Roles for Synonymous Codon Usage in Protein Biogenesis

Understanding the Genetic Code

The universal triple-nucleotide genetic code is often viewed as a given, randomly selected through evolution. However, as summarized in this article, many observations and deductions within structural and thermodynamic frameworks help to explain the forces that must have shaped the code during the early evolution of life on Earth.

Nature and Regulation of Protein Folding on the Ribosome

Co-translational protein folding is an essential process by which cells ensure the safe and efficient production and assembly of new proteins in their functional native states following biosynthesis on the ribosome. In this review, we describe recent progress in probing the changes during protein synthesis of the free energy landscapes that underlie co-translational folding and discuss the critical coupling between these landscapes and the rate of translation that ultimately determines the success or otherwise of the folding process. Recent developments have revealed a variety of mechanisms by which both folding and translation can be modulated or regulated, and we discuss how these effects are utilised by the cell to optimise the outcome of protein biosynthesis.

Compositional properties and codon usage pattern of mitochondrial ATP gene in different classes of Arthropoda

Codon usage bias (CUB) is defined as the usage of synonymous codons unequally for an amino acid in a gene transcript. It is influenced by both mutation pressure and natural selection and is a species-specific property. In our current study, we used bioinformatic methods to investigate the coding sequences of mitochondrial adenosine triphosphate gene (MT-ATP) in different classes of arthropoda to know the codon usage pattern of the gene as no work was described earlier. The analysis of compositional properties suggested that the gene is AT rich. The effective number of codons revealed the CUB of both ATP6 and ATP8 gene was moderate. Heat map showed that the codons ending with AT were negatively associated with GC3 while the codons ending with GC were positively associated with GC3 in all the classes of arthropoda. Correspondence study revealed that the pattern of codon usage of ATP6 and ATP8 genes differed across classes. Neutrality plot suggested the codon usage bias of these two genes in phylum arthropoda was influenced by both mutation pressure and natural selection.

Chronic obstructive pulmonary disease: A crosstalk on nucleotide compositional dynamics and codon usage patterns of the genes involved in disease

Chronic obstructive pulmonary disease (COPD), a lung disease, affects a large number of people worldwide, leading to death. Here, we analyzed the compositional features and trends of codon usage of the genes influencing COPD to understand molecular biology, genetics, and evolutionary relationships of these genes as no work was reported yet. Coding sequences of COPD genes were found to be rich in guanine-cytosine (GC) content. A high value (34-60) of the effective number of codons of the genes indicated low codon usage bias (CUB). Correspondence analysis suggested that the COPD genes were distinct in their codon usage patterns. Relative synonymous codon usage values of codons differed between the more preferred codons and the less-preferred ones. Correlation analysis between overall nucleotides and those at third codon position revealed that mutation pressure might influence the CUB of the genes. The high correlation between GC12 and GC3 signified that directional mutation pressure might have operated at all the three codon positions in COPD genes.

Analysis of codon usage patterns in "Lonicerae Flos" (Lonicera macranthoides Hand. -Mazz.) based on transcriptome data

Lonicera macranthoides Hand. -Mazz. is an important medicinal and economical plant in China, however, the codon usage bias (CUB) in L. macranthoides genes is still unknown. In this study, L. macranthoides transcriptome sequencing has been completed, and codon usage patterns in 36,090 reconstructed genes from the L. macranthoides transcriptome were examined. The mean GC content and GC3 value is 44.9% and 43.1%, respectively, which indicates that nucleotide contents of L. macranthoides genome is somewhat AT rich, and its codon bias pattern tends to use A/T-ending codons. According to neutrality plot, ENC plot, PR2-Bias plot and correspondence analysis, we know that both compositional constraint under selection and mutation could affect the CUB in L. macranthoides, and the mutation is the most determinant factor. Meanwhile, gene expression levels can influence its codon usage pattern. Furthermore, we identified 29 optimal codons and most of them ended with A/U. The study will lay a foundation for future research on gene prediction, genetic engineering and molecular evolution in L. macranthoides.

Dual expression of CCA-adding enzyme and RNase T in Escherichia coli generates a distinct cca growth phenotype with diverse applications

Correct synthesis and maintenance of functional tRNA 3′-CCA-ends is a crucial prerequisite for aminoacylation and must be achieved by the phylogenetically diverse group of tRNA nucleotidyltransferases. While numerous reports on the in vitro characterization exist, robust analysis under in vivo conditions is lacking. Here, we utilize Escherichia coli RNase T, a tRNA-processing enzyme responsible for the tRNA-CCA-end turnover, to generate an in vivo system for the evaluation of A-adding activity. Expression of RNase T results in a prominent growth phenotype that renders the presence of a CCA- or A-adding enzyme essential for cell survival in an E. coli Δcca background. The distinct growth fitness allows for both complementation and selection of enzyme variants in a natural environment. We demonstrate the potential of our system via detection of altered catalytic efficiency and temperature sensitivity. Furthermore, we select functional enzyme variants out of a sequence pool carrying a randomized codon for a highly conserved position essential for catalysis. The presented E. coli-based approach opens up a wide field of future studies including the investigation of tRNA nucleotidyltransferases from all domains of life and the biological relevance of in vitro data concerning their functionality and mode of operation.

"CodonWizard" - An intuitive software tool with graphical user interface for customizable codon optimization in protein expression efforts

Optimization of coding sequences to maximize protein expression yield is often outsourced to external service providers during commercial gene synthesis and thus unfortunately remains a black box for many researchers. The presented software program "CodonWizard" offers scientists a powerful but easy-to-use tool for customizable codon optimization: The intuitive graphical user interface empowers even scientists inexperienced in the art to straightforward design, modify, test and save complex codon optimization strategies and to publicly share successful otimization strategies among the scientific community. "Codon Wizard" provides highly flexible features for sequence analysis and completely customizable modification/optimization of codon usage of any given input sequence data (DNA/RNA/peptide) using freely combinable algorithms, allowing for implementation of contemporary, well-established optimization strategies as well as novel, proprietary ones alike. Contrary to comparable tools, "Codon Wizard" thus finally opens up ways for an empirical approach to codon optimization and may also >be used completely offline to protect resulting intellectual property. As a benchmark, the reliability, intuitiveness and utility of the application could be demonstrated by increasing the yield of recombinant TEV-protease expressed in E. coli by several orders of magnitude after codon optimization using "CodonWizard" - Permanently available for download on the web at http://schwalbe.org.chemie.uni-frankfurt.de/node/3324.

