Amino Acid Sequence Of Protein Research Articles

DGDTA: dynamic graph attention network for predicting drug–target binding affinity

BackgroundObtaining accurate drug–target binding affinity (DTA) information is significant for drug discovery and drug repositioning. Although some methods have been proposed for predicting DTA, the features of proteins and drugs still need to be further analyzed. Recently, deep learning has been successfully used in many fields. Hence, designing a more effective deep learning method for predicting DTA remains attractive.ResultsDynamic graph DTA (DGDTA), which uses a dynamic graph attention network combined with a bidirectional long short-term memory (Bi-LSTM) network to predict DTA is proposed in this paper. DGDTA adopts drug compound as input according to its corresponding simplified molecular input line entry system (SMILES) and protein amino acid sequence. First, each drug is considered a graph of interactions between atoms and edges, and dynamic attention scores are used to consider which atoms and edges in the drug are most important for predicting DTA. Then, Bi-LSTM is used to better extract the contextual information features of protein amino acid sequences. Finally, after combining the obtained drug and protein feature vectors, the DTA is predicted by a fully connected layer. The source code is available from GitHub at https://github.com/luojunwei/DGDTA.ConclusionsThe experimental results show that DGDTA can predict DTA more accurately than some other methods.

First report of a novel polymorphism and genetic characteristics of the leporine prion protein (PRNP) gene.

Transmissible spongiform encephalopathies (TSEs) have been reported in a broad spectrum of hosts. The genetic polymorphisms and characteristics of the prion protein (PRNP) gene have a vital impact on the development of TSEs. Notably, natural TSE infection cases have never been reported in rabbits, and genetic variations of the leporine PRNP gene have not been investigated to date. To identify leporine PRNP gene polymorphism, we performed amplicon sequencing in 203 rabbits. We report a novel single nucleotide polymorphism on the leporine PRNP gene. In addition, we performed a comparative analysis of amino acid sequences of prion protein (PrP) across several hosts using ClustalW2. Furthermore, we evaluated the effect of changes of unique leporine PrP amino acids with those conserved among various species using Swiss-Pdb Viewer. Interestingly, we found seven unique leporine amino acids, and the change of unique leporine amino acids with those conserved among other species, including S175N, Q221K, Q221R, A226Y, A230G, and A230S, was predicted to reduce hydrogen bonds in leporine PrP.

Potential quorum-sensing inhibitor of Hafnia alvei H4-theaflavin-3,3´-digallate analyzed by virtual screening and molecular simulation.

Hafnia species can cause food spoilage via the quorum-sensing (QS) system. Thus, strategies that target QS in these bacteria might be a good approach to safeguard the quality of processed food. In this study, the amino acid sequence of the LasI Ha protein, a key QS regulator from Hafnia alvei H4, was used to construct its 3D structure for the virtual screening of potential QS inhibitors (QSIs) from the Bioactive Compound database. Four potential QSIs were obtained, and these were all theaflavins (TFs). Among them, theaflavin-3,3´-digallate (TF3) was found to outperform the others, displaying a higher docking score according to molecular docking analysis, and required only a sub-minimal inhibitory concentration (31.25 mM) to cause a significant decrease in the production of the autoinducer N-acyl homoserine lactone in H. alvei H4 and up to 60.5% inhibition of its motility. Furthermore, molecular simulation results indicated that TF3 could stably bind to a cavity within LasI Ha to form stable hydrogen bonds and hydrophobic interactions with various key residues of the protein to exert the inhibitory effect. Thus, TF3 may be considered a potential compound to protect against food spoilage caused by H. alvei H4 via the quorum quenching. IMPORTANCE Hafnia alvei, the main strain studied in this paper, is often isolated from spoiled foods, especially refrigerated protein-based raw foods, and is generally considered to be a spoilage bacterium whose spoilage-causing properties may be closely related to its own very strong population-sensing activity, so the strategy of quorum quenching against H. alvei H4 may be a good way to guarantee the quality of processed foods. Given the current global requirements for food safety and quality, coupled with negative consumer perceptions of the excessive inclusion of synthetic chemicals in food products, the use of natural compounds as QSIs in the storage of aquatic food products would seem more attractive.

