Transcript Level and Sequence Matching Are Key Determinants of Off-Target Effects in RNAi

Double-stranded RNA (dsRNA) pesticides, those based on RNA interference (RNAi) technology utilizing dsRNA, have shown potential for pest control. However, the off-target effects of dsRNA pose limitations to the widespread application of RNAi and raise concerns regarding potential side effects on other beneficial organisms. The precise impact and underlying factors of these off-target effects are still not well understood. Here, we found that the transcript level and sequence matching jointly regulate off-target effects of dsRNA. The much lower expressed target genes were knocked down to a lesser extent than genes with higher expression levels, and the critical sequence identity of off-target effects is approximately 80%. Moreover, off-target effects could be triggered by a contiguous matching sequence length exceeding 15 nt as well as nearly perfectly matching sequences with one or two base mismatches exceeding 19 nt. Increasing the dosage of dsRNA leads to more severe off-target effects. However, the length of mismatched dsRNA, the choice of different RNAi targets, and the location of target sites within the same gene do not affect the severity of off-target effects. These parameters can be used to guide the design of possibly selective sequences for RNAi, optimize the specificity and efficiency of dsRNA, and facilitate practical applications of RNAi for pest control.

Structures of distantly related interacting protein homologs are less divergent than non-interacting homologs

Homologous proteins can display high structural variation due to evolutionary divergence at low sequence identity. This classical inverse relationship between sequence identity and structural similarity, established many years ago, has remained true between homologous proteins of known structure over time. However, a large number of heteromeric proteins also exist in the structural data bank, where the interacting subunits belong to the same fold and maintain low sequence identity between themselves. It is not clear if there is any selection pressure to deviate from the inverse sequence-structure relationship for such interacting distant homologs, in comparison to pairs of homologs which are not known to interact. We examined 12,824 fold pairs of interacting homologs of known structure, which includes both heteromers and multi-domain proteins. These were compared with monomeric proteins, resulting in 26,082 fold pairs as a dataset of non-interacting homologous systems. Interacting homologs were found to retain higher structural similarity than non-interacting homologs at diminishing sequence identity in a statistically significant manner. Interacting homologs are more similar in their 3D structures than non-interacting homologs and have a preference towards symmetric association. There appears to be a structural constraint between remote homologs due to this commitment.

Genetic Diversity and Epidemic Types of Porcine Reproductive and Respiratory Syndrome (PRRS) Virus in Japan from 2018 to 2020

To clarify the genetic diversity of the porcine reproductive and respiratory syndrome virus (PRRSV) in Japan in recent years, we determined the nucleotide sequence of open reading frame 5 of 2482 PRRSV sequences obtained from samples collected from pigs between January 2018 and December 2020. As a result of molecular phylogenetic analysis, Cluster II represented the largest proportion (44.9−50.6%) throughout the study period, followed by Cluster IV (34.0−40.8%), Cluster III (7.8−12.1%), Cluster I (3.1−6.7%), and Cluster V (0.1−0.2%). The relative distributions between Clusters varied between geographic regions and between years: in 2018, Cluster II was the most prevalent in all regions. In 2019, Cluster II was dominant in the Hokkaido and Tohoku regions, while in other regions Cluster IV was dominant. In 2020, Cluster IV was dominant in the Kanto/Tosan and Kyushu/Okinawa regions, whilst in other regions Cluster II was predominant. Compared with a previous study, the proportions of genome sequences classified in Clusters II and IV significantly increased (p = 0.042 and 0.018, respectively) and those classified in Cluster III significantly decreased (p < 0.01). The widespread use of live attenuated vaccines using strains that belong to Cluster II might have accounted for these changes in the relative distribution between Clusters.

Early secreted antigenic target of 6 kda-like proteins of mycobacterium tuberculosis: Diagnostic and vaccine relevance

BACKGROUND

Early secreted antigenic target of 6 kDa (ESAT6) is low-molecular-weight and immunodominant protein of Mycobacterium tuberculosis with relevance to diagnosis and vaccine development. Analysis of the M. tuberculosis genome has shown the existence of 23 ESAT6-like genes. This study was aimed to determine M. tuberculosis-specificity vis-à-vis crossreactivity of ESAT6-like genes and encoded proteins and their potential in the diagnosis and vaccine development.

METHODS

All ESAT6-like proteins were characterized using the webserver Tuberculist. The sequence identities were determined using basic local alignment search tool.