Different mitogenomic codon usage patterns between damselflies and dragonflies and nine complete mitogenomes for odonates

Damselflies and dragonflies, of the order Odonata, have distinct body plans and predatory abilities. Knowledge of their various evolutionary histories will allow for an understanding of the genetic and phenotypic evolution of insects. Mitogenomes are suitable materials to elucidate this, but the mitogenome of only a few odonates have been annotated. Herein, we report the complete mitogenome of nine odonates, including seven dragonflies and two damselflies, and a comprehensive analysis of the codon usage in 31 Odonata mitogenomes with the aim to estimate their evolutionary characteristics. Overall, a weak codon bias exists among odonate mitogenomes, although this favours AT-ending codons. Damselflies have a weaker codon usage bias than dragonflies, and 37 codons have significantly different usages. Both directional mutation and purifying selection shape damselfly and dragonfly mitogenomes. Although inevitable, directional mutation bias plays a minor role, whereas purifying selection pressure is the dominant evolutionary force. A higher selection pressure is observed in dragonflies than in damselflies, but it mainly acts on codon usage patterns rather than amino acid translation. Our findings suggest that dragonflies might have more efficient mitochondrial gene expression levels than damselflies, producing more proteins that support their locomotion and predatory abilities.

Analysis of codon usage patterns and influencing factors in Nipah virus

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Nipah virus (NiV) genes are AT-rich.

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Codon usage bias of NiV genes is low.

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Patterns of codon usage bias differ across the genomes of NiV.

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Both mutation pressure and natural selection influenced codon usage bias of NiV genes.

Codon usage bias (CUB) is the unequal usage of synonymous codons of an amino acid in which some codons are used more often than others and is widely used in understanding molecular biology, genetics, and functional regulation of gene expression. Nipah virus (NiV) is an emerging zoonotic paramyxovirus that causes fatal disease in both humans and animals. NiV was first identified during an outbreak of a disease in Malaysia in 1998 and then occurred periodically since 2001 in India, Bangladesh, and the Philippines. We used bioinformatics tools to analyze the codon usage patterns in a genome-wide manner among 11 genomes of NiV as no work was reported yet. The compositional properties revealed that the overall GC and AT contents were 41.96 and 58.04%, respectively i.e. Nipah virus genes were AT-rich. Correlation analysis between overall nucleotide composition and its 3^rd codon position suggested that both mutation pressure and natural selection might influence the CUB across Nipah genomes. Neutrality plot revealed natural selection might have played a major role while mutation pressure had a minor role in shaping the codon usage bias in NiV genomes.

Colistin Resistant A. baumannii: Genomic and Transcriptomic Traits Acquired Under Colistin Therapy

Even though colistin-based treatment represents the antimicrobial-regimen backbone for the management of multidrug-resistant Gram-negative infections, colistin resistance is still rare, at least as a full resistance, in Acinetobacter baumannii (Ab). We investigated the genomics and transcriptomics of two clinical Extensively Drug Resistance (XDR) colistin-susceptible/resistant (COL-S/R) Ab strain-pairs in which COL-resistance was developed after exposure to colistin therapy. The molecular characterization of the strains showed that all strains belonged to PFGE-A, ST-281, OXA-23 producers, Global Clone-II, and were resistant to imipenem, meropenem, ampicillin/sulbactam, ciprofloxacin, gentamicin, amikacin, trimethoprim/sulfamethoxazole, and susceptible to tigecycline, in agreement with NGS-acquired resistome. COL-R vs. COL-S Ab comparative genomics, mapping on Ab ATCC 17978 and Ab ACICU Reference Genomes, revealed a closely related genomic phylogeny, especially between strain-pair isolates, and distinctive common genomic non-synonymous SNPs (nsSNPs) in COL-R Ab strains. Furthermore, pmrB and pmrC nsSNPs were found. Notably we recovered, for the first time, lpxC and lpxD nsSNPs previously described only in "in-vitro" mutants and associated with colistin resistance in a clinical COL-R Ab. COL-R vs. COL-S Ab comparative transcriptomics evidenced a strain-dependent response to the colistin resistance onset highly variable among the single COL-R strains vs. their COL-S parents and merely seven common over-expressed transcripts, i.e. the PgaB lipoprotein for biofilm-matrix production, the diacylglycerol kinase for the lipid recycling in the membrane-derived oligosaccharide cycle, a membrane non-ribosomal peptide synthetase, the Lipid A phosphoethanol aminotransferase PmrC, and three hypothetical proteins. The transcript analysis of the "COL-R related genes" and the RNA-seq data confirmed pmrCAB over-expression responsible for a greater positive net cell-charge, and lpxACD under-expression in COL-R causing a decreased LPS production, as main mechanisms of colistin resistance. Our study reports the COL-R Ab genomic and transcriptomic signatures reflecting the interplay between several direct and indirect potential adaptations to antimicrobial pressure, including the occurrence of SNP accumulation hotspot loci in genes related to intrinsic or adaptive colistin resistance, surface adhesion proteins and porins, and over-expressed genes involved in different pathways, i.e. biofilm production, oxidative stress response, extensive drug and COL resistance.

Identification and comparison of allergenicity of native and recombinant fish major allergen parvalbumins from Japanese flounder (Paralichthys olivaceus)

Compared with native parvalbumin, recombinant β-parvalbumin based on the optimized DNA sequence can be used in fish allergen confirmation.

Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses

Cells adapt to stress by altering gene expression at multiple levels. Here, we propose a new mechanism regulating stress-dependent gene expression at the level of translation, with coordinated interplay between the tRNA epitranscriptome and biased codon usage in families of stress-response genes. In this model, auxiliary genetic information contained in synonymous codon usage enables regulation of codon-biased and functionally related transcripts by dynamic changes in the tRNA epitranscriptome. This model partly explains the association between synchronous stress-dependent epitranscriptomic marks and significant multi-codon usage skewing in families of translationally regulated transcripts. The model also predicts translational adaptation during viral infections.

Can Protein Expression Be Regulated by Modulation of tRNA Modification Profiles?

tRNAs are the central adaptor molecules in translation. Their decoding properties are influenced by post-transcriptional modifications, particularly in the critical anticodon-stem-loop (ASL) region. Synonymous codon choice, also called codon usage bias, affects both translation efficiency and accuracy, and ASL modifications play key roles in both of these processes. In combination with a handful of historical examples, recent studies integrating ribosome profiling, proteomics, codon-usage analyses, and modification quantifications show that levels of tRNA modifications can change under stress, during development, or under specific metabolic conditions and can modulate the expression of specific genes. Deconvoluting the different responses (global or specific) to tRNA modification deficiencies can be difficult because of pleiotropic effects, but, as more cases emerge, it does seem that tRNA modification changes could add another layer of regulation in the transfer of information from DNA to protein.

The stop-and-go traffic regulating protein biogenesis: How translation kinetics controls proteostasis

Generating a functional proteome requires the ribosome to carefully regulate disparate co-translational processes that determine the fate of nascent polypeptides. With protein synthesis being energetically expensive, the ribosome must balance the costs of efficiently making a protein with those of properly folding it. Emerging as a primary means of regulating this trade-off is the nonuniform rate of translation elongation that defines translation kinetics. The varying speeds with which the ribosome progresses along a transcript have been implicated in several aspects of protein biogenesis, including co-translational protein folding and translational fidelity, as well as gene expression by mediating mRNA decay and protein quality control pathways. The optimal translation kinetics required to efficiently execute these processes can be distinct. Thus, the ribosome is tasked with tightly regulating translation kinetics to balance these processes while maintaining adaptability for changing cellular conditions. In this review, we first discuss the regulatory role of translation elongation in protein biogenesis and what factors influence elongation kinetics. We then describe how changes in translation kinetics signal downstream pathways that dictate the fate of nascent polypeptides. By regulating these pathways, the kinetics of translation elongation has emerged as a critical tool for driving gene expression and maintaining proteostasis through varied mechanisms, including nascent chain folding and binding different ribosome-associated machinery. Indeed, a growing number of examples demonstrate the important role of local changes in elongation kinetics in modulating the pathophysiology of human disease.

Interactions between the mRNA and Rps3/uS3 at the entry tunnel of the ribosomal small subunit are important for no-go decay

No-go Decay (NGD) is a process that has evolved to deal with stalled ribosomes resulting from structural blocks or aberrant mRNAs. The process is distinguished by an endonucleolytic cleavage prior to degradation of the transcript. While many of the details of the pathway have been described, the identity of the endonuclease remains unknown. Here we identify residues of the small subunit ribosomal protein Rps3 that are important for NGD by affecting the cleavage reaction. Mutation of residues within the ribosomal entry tunnel that contact the incoming mRNA leads to significantly reduced accumulation of cleavage products, independent of the type of stall sequence, and renders cells sensitive to damaging agents thought to trigger NGD. These phenotypes are distinct from those seen in combination with other NGD factors, suggesting a separate role for Rps3 in NGD. Conversely, ribosomal proteins ubiquitination is not affected by rps3 mutations, indicating that upstream ribosome quality control (RQC) events are not dependent on these residues. Together, these results suggest that Rps3 is important for quality control on the ribosome and strongly supports the notion that the ribosome itself plays a central role in the endonucleolytic cleavage reaction during NGD.

In all organisms, optimum cellular fitness depends on the ability of cells to recognize and degrade aberrant molecules. Messenger RNA is subject to alterations and, as a result, often presents roadblocks for the translating ribosomes. It is not surprising, then, that organisms evolved pathways to resolve these valuable stuck ribosomes. In eukaryotes, this process is called no-go decay (NGD) because it is coupled with decay of mRNAs that are associated with ribosomes that do not ‘go’. This decay process initiates with cleavage of the mRNA near the stall site, but some important details about this reaction are lacking. Here, we show that the ribosome itself is very central to the cleavage reaction. In particular, we identified a pair of residues of a ribosomal protein to be important for cleavage efficiency. These observations are consistent with prior structural studies showing that the residues make intimate contacts with the incoming mRNA in the entry tunnel. Altogether our data provide important clues about this quality-control pathway and suggest that the endonuclease not only recognizes stalled ribosomes but may have coevolved with the translation machinery to take advantage of certain residues of the ribosome to fulfill its function.

Compositional properties and codon usage of TP73 gene family

The TP73 gene is considered as one of the members of TP53 gene family and shows much homology to p53 gene. TP73 gene plays a pivotal role in cancer studies in addition to other biological functions. Codon usage bias (CUB) is the phenomenon of unequal usage of synonymous codons for an amino acid wherein some codons are more frequently used than others and it reveals the evolutionary relationship of a gene. Here, we report the pattern of codon usage in TP73 gene using various bioinformatic tools as no work was reported yet. Nucleotide composition analysis suggested that the mean nucleobase C was the highest, followed by G and the gene was GC rich. Correlation analysis between codon usage and GC3 suggested that most of the GC-ending codons showed positive correlation while most of the AT-ending codons showed negative correlation with GC3 in the coding sequences of TP73 gene variants in human. The CUB is moderate in human TP73 gene as evident from intrinsic codon deviation index (ICDI) analysis. Nature selected against two codons namely ATA (isoleucine) and AGA (arginine) in the coding sequences of TP73 gene during the course of evolution. A significant correlation (p < 0.05) was found between overall nucleotide composition and its composition at the 3rd codon position, indicating that both mutation pressure and natural selection might influence the CUB. The correlation analysis between ICDI and biochemical properties of protein suggested that variation of CUB was associated with degree of hydrophobicity and length of protein.

