Common Codon Research Articles

The mitochondrial genome of the marine gastropod Neverita didyma (Roding, 1798) (Mollusca: Gastropoda)

In this study, the complete mitochondrial genome of the Neverita didyma (Mollusca: Gastropoda) was sequenced. The mitochondrial genome is 15,252 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes. The overall nucleotides base composition of the heavy strand is 30.47% for A, 14.09%% for C, 15.89%for G, and 39.56% for T with an AT-rich feature (70.03%). All the protein-coding genes begin with an ATG codon, the common termination codon is TAA, except for nd2 and nd4l terminated with TAG and nd5 terminated by incomplete codon TA. Seen from the phylogenetic tree, Naticarius hebraeus, and N. didyma from the same Superfamily (Naticoidea) clustered into one branch. The data would provide useful data for further studies on population genetics and molecular systematics.

Complete mitochondrial genome of the Sternaspis scutata (Sternaspidae, Annelida)

IIn this study, the complete mitochondrial genome of the Sternaspis scutata wassequenced. The mitochondrial genome is 15 300 bp in length, containing 13 protein-coding sequences, 2 rRNAs, 21 tRNAs and 1 non-coding region. All these genes are in the heavy strand. Most protein-coding genes begin with an ATG codon, while NAD4L utilize ATT. The common termination codon is TAA, except for atp6 terminated with TAG, and cox2, atp8, nad2, nad6 terminated by incomplete codon T. Seen from the phylogenetic tree, Sternaspis scutata, Pista cristata and Terebellides stroemii from the same Order (Terebellida) clustered into one branch.

Species specificity and host affinity rather than tissue tropism controls codon usage pattern in respiratory mycoplasmosis

Respiratory Mycoplasmosis (rMyc) is a devastating respiratory disease causing serious pneumonia in camels, cattle and human causing fatalities and high economic loss. Codon usage pattern is an important measure of host-parasite relationship, parasites adaptation and evolution. In this work, two important species of rMyc affecting human (Mycoplasma pneumoniae) and camels (Mycoplasma mycoides) were analysed for finding their codon usage bias, factors affecting their genomes composition and their relation to their host including adaptation and disease pathogenesis. In spite of their reduced genome size, rMyc showed comprehensive and host-independent codon usage machinery with wide variability and incompatibility with their host pattern. Although, rMyc are common infectious agents of respiratory tract, they showed completely diverse codon usage, adaptation and pathogenesis profiles. M. mycoides showed strict highly biased A/T selection in their genomic composition, preferred codons and at the 3rd position of codons as well as highly divergent codon usage pattern compared with its host. M. pneumoniae showed more attempts in adaptation to mammalian host environment by showing codon usage pattern almost similar to their host. High GC content in genome, low number of overbiased and underbiased codons, high ENc values and balanced use of GC and AT in preferred codons N3s were among the factors of adaptation to its habitat. There was immune selection among rMyc. M. mycoides is more immune resistant by showing lower CpG dinucleotide frequency compared with M. pneumoniae. The higher and faster gene expression in M. mycoides, and to a lesser extent M. pneumoniae, devoted from low ENc values accounts for high pathogenicity and acute disease. Common evolutionary origin and variable codon usage indices account for variable attempts among Mycoplasma species to adapt their habitat regardless their tissue tropism or host specificity.

Phylogenetic Uniqueness of Honeybee Apis Cerana from the Korean Peninsula Inferred from The Mitochondrial, Nuclear, and Morphological Data

Abstract Apis cerana is an Eastern honeybee species distributed throughout Asia and closely related to the Western honeybee species Apis mellifera distributed across all of Africa, Europe and Western Asia, and subdivided into thirty confirmed subspecies. Currently, A. cerana is an endangered bee species in contrast to A. mellifera. We sequenced and annotated the complete mitochondrial genome of A. cerana from the Jeollanam-do province of South Korea and uploaded to the DDBJ/Genbank database(AP018431). MtDNA sequence is 15.925 bp long, has 84% AT-content and 16% GC-content and contains 22 tRNA genes, 13 protein-coding genes, two ribosomal RNA genes, one AT-rich region and four non-coding intergenic regions (NC1-4). All protein-coding genes are started by ATT and ATG codons, except the genes ATP8 and ND4, which started by ATC and ATA, respectively, and are stopped by the common codons TAA and TAG. A comparative analysis of the whole mtDNA sequences of A. cerana from Korea and Taiwan, A. c. cerana from China and A. c. japonica from Japan showed that the genetic divergence of the Korean A. cerana sample from subspecies A. c. cerana (2.57%) and A. c. japonica (2.58%) matched to the level of genetic divergence of mtDNA between animal subspecies (0.8-8%). Based on the comparative analysis of complete mtDNA (~16,000 bp), two nuclear gene VG and EF1- α sequences (~8,000 bp) and morphological measurements (six parameters), we assumed that Korean A. cerana, Chinese A. c. cerana and Japanese A. c. japonica are different subspecies at an early stage of sub-speciation and could be called further as subspecies of Apis cerana koreana.

