Distinct ribosome states trigger diverse mRNA quality control pathways

Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully-designed reporter mRNAs to perform genetic screens and functional assays in S. cerevisiae. We characterize the roles of Hel2 and Syh1 in coordinating translational repression and mRNA decay on NGD reporter mRNAs, finding that Syh1 acts as the primary link to mRNA decay in NGD. Importantly, we observe that these NGD factors are not involved in the degradation of mRNAs enriched in non-optimal codons. Further, we establish that a key factor previously implicated in COMD, Not5, contributes modestly to the degradation of an NGD-targeted mRNA. Finally, we use ribosome profiling to reveal distinct ribosomal states associated with each reporter mRNA that readily rationalize the contributions of NGD and COMD factors to degradation of these reporters. Taken together, these results provide new mechanistic insight into the role of Syh1 in NGD and define the molecular triggers that determine how distinct pathways target mRNAs for degradation in yeast.

Deciphering Codon Usage Patterns in Genome of Cucumis sativus in Comparison with Nine Species of Cucurbitaceae

Cucumber is the most important vegetable crop in the Cucurbitaceae family. Condon usage bias (CUB) is a valuable character of species evolution. However, there is little research on the CUB of cucumber. Thus, this study analyzes the codon usage patterns of cucumber and its relatives within Cucurbitaceae on the genomic level. The analysis of fundamental indicators of codon characteristics shows that it was slightly GC poor, and there was weak codon usage bias in cucumber. We conduct the analysis of neutrality plot, ENC plot, P2 index, and COA indicates that the nucleotide composition, mutation pressure, and translational selection might play roles in CUB in cucumber and its relatives. Among these factors, nucleotide composition might play the most critical role. Based on these analyses, 30 optimal codons were identified in cucumber, most of them ending with U or A. Meanwhile, based on the RSCU values of species, a cluster tree was constructed, in which the situation of cucumber is consistent with the current taxonomic and evolutionary studies in Cucurbitaceae. This study systematically compared the CUB patterns and shaping factors of cucumber and its relatives, laying a foundation for future research on genetic engineering and evolutionary mechanisms in Cucurbitaceae.

Comparative analysis of transcriptomic data shows the effects of multiple evolutionary selection processes on codon usage in Marsupenaeus japonicus and Marsupenaeus pulchricaudatus

Background Kuruma shrimp, a major commercial shrimp species in the world, has two cryptic or sibling species, Marsupenaeus japonicus and Marsupenaeus pulchricaudatus. Codon usage analysis would contribute to our understanding of the genetic and evolutionary characteristics of the two Marsupenaeus species. In this study, we analyzed codon usage and related indices using coding sequences (CDSs) from RNA-seq data. Results Using CodonW 1.4.2 software, we performed the codon bias analysis of transcriptomes obtained from hepatopancreas tissues, which indicated weak codon bias. Almost all parameters had similar correlations for both species. The gene expression level (FPKM) was negatively correlated with A/T3s. We determined 12 and 14 optimal codons for M. japonicus and M. pulchricaudatus, respectively, and all optimal codons have a C/G-ending. The two Marsupenaeus species had different usage frequencies of codon pairs, which contributed to further analysis of transcriptional differences between them. Orthologous genes that underwent positive selection (ω > 1) had a higher correlation coefficient than that of experienced purifying selection (ω < 1). Parity Rule 2 (PR2) and effective number of codons (ENc) plot analysis showed that the codon usage patterns of both species were influenced by both mutations and selection. Moreover, the average observed ENc value was lower than the expected value for both species, suggesting that factors other than GC may play roles in these phenomena. The results of multispecies clustering based on codon preference were consistent with traditional classification. Conclusions This study provides a relatively comprehensive understanding of the correlations among codon usage bias, gene expression, and selection pressures of CDSs for M. japonicus and M. pulchricaudatus. The genetic evolution was driven by mutations and selection pressure. Moreover, the results point out new insights into the specificities and evolutionary characteristics of the two Marsupenaeus species.