Genetic variation in KCNQ4 gene is associated with susceptibility to noise-induced hearing loss in a Chinese population

Noise-induced hearing loss (NIHL), one of the most widespread occupational health risks worldwide, is a kind of complex disorder resulting from both genetic and environmental factors. KCNQ4 channels are crucial to the internal ear potassium recycling. To explore whether KCNQ4 polymorphism is associated with individual susceptibility to NIHL, we performed this genetic association study on 571 NIHL cases and 639 normal hearing controls selected from about 2700 Chinese noise-exposed workers. General information and audiometric data were obtained through questionnaires and pure-tone audiometry (PTA). DNA samples were collected and genotyping for three selected SNPs (rs709688, rs2769256 and rs4660468) was performed. Significant differences were observed between cases and controls for the genotype frequency and allele frequency in rs4660468, suggesting that rs4660468 CT/TT genotype and T allele may be risk factors for NIHL. In subjects exposed to noise for more than 16 years (OR = 1.23, 95% CI = 1.09-1.53) and those who exposed to noise >92 dB (OR = 1.29, 95% CI = 1.08-1.69), increased risks of NIHL were found after stratified analysis for rs4660468. Our results suggest that rs4660468 T allele of KCNQ4 involves with a higher risk of NIHL and could be one biomarker of susceptibility for Chinese noise exposed workers.

Hepatitis A Virus Codon Usage: Implications for Translation Kinetics and Capsid Folding

Codon usage bias is universal to all genomes. Hepatitis A virus (HAV) codon usage is highly biased and deoptimized with respect to its host. Accordingly, HAV is unable to induce cellular translational shutoff and its internal ribosome entry site (IRES) is inefficient. Codon usage deoptimization may be seen as a hawk (host cell) versus dove (HAV) game strategy for accessing transfer RNA (tRNA). HAV avoids use of abundant host cell codons and thereby eludes competition for the corresponding tRNAs. Instead, codons that are abundant or rare in cellular messenger RNAs (mRNAs) are used relatively rarely in its genome, although intermediately abundant host cell codons are abundant in the viral genome. Rare codons in the capsid coding region slow down the translation elongation rate, and in doing so intrinsically modulate capsid folding, which is critical to the stability of a virus transmitted through the fecal-oral route. HAV is a paradigmatic example of what has been proposed as a codon usage "code" for protein structure.

Upgrading aminoacyl-tRNA synthetases for genetic code expansion

Synthesis of proteins with non-canonical amino acids via genetic code expansion is at the forefront of synthetic biology. Progress in this field has enabled site-specific incorporation of over 200 chemically and structurally diverse amino acids into proteins in an increasing number of organisms. This has been facilitated by our ability to repurpose aminoacyl-tRNA synthetases to attach non-canonical amino acids to engineered tRNAs. Current efforts in the field focus on overcoming existing limitations to the simultaneous incorporation of multiple non-canonical amino acids or amino acids that differ from the l-α-amino acid structure (e.g. d-amino acid or β-amino acid). Here, we summarize the progress and challenges in developing more selective and efficient aminoacyl-tRNA synthetases for genetic code expansion.

Quantifying codon usage in signal peptides: Gene expression and amino acid usage explain apparent selection for inefficient codons

The Sec secretion pathway is found across all domains of life. A critical feature of Sec secreted proteins is the signal peptide, a short peptide with distinct physicochemical properties located at the N-terminus of the protein. Previous work indicates signal peptides are biased towards translationally inefficient codons, which is hypothesized to be an adaptation driven by selection to improve the efficacy and efficiency of the protein secretion mechanisms. We investigate codon usage in the signal peptides of E. coli using the Codon Adaptation Index (CAI), the tRNA Adaptation Index (tAI), and the ribosomal overhead cost formulation of the stochastic evolutionary model of protein production rates (ROC-SEMPPR). Comparisons between signal peptides and 5'-end of cytoplasmic proteins using CAI and tAI are consistent with a preference for inefficient codons in signal peptides. Simulations reveal these differences are due to amino acid usage and gene expression - we find these differences disappear when accounting for both factors. In contrast, ROC-SEMPPR, a mechanistic population genetics model capable of separating the effects of selection and mutation bias, shows codon usage bias (CUB) of the signal peptides is indistinguishable from the 5'-ends of cytoplasmic proteins. Additionally, we find CUB at the 5'-ends is weaker than later segments of the gene. Results illustrate the value in using models grounded in population genetics to interpret genetic data. We show failure to account for mutation bias and the effects of gene expression on the efficacy of selection against translation inefficiency can lead to a misinterpretation of codon usage patterns.

Coping with stress by regulating tRNAs

Stress conditions curtail the energetically costly process of messenger RNA translation. In this issue of Science Signaling, Torrent et al. report key evidence for a direct link between codon usage and translation regulation in response to stress.

The adaptation of codon usage of +ssRNA viruses to their hosts

Viruses depend on their host's cellular structure to survive. Most of them do not have tRNAs, their translation relies on hosts' tRNA pools. Over the course of evolution, viruses needed to optimally exploit cellular processes of their host. Thus, codon usage of a virus should coevolve with its host to efficiently and rapidly replicate. Some viruses can invade a broad spectrum of hosts (BSTVs), while others can invade a narrow spectrum only (NSTVs). Consequently, we test the hypothesis that similarity of codon usage preference and the degree of matching between BSTVs and their hosts will be lower than that of NSTVs, which only need to coevolve with few hosts. We compare the patterns of codon usage in 255 virus genomes to test this hypothesis. Our results show that NSTVs have a higher degree of matching to their hosts' tRNA pools than BSTVs. Further, analysis of the effective number of codons (ENC) infers that codon usage bias of NSTVs is relatively stronger than that of BSTVs. Thus, codon usage of NSTVs tends to better match their host than that of BSTVs. This supports the hypothesis that viruses adapt to the expression system of their host(s).

