Role of a holo-insertase complex in the biogenesis of biophysically diverse ER membrane proteins.

Mammalian membrane proteins perform essential physiologic functions that rely on their accurate insertion and folding at the endoplasmic reticulum (ER). Using forward and arrayed genetic screens, we systematically studied the biogenesis of a panel of membrane proteins, including several G-protein-coupled receptors (GPCRs). We observed a central role for the insertase, the ER membrane protein complex (EMC), and developed a dual-guide approach to identify genetic modifiers of the EMC. We found that the back of Sec61 (BOS) complex, a component of the multipass translocon, was a physical and genetic interactor of the EMC. Functional and structural analysis of the EMC⋅BOS holocomplex showed that characteristics of a GPCR's soluble domain determine its biogenesis pathway. In contrast to prevailing models, no single insertase handles all substrates. We instead propose a unifying model for coordination between the EMC, the multipass translocon, and Sec61 for the biogenesis of diverse membrane proteins in human cells.

Single-tissue proteomics in Caenorhabditis elegans reveals proteins resident in intestinal lysosome-related organelles.

The nematode intestine is the primary site for nutrient uptake and storage as well as the synthesis of biomolecules; lysosome-related organelles known as gut granules are important for many of these functions. Aspects of intestine biology are not well understood, including the export of the nutrients it imports and the molecules it synthesizes, as well as the complete functions and protein content of the gut granules. Here, we report a mass spectrometry (MS)-based proteomic analysis of the intestine of the Caenorhabditis elegans and of its gut granules. Overall, we identified approximately 5,000 proteins each in the intestine and the gonad and showed that most of these proteins can be detected in samples extracted from a single worm, suggesting the feasibility of individual-level genetic analysis using proteomes. Comparing proteomes and published transcriptomes of the intestine and the gonad, we identified proteins that appear to be synthesized in the intestine and then transferred to the gonad. To identify gut granule proteins, we compared the proteome of individual intestines deficient in gut granules to the wild type. The identified gut granule proteome includes proteins known to be exclusively localized to the granules and additional putative gut granule proteins. We selected two of these putative gut granule proteins for validation via immunohistochemistry, and our successful confirmation of both suggests that our strategy was effective in identifying the gut granule proteome. Our results demonstrate the practicability of single-tissue MS-based proteomic analysis in small organisms and in its future utility.

SARS-CoV-2 couples evasion of inflammatory response to activated nucleotide synthesis.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolves rapidly under the pressure of host immunity, as evidenced by waves of emerging variants despite effective vaccinations, highlighting the need for complementing antivirals. We report that targeting a pyrimidine synthesis enzyme restores inflammatory response and depletes the nucleotide pool to impede SARS-CoV-2 infection. SARS-CoV-2 deploys Nsp9 to activate carbamoyl-phosphate synthetase, aspartate transcarbamoylase, and dihydroorotase (CAD) that catalyzes the rate-limiting steps of the de novo pyrimidine synthesis. Activated CAD not only fuels de novo nucleotide synthesis but also deamidates RelA. While RelA deamidation shuts down NF-κB activation and subsequent inflammatory response, it up-regulates key glycolytic enzymes to promote aerobic glycolysis that provides metabolites for de novo nucleotide synthesis. A newly synthesized small-molecule inhibitor of CAD restores antiviral inflammatory response and depletes the pyrimidine pool, thus effectively impeding SARS-CoV-2 replication. Targeting an essential cellular metabolic enzyme thus offers an antiviral strategy that would be more refractory to SARS-CoV-2 genetic changes.

Increasing Proteome Coverage Through a Reduction in Analyte Complexity in Single-Cell Equivalent Samples.

