Codon Positions Research Articles

Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects

In December 2019, rising pneumonia cases caused by a novel β-coronavirus (SARS-CoV-2) occurred in Wuhan, China, which has rapidly spread worldwide, causing thousands of deaths. The WHO declared the SARS-CoV-2 outbreak as a public health emergency of international concern, since then several scientists are dedicated to its study. It has been observed that many human viruses have codon usage biases that match highly expressed proteins in the tissues they infect and depend on the host cell machinery for the replication and co-evolution. In this work, we analysed 91 molecular features and codon usage patterns for 339 viral genes and 463 human genes that consisted of 677,873 codon positions. Hereby, we selected the highly expressed genes from human lung tissue to perform computational studies that permit to compare their molecular features with those of SARS, SARS-CoV-2 and MERS genes. The integrated analysis of all the features revealed that certain viral genes and overexpressed human genes have similar codon usage patterns. The main pattern was the A/T bias that together with other features could propitiate the viral infection, enhanced by a host dependant specialization of the translation machinery of only some of the overexpressed genes. The envelope protein E, the membrane glycoprotein M and ORF7 could be further benefited. This could be the key for a facilitated translation and viral replication conducting to different comorbidities depending on the genetic variability of population due to the host translation machinery. This is the first codon usage approach that reveals which human genes could be potentially deregulated due to the codon usage similarities between the host and the viral genes when the virus is already inside the human cells of the lung tissues. Our work leaded to the identification of additional highly expressed human genes which are not the usual suspects but might play a role in the viral infection and settle the basis for further research in the field of human genetics associated with new viral infections. To identify the genes that could be deregulated under a viral infection is important to predict the collateral effects and determine which individuals would be more susceptible based on their genetic features and comorbidities associated.

Comprehensive analysis of coding sequence architecture features and gene expression in Arachis duranensis.

Coding sequence (CDS) architecture affects gene expression levels in organisms. Codon optimization can increase the gene expression level. Therefore, understanding codon usage patterns has important implications for research on genetic engineering and exogenous gene expression. To date, the codon usage patterns of many model plants have been analyzed. However, the relationship between CDS architecture and gene expression in Arachis duranensis remains poorly understood. According to the results of genome sequencing, A. duranensis has many resistant genes that can be used to improve the cultivated peanut. In this study, bioinformatic approaches were used to estimate A. duranensis CDS architectures, including frequency of the optimal codon (Fop), polypeptide length and GC contents at the first (GC1), second (GC2) and third (GC3) codon positions. In addition, Arachis RNA-seq datasets were downloaded from PeanutBase. The relationships between gene expression and CDS architecture were assessed both under normal growth as well as nematode and drought stress conditions. A total of 26 codons with high frequency were identified, which preferentially ended with A or T in A. duranensis CDSs under the above-mentioned three conditions. A similar CDS architecture was found in differentially expressed genes (DEGs) under nematode and drought stresses. The GC1 content differed between DEGs and non-differentially expressed genes (NDEGs) under both drought and nematode stresses. The expression levels of DEGs were affected by different CDS architectures compared with NDEGs under drought stress. In addition, no correlation was found between differential gene expression and CDS architecture neither under nematode nor under drought stress. These results aid the understanding of gene expression in A. duranensis.

Spatiotemporal adaptive evolution of an MHC immune gene in a frog-fungus disease system.

Genetic diversity of major histocompatibility complex (MHC) genes is linked to reduced pathogen susceptibility in amphibians, but few studies also examine broad spatial and temporal patterns of MHC and neutral genetic diversity. Here, we characterized range-wide MHC diversity in the Northern leopard frog, Rana pipiens, a species found throughout North America that is experiencing disease-related declines. We used previously sequenced neutral markers (mitochondrial DNA and microsatellites), sequenced an expressed MHC class IIß gene fragment, and measured infection prevalence and intensity of the global fungal pathogen Batrachochytrium dendrobatidis (Bd) across 14 populations. Four populations were sampled across two decades, enabling temporal comparisons of selection and demography. We recovered 37 unique MHC alleles, including 17 that were shared across populations. Phylogenetic and population genetic patterns between MHC and neutral markers were incongruent, and five MHC codon positions associated with peptide binding were under positive selection. MHC heterozygosity, but not neutral marker heterozygosity, was a significant factor explaining spatial patterns of Bd prevalence, whereas only environmental variables predicted Bd intensity. MHC allelic richness (AR) decreased significantly over time but microsatellite-based AR did not, highlighting a loss of functional immunogenetic diversity that may be associated with Bd selective pressures. MHC supertype 4 was significantly associated with an elevated risk of Bd infection, whereas one supertype 2 allele was associated with a nearly significant reduced risk of Bd. Taken together, these results provide evidence that positive selection contributes to MHC class IIß evolution in R. pipiens and suggest that functional MHC differences across populations may contribute to disease adaptation.