Nematostella vectensis exemplifies the exceptional expansion and diversity of opsins in the eyeless Hexacorallia

BackgroundOpsins are the primary proteins responsible for light detection in animals. Cnidarians (jellyfish, sea anemones, corals) have diverse visual systems that have evolved in parallel with bilaterians (squid, flies, fish) for hundreds of millions of years. Medusozoans (e.g., jellyfish, hydroids) have evolved eyes multiple times, each time independently incorporating distinct opsin orthologs. Anthozoans (e.g., corals, sea anemones,) have diverse light-mediated behaviors and, despite being eyeless, exhibit more extensive opsin duplications than medusozoans. To better understand the evolution of photosensitivity in animals without eyes, we increased anthozoan representation in the phylogeny of animal opsins and investigated the large but poorly characterized opsin family in the sea anemone Nematostella vectensis.ResultsWe analyzed genomic and transcriptomic data from 16 species of cnidarians to generate a large opsin phylogeny (708 sequences) with the largest sampling of anthozoan sequences to date. We identified 29 opsins from N. vectensis (NvOpsins) with high confidence, using transcriptomic and genomic datasets. We found that lineage-specific opsin duplications are common across Cnidaria, with anthozoan lineages exhibiting among the highest numbers of opsins in animals. To establish putative photosensory function of NvOpsins, we identified canonically conserved protein domains and amino acid sequences essential for opsin function in other animal species. We show high sequence diversity among NvOpsins at sites important for photoreception and transduction, suggesting potentially diverse functions. We further examined the spatiotemporal expression of NvOpsins and found both dynamic expression of opsins during embryonic development and sexually dimorphic opsin expression in adults.ConclusionsThese data show that lineage-specific duplication and divergence has led to expansive diversity of opsins in eyeless cnidarians, suggesting opsins from these animals may exhibit novel biochemical functions. The variable expression patterns of opsins in N. vectensis suggest opsin gene duplications allowed for a radiation of unique sensory cell types with tissue- and stage-specific functions. This diffuse network of distinct sensory cell types could be an adaptive solution for varied sensory tasks experienced in distinct life history stages in Anthozoans.

Arabidopsis transmembrane proteins regulate protein turnover as signaling molecules during internalization by means of ubiquitination

<p>This study attempts to characterize the structure, function, and other features of Arabidopsis thaliana based on its transmembrane protein amino acid sequence and assess its potential as a drug target and ubiquitination site. The transmembrane protein belongs to the Arabidopsis plant, but little is known about the structure-function of the protein, among others. We predicted the structure and transmembrane domains of the transmembrane protein by different bioinformatic tools, and the prediction results showed that its three poorly conserved transmembrane domains could be used as potential drug targeting sites. Among them, lysine ubiquitination sites play an important role in the recycling of plant membrane proteins, and we found the existence of ubiquitination sites by predicting the ubiquitination sites of transmembrane proteins, and this could be a new research direction in the future.<strong></strong></p>

Heme Pocket Structure and Its Functional Implications in an Ancestral Globin Protein.

Proteins have undergone evolutionary processes to achieve optimal stability, increased functionality, and novel functions. Comparative analysis of existent and ancestral proteins provides insights into the factors that influence protein stability and function. Ancestral sequence reconstruction allows us to deduce the amino acid sequences of ancestral proteins. Here, we present the structural and functional characteristics of an ancestral protein, AncMH, reconstructed to be the last common ancestor of hemoglobins and myoglobins. Our findings reveal that AncMH harbors heme and that the heme binds oxygen. Furthermore, we demonstrate that the ferrous heme in AncMH is pentacoordinated, similar to that of human adult hemoglobin and horse myoglobin. A detailed comparison of the heme pocket structure indicates that the heme pocket in AncMH is more similar to that of hemoglobin than that of myoglobin. However, the autoxidation of AncMH is faster than that of both hemoglobin and myoglobin. Collectively, our results suggest that ancestral proteins of hemoglobins and myoglobins evolved in steps, including the hexa- to pentacoordination transition, followed by stabilization of the oxygen-bound form.

