 42°C using Q-PCR. At 37°C, mRNA levels for all genes were consistent with previous studies, but at 42°C mRNA levels for four genes were significantly different from levels at 37°C. Transcript levels were higher for genes B and D; the promoter before gene B appears to be up-regulated at high temperature. Levels for genes F and G were reduced at high temperature, possibly due to increased efficiency of the transcription termination signal immediately upstream of gene F. These functional changes in φX174 gene regulation at high temperature have not been described previously. Studies of phage evolution at high temperatures indicate that this difference in transcript levels is subject to adaptation.

A systematic approach to increase the efficiency of membrane protein production in cell-free expression systems

High amounts of membrane protein samples are needed for structural or functional analysis and a first bottleneck is often to obtain sufficient production efficiencies. The reduced complexity of protein production in cell-free expression systems results in a frequent correlation of efficiency problems with the essential transcription/translation process. We present a systematic tag variation strategy for the rapid improvement of cell-free expression efficiencies of membrane proteins based on the optimization of translation initiation. A small number of rationally designed short expression tags is attached via overlap PCR to the 5-prime end of the target protein coding sequence. The generated pool of DNA templates is analyzed in a cell-free expression screen and the most efficient template is selected for further preparative scale protein production. The expression tags can be minimized to only a few codons and no further impact on the coding sequence is required. The complete process takes only few days and the synthesized PCR fragments can be used directly as templates for preparative scale cell-free reactions. The strategy is exemplified with the production of a set of G-protein coupled receptors and yield improvements of up to 32-fold were obtained. All proteins were finally synthesized in amounts sufficient for further quality optimization and initial crystallization screens.