The advancement of sophisticated instrumentation in mass spectrometry has catalyzed an in-depth exploration of complex proteomes. This exploration necessitates a nuanced balance in experimental design, particularly between quantitative precision and the enumeration of analytes detected. In bottom-up proteomics, a key challenge is that oversampling of abundant proteins can adversely affect the identification of a diverse array of unique proteins. This issue is especially pronounced in samples with limited analytes, such as small tissue biopsies or single-cell samples. Methods such as depletion and fractionation are suboptimal to reduce oversampling in single cell samples, and other improvements on LC and mass spectrometry technologies and methods have been developed to address the trade-off between precision and enumeration. We demonstrate that by using a monosubstrate protease for proteomic analysis of single-cell equivalent digest samples, an improvement in quantitative accuracy can be achieved, while maintaining high proteome coverage established by trypsin. This improvement is particularly vital for the field of single-cell proteomics, where single-cell samples with limited number of protein copies, especially in the context of low-abundance proteins, can benefit from considering analyte complexity. Considerations about analyte complexity, alongside chromatographic complexity, integration with data acquisition methods, and other factors such as those involving enzyme kinetics, will be crucial in the design of future single-cell workflows.

Lactiplantibacillus paraxiangfangensis sp. nov., isolated from traditional Chinese pickle.

Three Gram-stain-positive bacterial strains (designated 231-9T, 142-6 and 463-4) were isolated from traditional Chinese pickle, and were characterized using a polyphasic taxonomic approach. Results of 16S rRNA gene sequence analysis indicated that strains 231-9T, 142-6 and 463-4 were phylogenetically related to the type strains of Lactiplantibacillus xiangfangensis, Lactiplantibacillus garii, Lactiplantibacillus carotarum, Lactiplantibacillus plajomi and Lactiplantibacillus modestisalitolerans, having 98.6-99.9 % 16S rRNA gene sequence similarities. Strains 231-9T, 142-6 and 463-4 were most closely related to the type strain of L. xiangfangensis, having 99.9 % 16S rRNA gene, 95.6 % pheS, 99.4 % rpoA and 98.2 % concatenated pheS and rpoA sequence similarities. Relatively low pheS (95.6 %) sequence similarity indicated that strain 231-9T should be further identified. Strain 231-9T shared 99.7-99.9 % average nucleotide identity (ANI) and 98.8-98.9 % digital DNA-DNA hybridization (dDDH) values with strains 142-6 and 463-4, indicating that they belonged to the same species. The ANI and dDDH values between strain 231-9T and L. xiangfangensis LMG 26013T were 92.4-92.9 and 49.6 %, respectively, less than the threshold for species demarcation (95-96% ANI and 70 % dDDH values, respectively), indicating that strains 231-9T, 142-6 and 463-4 represented a novel species within the genus Lactiplantibacillus. Acid production from d-ribose, d-adonitol, d-galactose and lactose, activity of ß-galactosidase and ß-glucosidase, Voges-Proskauer reaction, hydrolysis of hippurate, resistance to 5 µg ml-1 erythromycin, 100 µg ml-1 tetracycline hydrochloride, 50 µg ml-1 bacitracin, 300 µg ml-1 each of gentamicin sulphate, streptomycin sulphate and neomycin sulphate, tolerance to 6 % NaCl could distinguish strains 231-9T, 142-6 and 463-4 from L. xiangfangensis 3.1.1T. Based upon the data of polyphasic characterization obtained in the present study, a novel species, Lactiplantibacillus paraxiangfangensis sp. nov., is proposed and the type strain is 231-9T (=JCM 36258T=CCTCC AB 2023133T).

Fluoranthene imide dimers with strong isomeric effects on the charge transport properties.

To date, the development of high-performance n-type organic semiconductors has remained challenging due to the scarcity of highly electron-deficient π-conjugated structural units and the difficulty of controlling intermolecular packing in the thin-film state. In addition, there have been few reports on the use of dimer design to tune the optoelectronic properties of materials. Herein, we report new cyano-substituted fluoranthene imide-based dimers (F16 and F17) for small-molecule n-type organic semiconductors. It is noteworthy that substituents at different positions lead to different film morphologies and very distinct thermal aggregation behaviors due to different dihedral angles. The self-assembly behavior of F17 improves thermal stability. Therefore, F17, which has a closer cyano groups structure, exhibits better field-effect transistor performance, with a maximum mobility of 6.6 × 10-4 cm2 V-1 s-1, while F16 does not exhibit any transistor performance.

Lapidilactobacillus salsurivasis sp. nov., Secundilactobacillus muriivasis sp. nov., and Streptococcus parasalivarius sp. nov., isolated from Traditional Chinese Pickle.