Exploring the impact of RNA editing on mitochondrial phylogenetic analyses in liverworts, an early land plant lineage

AbstractPlant mitochondrial protein‐coding genes are slow evolving, and therefore are less subject to substitution saturation, and therefore perhaps more suitable for resolving deep relationships of high taxonomic categories. Plant mitochondrial genes hold, however, hundreds of RNA editing sites, involving mostly non‐synonymous substitutions in the first and second codon positions, which has been reported to affect phylogenetic reconstructions. We have previously identified ca. 4700 mitochondrial RNA editing sites within a group of liverworts representing the ordinal diversity of liverworts, allowing us to critically evaluate the impacts of RNA editing sites on phylogenetic reconstructions in liverworts. Our phylogenetic inferences are mostly congruent on topology inferred from the original mitochondrial gene dataset, dataset with RNA editing sites corrected, and dataset with RNA editing sites excluded. The RNA editing site excluded dataset recovered a topology identical to that of the RNA editing site corrected dataset, supporting the sister relationship of Ptilidium and Jungermanniales, whereas the original dataset supported the sister relationship of Ptilidium and Jungermanniidae. The controversial placements of Ptilidium could be explained by site‐wise log‐likelihood analysis, as the majority of liverwort RNA editing sites supported the sister relationship of Ptilidium and Jungermanniidae, hence the correction or exclusion of the RNA editing sites changed the tree topology and supported the sister relationship of Ptilidium and Jungermanniales. Our study shows that RNA editing sites potentially impact phylogenetic analyses, suggesting that both genome and transcriptome derived data should be used with caution for phylogenetic reconstruction with genes hosting vast numbers of RNA editing sites such as plant organellar genes.

Mitochondrial genes from 18 angiosperms fill sampling gaps for phylogenomic inferences of the early diversification of flowering plants

AbstractThe early diversification of angiosperms is thought to have been a rapid process, which may complicate phylogenetic analyses of early angiosperm relationships. Plastid and nuclear phylogenomic studies have raised several conflicting hypotheses regarding overall angiosperm phylogeny, but mitochondrial genomes have been largely ignored as a relevant source of information. Here we sequenced mitochondrial genomes from 18 angiosperms to fill taxon‐sampling gaps in Austrobaileyales, magnoliids, Chloranthales, Ceratophyllales, and major lineages of eudicots and monocots. We assembled a data matrix of 38 mitochondrial genes from 107 taxa to assess how well mitochondrial genomic data address current uncertainties in angiosperm relationships. Although we recovered conflicting phylogenies based on different data sets and analytical methods, we also observed congruence regarding deep relationships of several major angiosperm lineages: Chloranthales were always inferred to be the sister group of Ceratophyllales, Austrobaileyales to mesangiosperms, and the unplaced Dilleniales was consistently resolved as the sister to superasterids. Substitutional saturation, GC compositional heterogeneity, and codon‐usage bias are possible reasons for the noise/conflict that may impact phylogenetic reconstruction; and angiosperm mitochondrial genes may not be substantially affected by these factors. The third codon positions of the mitochondrial genes appear to contain more parsimony‐informative sites than the first and second codon positions, and therefore produced better resolved phylogenetic relationships with generally strong support. The relationships among these major lineages remain incompletely resolved, perhaps as a result of the rapidity of early radiations. Nevertheless, data from mitochondrial genomes provide additional evidence and alternative hypotheses for exploring the early evolution and diversification of the angiosperms.

The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing.

BackgroundThe coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts.MethodsSequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitogenome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes.ResultsThe complete circular mitogenome of O. rhinoceros is 20,898 bp in length, with a gene content canonical for insects (13 PCGs, two rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lineages in the Scarabaeidae. In silico PCR-RFLP analysis recovered the correct fragment set that is diagnostic for the CRB-G haplogroup. These results validate the high-quality of the O. rhinoceros mitogenome sequence and annotation.