A Novel Variant of Avian Reovirus Is Pathogenic to Vaccinated Chickens.

Avian reovirus (ARV) infections, characterized by severe arthritis, tenosynovitis, pericarditis, and poor weight gain, have become increasingly serious in recent years. The economic impact is significant as it causes growth inhibition and immunosuppression. Some commercial poultry in China have been widely vaccinated with available ARV vaccines; however, infections continue to occur even after vaccination. This study aimed to isolate a novel variant, ARV-SD19/11103, from the joint tissues of infected broiler chickens vaccinated with ARV vaccines in Shandong Province. Genetic evolution analysis of the major protective antigen σC gene in ARVs showed that ARV-SD19/11103 was located in the genotype cluster I but not in the same sub-cluster as the S1133 vaccine strain. The amino acid sequence similarity between SD19/11103 and vaccine strains S1133, 1733, and 2408 was <80%. After analyzing the amino acid sequences of the σC protein, 33 amino acid differences were found between the new variant isolate and the vaccine strains. This novel variant showed obvious pathogenicity in specific pathogen-free chicken embryos and chicks and could cause serious disease in chickens vaccinated with commercially available ARV vaccines. Cross-neutralization experiments further demonstrated a significant antigenic difference between the novel variant and genotype cluster I ARV strains. The novel variant strain isolated in this study provides an important theoretical basis for understanding the prevalence and genetic evolutionary characteristics of ARV variant strains in our country. This study identified the causes of ARVs circulating and emphasizes the needs for developing new vaccines against novel ARV variants.

Comparative of the complete chloroplast genome and RNA editing of Eucalyptus camaldulensis T5 clone, an elite variety in Thailand

Abstract. Racharak P, Suttangkakul A, Vuttipongchaikij S. 2023. Comparative of the complete chloroplast genome and RNA editing of Eucalyptus camaldulensis T5 clone, an elite variety in Thailand. Biodiversitas24: 3774-3784. Eucalyptus camaldulensis, T5 clone, the excellent fast-growing tree plantation in Thailand, was analyzed for the complete chloroplast genome and RNA editing. The complete chloroplast genome revealed a total genome size of 160,204 bp that divided into a large single copy (LSC) (88,904 bp) and a small single copy region (SSC) (18,506 bp) by inverted repeat regions (IR) containing 26,397 bp. A circular mapping genome and gene order showed the circle antiparallel mapping gene of 135 genes, including 37 tRNAs, 10 rRNAs, and 1 pseudogene. GC content of the genome was 36.87%. The comparative genomes analysis between the T5 clone and E. camaldulensis from the NCBI database suggested that the thymine (T) and adenine (A) strongly impacted the indel and transversion process, which could be a point of mutation in the genome. Furthermore, 24 specific genes were used to investigate RNA editing. From all genes, only 11 genes were edited with C to U conversion.Triplet codons, tUA, tUt, tUg and Ugg were the most frequently edited codon and expressions; the crucial influence of amino acid alterations. Due to RNA editing events, the physicochemical properties of amino acids were changed from polar to nonpolar amino acids and from hydrophilic to hydrophobic amino acids. Physicochemical properties conversion is necessary to form complete amino acid sequences for several essential chloroplast proteins. The event might be the accumulation of amino acid alterations causing phenotypic variation for plant adaptation and evolution.

In Silico Physicochemical Characterization of Fusion Proteins from Emerging Amazonian Arboviruses.