Four Gram-stain-positive bacterial strains (designated 475-2T, 46-6BT, 778-2T and A810-3), isolated from traditional Chinese pickle, were characterized using a polyphasic taxonomic approach. Strain 475-2T was most closely related to the type strain of Lapidilactobacillus achengensis, having 99.9% 16S rRNA gene sequence similarity, 94.1-95.1% average nucleotide identity (ANI) and 57.6% digital DNA-DNA hybridization (dDDH) values. Strain 46-6BT was most closely related to the type strain of Secundilactobacillus similis, having 99.8% 16S rRNA gene sequence similarity, 94.3-94.9% ANI and 58.9-59.2% dDDH values. Strains 778-2T and A810-3 were phylogenetically related to the type strains of Streptococcus salivarius, Streptococcus thermophilus and Streptococcus vestibularis, having 99.7-99.9% 16S rRNA gene sequence similarities, 89.1-94.4% ANI and 39.0-55.5% dDDH values. Based upon the data obtained in the present study, three novel species, Lapidilactobacillus salsurivasis sp. nov., Secundilactobacillus muriivasis sp. nov. and Streptococcus parasalivarius sp. nov., are proposed and the type strains are 475-2T (= JCM 36613T = CCTCC AB 2023258T = LMG 33412T), 46-6BT (= JCM 36612T = CCTCC AB 2023259T = LMG 33411T) and 778-2T (= JCM 36614T = CCTCC AB 2023257T = LMG 33413T), respectively.

Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization.

BACKGROUND: The analysis of mass spectrometry-based quantitative proteomics data can be challenging given the variety of established analysis platforms, the differences in reporting formats, and a general lack of approachable standardized post-processing analyses such as sample group statistics, quantitative variation and even data filtering. We developed tidyproteomics to facilitate basic analysis, improve data interoperability and potentially ease the integration of new processing algorithms, mainly through the use of a simplified data-object. RESULTS: The R package tidyproteomics was developed as both a framework for standardizing quantitative proteomics data and a platform for analysis workflows, containing discrete functions that can be connected end-to-end, thus making it easier to define complex analyses by breaking them into small stepwise units. Additionally, as with any analysis workflow, choices made during analysis can have large impacts on the results and as such, tidyproteomics allows researchers to string each function together in any order, select from a variety of options and in some cases develop and incorporate custom algorithms. CONCLUSIONS: Tidyproteomics aims to simplify data exploration from multiple platforms, provide control over individual functions and analysis order, and serve as a tool to assemble complex repeatable processing workflows in a logical flow. Datasets in tidyproteomics are easy to work with, have a structure that allows for biological annotations to be added, and come with a framework for developing additional analysis tools. The consistent data structure and accessible analysis and plotting tools also offers a way for researchers to save time on mundane data manipulation tasks.

Elevation of Lentilactobacillus rapi subsp. dabitei Li et al. 2022 to the species level as Lentilactobacillus dabitei sp. nov.

Lentilactobacillus rapi subsp. dabitei was proposed by Li et al. in 2022. The type strains of L. rapi subsp. dabitei and L. rapi subsp. rapi shared 93.1 % average nucleotide identity and 52.8 % digital DNA-DNA hybridization values. Strain IMAU80584T was proposed as a novel subspecies of L. rapi rather than a novel species of the genus Lentilactobacillus on the basis of similar phenotypic characteristics (including growth temperature and pH, tolerance to NaCl and features based on API 50CH and API ZYM). However, the phenotypic investigation performed by Li et al. was insufficient because some physiological and biochemical characteristics recommended by Mattarelli et al. were not included. In the present study, the taxonomic relationship between L. rapi subsp. dabitei and L. rapi subsp. rapi was re-evaluated. Based upon the data obtained in the present study, we propose to elevate L. rapi subsp. dabitei to the species level as Lentilactobacillus dabitei sp. nov. The type strain is IMAU80584T (=GDMCC 1.2566T=JCM 34647T).

Distressed Communities Index in Patients Undergoing Transcatheter Aortic Valve Implantation in an Affluent County in New York.