The nucleotide usages significantly impact synonymous codon usage in Mycoplasma hyorhinis.

Five annotated genomes of Mycoplasma hyorhinis were analyzed for clarifying evolutionary dynamics driving the overall codon usage pattern. Information entropy used for estimating nucleotide usage pattern at the gene level indicates that multiple evolutionary dynamics participate in forcing nucleotide usage bias at every codon position. Moreover, nucleotide usage bias directly contributes to synonymous codon usage biases with two different extremes. The overrepresented codons tended to have A/T in the third codon position, and the underrepresented codons strongly used G/C in the third position. Furthermore, correspondence analysis and neutrality plot reflect an obvious interplay between mutation pressure and natural selection mediating codon usage in M. hyorhinis genome. Due to significant bias in usages between A/T and G/C at the gene level, different selective forces have been proposed to contribute to codon usage preference in M. hyorhinis genome, including nucleotide composition constraint derived from mutation pressure, translational selection involved in natural selection, and strand-specific mutational bias represented by different nucleotide skew index. The systemic analyses of codon usage for M. hyorhinis can enable us to better understand the mechanisms of evolution in this species.

Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae.

The present study was carried out on 62 genome sequences of members of the family Anelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constraints, indicating that compositional properties might have influenced the CUB. A highly significant correlation was observed between the overall base content and the base content at the third codon position, indicating that mutations might have affected the CUB. A highly significant positive correlation was observed between GC12 and GC3 (r = 0.904, p < 0.01), which indicated that directional mutation pressure influenced all three codon positions. A neutrality plot revealed that the contribution of mutation and natural selection in determining the CUB was 58.6% and 41.4%, respectively.Electronic supplementary materialThe online version of this article (10.1007/s00705-020-04890-2) contains supplementary material, which is available to authorized users.

Quantitative elucidation of associations between nucleotide identity and physicochemical properties of amino acids and the functional insight

Studies on codon property would deepen our understanding of the origin of primitive life and enlighten biotechnical application. Here, we proposed a quantitative measurement of codon-amino acid association and found that seven out of 13 physicochemical properties have stronger associations with the nucleotide identity at the second codon position, indicating that protein structure and function may associate more closely with it than the other two sites. When extending the effect of codon-amino acid association to protein level, it was found that the correlation between the second codon position (measured by the relative frequencies of nucleobase T and A at this codon site) and hydrophobicity (by the form of GRAVY value) became stronger with 96% genomes having R > 0.90 and p < 1e-60. Furthermore, we revealed that informational genes encoding proteins have lower GRAVY values than operational proteins (p < 3e-37) in both prokaryotic and eukaryotic genomes. The above results reveal a complete link from codon identity (A2 versus T2) to amino acid property (hydrophilic versus hydrophobic) and then to protein functions (informational versus operational). Hence, our work may help to understand how the nucleotide sequence determines protein function.

Differential genetic variability at two mtDNA COI regions does not imply mismatches in Odonata molecular identification performances

Molecular-based approaches for species identification and delimitation strongly rely, in terms of universality and efficiency, on the selected markers. Conventionally, when adopting a DNA barcoding approach to discriminate (or identify) metazoans species, the marker choice falls on the 658 base pair region at the 5ʹ end of the mitochondrial COI gene. However, a growing number of studies suggest to use alternative and more variable genetic regions, even from the same gene, such as the 3ʹ end of the COI. In this work, we compared the identification performance of the 5ʹ and 3ʹ end COI regions on a large sequence dataset of odonate species, an order of arthropods among the most studied in terms of conservation importance for aquatic ecosystems. The genetic datasets comprised a total of 236 specimens, 113 species, 51 genera and 12 families spanning the two odonate suborders Zygoptera and Anisoptera, and were analysed under an integrative multiple approach including descriptive statistics and variability of the sequences, phylogenetic reconstructions, DNA-based species delimitations, genetic distances, identification of diagnostic characters and saturation plots. All analyses were congruent in recovering the COI-3ʹ region to be slightly more variable than the COI-5ʹ one, and both regions showed a saturation of transversion at the third codon position. However, phylogenetic reconstructions, genetic distances, and diagnostic characters identification resulted in a similar discrimination power for the two COI regions. Therefore, the COI-3ʹ region does not add much information to the standard COI-5ʹ barcode region, which has in turn largely been demonstrated to successfully delineate invertebrate communities through DNA and eDNA metabarcoding, and to have a much more extensive taxonomic coverage in public databases. Overall, the DNA barcoding inventory assembled in this study will provide valuable insights into the systematics and conservation of many odonate species with implications for future DNA and eDNA monitoring-based studies.

