A unified mechanism for intron and exon definition and back-splicing.

The molecular mechanisms of exon definition and back-splicing are fundamental unanswered questions in pre-mRNA splicing. Here we report cryo-electron microscopy structures of the yeast spliceosomal E complex assembled on introns, providing a view of the earliest event in the splicing cycle that commits pre-mRNAs to splicing. The E complex architecture suggests that the same spliceosome can assemble across an exon, and that it either remodels to span an intron for canonical linear splicing (typically on short exons) or catalyses back-splicing to generate circular RNA (on long exons). The model is supported by our experiments, which show that an E complex assembled on the middle exon of yeast EFM5 or HMRA1 can be chased into circular RNA when the exon is sufficiently long. This simple model unifies intron definition, exon definition, and back-splicing through the same spliceosome in all eukaryotes and should inspire experiments in many other systems to understand the mechanism and regulation of these processes

Author Correction: CryoEM structure of Saccharomyces cerevisiae U1 snRNP offers insight into alternative splicing.

The originally published version of this Article contained several errors in Figure 2, panel a: the basepair register in SL3-4 of yeast U1 snRNA was depicted incorrectly; the basepair for A287-U295 in yeast U1 snRNA was erroneously present; basepairs for U84-G119, G309-U532, A288-U295 and U289-A294 in yeast U1 snRNA were missing; the bulging nucleotide in SL3 of human U1 snRNA was depicted as G instead of C; and the dashed boxes defining the 5' ss binding site and Sm site in both human and yeast snRNAs were not drawn accurately. These have now been corrected in both the PDF and HTML versions of the Article

A novel bacterium-like particles platform displaying antigens by new anchoring proteins induces efficacious immune responses

Bacterium-like particles (BLP) are the peptidoglycan skeleton particles of lactic acid bacteria, which have high safety, mucosal delivery efficiency, and adjuvant effect. It has been widely used in recent years in the development of vaccines. Existing anchoring proteins for BLP surfaces are few in number, so screening and characterization of new anchoring proteins are necessary. In this research, we created the OACD (C-terminal domain of Escherichia coli outer membrane protein A) to serve as an anchoring protein on the surface of BLP produced by the immunomodulatory bacteria Levilactobacillus brevis 23017. We used red fluorescent protein (RFP) to demonstrate the novel surface display system’s effectiveness, stability, and ability to be adapted to a wide range of lactic acid bacteria. Furthermore, this study employed this surface display method to develop a novel vaccine (called COB17) by using the multi-epitope antigen of Clostridium perfringens as the model antigen. The vaccine can induce more than 50% protection rate against C. perfringens type A challenge in mice immunized with a single dose and has been tested through three routes. The vaccine yields protection rates of 75% for subcutaneous, 50% for intranasal, and 75% for oral immunization. Additionally, it elicits a strong mucosal immune response, markedly increasing levels of specific IgG, high-affinity IgG, specific IgA, and SIgA antibodies. Additionally, we used protein anchors (PA) and OACD simultaneous to show several antigens on the BLP surface. The discovery of novel BLP anchoring proteins may expand the possibilities for creating mucosal immunity subunit vaccines. Additionally, it may work in concert with PA to provide concepts for the creation of multivalent or multiple vaccines that may be used in clinical practice to treat complex illnesses

Result of a year-long animal survey in a state-owned forest farm in Beijing, China

BackgroundArtificial forest can have great potential in serving as habitat to wildlife, depending on different management methods. As the state-owned forest farms now play a new role in ecological conservation in China, the biological richness of this kind of land-use type is understudied. Once owned by a mining company, a largest state-owned forest farm, Jingxi Forest Farm, has been reformed to be a state-owned forest farm with the purpose of conservation since 2017. Although this 116.4 km2 forest farm holds a near-healthy montaine ecosystem very representative in North China, a large proportion of artificial coniferous forest in the forest farm has been proven to hold less biodiversity than natural vegetation. This situation, however, provides a great opportunity for ecological restoration and biodiversity conservation. Therefore, from November 2019 to December 2020, we conducted a set of biodiversity surveys, whose results will serve as a baseline for further restoration and conservation.New informationHere, we report the result of a multi-taxa fauna diversity survey conducted in Jingxi Forest Farm mainly in year 2020 with explicit spatial information. It is the first survey of its kind conducted in this area, revealing a total of 19 species of mammals, 86 birds, four reptiles, two amphibians and one fish species, as well as 101 species of insects. Four species of mammals are identified as data-poor species as they have less than 100 occurrence records with coordination in the GBIF database. One species of insect, representing one new provincial record genus of Beijing, is reported