The complete mitochondrial genome of a walnut weevil, Alcidodes juglans Chao (Coleoptera: Curculionidae)

The walnut weevil, Alcidodes juglans Chao (Coleoptera: Curculionidae), is an important agricultural pest and distributed widely in China. The complete mitochondrial genome of A. juglans is 15,638 bp long, and consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes, 21 transfer RNA (tRNA) genes and a putative control region (GenBank accession No. MH819192). The trnI gene has not been observed in the A. juglans mitogenome. The nucleotide composition is significantly biased (A, G, C, and T was 38.35%, 10.02%, 14.96%, and 36.67%, respectively) with A + T contents of 75.02%. All of the 21 tRNAs have the typical cloverleaf structure, with an exception for trnS1 (AGN). All PCGs are initiated by ATN codons, except for cox1 with AAT instead. Ten PCGs use a common stop codon of TAA or TAG, whereas the remaining three were terminated with a single T. The phylogenetic relationships based on neighbour-joining method showed that A. juglans is closely related to Naupactus xanthographus, which is in accordance with the traditional morphological classification.

Codon usage regulates human KRAS expression at both transcriptional and translational levels

KRAS and HRAS are highly homologous oncogenic Ras GTPase family members that are mutated in a wide spectrum of human cancers. Despite having high amino acid identity, KRAS and HRAS have very different codon usage biases: the HRAS gene contains many common codons, and KRAS is enriched for rare codons. Rare codons in KRAS suppress its protein expression, which has been shown to affect both normal and cancer biology in mammals. Here, using HRAS or KRAS expression in different human cell lines and in vitro transcription and translation assays, we show that KRAS rare codons inhibit both translation efficiency and transcription and that the contribution of these two processes varies among different cell lines. We observed that codon usage regulates mRNA translation efficiency such that WT KRAS mRNA is poorly translated. On the other hand, common codons increased transcriptional rates by promoting activating histone modifications and recruitment of transcriptional coactivators. Finally, we found that codon usage also influences KRAS protein conformation, likely because of its effect on co-translational protein folding. Together, our results reveal that codon usage has multidimensional effects on protein expression, ranging from effects on transcription to protein folding in human cells.

Utilization of rare codon-rich markers for screening amino acid overproducers

The translation of rare codons relies on their corresponding rare tRNAs, which could not be fully charged under amino acid starvation. Theoretically, disrupted or retarded translation caused by the lack of charged rare tRNAs can be partially restored by feeding or intracellular synthesis of the corresponding amino acids. Inspired by this assumption, we develop a screening or selection system for obtaining overproducers of a target amino acid by replacing its common codons with the corresponding synonymous rare alternative in the coding sequence of selected reporter proteins or antibiotic-resistant markers. Results show that integration of rare codons can inhibit gene translations in a frequency-dependent manner. As a proof-of-concept, Escherichia coli strains overproducing l-leucine, l-arginine or l-serine are successfully selected from random mutation libraries. The system is also applied to Corynebacterium glutamicum to screen out l-arginine overproducers. This strategy sheds new light on obtaining and understanding amino acid overproduction strains.

The right proteins at the right time

Stress Responses Cells must tailor protein synthesis so that proteins that enable growth and proliferation and those that enable adaptation under stressful conditions are produced at the appropriate times. Torrent et al. found that yeast genes encoding proteins involved in growth and proliferation used common codons, whereas those encoding stressresponse proteins tended to use rare codons (see the Focus by Pechmann). Stress skewed the transfer RNA (tRNA) pool toward those tRNAs that recognize rare codons. Furthermore, stress proteins were translated faster than those involved in growth and proliferation. Sci. Signal. 11 , eaat6409, eaau1098 (2018).

The complete mitochondrial genome of the bazaar fly, Musca sorbens Wiedemann (Diptera: Muscidae)

The bazaar fly, Musca sorbens (Diptera: Muscidae) Wiedemann, 1830 is a world-wide species with sanitary, medical, and veterinary importance. The complete mitochondrial genome of M. sorbens is sequenced to better understand the mitogenomic characteristics and phylogeny of this species. The circular mitogenome is 16,120 bp in length, contains 13 protein-coding genes (PCGs), 22 tRNA genes (tRNAs), two rRNA genes, and an AT-rich control region. The mitogenome comprises an A + T content of 77.4%. All PCGs start with “ATN” codons except for COI which starts with TCG, and terminate with the common stop codons TNN. A phylogenetic tree, including six Muscidae species, is reconstructed based on the whole mitogenome sequences. The interspecific distances of mitogenomes between the six Muscidae species range from 0.059 to 0.168.