NLRP3 expression in mesencephalic neurons and characterization of a rare NLRP3 polymorphism associated with decreased risk of Parkinson's disease

Neuroinflammation is a well-characterized pathophysiology occurring in association with the progression of Parkinson's disease. Characterizing the cellular and molecular basis of neuroinflammation is critical to understanding its impact on the incidence and progression of PD and other neurologic disorders. Inflammasomes are intracellular pro-inflammatory pattern-recognition receptors capable of initiating and propagating inflammation. These cellular complexes are well characterized in the innate immune system and activity of the NLRP3 inflammasome has been reported in microglia. NLRP3 inflammasome activity has been associated with Alzheimer's disease, and recent reports, from our laboratory and others, indicate that Nlrp3 is required for neuroinflammation and nigral cell loss in animal models of PD. NLRP3 has not yet been characterized in PD patients. Here we characterize NLRP3 in PD using immunohistologic and genetic approaches. Histologic studies revealed elevated NLRP3 expression in mesencephalic neurons of PD patients. Analysis of exome sequencing data for genetic variation of NLRP3 identified multiple single-nucleotide polymorphisms (SNPs) including rs7525979 that was associated with a significantly reduced risk of developing PD. Mechanistic studies conducted in HEK293 cells indicated that the synonymous SNP, NLRP3 rs7525979, alters the efficiency of NLRP3 translation impacting NLRP3 protein stability, ubiquitination state, and solubility. These data provide evidence that dopaminergic neurons are a cell-of-origin for inflammasome activity in PD and are consistent with recent animal studies, suggesting that inflammasome activity may impact the progression of PD.

Timing during translation matters: synonymous mutations in human pathologies influence protein folding and function

Ribosomes translate mRNAs with non-uniform speed. Translation velocity patterns are a conserved feature of mRNA and have evolved to fine-tune protein folding, expression and function. Synonymous single-nucleotide polymorphisms (sSNPs) that alter programmed translational speed affect expression and function of the encoded protein. Synergistic advances in next-generation sequencing have led to the identification of sSNPs associated with disease penetrance. Here, we draw on studies with disease-related proteins to enhance our understanding of mechanistic contributions of sSNPs to functional alterations of the encoded protein. We emphasize the importance of identification of sSNPs along with disease-causing mutations to understand genotype-phenotype relationships.

Gain of function of sporadic/familial hemiplegic migraine-causing SCN1A mutations: Use of an optimized cDNA

INTRODUCTION

Familial hemiplegic migraine 3 is an autosomal dominant headache disorder associated with aura and transient hemiparesis, caused by mutations of the neuronal voltage-gated sodium channel Nav1.1. While a gain-of function phenotype is generally assumed to underlie familial hemiplegic migraine, this has not been fully explored. Indeed, a major obstacle in studying in vitro neuronal sodium channels is the difficulty in propagating and mutagenizing expression plasmids containing their cDNAs. The aim of this work was to study the functional effect of two previously uncharacterized hemiplegic migraine causing mutations, Leu1670Trp (L1670W) and Phe1774Ser (F1774S).

METHODS

A novel SCN1A containing-plasmid was designed in silico and synthesized, and migraine mutations were inserted in this background. Whole-cell patch clamp was performed to investigate the functional properties of mutant Nav1.1 transiently expressed in Human Embryonic Kidney 293 cells.

RESULTS AND CONCLUSIONS

We generated an optimized Nav1.1 expression plasmid that was extremely simple to handle and used the novel plasmid to study the functional effects of two migraine mutations. We observed that L1670W, but not F1774S, reduced current density and that both mutations led to a dramatic increase in persistent sodium currents, a depolarizing shift of the steady state-inactivation voltage-dependence, and a faster recovery from inactivation. The results are consistent with a major gain-of function effect underlying familial hemiplegic migraine 3. Our optimization strategy will help to characterize in an efficient manner the effect in vitro of mutations of neuronal voltage-gated sodium channels.

The analysis of genome composition and codon bias reveals distinctive patterns between avian and mammalian circoviruses which suggest a potential recombinant origin for Porcine circovirus 3

Members of the genus Circovirus are host-specific viruses, which are totally dependent on cell machinery for their replication. Consequently, certain mimicry of the host genome features is expected to maximize cellular replicative system exploitation and minimize the recognition by the innate immune system. In the present study, the analysis of several genome composition and codon bias parameters of circoviruses infecting avian and mammalian species demonstrated the presence of quite distinctive patterns between the two groups. Remarkably, a higher deviation from the expected values based only on mutational patterns was observed for mammalian circoviruses both at dinucleotide and codon levels. Accordingly, a stronger selective pressure was estimated to shape the genome of mammalian circoviruses, particularly in the Cap encoding gene, compared to avian circoviruses. These differences could be attributed to different physiological and immunological features of the two host classes and suggest a trade-off between a tendency to optimize the capsid protein translation while minimizing the recognition of the genome and the transcript molecules. Interestingly, the recently identified Porcine circovirus 3 (PCV-3) had an intermediate pattern in terms of genome composition and codon bias. Particularly, its Rep gene appeared closely related to other mammalian circoviruses (especially bat circoviruses) while the Cap gene more closely resembled avian circoviruses. These evidences, coupled with the high selective forces apparently modelling the PCV-3 Cap gene composition, suggest the potential recombinant origin, followed or preceded by a host jump, of this virus.