Reduced binding activity of vaccine serum to omicron receptor-binding domain

Coronavirus disease 2019 (COVID-19) vaccination regimens contribute to limiting the spread of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2). However, the emergence and rapid transmission of the SARS-CoV-2 variant Omicron raise a concern about the efficacy of the current vaccination strategy. Here, we expressed monomeric and dimeric receptor-binding domains (RBDs) of the spike protein of prototype SARS-CoV-2 and Omicron variant in E. coli and investigated the reactivity of anti-sera from Chinese subjects immunized with SARS-CoV-2 vaccines to these recombinant RBDs. In 106 human blood samples collected from 91 participants from Jiangxi, China, 26 sera were identified to be positive for SARS-CoV-2 spike protein antibodies by lateral flow dipstick (LFD) assays, which were enriched in the ones collected from day 7 to 1 month post-boost (87.0%) compared to those harvested within 1 week post-boost (23.8%) (P < 0.0001). A higher positive ratio was observed in the child group (40.8%) than adults (13.6%) (P = 0.0073). ELISA results showed that the binding activity of anti-SARS-CoV-2 antibody-positive sera to Omicron RBDs dropped by 1.48- to 2.07-fold compared to its homogeneous recombinant RBDs. Thus, our data indicate that current SARS-CoV-2 vaccines provide restricted humoral protection against the Omicron variant

<i>CsSE59</i> Encoding Invertase/Pectin Methyl Esterase Inhibitor Is a Candidate Gene Conferring the Virescent True Leaf Phenotype in Cucumber

Leaf color mutants are the ideal materials to study the regulation mechanisms of chlorophyll biosynthesis and chloroplast development or as markers for crop breeding. In this study, we identified a virescent true leaf mutant se59 from the ethyl methane sulfonate (EMS)-induced mutant lines of cucumber (Cucumis sativus L.). The se59 mutant showed normal cotyledons, but the true leaf displays light green at early growth stage, which can recover normal green later. The se59 locus was controlled by a single recessive nuclear gene. The grana stacking in the chloroplasts of se59 decreased significantly, and both the photosynthetic ability and the photosynthetic pigment contents of the se59 were significantly lower than those of wild type. The results of BSA-seq and genotyping showed that an Invertase/Pectin Methyl Esterase Inhibitor (INV/PMEI) protein encoded by CsSE59 is a candidate gene for the virescent true leaf mutant. The expression level of CsSE59 in stem, leaf and root is high. Based on the transcriptome analysis of the first true leaf of se59 mutant, the expression levels of 17 leaf color related genes changed significantly, suggesting CsSE59 may regulate virescent true leaf by interacting with some of these genes in cucumber. The identification of CsSE59 is helpful to clarify the role of INV/PMEI in chloroplast development and to understand the mechanisms of leaf color variation in cucumber

Comprehensive Genomic Analysis and Expression Profile of <i>Hsp70</i> Gene Family Related to Abiotic and Biotic Stress in Cucumber

Heat shock protein 70 (Hsp70) is a class of HSPs involved in plant growth and development, stress response and regulation. The Hsp70 proteins exist widely in the plant world, but the detail information about Hsp70s is still unclear in cucumber. Based on the available cucumber genome, a total of 12 Hsp70 genes (CsHsp70-1 to CsHsp70-12) were identified in this study, and they were distributed among five out of seven chromosomes. The CsHsp70s were divided into four groups based on a phylogenetic analysis by using protein sequences from cucumber and other plants, and their conserved motifs were relatively conserved. Gene duplication analysis showed that segmental duplication is the main driving force of expansion in cucumber CsHsp70 genes. Promoter analysis of CsHsp70 genes showed that they contained many cis-acting elements involved in hormone and stress responses. Expression analysis by RNA-seq and qRT-PCR indicated that the expression of most CsHsp70 genes was associated with multiple biotic and abiotic stresses in cucumber. This study introduces the characteristics of cucumber CsHsp70 genes and the regulation of their expression levels in various abiotic and biotic stresses, which provided a basis for functional exploration and utilization of CsHsp70 genes in the future

Molecular Cloning, Characterization, and Expression Analysis of SIMILAR TO RCD-ONE (SRO) Family Genes Responding to Abiotic and Biotic Stress in Cucumber