BACKGROUND: The clinical impact of the distressed communities index (DCI), a composite measure of economic well-being based on the U.S. zip code, is becoming increasingly recognized. Ranging from 0 (prosperous) to 100 (distressed), DCI's association with cardiovascular outcomes remains unknown. We aimed to study the association of the DCI with presentation and outcomes in adults with severe symptomatic aortic stenosis (AS) undergoing transcatheter aortic valve intervention (TAVR) in an affluent county in New York. METHODS: The study population included 286 patients with severe symptomatic AS or degeneration of a bioprosthetic valve who underwent TAVR with a newer generation transcatheter heart valve (THV) from December 2015 to June 2018 at an academic tertiary medical center. DCI for each patient was derived from their primary residence zip code. Patients were classified into DCI deciles and then categorized into 4 groups. The primary and secondary outcomes of interest were 30-day, 1-year, and 3-year mortality, respectively. RESULTS: Among 286 patients studied, 26%, 28%, 28%, and 18% were categorized into DCI groups 1-4, respectively (DCI <10: n = 73; DCI 10-20: n = 81; DCI 20-30: n = 80; DCI >30: n = 52). Patients in group 4 were younger with worse kidney function compared to patients in groups 1 and 2. They also had smaller aortic annuli and were more likely to receive a smaller THV. No significant difference in hospital length of stay or distribution of in-hospital, 30-day, 1-year, and 3-year mortality was demonstrated. CONCLUSIONS: While the DCI was associated with differences in the clinical and anatomic profile, it was not associated with differences in clinical outcomes in this prospective observational study of adults undergoing TAVR suggesting that access to care is the likely discriminator.

Characterization of orange-spotted grouper (Epinephelus coioides) interferon regulatory factor 4 regulated by heat shock factor 1 during heat stress in response to antiviral immunity.

Interferon regulatory factor 4 (IRF4), in conjunction with thermogenic regulation, is a negative regulator of immune responses. Therefore, we examined whether temperature changes regulated the antiviral response of IRF4 in nervous necrosis virus (NNV)-infected orange-spotted groupers. We found that osgIRF4 mRNA expression was responsive to poly I:C stimulation and NNV infection. In vitro overexpression of osgIRF4 caused a marked decrease in the promoter activity of the antiviral protein Mx1, and magnified NNV replication. Notably, we showed that the IAD domain of osgIRF4 exerted a dominant inhibitory effect on the Mx1 promoter. Furthermore, on exposure to high temperatures, the action of osgIRF4 was dependent on heat shock factor 1 (HSF1) expression. Additionally, small interfering RNA knockdown of HSF1 abrogated high temperature-mediated osgIRF4 activity. These findings suggest that osgIRF4 is an essential negative regulator of innate antiviral immunity and enhances viral replication during heat stress in the orange-spotted grouper.

Cloning and characterisation of type I interferon receptor 1 in orange-spotted grouper (Epinephelus coioides) for response to nodavirus infection.

Grouper is known as a highly economical teleost species in the Asian aquaculture industry; however, intensive culture activities easily cause disease outbreak, especially viral disease. For the prevention of viral outbreaks, interferon (IFN) is among the major defence systems being studied in different species. Fish type I IFNs are known to possess antiviral properties similar to mammalian type I IFNs. In order to stimulate antiviral function, IFN will bind to its cognate receptor, the type I interferon receptor (IFNAR), composed of heterodimeric receptor subunits known as IFNAR1 and IFNΑR2. The binding of type I interferon to receptors assists in the transduction of signals from the external to internal environments of cells to activate biological responses. In order to study the function of IFN, we first need to understand IFN receptors. In this study, we cloned and identified IFNAR1 in orange-spotted grouper (osgIFNAR1) and noted the up-regulated mRNA expression of the receptor and downstream effectors in the head kidney cells with cytokine treatment. The transcriptional expression of osgIFNAR1, which is characterised using polyinosinic-polycytidylic acid (poly[I:C]) and lipopolysaccharide (LPS) treatments, indicated the involvement of osgIFNAR1 in the immune response of grouper. The subcellular localisation of osgIFNAR1 demonstrated scattering across the grouper cell. Viral infection showed the negative feedback regulation of osgIFNAR1 in grouper larvae. Further loss of function of IFNAR1 showed a decreased expression of the virus. This study reported the identification of osgIFNAR1 and characterisation of receptor sensitivity towards immunostimulants, cytokine response, and viral challenge in the interferon pathway of orange-spotted grouper and possible different role of the receptor in viral production. Together, these results provide a frontline report of the potential function of osgIFNAR1 in the innate immunity of teleost.