Mayaro (MAYV), Saint Louis encephalitis (SLEV), and Oropouche (OROV) viruses are neglected members of the three main families of arboviruses with medical relevance that circulate in the Amazon region as etiological agents of outbreaks of febrile illnesses in humans. As enveloped viruses, MAYV, SLEV, and OROV largely depend on their class II fusion proteins (E1, E, and Gc, respectively) for entry into the host cell. Since many aspects of the structural biology of such proteins remain unclear, the present study aimed at physicochemically characterizing them by an in silico approach. The complete amino acid sequences of MAYV E1, SLEV E, and OROV Gc proteins derived by conceptual translation from annotated coding regions in the reference sequence genome of the respective viruses were obtained from the NCBI Protein database in the FASTA format and then submitted to the ClustalO, Protcalc, Pepstats, Predator, Proscan, PCprof, Phyre2, and 3Drefine web servers for the determination of sequence identities, the estimation of residual properties, the prediction of secondary structures, the identification of potential post-translational modifications, the recognition of antigenic propensities, and the modeling/refinement of three-dimensional structures. Sequence identities were 20.44%, 18.82%, and 13.70% between MAYV/SLEV, SLEV/OROV, and MAYV/OROV fusion proteins, respectively. As for the residual properties, MAYV E1 and SLEV E proteins showed a predominance of the non-polar profile (56% and 55% of the residues, respectively), whereas the OROV Gc protein showed a predominance of the polar profile (52% of the residues). Regarding predicted secondary structures, MAYV E1 and SLEV E proteins showed fewer alpha-helices (16.51% and 15.17%, respectively) than beta-sheets (21.79% and 25.15%, respectively), while the opposite was observed in the OROV Gc protein (20.39% alpha-helices and 12.14% beta-sheets). Regarding post-translational modifications, MAYV E1, SLEV E, and OROV Gc proteins showed greater relative potential for protein kinase C phosphorylation, N-myristoylation, and casein kinase II phosphorylation, respectively. Finally, antigenic propensities were higher in the N-terminus half than in the C-terminus half of these three proteins, whose three-dimensional structures revealed three distinctive domains. In conclusion, MAYV E1 and SLEV E proteins were found to share more physicochemical characteristics with each other than the OROV Gc protein, although they are all grouped under the same class of viral fusion proteins.

Structure Analysis of the MatA Locus of Sexual Compatibility in the Edible Mushroom Pleurotus ostreatus

The edible oyster mushroom Pleurotus ostreatus is one of the most cultivated species worldwide. Morphogenesis associated with the maturation of fruit bodies is controlled by two unlinked loci of sexual compatibility matA and matB with multiple alleles (tetrapolar system of sexual compatibility). Quantitative analysis of the alleles of mating compatibility loci in 17 natural isolates collected in the Moscow region was performed in mon–mon (monokaryons–monokaryon) and di–mon (dikaryon–monokaryon) crossings. Four monokaryotic testers strains which were heteroallelic at both mating type loci were obtained for each of the five natural mushroom isolates by using original technique of sterile spore prints on Petri dishes and mon–mon crossing. Twelve natural isolates were crossed via di-mon mating with the four monokaryotic testers M-38. Genetic analysis of the alleles of sexual compatibility loci in 17 natural isolates revealed multiple alleles at both loci: at least ten alleles at matA locus and eight alleles at matB locus. Structural organization analysis of the matA locus was performed in silico for homokaryotic strains PC9 and PC15 based on the whole-genome sequencing data available at DOE Joint Genome Institute. The matA locus has an extremely divergent structure: there are one copy of the homeodomain gene hd1 and one copy of the hd2 gene in the PC9 strain, whereas the matA locus of the PC15 strain is composed by two copies of hd1.1 and hd1.2 genes (class HD1 homeodomain proteins) and one copy of hd2 gene (class HD2 proteins). Comprehensive analysis of amino acid sequences of HD1 and HD2 homeodomain proteins demonstrated that the proteins have a globular structure with the nuclear localization and contain a variable N-terminus and a more conserved DNA-binding domain with a specific conserved motif WFXNXR in the third ɑ-helix. The results suggest that multiple alleles of the matA locus of sexual compatibility in basidiomycete fungi is achieved due to both different copy number of the coding hd genes within the locus and the variability of the coding gene sequences.