Patterns of genome-wide codon usage bias in tobacco, tomato and potato

Understanding codon usage patterns and their shaping factors in members of the Solanaceae family may reflect important features of their evolutionary history. Here, we investigated codon usage bias (CUB) over the whole genome of tobacco, tomato and potato. Analyzing the effective number of codons (ENc) revealed a weak CUB over the whole genome of the three genomes. The correlation analysis between the ENc and the nucleotide content at the third codon position indicated that genes with high ENc have high A/T and low G/C contents. Analyzing nucleotide composition and the relative synonymous codon usage confirmed that the three genomes are AT-rich and favor codons ending with T and/or A. Comparing CUB in each of the three genomes revealed that approximately 50% and 45% of the genes were dominated by mutational and natural selection, respectively. The remaining 5% of the genes were affected by combined factors of mutation and translation selection. The first four axes of the correspondence analysis (CA) were the major contributors to the variation within the codon sequences (CDS) of the three genomes. Results of a multi-regression analysis between the 4 axes and the CUB indices verified the fact that natural selection and directional mutation for base composition along with other factors could describe the variations in the CUB within the CDS of the three genomes. In conclusion, the CUB of the three species showed the same weak trend and that mutation and natural selection were the main factors influencing the nuclear genes of the three genomes.

Identification of Translation Start Sites in Bacterial Genomes.

The knowledge of translation start sites is crucial for annotation of genes in bacterial genomes. However, systematic mapping of start codons in bacterial genes has mainly relied on predictions based on protein conservation and mRNA sequence features which, although useful, are not always accurate. We recently found that the pleuromutilin antibiotic retapamulin (RET) is a specific inhibitor of translation initiation that traps ribosomes specifically at start codons, and we used it in combination with ribosome profiling to map start codons in the Escherichia coli genome. This genome-wide strategy, that was named Ribo-RET, not only verifies the position of start codons in already annotated genes but also enables identification of previously unannotated open reading frames and reveals the presence of internal start sites within genes. Here, we provide a detailed Ribo-RET protocol for E. coli. Ribo-RET can be adapted for mapping the start codons of the protein-coding sequences in a variety of bacterial species.

Diverse phylogenomic datasets uncover a concordant scenario of laurasiatherian interordinal relationships

Resolving the interordinal relationships in the mammalian superorder Laurasiatheria has been among the most intractable problems in higher-level mammalian systematics, with many conflicting hypotheses having been proposed. The present study collected three different sources of genome-scale data with comprehensive taxon sampling of laurasiatherian species, including two protein-coding datasets (4,186 protein-coding genes for an amino acid dataset comprising 2,761,247 amino acid residues and a nucleotide dataset comprising 5,516,340 nucleotides from 1st and 2nd codon positions), an intronic dataset (1,210 introns comprising 1,162,723 nucleotides) and an ultraconserved elements (UCEs) dataset (1,246 UCEs comprising 1,946,472 nucleotides) from 40 species representing all six laurasiatherian orders and 7 non-laurasiatherian outgroups. Remarkably, phylogenetic trees reconstructed with the four datasets using different tree-building methods (RAxML, FastTree, ASTRAL and MP-EST) all supported the relationship (Eulipotyphla, (Chiroptera, ((Carnivora, Pholidota), (Cetartiodactyla, Perissodactyla)))). We find a resolution of interordinal relationships of Laurasiatheria among all types of markers used in the present study, and the likelihood ratio tests for tree comparisons confirmed that the present tree topology is the optimal hypothesis compared to other examined hypotheses. Jackknifing subsampling analyses demonstrate that the results of laurasiatherian tree reconstruction varied with the number of loci and ordinal representatives used, which are likely the two main contributors to phylogenetic disagreements of Laurasiatheria seen in previous studies. Our study provides significant insight into laurasiatherian evolution, and moreover, an important methodological strategy and reference for resolving phylogenies of adaptive radiation, which have been a long-standing challenge in the field of phylogenetics.