Genetic mutations at rifampicin resistance-determining region of RpoB gene in conferring resistance to isolated multidrug-resistant tuberculosis strains

Introduction: Drug resistant tuberculosis (TB) among the new and retreatment cases was seen to be 5%. Multidrug resistant TB to at least isoniazid and Rifampicin is an alarming threat to the community and the scenario is even worse for retreatment cases showing rising trend over the years. A systematic analysis of the nature of the resistance conferred may contribute in understanding the common as well as rare genetic alterations that ultimately led to the genotypic resistance. The study thus involves a probe into the most common and rare patterns of genetic mutation that have led to the rifampicin resistance among the retreatment cases. The common and rare codons along with their change in amino acid sequences involved in conferring the resistance were looked for. Methods: The detection of the patterns genetic mutation is done by the Genotype MTBDR plus V2 kits (Hains Life Sciences) based on DNA strip technology (line probe assay). Results: The analysis has shown that only around 14.93% cases reflected exclusive mutations at around 531-533 region of the RpoB gene. Presence of both the wild and mutant gene segments simultaneously (WildType [WT] and MUT3) accounted to a striking percentage of 60.3% showing a heterogenous generation of susceptible and resistant strains at the same time. This pattern analysis showing maximum of heterogenous strains may be suggestive of capturing a generation under the process of conversion from WT to mutant type. About 95% reproducibility in liquid culture system further established the fact that most of the strains might be a cause for the rising attrition toward the first line of drugs. Conclusion: This pattern analysis showing maximum of heterogenous strains may be suggestive of capturing a generation under the process of conversion. The retrospective analysis showed how heterogenous population prevailed in the retreatment groups.

%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.

The complete mitochondrial genome analysis of Eristalis tenax (Diptera, Syrphidae)

The complete mitochondrial genome of Eristalis tenax (Linnaeus, 1758) (Diptera, Syrphidae) is reported here. This is the first sequenced mitogenome from the subfamily Milesiinae. The whole mitochondrial genome is 16,091 bp in length and contains 37 canonical genes, which include 22 transfer RNA genes, 13 protein-coding genes and two ribosomal RNA genes, the control region is 1125 bp in length. Most PCGs start with standard ATN codons, while CO1 and ND1 use TTG, CO3 uses TGG as start codons. All PCGs terminate in the common stop codons TAA. In addition, the nucleotide composition of the coding region was 40.0% of A, 40.1% of T, 11.2% of C, 8.7% of G and 80.1% of A + T content. The phylogenetic tree shows that Syrphidae is the sister group of Pipunculidae.

Complete mitochondrial genome of Bombus breviceps (Hymenoptera: Apidae)

The complete mitochondrial genome of Bombus breviceps, which belongs to the subgenus of Alpigenobombus in Bombus genus, was sequenced. This circular mitogenome is 16,743 bp (83.5% AT) in length, with two rRNA genes, 22 tRNA genes, and 13 protein-coding genes. All protein-coding genes are initiated with the common invertebrate initiation codon except TTA for ND2, and terminated by the typical stop codon TAA or TAG. tRNA-Ser (TCT) lacks a dihydrouridine (DHU) arm while other tRNA genes form a cloverleaf structure. Phylogenetic analysis shows that genus Bombus has a closer relationship with genus Melipona than any other genera in Apidae family, and B. breviceps clusters closer to B. lapidarius than any other bumblebees with sequenced mitogenome.

Erratum to: The complete mitochondrial genome of Naemorhedus griseus (Artiodactyla: Bovidae) and its phylogenetic implications

The Chinese goral (Naemorhedus griseus) has been categorized as vulnerable species by the World Conservation Union and listed as a Class I protected species in China for its over-hunting for meat, fur and medicines. In order to provide efficient genetic resources for the conservation and preservation of the endangered species, the complete mitochondrial genome of this species was determined and analyzed. It is 16,446 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, one origin of replication on the light-strand (OL) and a control region. Most of the PCGs use ATG as the common initiation codon, while ND2, ATP6 and ND3 use ATA and ND5 uses ATC as the initiation codon. Most of them have TAA or TAG as the stop codon, except COIII, ND3 and ND4 use an incomplete stop codon T or TA and Cyt b uses an uncommon AGA. An ML tree involving 19 Caprinae species was constructed, which will contribute to phylogenetic studies of Caprinae and further conservation strategies for the Chinese goral.