Characterization of the common bed bug's eggshell and egg glue proteins

An insect egg is one of the most vulnerable stages of insect life, and the evolutionary success of a species depends on the eggshell protecting the embryo and the egg glue securing the attachment. The common bed bug (Cimex lectularius), notorious for its painful and itchy bites, infests human dwellings to feed on blood. They are easier to find these days as they adapt to develop resistance against commonly used insecticides. In this study, we identify and characterize the eggshell protein and the probable egg glue protein (i.e. keratin associated protein 5–10 like protein) of the bed bug by using mass spectrometry and bioinformatics analysis. Furthermore, by using transcription profiling and in vivo RNA interference, we show evidences that the keratin associated protein 5–10 like protein functions as the glue protein. Finally, structural characterizations on the two proteins are performed using recombinant proteins. Amino acid sequences of various insect eggshell and egg glue proteins support their independent evolution among different insect groups. Hence, inhibiting the function of these proteins related to the earliest stage of life can achieve species-specific population control. In this respect, our results would be a starting point in developing new ways to control bed bug population.

&lt;i&gt;In silico&lt;/i&gt; analysis of genomes of Bacillus anthracis strains belonging to major genetic lineages

Introduction. The global phylogenetic population structure of Bacillus anthracis is represented by major genetic lineages (A, B and C) with nonuniform distribution of isolates, which still cannot be explained. Identification of characteristics of genomes of strains from three lineages, which can affect their spread, is of high importance.&#x0D; The aim of the study is to explore genomic characteristics of different genetic lineages, which may have an effect on their distribution, by using the in silico analysis of a representative subset of B. anthracis strains.&#x0D; Materials and methods. The whole-genome sequences of 49 B. anthracis strains and Bacillus cereus biovar anthracis CI strain were studied. The in silico analysis was performed to identify polymorphisms using BLASTn, MEGA X, Tandem Repeat Finder, Parsnp the Harvest Suite software.&#x0D; Results. The genome variability depended on single nucleotide polymorphisms, single-nucleotide repeats, number of tandem repeats, substitutions and indels. In strains from lineages B and C, they outnumbered 1.613.4 times and in the B. cereus biovar anthracis strain 5150 times those in B. anthracis strains from lineage A. Significant substitutions in housekeeping genes and pathogenicity factor genes caused changes in amino acid sequences in proteins significantly more frequently in B. anthracis strains from major lineages B and C.&#x0D; Based on the molecular typing and a multi-virulence-locus sequence typing analysis (MVLST) with a discrimination index of 0.9633, strains were classified into three major genetic lineages including groups different from the canonical group.&#x0D; Conclusion. The distinctive feature of B. anthracis genomes is that they have a larger number of significant nucleotide substitutions in pathogenicity factor genes and housekeeping genes of strains belonging to major lineages B and C compared to lineage A. Changes in proteins encoded by them can cause differences in ecological adaptation and in prevalence, which are higher in strains of lineage A. MVLST having a high discriminating capacity can be used as an additional method to B. anthracis molecular typing.

STUDY OF NON-CODING AREAS OF THE DNA GENOME OF DIFFERENT ANIMAL SPECIES

STUDY OF NON-CODING AREAS OF THE DNA GENOME OF DIFFERENT ANIMAL SPECIES

Detection and Genetic Characterization of Astroviruses in Brain Tissues of Wild Raccoon Dogs.