Natural Selection Plays an Important Role in Shaping the Codon Usage of Structural Genes of the Viruses Belonging to the Coronaviridae Family.

Viruses belonging to the Coronaviridae family have a single-stranded positive-sense RNA with a poly-A tail. The genome has a length of ~29.9 kbps, which encodes for genes that are essential for cell survival and replication. Different evolutionary constraints constantly influence the codon usage bias (CUB) of different genes. A virus optimizes its codon usage to fit the host environment on which it savors. This study is a comprehensive analysis of the CUB for the different genes encoded by viruses of the Coronaviridae family. Different methods including relative synonymous codon usage (RSCU), an Effective number of codons (ENc), parity plot 2, and Neutrality plot, were adopted to analyze the factors responsible for the genetic evolution of the Coronaviridae family. Base composition and RSCU analyses demonstrated the presence of A-ended and U-ended codons being preferred in the 3rd codon position and are suggestive of mutational selection. The lesser ENc value for the spike ‘S’ gene suggests a higher bias in the codon usage of this gene compared to the other structural genes. Parity plot 2 and neutrality plot analyses demonstrate the role and the extent of mutational and natural selection towards the codon usage pattern. It was observed that the structural genes of the Coronaviridae family analyzed in this study were at the least under 84% influence of natural selection, implying a major role of natural selection in shaping the codon usage.

Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7).

Salmon pancreas disease virus, more commonly known as salmonid alphavirus (SAV), is a single-stranded positive sense RNA virus and the causative agent of pancreas disease and sleeping disease in salmonids. In this study, a unique strain of SAV previously isolated from ballan wrasse was subjected to whole genome sequencing using nanopore sequencing. In order to accurately examine the evolutionary history of this strain in comparison to other SAV strains, a partitioned phylogenetic analysis was performed to account for variation in the rate of evolution for both individual genes and codon positions. Partitioning the genome alignments almost doubled the observed branch lengths in the phylogenetic tree when compared to the more common approach of applying one model of substitution across the genome and significantly increased the statistical fit of the best-fitting models of nucleotide substitution. Based on the genomic data, a valid case can be made for the viral strain examined in this study to be considered a new SAV genotype. In addition, this study adds to a growing number of studies in which SAV has been found to infect non-salmonid fish, and as such we have suggested that the viral species name be amended to the more inclusive 'piscine alphavirus'.

Phylogenomics Analysis of SARS-CoV2 Genomes Reveals Distinct Selection Pressure on Different Viral Strains.

We are witnessing a tremendous outbreak of a novel coronavirus (SARS-CoV2) across the globe. Upon exposure to different population and changing environment, the viral strain might experience different mutational bias that leads to genetic diversity among the viral population. Also, the diversification can be influenced by distinct selection pressure on different viral genomes. We have carried out a comparative genomic analysis of 82 SARS-CoV2 genomes. We have evaluated their evolutionary divergence, substitution pattern, and rates. Viral genomes under distinct selection pressure have been identified. Sites that experience strong selection pressure also have been identified. Our result shows that the translational preference of a few codons is strongly correlated with the mutational bias imposed by genome compositional constraint and influenced by natural selection. Few genomes are evolving with a higher mutational rate with a distinct signature of nucleotide substitution in comparison to others. Four viral strains are under the effect of purifying selection, while nine SARS-CoV2 genomes are under strong positive selection bias. Site analysis indicates a strong positive selection pressure on two codon positions at 3606th and 8439th positions. Our study elucidates adaptation of few SARS-CoV2 viral strain during the outbreak shaping by natural selection and genomic compositional constraints.

Molecular evidence on the emergence of benzimidazole resistance SNPs in field isolates of Marshallagia marshalli (Nematoda: Trichostrongylidae) in sheep.

The infection with members of the Trichostrongylid nematodes has been frequently reported from sheep and goats. Because of the widespread use of Benzimidazoles (BZs), the resistance suspected to occur in some worms populations. In this study, we focused on the prevalent nematode, Marshallagia marshalli, from the abomasa of sheep. Samples were obtained from at least 10 infected farms and diagnosed with morphological and molecular methods. For resistance analysis, genomic DNA from pooled adult samples of all farms were analysed for the beta tubulin gene to detect any polymorphisms at codon positions of F167Y, E198A and F200Y. According to the results, seven farms (70%) revealed resistance (R) allele at F200Y with relatively high frequency. No other mutations were identified at the other two positions. Also, except for one homozygous (RR) occasion, the isolates with R allele had heterozygous (RS) genotype. This finding indicates that the worm populations are still affected by drugs of the BZ class. However, the genetic data also notes on developing resistance mechanisms in M. marshalli populations in sheep.