A multiplex ARMS PCR approach to detection of common β-globin gene mutations

Backgroundβ-thalassaemia is a group of inherited single-gene disorders worldwide. Each ethnic population has its own common mutations. Heterogeneity of β-thalassaemia mutations in multi-ethnic population of Surat, makes molecular diagnosis expensive and time consuming. MethodsSpecific primers were used to differentiate four common mutations, IVS I-5 (G→C), Codon 41/42 (- TCTT), 619-bp deletion and FS 8/9 (+G), by a simple PCR involving a multiplex amplification refractory mutation system. ResultsSeveral high prevalence β-Thalassemia trait groups constituted by Muslims, Patels, Sindhis, ModhBanias, and Mahayavanshi. Four most common mutations detected in them are IVS I-5 (G→C), Codon 41/42 (- TCTT), 619-bp deletion and FS 8/9 (+G). We identified each of these β-thalassemia mutations in multiplexed ARMS from positive control samples. Our multiplex-ARMS-PCR system was first standardized on positive DNA samples with above known four most common β-thalassemia mutations, and these positive samples had been diagnosed with β-thalassemia and also all these samples belonged to Surat ethnic groups. The system was subsequently tested on 110 blood samples from different ethnic backgrounds with unknown β-thalassemia mutations which were in all specimens. ConclusionThe ARMS multiplex system was found reliable, cost effective, fast and most applicable for mutation screening of Thalassemia in Surat populations.

Codon bias imposes a targetable limitation on KRAS-driven therapeutic resistance

KRAS mutations drive resistance to targeted therapies, including EGFR inhibitors in colorectal cancer (CRC). Through genetic screens, we unexpectedly find that mutant HRAS, which is rarely found in CRC, is a stronger driver of resistance than mutant KRAS. This difference is ascribed to common codon bias in HRAS, which leads to much higher protein expression, and implies that the inherent poor expression of KRAS due to rare codons must be surmounted during drug resistance. In agreement, we demonstrate that primary resistance to cetuximab is dependent upon both KRAS mutational status and protein expression level, and acquired resistance is often associated with KRASQ61 mutations that function even when protein expression is low. Finally, cancer cells upregulate translation to facilitate KRASG12-driven acquired resistance, resulting in hypersensitivity to translational inhibitors. These findings demonstrate that codon bias plays a critical role in KRAS-driven resistance and provide a rationale for targeting translation to overcome resistance.

Genotypic distribution of multidrug-resistant and extensively drug-resistant tuberculosis in northern Thailand.

BackgroundMultidrug/extensively drug-resistant tuberculosis (M/XDR-TB) is a major public health problem, and early detection is important for preventing its spread. This study aimed to demonstrate the distribution of genetic site mutation associated with drug resistance in M/XDR-TB in the northern Thai population.MethodsThirty-four clinical MTB isolates from M/XDR-TB patients in the upper northern region of Thailand, who had been identified for drug susceptibility using the indirect agar proportion method from 2005 to 2012, were examined for genetic site mutations of katG, inhA, and ahpC for isoniazid (INH) drug resistance and rpoB for rifampicin (RIF) drug resistance. The variables included the baseline characteristics of the resistant gene, genetic site mutations, and drug susceptibility test results.ResultsAll 34 isolates resisted both INH and RIF. Thirty-two isolates (94.1%) showed a mutation of at least 1 codon for katG, inhA, and ahpC genes. Twenty-eight isolates (82.4%) had a mutation of at least 1 codon of rpoB gene. The katG, inhA, ahpC, and rpoB mutations were detected in 20 (58.7%), 27 (79.4%), 13 (38.2%), and 28 (82.3%) of 34 isolates. The 3 most common mutation codons were katG 315 (11/34, 35.3%), inhA 14 (11/34, 32.4%), and inhA 114 (11/34, 32.4%). For this population, the best genetic mutation test panels for INH resistance included 8 codons (katG 310, katG 340, katG 343, inhA 14, inhA 84, inhA 86, inhA 114, and ahpC 75), and for RIF resistance included 6 codons (rpoB 445, rpoB 450, rpoB 464, rpoB 490, rpoB 507, and rpoB 508) with a sensitivity of 94.1% and 82.4%, respectively.ConclusionThe genetic mutation sites for drug resistance in M/XDR-TB are quite variable. The distribution of these mutations in a certain population must be studied before developing the specific mutation test panels for each area. The results of this study can be applied for further molecular M/XDR-TB diagnosis in the upper northern region of Thailand.