Astroviruses (AstVs) have been detected in a wide range of animal species, including mammals and birds. Recently, a novel AstV associated with neurological symptoms has been detected in the brains of some mammals. Raccoon dog AstV has been reported recently in China. However, there have been no reports in South Korea. Therefore, the present study aimed to detect and genetically characterize AstVs in the intestine and brain tissues of 133 wild raccoon dogs collected in Korea between 2017 and 2019. Of the seven raccoon dogs, AstVs were detected in six intestinal tissues and four brain tissues. Analysis of the capsid protein amino acid sequences of raccoon dog AstVs detected in Korea revealed a high similarity to canine AstVs, suggesting possible interspecies transmission between raccoon dogs and dogs. Phylogenetic and capsid protein amino acid sequence analysis of raccoon dog AstVs detected in the brain the 17-148B strain belonging to the HMO clade and exhibiting conserved sequences found in neurotropic AstVs (NT-AstVs), indicating their potential as NT-AstVs. However, the pathogenicity and transmission routes of the raccoon dog AstV detected in Korea have not yet been elucidated, so further research and continued surveillance for AstV in wild raccoon dogs are needed.

Isolation and genomic characterization of one novel goose astrovirus causing acute gosling gout in China

Novel goose astrovirus (NGAstV) is a member of the genus Avain Avastrovirus (AAstV) and the family Astroviridae. NGAstV-associated gout disease has caused huge economic losses to the goose industry worldwide. Since early 2020, NGAstV infections characterized by articular and visceral gout emerged continuously in China. Herein, we isolated a GAstV strain from goslings with fatal gout disease and sequenced its complete genome nucleotide sequence. Then we conducted systematic genetic diversity and evolutionary analysis. The results demonstrated that two genotypic species of GAstV (GAstV-I and GAstV-II) were circulating in China, and GAstV-II sub-genotype IId had become the dominant one. Multiple alignments of amino acid sequences of GAstV capsid protein revealed that several characteristic mutations (E456D, A464N, and L540Q) in GAstV-II d strains, as well as additional residues in the newly identified isolate which varied over time. These findings enrich the understanding of the genetic diversity and evolution of GAstV and may facilitate the development of effective preventive strategies.

Cloning and analysis of DlERF23 gene in flower induction

Irregular flowering is a serious problem in longan production. Identifying the flower induction-related genes and analyzing their regulation mechanism is the key to solve this problem. The APETALA2/ethylene responsive factor (AP2/ERF) superfamily members are transcription factors (TFs) that regulate diverse developmental processes, including flowering time, and stress responses in plants. However, there is still no research about AP2/ERF involved in the regulation of longan flower induction. In the present study, a AP2/ERF TF member DlERF23 was cloned from longan (Dimocarpus longan). It has a typical AP2 domain with the coding sequence (CDS) of DlERF23 is 552 bp in length and encodes 184 amino acids. The molecular weight of DlERF23 protein was 20.41 kda and the theoretical isoelectric point (PI) was 7.69. The amino acid sequence of DlERF23 protein had the highest similarity with CsERF23 (XP_006478313.1) of Citrus sinensis and CcERF23 (XP_006441807.2) of Citrus clementina. The results of qRT-PCR showed that the relative expression level of DlERF23 gene in pericarp was higher, followed by stem, leave, flower and flower bud. Meanwhile, DlERF23 gene significant down-regulated in the early stage of flower induction in ‘Sijimi’ (SJ) longan and up-regulated in the late stage of flower induction in ‘Shixia’ (SX). The results of transient expression of Arabidopsis protoplasts showed that the fluorescence signal was mainly concentrated in the nucleus. Moreover, overexpression of DlERF23 in Arabidopsis promoted early flowering. These results provide useful information for revealing the biological roles of DlERF23 in longan and increase our understanding of the AP2/ERF superfamily members in fruit trees.

Comparison of the gut virus communities between patients with Crohn's disease and healthy individuals.