Evidence from simulation studies for selective constraints on the codon usage of the Angiosperm psbA gene

The codon usage of the Angiosperm psbA gene is atypical for flowering plant chloroplast genes but similar to the codon usage observed in highly expressed plastid genes from some other Plantae, particularly Chlorobionta, lineages. The pattern of codon bias in these genes is suggestive of selection for a set of translationally optimal codons but the degree of bias towards these optimal codons is much weaker in the flowering plant psbA gene than in high expression plastid genes from lineages such as certain green algal groups. Two scenarios have been proposed to explain these observations. One is that the flowering plant psbA gene is currently under weak selective constraints for translation efficiency, the other is that there are no current selective constraints and we are observing the remnants of an ancestral codon adaptation that is decaying under mutational pressure. We test these two models using simulations studies that incorporate the context-dependent mutational properties of plant chloroplast DNA. We first reconstruct ancestral sequences and then simulate their evolution in the absence of selection on codon usage by using mutation dynamics estimated from intergenic regions. The results show that psbA has a significantly higher level of codon adaptation than expected while other chloroplast genes are within the range predicted by the simulations. These results suggest that there have been selective constraints on the codon usage of the flowering plant psbA gene during Angiosperm evolution.

Comparative analysis of codon usage patterns in chloroplast genomes of five Miscanthus species and related species

Miscanthus is not only a perennial fiber biomass crop, but also valuable breeding resource for its low-nutrient requirements, photosynthetic efficiency and strong adaptability to environment. In the present study, the codon usage patterns of five different Miscanthus plants and other two related species were systematically analyzed. The results indicated that the cp genomes of the seven representative species were preference to A/T bases and A/T-ending codons. In addition, 21 common high-frequency codons and 4–11 optimal codons were detected in the seven chloroplast genomes. The results of ENc-plot, PR2-plot and neutrality analysis revealed the codon usage patterns of the seven chloroplast genomes are influenced by multiple factors, in which nature selection is the main influencing factor. Comparative analysis of the codon usage frequencies between the seven representative species and four model organisms suggested that Arabidopsis thaliana, Populus trichocarpa and Saccharomyces cerevisiae could be considered as preferential appropriate exogenous expression receptors. These results might not only provide important reference information for evolutionary analysis, but also shed light on the way to improve the expression efficiency of exogenous gene in transgenic research based on codon optimization.

Analysis of Codon Usage Patterns in Giardia duodenalis Based on Transcriptome Data from GiardiaDB

Giardia duodenalis, a flagellated parasitic protozoan, the most common cause of parasite-induced diarrheal diseases worldwide. Codon usage bias (CUB) is an important evolutionary character in most species. However, G. duodenalis CUB remains unclear. Thus, this study analyzes codon usage patterns to assess the restriction factors and obtain useful information in shaping G. duodenalis CUB. The neutrality analysis result indicates that G. duodenalis has a wide GC3 distribution, which significantly correlates with GC12. ENC-plot result—suggesting that most genes were close to the expected curve with only a few strayed away points. This indicates that mutational pressure and natural selection played an important role in the development of CUB. The Parity Rule 2 plot (PR2) result demonstrates that the usage of GC and AT was out of proportion. Interestingly, we identified 26 optimal codons in the G. duodenalis genome, ending with G or C. In addition, GC content, gene expression, and protein size also influence G. duodenalis CUB formation. This study systematically analyzes G. duodenalis codon usage pattern and clarifies the mechanisms of G. duodenalis CUB. These results will be very useful to identify new genes, molecular genetic manipulation, and study of G. duodenalis evolution.

Tempo of degeneration across independently evolved non-recombining regions

Recombination is beneficial over the long term, allowing more effective selection. Despite long-term advantages of recombination, local recombination suppression is known to evolve and lead to genomic degeneration, in particular on sex and mating-type chromosomes, sometimes linked to severe genetic diseases. Here, we investigated the tempo of degeneration in non-recombining regions, i.e., the function curve for the accumulation of deleterious mutations over time, taking advantage of 17 independent events of large recombination suppression identified on mating-type chromosomes of anther-smut fungi, including five newly identified in the present study. Using high-quality genomes assemblies of alternative mating types of 13 Microbotryum species, we estimated the degeneration levels in terms of accumulation of non-optimal codons and non-synonymous substitutions in non-recombining regions. We found a reduced frequency of optimal codons in the non-recombining regions on mating-type chromosomes compared to autosomes. We showed that the lower frequency of optimal codons in non-recombining regions was not due to less frequent GC-biased gene conversion or lower ancestral expression levels compared to recombining regions. We estimated that the frequency of optimal codon usage decreased linearly at a rate of 0.989 per My. The non-synonymous over synonymous substitution rate (dN/dS) increased rapidly after recombination suppression and then reached a plateau. To our knowledge this is the first study to disentangle effects of reduced selection efficacy from GC-biased gene conversion in the evolution of optimal codon usage to quantify the tempo of degeneration in non-recombining regions, leveraging on multiple independent recombination suppression events. Understanding the tempo of degeneration is important for our knowledge on genomic evolution, on the origin of genetic diseases and on the maintenance of regions without recombination.