A Single Nucleotide Polymorphism in the Vitamin D Receptor Gene Is Associated With Decreased Levels of the Protein and a Penetrating Pattern in Crohn's Disease

BACKGROUND

Vitamin D signaling modulates inflammation through the vitamin D receptor (VDR). The synonymous single nucleotide polymorphism (SNP) rs731236, located in the VDR gene, has been associated with a higher risk of Crohn's disease (CD). We analyzed differences in VDR expression levels among CD patients who were homozygous for allelic variants in this SNP and their relevance for disease course.

METHODS

DNA was extracted from blood samples of CD patients, and SNP genotyping was performed by polymerase chain reaction-restriction fragment length polymorphism. Fresh blood from patients was used to isolate peripheral blood mononuclear cells (PBMCs) or to determine the expression of adhesion molecules by flow cytometry. We analyzed the gene expression of VDR and several cytokines in PBMCs using real-time polymerase chain reaction and the protein levels of VDR, NFκB, and IκBα by immunoblot. In addition, we collected complete clinical data for a group of 103 patients, including age at diagnosis, disease location, and disease behavior to compare patient characteristics with respect to genotype.

RESULTS

We found that CD patients who were homozygous for the risk allele presented lower levels of VDR protein in PBMCs, and that this was associated with an upregulation of IL1β mRNA and activation of lymphocytic adhesion molecules. These patients had a higher risk of developing a B3-penetrating phenotype and of needing to undergo surgery.

CONCLUSION

Our data highlight the relevance of vitamin D/VDR signaling in modulating the subjacent inflammation that leads to CD-related complications.

Accessibility of the Shine-Dalgarno Sequence Dictates N-Terminal Codon Bias in E. coli

Despite considerable efforts, no physical mechanism has been shown to explain N-terminal codon bias in prokaryotic genomes. Using a systematic study of synonymous substitutions in two endogenous E. coli genes, we show that interactions between the coding region and the upstream Shine-Dalgarno (SD) sequence modulate the efficiency of translation initiation, affecting both intracellular mRNA and protein levels due to the inherent coupling of transcription and translation in E. coli. We further demonstrate that far-downstream mutations can also modulate mRNA levels by occluding the SD sequence through the formation of non-equilibrium secondary structures. By contrast, a non-endogenous RNA polymerase that decouples transcription and translation largely alleviates the effects of synonymous substitutions on mRNA levels. Finally, a complementary statistical analysis of the E. coli genome specifically implicates avoidance of intra-molecular base pairing with the SD sequence. Our results provide general physical insights into the coding-level features that optimize protein expression in prokaryotes.

Cobalamin-Dependent C-Methyltransferases From Marine Microbes: Accessibility via Rhizobia Expression

Cobalamin-dependent radical S-adenosylmethionine (rSAM) methyltransferases catalyze chemically challenging methylation reactions on diverse natural products at unactivated carbon centers. In vivo reconstitution and biosynthetic studies of natural product gene clusters encoding these enzymes are often severely limited by ineffective heterologous expression hosts, including the otherwise versatile Escherichia coli. In this chapter, we describe the use of rhizobia bacteria as effective expression hosts for cobalamin-dependent rSAM C-methyltransferases. We chose the natural product pathway encoding the heavily modified cytotoxic peptides, the polytheonamides, as our model pathway due to the presence of two methyltransferases responsible for a total of 17 C-methylations. Detailed protocols are given for vector construction, transformation, and heterologous expression in Rhizobium leguminosarum bv. viciae 3841. Additional methods pertaining to analytical separation and mass spectrometric analysis of modified peptides are also entailed. As genomics continues to uncover new enzymes and pathways from unknown and uncultivated microbes, use of metabolically distinct heterologous expression hosts like rhizobia will be a necessary tool to unravel the catalytic and metabolic diversity of marine microbial life.

Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation

Acquisition of mutations is central to evolution; however, the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, may alleviate the effects of destabilizing mutations thus promoting sequence diversification. To illuminate how chaperones can influence protein evolution, we examined the effect of reduced activity of the chaperone Hsp90 on poliovirus evolution. We find that Hsp90 offsets evolutionary trade-offs between protein stability and aggregation. Lower chaperone levels favor variants of reduced hydrophobicity and protein aggregation propensity but at a cost to protein stability. Notably, reducing Hsp90 activity also promotes clusters of codon-deoptimized synonymous mutations at inter-domain boundaries, likely to facilitate cotranslational domain folding. Our results reveal how a chaperone can shape the sequence landscape at both the protein and RNA levels to harmonize competing constraints posed by protein stability, aggregation propensity, and translation rate on successful protein biogenesis.

Codon harmonization - going beyond the speed limit for protein expression

Codon usage distribution has been soundly used by nature to fine tune protein biogenesis. Alteration of the mRNA structure or sequential scheduling of codons can profoundly affect translation, thus altering protein yield, functionality, solubility, and proper folding. Building on these observations, here, we present an evaluation of different recently designed algorithms of sequence adaptation based on Codon Adaptation Index (CAI) profiling. The first algorithm globally harmonizes synonymous codons in the original sequence in full respect to the heterologous expression host codon usage. The second recodes the sequence in accordance with the native sequence CAI profile. Our data, generated on three model proteins, highlights the importance to consider gene recoding as a parameter itself for recombinant protein expression improvement.

Factors affecting synonymous codon usage of housekeeping genes in Drosophila melanogaster

Housekeeping genes (HK genes) are required for cell survival and the maintenance of basic cellular functions. The investigation of factors affecting codon usage patterns in HK genes of insects can help in understanding the molecular evolution of insects and aid the development of insect pest management strategies. In this study, we employed bioinformatics approaches to analyze the codon usage bias (CUB) of HK genes in the insect model organism, Drosophila melanogaster. A comparison of CUB between 1107 HK genes and 1084 high tissue specificity genes suggested that HK genes have higher CUB in D. melanogaster. In addition, we found that CUB inversely correlates with the non-synonymous substitution rate of HK genes. Therefore, we attempted to identify the factors that potentially influence the codon usage pattern of HK genes. Our results suggest that mutation pressure and natural selection highly correlate with CUB in the HK genes of D. melanogaster and that two topological properties of HK proteins (proportion of protein interacting length and protein connectivity) also correlate with CUB in the HK genes of D. melanogaster. This study provides insight into CUB in the HK genes of D. melanogaster, and the results can support future investigations of potential applications in agricultural and biomedical field.