Lack of association of HFE gene polymorphism with high body iron status in Pakistani patients with type 2 diabetes mellitus.

The Aim of this study was to investigate the relationship of 3 common polymorphisms in the HFE gene (C282Y, H63D and S65C) with high body iron status in a population of Pakistani subjects with type 2 diabetes mellitus (DM) and to explore if there is any novel mutation in HFE gene in a sample of Pakistani subjects with type 2 DM. In a case-control design, 200 healthy controls and 200 consecutive adult subjects with type 2 DM (both gender; age range of 30-70 years) were enrolled with informed consent. Their serum samples were analyzed for body iron status (ratio of concentration of soluble transferrin receptor to ferritin concentration). DNA from blood was screened for HFE gene polymorphisms via polymerase chain reaction, followed by restriction fragment length polymorphism or via Sanger sequencing to identify any novel mutation(s) in HFE gene. We found that there was lack of any association between HFE polymorphism and body iron status in Pakistani subjects with type 2 DM and healthy controls. H63D was the most common polymorphism found in this population. Single base substitution of G nucleotide instead of C at the codon position 187 in the HFE gene exon 2 was discovered in one subject with DM. There was also a lack of association between D allele (variant allele of H63D) and type 2 DM. A significant relationship was found between CG genotype and abnormal albuminuria in subjects with type 2 DM (p = 0.036). In conclusion, HFE gene polymorphism is not associated either with high body iron status or type 2 DM in a hospital based Pakistani population and variant allele of H63D polymorphism appears to be associated with diabetic nephropathy.

Poly(A)-Binding Protein Regulates the Efficiency of Translation Termination

Multiple factors influence translation termination efficiency, including nonsense codon identity and immediate context. To determine whether the relative position of a nonsense codon within an open reading frame (ORF) influences termination efficiency, we quantitate the production of prematurely terminated and/or readthrough polypeptides from 26 nonsense alleles of 3 genes expressed in yeast. The accumulation of premature termination products and the extent of readthrough for the respective premature termination codons (PTCs) manifest a marked dependence on PTC proximity to the mRNA 3' end. Premature termination products increase in relative abundance, whereas readthrough efficiencies decrease progressively across different ORFs, and readthrough efficiencies for a PTC increase in response to 3' UTR lengthening. These effects are eliminated and overall translation termination efficiency decreases considerably in cells harboring pab1 mutations. Our results support a critical role for poly(A)-binding protein in the regulation of translation termination and also suggest that inefficient termination is a trigger for nonsense-mediated mRNA decay (NMD).

HCV Genetic Diversity Can Be Used to Infer Infection Recency and Time since Infection.

HIV-1 genetic diversity can be used to infer time since infection (TSI) and infection recency. We adapted this approach for HCV and identified genomic regions with informative diversity. We included 72 HCV/HIV-1 coinfected participants of the Swiss HIV Cohort Study, for whom reliable estimates of infection date and viral sequences were available. Average pairwise diversity (APD) was calculated over each codon position for the entire open reading frame of HCV. Utilizing cross validation, we evaluated the correlation of APD with TSI, and its ability to infer TSI via a linear model. We additionally studied the ability of diversity to classify infections as recent (infected for <1 year) or chronic, using receiver-operator-characteristic area under the curve (ROC-AUC) in 50 patients whose infection could be unambiguously classified as either recent or chronic. Measuring HCV diversity over third or all codon positions gave similar performances, and notable improvement over first or second codon positions. APD calculated over the entire genome enabled classification of infection recency (ROC-AUC = 0.76). Additionally, APD correlated with TSI (R2 = 0.33) and could predict TSI (mean absolute error = 1.67 years). Restricting the region over which APD was calculated to E2-NS2 further improved accuracy (ROC-AUC = 0.85, R2 = 0.54, mean absolute error = 1.38 years). Genetic diversity in HCV correlates with TSI and is a proxy for infection recency and TSI, even several years post-infection.