Characterization of betanodavirus quasispecies influences on the subcellular localization and expression of tumor necrosis factor (TNF).

The aim of this study was to investigate the influence of variant coat proteins (CPs) from different quasispecies of betanodavirus on diverse aspects of nodavirus-induced pathogenesis. It is known that variant CPs can acquire either nuclear or cytoplasmic localization, depending on the nodavirus CP genotype, and this variation may arise during viral replication and influence the regulation of host and viral gene transcription. To investigate the role of these variant CPs in pathogenesis, six variant CP expression plasmids were constructed, each containing different quasispecies CP variants from nodavirus genotype red spotted grouper nervous necrosis virus (RGNNV). The CP expression plasmids were transiently transfected into grouper GF-1 cells. At different times, the cell cycle and cell proliferation were assayed using flow cytometry and methyl thiazolyl tetrazolium (MTT) assays, respectively. The proportion of G2/M-phase GF-1 cells transfected with CP expression plasmids was higher than that of cells transfected with the blank plasmid, especially in regards to quasispecies 2 (QS2). The proliferation ratio of cells transfected with the CP expression plasmids was significantly higher than that of cells transfected with the blank plasmid, with the exception of QS6. We also found that the different quasispecies CPs downregulated the promoter activity of the tumor necrosis factor (TNF) gene to different degrees. In addition, this is the first report showing the betanodavirus CP derived from different quasispecies of RGNNV provide evidence of a chronically nodavirus-infected grouper. Overall, this study represents the first comprehensive analysis of variant CPs from grouper with persistent nodavirus infections and their effects on different aspects of pathogenesis.

Author Correction: Plumbagin attenuates cancer cell growth and osteoclast formation in the bone microenvironment of mice.

During re-read of our previously article Plumbagin attenuates cancer cell growth and osteoclast formation in the bone microenvironment of micepublished in Acta Pharmacologica Sinica, we were regretted to point out a mistake shown in Fig. 2a. The representative figure chosen to indicate the inhibitory effect of 4 mg/kg of plumbagin treatment at 1 week against MDA-MB-231SArfp cells localization within bone environment was incorrect due to the mishandling in manuscript preparation. Although this correction does not affect the results and conclusion of the paper, all the authors agree on the correction of our negligence as providing the corrected Fig. 2a presented below. We feel sorry and apologize for all the inconvenience it caused.An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Dihydromyricetin Inhibits Inflammation of Fibroblast-Like Synoviocytes through Regulation of Nuclear Factor-κB Signaling in Rats with Collagen-Induced Arthritis.

Dihydromyricetin (DMY), the main flavonoid of Ampelopsis grossedentata, has potent anti-inflammatory activity. However, the effect of DMY on chronic autoimmune arthritis remains undefined. In this study, we investigated the therapeutic effects of DMY on collagen-induced arthritis (CIA). Wistar rats were immunized with bovine type II collagen to establish CIA and were then administered DMY intraperitoneally (5, 25, and 50 mg/kg) every other day for 5 weeks. Paw swelling, clinical scoring, and histologic analysis were assessed to determine the therapeutic effects of DMY on the development of arthritis in CIA rats. The results showed that treatment with DMY significantly reduced erythema and swelling in the paws of CIA rats. Pathologic analysis of the knee joints and peripheral blood cytokine assay results confirmed the antiarthritic effects of DMY on synovitis and inflammation. Fibroblast-like synoviocytes (FLSs) were isolated from the synovium of CIA rats and treated with 10 ng/ml interleukin (IL)-1ß DMY significantly inhibited the proliferation, migration, and inflammation of IL-1ß-induced FLSs, whereas it significantly increased IL-1ß-induced FLS apoptosis in a dose-dependent manner (6.25-25 µM). Moreover, DMY suppressed phosphorylation of IκB kinase (IKK) and inhibitor of NF-κB α and subsequently reduced the IL-1ß-induced nucleus translocation of NF-κB in FLSs. Through a molecular docking assay, we demonstrated that DMY could directly bind to the Thr9 and Asp88 residues in IKKα and the Asp95, Asn142, and Gln167 residues in IKKß These findings demonstrate that DMY could alleviate inflammation in CIA rats and attenuate IL-1ß-induced activities in FLSs through suppression of NF-κB signaling.