RESULTS

The genes for six ESAT6-like proteins were located in M. tuberculosis-specific genomic regions of differences (RDs), i.e., EsxA and EsxB in RD1, EsxO and EsxP in RD7, and EsxV and EsxW in RD9. The genes for other ESAT6-like proteins were located in the genomic regions shared with other mycobacteria. Based on sequence identities, the ESA6-like proteins were divided into four subfamilies of 15 proteins and no subfamily of 8 proteins. The members of subfamilies 1-4 shared extensive sequence identities among the members of each subfamily. Each member of subfamily 1 (EsxI, EsxL, EsxN, EsxO, EsxV) and subfamily 2 (EsxJ, EsxK, EsxM, EsxP, EsxW) were homologs. Hence, the gene sequences identical to EsxO and EsxP located in RD7, and EsxV and EsxW located in RD9 were also present in the regions of M. tuberculosis genome shared with other mycobacteria.

CONCLUSION

Because of their specificity to M. tuberculosis, only EsxA (ESAT6) and EsxB (CFP10) will be useful in the specific diagnosis. However, other ESAT6-like proteins may be useful for vaccine development against tuberculosis.

The ABC transporter G subfamily in Arabidopsis thaliana

ABC transporters are ubiquitously present in all kingdoms and mediate the transport of a large spectrum of structurally different compounds. Plants possess high numbers of ABC transporters in relation to other eukaryotes; the ABCG subfamily in particular is extensive. Earlier studies demonstrated that ABCG transporters are involved in important processes influencing plant fitness. This review summarizes the functions of ABCG transporters present in the model plant Arabidopsis thaliana. These transporters take part in diverse processes such as pathogen response, diffusion barrier formation, or phytohormone transport. Studies involving knockout mutations reported pleiotropic phenotypes of the mutants. In some cases, different physiological roles were assigned to the same protein. The actual transported substrate(s), however, still remain to be determined for the majority of ABCG transporters. Additionally, the proposed substrate spectrum of different ABCG proteins is not always reflected by sequence identities between ABCG members. Applying only reverse genetics is thereby insufficient to clearly identify the substrate(s). We therefore stress the importance of in vitro studies in addition to in vivo studies in order to (i) clarify the substrate identity; (ii) determine the transport characteristics including directionality; and (iii) identify dimerization partners of the half-size proteins, which might in turn affect substrate specificity.

Off-target effects of RNAi correlate with the mismatch rate between dsRNA and non-target mRNA

RNAi is a potent technique for the knockdown of target genes. However, its potential off-target effects limit the widespread applications in both reverse genetic analysis and genetic manipulation. Previous efforts have uncovered rules underlying specificity of siRNA-based silencing, which has broad applications in humans, but the basis for specificity of dsRNAs, which are better suited for use as insecticides, is poorly understood. Here, we investigated the rules governing dsRNA specificity. Mutational analyses showed that dsRNAs with >80% sequence identity with target genes triggered RNAi efficiently. dsRNAs with ≥16 bp segments of perfectly matched sequence or >26 bp segments of almost perfectly matched sequence with one or two mismatches scarcely distributed (single mismatches inserted between ≥5 bp matching segments or mismatched couplets inserted between ≥8 bp matching segments) also able to trigger RNAi. Using these parameters to predict off-target risk, dsRNAs can be designed to optimize specificity and efficiency, paving the way to the widespread, rational application of RNAi in pest control.

Genetic Analysis of Cachavirus-Related Parvoviruses Detected in Pet Cats: The First Report From China

In this study, members of the Carnivore chaphamaparvovirus species 1, closely related to a virus previously reported in dog feces named cachavirus was identified for the first time in feces of Chinese cats. Screening tests using rectal swabs from 171 diarrheic and 378 healthy cats collected from Henan, Anhui, and Zhejiang provinces in China revealed two samples from diarrheic cats that were positive for cachavirus, but statistical analysis indicated no association between the presence of the virus and clinical signs (p > 0.05). Subsequently, two partial genome sequences [from nucleotides 479–4123, according to the strains from dogs (cachavirus)] of the two strains from cats (cachavirus-cat1 and -cat2) were amplified. The NS1 and VP1 sites of cachavirus-cat1 and -cat2 shared a high identity of 91.9 and 97.0% with reported cachaviruses, respectively, but lower identity of 74.8 and 73.2% with another carnivore chaphamaparvovirus named fechaviruses detected in cats, respectively, indicated the two strains might origin from dogs. These findings improve our understanding of the diversity and tropism of viruses in Carnivore chaphamaparvovirus species 1 which now include both dogs and now cats viruses.