SIMILAR TO RCD-ONE (SRO) is a plant-specific small protein family that controls many biological processes including physiological development and stress responses. The SRO gene family has been studied in several plant species, but no detailed characterization and expression profiles of this important gene family were performed in cucumber. In this study, we characterize the SRO genes in cucumber, and determined their transcript levels in various tissues and under exposure to diverse biotic and abiotic stressors. Four SRO genes (named as CsSRO1&ndash;CsSRO4) were identified and isolated, which were distributed on three different chromosomes. Gene duplication analysis showed that only one pair of segmental duplication event was identified, but no tandem duplication events were detected. All CsSROs consist of the PARP domain and a C-terminal RST domain, while the N-terminal WWE domain was only present in CsSRO2 and CsSRO4. SROs from 15 plant species are divided into two groups (I and II), and group I can be further divided into four subgroups (Ia to Id) according to the phylogenetic tree. The conserved motif and gene structure analyses showed that SROs within the same branch of the phylogenetic tree have analogous conserved motifs configuration and gene structures. However, SRO genes possessed variable numbers of introns in different subgroups, which may affect the evolution of new family members. RNA-Seq data and qRT-PCR results showed that the four CsSRO genes have distinct expression pattern in various tissues and under diverse stresses, suggesting their multiple functions in plant growth and stress responses. The findings provide a basis for further research aiming at functional characterization of the regulatory mechanism to reveal the roles of CsSRO genes in developmental and stress-related processes of cucumber

Genome-Wide Survey and Expression Analysis of B-Box Family Genes in Cucumber Reveal Their Potential Roles in Response to Diverse Abiotic and Biotic Stresses

As a class of zinc finger transcription factors, B-box (BBX) proteins play diverse roles in numerous biological processes, and they have been identified in a series of plant species in recent years. However, the roles of BBX genes in regulating cucumber growth regulation and stress response have not yet been established. Here, a total of 22 BBX family genes were identified via an analysis of the latest cucumber genome data, which were classified into five groups (I–V) on the basis of their phylogenetic features and number of B-box domains and CCT domains. The CsBBX genes were unevenly distributed across the seven cucumber chromosomes, and segmental duplication was found to play a significant role in the expansion of the cucumber BBX gene family. Gene structure and motif composition analysis suggested that the evolutionarily close CsBBXs have similar conserved motif composition and gene structure. Most CsBBX genes possessed 1–3 introns, and intron gain rather than intron loss could contribute to the different structures of CsBBX genes across different groups during their evolution. Promoter analysis revealed the presence of 13 kinds of hormone-related and nine kinds of stress-related cis-regulatory elements in the promoter regions of these CsBBX genes. Expression analysis via RNA-seq and qRT-PCR suggested that the CsBBX genes exhibit differential expression in different tissues and in response to various abiotic and biotic stresses. This work constitutes a starting point for further revealing the function of the CsBBX genes and sheds light on the potential molecular mechanism of stress resistance in cucumber

Genome-Wide Survey and Expression Analysis of B-Box Family Genes in Cucumber Reveal Their Potential Roles in Response to Diverse Abiotic and Biotic Stresses

As a class of zinc finger transcription factors, B-box (BBX) proteins play diverse roles in numerous biological processes, and they have been identified in a series of plant species in recent years. However, the roles of BBX genes in regulating cucumber growth regulation and stress response have not yet been established. Here, a total of 22 BBX family genes were identified via an analysis of the latest cucumber genome data, which were classified into five groups (I&ndash;V) on the basis of their phylogenetic features and number of B-box domains and CCT domains. The CsBBX genes were unevenly distributed across the seven cucumber chromosomes, and segmental duplication was found to play a significant role in the expansion of the cucumber BBX gene family. Gene structure and motif composition analysis suggested that the evolutionarily close CsBBXs have similar conserved motif composition and gene structure. Most CsBBX genes possessed 1&ndash;3 introns, and intron gain rather than intron loss could contribute to the different structures of CsBBX genes across different groups during their evolution. Promoter analysis revealed the presence of 13 kinds of hormone-related and nine kinds of stress-related cis-regulatory elements in the promoter regions of these CsBBX genes. Expression analysis via RNA-seq and qRT-PCR suggested that the CsBBX genes exhibit differential expression in different tissues and in response to various abiotic and biotic stresses. This work constitutes a starting point for further revealing the function of the CsBBX genes and sheds light on the potential molecular mechanism of stress resistance in cucumber