The escalating incidence of Crohn's disease (CD), a debilitating ailment that ravages individuals and their families, has become a formidable issue over recent decades. In this study, fecal samples from patients with CD and healthy individuals were investigated by means of viral metagenomics. The fecal virome was analyzed and some suspected disease-causing viruses were described. A polyomavirus named HuPyV with 5,120 base pairs (bp) was found in the disease group. In a preliminary analysis employing large T region-specific primers, it was found that HuPyV was present in 3.2% (1/31) of healthy samples and 43.2% (16/37) of disease samples. Additionally, two other viruses from the anellovirus and CRESS-DNA virus families were found in fecal samples from CD patients. The complete genome sequences of these two viruses were described respectively, and the phylogenetic trees have been built using the anticipated amino acid sequences of the viral proteins. Further research is required to elucidate the relationship between these viruses and the onset and development of Crohn's disease.

Backward Pattern Matching on Elastic-Degenerate Strings

The concept of elastic-degenerate strings (EDS) was introduced as a way of representing a sequenced population of the same species. Several online elastic-degenerate string matching (EDSM) algorithms were presented so far. Some of them provide a practical implementation. We propose a new on-line EDSM algorithm BNDM-EDS. Our algorithm combines two traditional algorithms BNDM and Shift-And that were adapted to the specificities needed by Elastic-Degenerate Strings. BNDM-EDS is running in {mathcal {O}}(Nmlceil frac{m}{w}rceil ) worst-case time. This implies {mathcal {O}}(Nm) time for small patterns, where m is the length of the searched pattern, N is the size of EDS, and w is the size of the computer word. The algorithm uses {mathcal {O}}(N + n) space, where n is the length of EDS. BNDM-EDS requires a simple preprocessing step with time and space {mathcal {O}}(m). We further present an extended version of the algorithm called BNDM-EDS-AA, which allows searching for proteins (amino acid sequences) encoded in DNA EDS. Though BNDM-EDS-AA considers more complex patterns than BNDM-EDS, it keeps its time and space efficiency. Experimental results on real genomic data show the superiority of BNDM-EDS over state-of-the-art algorithms. We also experimentally evaluate the efficiency of BNDM-EDS-AA for different pattern complexities, and evaluate the scaling of both BNDM-EDS and BNDM-EDS-AA with varying attributes of EDS datasets.

RNA recoding in cephalopods tailors microtubule motor protein function

RNA editing is a widespread epigenetic process that can alter the amino acid sequence of proteins, termed "recoding." In cephalopods, most transcripts are recoded, and recoding is hypothesized to be an adaptive strategy to generate phenotypic plasticity. However, how animals use RNA recoding dynamically is largely unexplored. We investigated the function of cephalopod RNA recoding in the microtubule motor proteins kinesin and dynein. We found that squid rapidly employ RNA recoding in response to changes in ocean temperature, and kinesin variants generated in cold seawater displayed enhanced motile properties in single-molecule experiments conducted in the cold. We also identified tissue-specific recoded squid kinesin variants that displayed distinct motile properties. Finally, we showed that cephalopod recoding sites can guide the discovery of functional substitutions in non-cephalopod kinesin and dynein. Thus, RNA recoding is a dynamic mechanism that generates phenotypic plasticity in cephalopods and can inform the characterization of conserved non-cephalopod proteins.

Rapid Identification of Jasmine Virus H Infecting Ixora coccinea by Nanopore Metatranscriptomics.

The global climate change and international trade have facilitated the movement of plants across borders, increasing the risk of introducing novel plant viruses in new territories. Ixora coccinea exhibited virus-like foliar symptoms, including mosaic and mild mottle. An Oxford Nanopore Technologies-based compact and portable MinION platform was used to identify the causal viral pathogen. The complete genome sequence of jasmine virus H (JaVH; 3867 nt, JaVH-CNU) was determined and found to share 88.4-90.3% nucleotide identity with that of Jasminum sambac JaVH isolate in China. Phylogenetic analysis based on the complete amino acid sequences of RNA-dependent RNA polymerase and coat protein revealed that JaVH-CNU was grouped separately with other JaVH isolates. This is the first report of a natural JaVH infection of &gt;i&lt;I. coccinea. The application of rapid nanopore sequencing for plant virus identification was demonstrated and is expected to provide accurate and rapid diagnosis for virus surveillance.