Identification of a new nucleotide binding site by structural alignment and site directed mutagenesis

Nucleotide binding proteins are involved in many important cellular processes and form one of the largest protein families. Traditionally, the identification of nucleotide binding motif, such as the ATP binding P-loop, has relied on the comparison of protein sequences, consideration of the function of each of the proteins and the identification of signature motifs within the sequence. Sometimes, it is difficult to identify nucleotide binding proteins based on sequence alignment because of increased evolutionary distances. In such cases, structural alignments can provide a better guide for comparing specific features of sequences because the overall structures of these motifs are conserved despite low sequence identity. In the present study, on the basis of bioinformatics and structural comparison of three representative protein structures of Ham1 superfamily, YjjX, YggV, and YhdE, previously identified as nucleotide binding proteins, we have identified a novel nucleotide binding motif (T/SXXXXK/R). The importance of this signature motif in binding of nucleotides was validated using site directed mutagenesis. Mutations of conserved residues of the loop either decreased or completely abolished the nucleotide binding activity of the protein. We used the conserved motif identified in the study to search for other proteins having a similar motif. Two proteins, GTP cyclohydrolase II and dephospho-CoA pyrophosphorylase showed presence of the loop, suggesting that this nucleotide binding motif is not unique in the Ham1 superfamily, but represents a novel NTP recognition motif.

Two Paralogous Genes Encoding Auxin Efflux Carrier Differentially Expressed in Bitter Gourd (Momordica charantia)

The phytohormone auxin regulates various developmental programs in plants, including cell growth, cell division and cell differentiation. The auxin efflux carriers are essential for the auxin transport. To show an involvement of auxin transporters in the coordination of fruit development in bitter gourd, a juicy fruit, we isolated novel cDNAs (referred as McPIN) encoding putative auxin efflux carriers, including McPIN1, McPIN2 (allele of McPIN1) and McPIN3, from developing fruits of bitter gourd. Both McPIN1 and McPIN3 genes possess six exons and five introns. Hydropathy analysis revealed that both polypeptides have two hydrophobic regions with five transmembrane segments and a predominantly hydrophilic core. Phylogenetic analyses revealed that McPIN1 shared the highest homology to the group of Arabidopsis, cucumber and tomato PIN1, while McPIN3 belonged to another group, including Arabidopsis and tomato PIN3 as well as PIN4. This suggests different roles for McPIN1 and McPIN3 in auxin transport involved in the fruit development of bitter gourd. Maximum mRNA levels for both genes were detected in staminate and pistillate flowers. McPIN1 is expressed in a particular period of early fruit development but McPIN3 continues to be expressed until the last stage of fruit ripening. Moreover, these two genes are auxin-inducible and qualified as early auxin-response genes. Their expression patterns suggest that these two auxin transporter genes play a pivotal role in fruit setting and development.

Cannabinoid receptors are widely expressed in goldfish: molecular cloning of a CB2-like receptor and evaluation of CB1 and CB2 mRNA expression profiles in different organs

Cannabinoids, the bioactive constituents of Cannabis sativa, and endocannabinoids, among which the most important are anandamide and 2-arachidonoylglycerol, control various biological processes by binding to specific G protein-coupled receptors, namely CB1 and CB2 cannabinoid receptors. While a vast amount of information on the mammalian endocannabinoid system does exist, few data have been reported on bony fish. In the goldfish, Carassius auratus, the CB1 receptor has been cloned and its distribution has been analyzed in the retina, brain and gonads, while CB2 had not yet been isolated. In the present paper, we cloned the goldfish CB2 receptor and show that it presents a quite high degree of amino acid identity with zebrafish Danio rerio CB2A and CB2B receptors, while the percentage of identity is lower with the puffer fish Fugu rubripes CB2, as also confirmed by the phylogenetic analysis. The sequence identity becomes much lower when comparing the goldfish and the mammalian CB2 sequences; as for other species, goldfish CB2 and CB1 amino acid sequences share moderate levels of identity. Western-blotting analysis shows the CB2 receptor as two major bands of about 53 and 40 kDa and other faint bands with apparent molecular masses around 70, 57 and 55 kDa. Since the distribution of a receptor could give information on its physiological role, we evaluated and compared CB1 and CB2 mRNA expression in different goldfish organs by means of qReal-Time PCR. Our results show that both CB1 and CB2 receptors are widely expressed in the goldfish, displaying some tissue specificities, thus opening the way for further functional studies on bony fish and other nonmammalian vertebrates.

Exploring residues crucial for nitrilase function by site directed mutagenesis to gain better insight into sequence-function relationships

Nitrilases represent a very important class of enzymes having an array of applications. In the present scenario, where the indepth information about nitrilases is limited, the present work is an attempt to shed light on the residues crucial for the nitrilase activity. The nitrilase sequences demonstrating varying degree of identity with P. putida nitrilase were explored. A stretch of residues, fairly conserved throughout the range of higher (96%) to lower (27%) sequence identity among different nitrilases was selected and investigated for the possible functional role in nitrilase enzyme system. Subsequently, the alanine substitution mutants (T48A, W49A, L50A, P51A, G52A, Y53A and P54A) were generated. Substitution of the rationally selected conserved residues altered the substrate recognition ability, catalysis and affected the substrate specificity but had very little impact on enantioselectivity and pattern of nitrile hydrolysis.