Codon based co-occurrence network motifs in human mitochondria

The nucleotide polymorphism in the human mitochondrial genome (mtDNA) tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, genome-wide nucleotide co-occurrence networks were constructed using data comprised of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns among codon and non-codon positions. We found evidence that the evolution of human mitochondria DNA is dominated by adaptive forces, particularly mutation and selection, which was supported by many previous studies. The diversity observed in the mtDNA was compared with mutations, co-occurring mutations, network motifs considering codon positions as causing agent. This comparison showed that long-range nucleotide co-occurrences have a large effect on genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analysis also showed that variable nucleotide positions of different human sub-populations implemented the independent mtDNA evolution to its geographical dispensation. Ergo, this study has provided both a network framework and a codon glance to investigate co-occurring genomic variations that are critical in underlying complex mitochondrial evolution.

Evolutionary analysis of polyproline motifs in Escherichia coli reveals their regulatory role in translation

Translation of consecutive prolines causes ribosome stalling, which is alleviated but cannot be fully compensated by the elongation factor P. However, the presence of polyproline motifs in about one third of the E. coli proteins underlines their potential functional importance, which remains largely unexplored. We conducted an evolutionary analysis of polyproline motifs in the proteomes of 43 E. coli strains and found evidence of evolutionary selection against translational stalling, which is especially pronounced in proteins with high translational efficiency. Against the overall trend of polyproline motif loss in evolution, we observed their enrichment in the vicinity of translational start sites, in the inter-domain regions of multi-domain proteins, and downstream of transmembrane helices. Our analysis demonstrates that the time gain caused by ribosome pausing at polyproline motifs might be advantageous in protein regions bracketing domains and transmembrane helices. Polyproline motifs might therefore be crucial for co-translational folding and membrane insertion.

Polyproline motifs induce ribosome stalling during translation, but the functional significance of this effect remains unclear. Our evolutionary analysis of polyproline motifs reveals that they are disfavored in E. coli proteomes as a consequence of the reduced translation efficiency, supporting the conjecture that translation efficiency-based evolutionary pressure shapes protein sequences. Enrichment of polyproline motifs in the protein regions bracketing structural domains and transmembrane helices indicates their regulatory role in co-translational protein folding and transmembrane helix insertion. Polyproline motifs could thus serve as protein-level cis-acting elements, which directly regulate the rate of translation elongation.

Principles of Protein Stability and Their Application in Computational Design

Proteins are increasingly used in basic and applied biomedical research. Many proteins, however, are only marginally stable and can be expressed in limited amounts, thus hampering research and applications. Research has revealed the thermodynamic, cellular, and evolutionary principles and mechanisms that underlie marginal stability. With this growing understanding, computational stability design methods have advanced over the past two decades starting from methods that selectively addressed only some aspects of marginal stability. Current methods are more general and, by combining phylogenetic analysis with atomistic design, have shown drastic improvements in solubility, thermal stability, and aggregation resistance while maintaining the protein's primary molecular activity. Stability design is opening the way to rational engineering of improved enzymes, therapeutics, and vaccines and to the application of protein design methodology to large proteins and molecular activities that have proven challenging in the past.

Local genic base composition impacts protein production and cellular fitness

The maintenance of a G + C content that is higher than the mutational input to a genome provides support for the view that selection serves to increase G + C contents in bacteria. Recent experimental evidence from Escherichia coli demonstrated that selection for increasing G + C content operates at the level of translation, but the precise mechanism by which this occurs is unknown. To determine the substrate of selection, we asked whether selection on G + C content acts across all sites within a gene or is confined to particular genic regions or nucleotide positions. We systematically altered the G + C contents of the GFP gene and assayed its effects on the fitness of strains harboring each variant. Fitness differences were attributable to the base compositional variation in the terminal portion of the gene, suggesting a connection to the folding of a specific protein feature. Variants containing sequence features that are thought to result in rapid translation, such as low G + C content and high levels of codon adaptation, displayed highly reduced growth rates. Taken together, our results show that purifying selection acting against A and T mutations most likely results from their tendency to increase the rate of translation, which can perturb the dynamics of protein folding.

Unraveling co-translational protein folding: Concepts and methods

Advances in techniques such as nuclear magnetic resonance spectroscopy, cryo-electron microscopy, and single-molecule and time-resolved fluorescent approaches are transforming our ability to study co-translational protein folding both in vivo in living cells and in vitro in reconstituted cell-free translation systems. These approaches provide comprehensive information on the spatial organization and dynamics of nascent polypeptide chains and the kinetics of co-translational protein folding. This information has led to an improved understanding of the process of protein folding in living cells and should allow remaining key questions in the field, such as what structures are formed within nascent chains during protein synthesis and when, to be answered. Ultimately, studies using these techniques will facilitate development of a unified concept of protein folding, a process that is essential for proper cell function and organism viability. This review describes current methods for analysis of co-translational protein folding with an emphasis on some of the recently developed techniques that allow monitoring of co-translational protein folding in real-time.