Analysis of Codon Bias in Mitochondrial Genome of Epinephelus Fuscoguttatus

Background: Epinephelus fuscoguttatus is one of the rare marine economic fishes with high economic value. At present, the researches on grouper mainly focus on artificial propagation, physiology and biochemistry, diseases and so on. However, there are few reports on mitochondrial genome level. The research aimed to analyze composition characteristics and usage preference of codon of mitochondrial genome in E. fuscoguttatus, and explored main factors of affecting the formation of codon preference, thereby providing theoretical basis for studying species evolution, genetics and breeding, and improving expression efficiency of exogenous genes. Results: GC content of mitochondrial genome of E. fuscoguttatus changed between 44.00% and 46.30%, with 45.40% of mean. Change range of CAI value was between 0.125 and 0.202, and the mean was 0.155. Effective number of codons (ENC) changed between 36.08 and 49.55, with 44.98 of mean. There were 32 codons that relative synonymous codon usage (RSCU) was more than 1, mainly ended with A/C. ENC-plot analysis found that all the genes were in the lower middle of the standard curve, and there was larger difference between actual and theoretical ENC, illustrating that codon bias was mainly affected by the choice. Correspondence analysis showed that the first axis contributed 58.85% of the difference, while the second, third and fourth axes contributed 14.59%, 7.66% and 5.43% of the difference respectively. Cumulative contribution rate of the first four vectors was 85.53%. Finally, nine optimal codons were selected: CUU, AUC, GUU, CCU, GCA, UAU, CGC, AGC and GGC.Conclusions: Codon usage preference of mitochondrial genome of E. fuscoguttatus was weak, and it preferred to use A/C terminated codon, and preference was mainly influenced by choice.

Codon Usage Patterns Analysis of Camellia oleifera Based on Transcriptome Data

Camellia oleifera is an essential oil woody plant. The development of the camellia industry can relieve the a China’s pressure of importing edible oil. However, there are few studies on the codon usage bias (CUB) in C. oleifera genes. In this study, the codon usage patterns were analyzed by 35,178 reconstructed genes from the C. oleifera transcriptome. The mean GC and GC3 content of all transcripts was 51.14% and 55.43% respectively. A total of 18 optimal codons were identified, 15 of them ending with A or U. Which indicated the use of A/U codons was high frequency. Furthermore, the natural selection and mutational pressure, both influenced CUB in C. oleifera, however the natural selection was the most deciding factor. The nucleotide excretion of C. oleifera genome is rich. C. oleifera prefers A/U ending codons, and nature selection is one of the most important factors affecting CUB. This study will lay a theoretical foundation for the research of molecular evolution and genetic engineering in C. oleifera.

Identification of the optimal codons for acetolactate synthase from weeds: an in-silico study

Although various studies of codon usage bias have been reported in a broad spectrum of organisms, no studies to date have examined codon usage bias for herbicide target genes. In this study, we analysed codon usage patterns for the acetolactate synthase (ALS) gene in eight monocot weeds and one model monocot. The base composition at the third codon position follows C3 &gt; G3 &gt; T3 &gt; A3. The values of the effective number of codons (ENC or Nc) indicate low bias, and ENC or Nc vs. GC3 plot suggests that this low bias is due to mutational pressure. Low codon adaptation index and codon bias index values further supported the phenomenon of low bias. Additionally, the optimal codons, along with over- and under-represented codons, were identified. Gene design using optimal codons rather than overall abundant codons produce improved protein expression results. Our results can be used for further studies, including eliciting the mechanisms of herbicide resistance (occurring due to elevation of gene expression levels) and the development of new compounds, their efficiency and risk assessment for herbicide resistance evolution.