Widespread position-specific conservation of synonymous rare codons within coding sequences.

Synonymous rare codons are considered to be sub-optimal for gene expression because they are translated more slowly than common codons. Yet surprisingly, many protein coding sequences include large clusters of synonymous rare codons. Rare codons at the 5’ terminus of coding sequences have been shown to increase translational efficiency. Although a general functional role for synonymous rare codons farther within coding sequences has not yet been established, several recent reports have identified rare-to-common synonymous codon substitutions that impair folding of the encoded protein. Here we test the hypothesis that although the usage frequencies of synonymous codons change from organism to organism, codon rarity will be conserved at specific positions in a set of homologous coding sequences, for example to tune translation rate without altering a protein sequence. Such conservation of rarity–rather than specific codon identity–could coordinate co-translational folding of the encoded protein. We demonstrate that many rare codon cluster positions are indeed conserved within homologous coding sequences across diverse eukaryotic, bacterial, and archaeal species, suggesting they result from positive selection and have a functional role. Most conserved rare codon clusters occur within rather than between conserved protein domains, challenging the view that their primary function is to facilitate co-translational folding after synthesis of an autonomous structural unit. Instead, many conserved rare codon clusters separate smaller protein structural motifs within structural domains. These smaller motifs typically fold faster than an entire domain, on a time scale more consistent with translation rate modulation by synonymous codon usage. While proteins with conserved rare codon clusters are structurally and functionally diverse, they are enriched in functions associated with organism growth and development, suggesting an important role for synonymous codon usage in organism physiology. The identification of conserved rare codon clusters advances our understanding of distinct, functional roles for otherwise synonymous codons and enables experimental testing of the impact of synonymous codon usage on the production of functional proteins.

Specific mutations in KRAS codon 12 are associated with worse overall survival in patients with advanced and recurrent colorectal cancer

Background:Activating mutations in KRAS have been suggested as potential predictive and prognostic biomarkers. However, the prognostic impact of specific point mutations remains less clear. This study assessed the prognostic impact of specific KRAS mutations on survival for patients with colorectal cancer.Methods:Retrospective review of patients KRAS typed for advanced and recurrent colorectal cancer between 2010 and 2015 in a UK Cancer Network.Results:We evaluated the impact of KRAS genotype in 392 patients. Mutated KRAS was detected in 42.9% of tumours. KRAS mutations were more common in moderate vs well-differentiated tumours. On multivariate analysis, primary tumour T stage (HR 2.77 (1.54–4.98), P=0.001), N stage (HR 1.51 (1.01–2.26), P=0.04), curative intent surgery (HR 0.51 (0.34–0.76), P=0.001), tumour grade (HR 0.44 (0.30–0.65), P=0.001) and KRAS mutation (1.54 (1.23–2.12), P=0.005) were all predictive of overall survival. Patients with KRAS codon 12 mutations had worse overall survival (HR 1.76 (95% CI 1.27–2.43), P=0.001). Among the five most common codon 12 mutations, only p.G12C (HR 2.21 (1.15–4.25), P=0.01) and p.G12V (HR 1.69 (1.08–2.62), P=0.02) were predictive of overall survival.Conclusions:For patients with colorectal cancer, p.G12C and p.G12V mutations in codon 12 were independently associated with worse overall survival after diagnosis.

Novel Genetic Variants of Hepatitis B Virus in Fulminant Hepatitis.

Fulminant hepatitis (FH) is a life-threatening liver disease characterised by intense immune attack and massive liver cell death. The common precore stop codon mutation of hepatitis B virus (HBV), A1896, is frequently associated with FH, but lacks specificity. This study attempts to uncover all possible viral nucleotides that are specifically associated with FH through a compiled sequence analysis of FH and non-FH cases from acute infection. We retrieved 67 FH and 280 acute non-FH cases of hepatitis B from GenBank and applied support vector machine (SVM) model to seek candidate nucleotides highly predictive of FH. Six best candidates with top predictive accuracy, 92.5%, were used to build a SVM model; they are C2129 (85.3%), T720 (83.0%), Y2131 (82.4%), T2013 (82.1%), K2048 (82.1%), and A2512 (82.1%). This model gave a high specificity (99.3%), positive predictive value (95.6%), and negative predictive value (92.1%), but only moderate sensitivity (64.2%). We successfully built a SVM model comprising six variants that are highly predictive and specific for FH: four in the core region and one each in the polymerase and the surface regions. These variants indicate that intracellular virion/core retention could play an important role in the progression to FH.