PDE11A negatively regulates lithium responsivity

Lithium responsivity in patients with bipolar disorder has been genetically associated with Phosphodiesterase 11A (PDE11A), and lithium decreases PDE11A mRNA in induced pluripotent stem cell-derived hippocampal neurons originating from lithium-responsive patients. PDE11 is an enzyme uniquely enriched in the hippocampus that breaks down cyclic AMP and cyclic GMP. Here we determined whether decreasing PDE11A expression is sufficient to increase lithium responsivity in mice. In dorsal hippocampus and ventral hippocampus (VHIPP), lithium-responsive C57BL/6J and 129S6/SvEvTac mice show decreased PDE11A4 protein expression relative to lithium-unresponsive BALB/cJ mice. In VHIPP, C57BL/6J mice also show differences in PDE11A4 compartmentalization relative to BALB/cJ mice. In contrast, neither PDE2A nor PDE10A expression differ among the strains. The compartment-specific differences in PDE11A4 protein expression are explained by a coding single-nucleotide polymorphism (SNP) at amino acid 499, which falls within the GAF-B homodimerization domain. Relative to the BALB/cJ 499T, the C57BL/6J 499A decreases PDE11A4 homodimerization, which removes PDE11A4 from the membrane. Consistent with the observation that lower PDE11A4 expression correlates with better lithium responsiveness, we found that Pde11a knockout mice (KO) given 0.4% lithium chow for 3+ weeks exhibit greater lithium responsivity relative to wild-type (WT) littermates in tail suspension, an antidepressant-predictive assay, and amphetamine hyperlocomotion, an anti-manic predictive assay. Reduced PDE11A4 expression may represent a lithium-sensitive pathophysiology, because both C57BL/6J and Pde11a KO mice show increased expression of the pro-inflammatory cytokine interleukin-6 (IL-6) relative to BALB/cJ and PDE11A WT mice, respectively. Our finding that PDE11A4 negatively regulates lithium responsivity in mice suggests that the PDE11A SNPs identified in patients may be functionally relevant.

%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding

Most amino acids can be encoded by more than one synonymous codon, but these are rarely used with equal frequency. In many coding sequences the usage patterns of rare versus common synonymous codons is nonrandom and under selection. Moreover, synonymous substitutions that alter these patterns can have a substantial impact on the folding efficiency of the encoded protein. This has ignited broad interest in exploring synonymous codon usage patterns. For many protein chemists, biophysicists and structural biologists, the primary motivation for codon analysis is identifying and preserving usage patterns most likely to impact high-yield production of functional proteins. Here we describe the core functions and new features of %MinMax, a codon usage calculator freely available as a web-based portal and downloadable script (http://www.codons.org). %MinMax evaluates the relative usage frequencies of the synonymous codons used to encode a protein sequence of interest and compares these results to a rigorous null model. Crucially, for analyzing codon usage in common host organisms %MinMax requires only the coding sequence as input; with a user-input codon frequency table, %MinMax can be used to evaluate synonymous codon usage patterns for any coding sequence from any fully sequenced genome. %MinMax makes no assumptions regarding the impact of transfer ribonucleic acid concentrations or other molecular-level interactions on translation rates, yet its output is sufficient to predict the effects of synonymous codon substitutions on cotranslational folding mechanisms. A simple calculation included within %MinMax can be used to harmonize codon usage frequencies for heterologous gene expression.

Codon optimality, bias and usage in translation and mRNA decay

The advent of ribosome profiling and other tools to probe mRNA translation has revealed that codon bias - the uneven use of synonymous codons in the transcriptome - serves as a secondary genetic code: a code that guides the efficiency of protein production, the fidelity of translation and the metabolism of mRNAs. Recent advancements in our understanding of mRNA decay have revealed a tight coupling between ribosome dynamics and the stability of mRNA transcripts; this coupling integrates codon bias into the concept of codon optimality, or the effects that specific codons and tRNA concentrations have on the efficiency and fidelity of the translation machinery. In this Review, we first discuss the evidence for codon-dependent effects on translation, beginning with the basic mechanisms through which translation perturbation can affect translation efficiency, protein folding and transcript stability. We then discuss how codon effects are leveraged by the cell to tailor the proteome to maintain homeostasis, execute specific gene expression programmes of growth or differentiation and optimize the efficiency of protein production.

Evidence of evolutionary selection for cotranslational folding

Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from cotranslational folding remain open questions. Here we report a genome-wide analysis that uncovers evidence of evolutionary selection for cotranslational folding. We describe a robust statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved. Surprisingly, we find that domain boundaries can explain only a small fraction of these conserved loci. Instead, we propose that regions enriched in slowly translated codons are associated with cotranslational folding intermediates, which may be smaller than a single domain. We show that the intermediates predicted by a native-centric model of cotranslational folding account for the majority of these loci across more than 500 Escherichia coli proteins. By making a direct connection to protein folding, this analysis provides strong evidence that many synonymous substitutions have been selected to optimize translation rates at specific locations within genes. More generally, our results indicate that kinetics, and not just thermodynamics, can significantly alter the efficiency of self-assembly in a biological context.

Competing Pathways and Multiple Folding Nuclei in a Large Multidomain Protein, Luciferase

Proteins obtain their final functional configuration through incremental folding with many intermediate steps in the folding pathway. If known, these intermediate steps could be valuable new targets for designing therapeutics and the sequence of events could elucidate the mechanism of refolding. However, determining these intermediate steps is hardly an easy feat, and has been elusive for most proteins, especially large, multidomain proteins. Here, we effectively map part of the folding pathway for the model large multidomain protein, Luciferase, by combining single-molecule force-spectroscopy experiments and coarse-grained simulation. Single-molecule refolding experiments reveal the initial nucleation of folding while simulations corroborate these stable core structures of Luciferase, and indicate the relative propensities for each to propagate to the final folded native state. Both experimental refolding and Monte Carlo simulations of Markov state models generated from simulation reveal that Luciferase most often folds along a pathway originating from the nucleation of the N-terminal domain, and that this pathway is the least likely to form nonnative structures. We then engineer truncated variants of Luciferase whose sequences corresponded to the putative structure from simulation and we use atomic force spectroscopy to determine their unfolding and stability. These experimental results corroborate the structures predicted from the folding simulation and strongly suggest that they are intermediates along the folding pathway. Taken together, our results suggest that initial Luciferase refolding occurs along a vectorial pathway and also suggest a mechanism that chaperones may exploit to prevent misfolding.