Author Correction: Synergistic suppression of human breast cancer cells by combination of plumbagin and zoledronic acid in vitro.

The authors regretted to find the mis-representative images in Fig. 3a, c and Fig. 4a, c when re-read our previously published article Synergistic suppression of human breast cancer cells by combination of plumbagin and zoledronic acid In vitro (DOI: 10.1038/aps.2015.42) in the journal of Acta Pharmacologica Sinica. This mistake occurred due to the careless compilation when the authors tried to show the synergistic effect against tumor apoptosis during figure presentation process. The right Fig. 3a, c and Fig. 4a, c were provided below. Despite that this correction does not affect the results and conclusions of the aforementioned paper, all the authors still consent on the correction of this negligence. We apologize to the Editor and the readership of the journal for any inconvenience caused. Your thoughtful understanding is highly appreciated.

[Treatment and Prognosis of Adult T Cell Acute Lymphoblastic Leukemia].

To analyze the treatment and prognosis of T cell acute lymphoblastic leukemia(T-ALL)in adults. Method The clinicobiogical and survival data of 68 adult patients with newly diagnosis T-ALL were retrospectively analzyed. Results The median age of these 68 patients was 23 years(14-60 years).T-ALL was more common in men(81%).After the first cycle of treatment,complete remission was achieved in 50 patients(73%).The highest complete remission(CR) rate was in patients with cortex T-ALL(100%),followed by other T-ALL(73%)and early T-cell precursor lymphoblastic leukemia(54%),(χ 2=5.712,P=0.058).The CR rate for adults aged >35 years was significantly lower than that of patients aged ≤ 35 years(40% vs. 79%,χ 2=6.364,P=0.012).The overall CR rate after the second treatment course was 93%.For patients treated with chemotherapy,autograft hematopoietic stem cell transplantation(auto-SCT),and allogeneic SCT,the median relapse free survival was 10 months,24 months,and not reached,respectively(P=0.002).The 5-year overall survival rate was 25% for all patients;for patients treated with chemotherapy,auto-SCT and allogeneic SCT,the median overall survival was 24 months,34 months,and 30 months,respectively(P=0.007),and the 5-year overall survival rate was 9%,33%,and 38%(P=0.037).Multivariate analysis showed leukocyte count ≥100×10 9/L was a risk factor for decreased relapse free survival(risk ratio 2.540,95%CI=1.058-6.099,P=0.037). Conclusion Adult T-ALL patients have poor prognosis,which may be improved by SCT.

Novel subunit vaccine with linear array epitope protect giant grouper against nervous necrosis virus infection.

Viral nervous necrosis caused by nervous necrosis virus (NNV) is one of the most severe diseases resulting in high fish mortality rates and high economic losses in the giant grouper industry. Various NNV vaccines have been evaluated, such as inactivated viruses, virus-like particles (VLPs), recombinant coat proteins, synthetic peptides of coat proteins, and DNA vaccines. However, a cheaper manufacturing process and effective protection of NNV vaccines for commercial application are yet to be established. Hence, the present study developed a novel subunit vaccine composed of a carrier protein, receptor-binding domain of Pseudomonas exotoxin A, and tandem-repeated NNV coat protein epitopes by using the structural basis of epitope prediction and the linear array epitope (LAE) technique. On the basis of the crystal structure of the NNV coat protein, the epitope was predicted from the putative target cell receptor-binding region to elicit neutralizing immune responses. The safety of the LAE vaccine was evaluated, and all vaccinated fish survived without any physiological changes. The coat protein-specific antibody titers in the vaccinated fish increased after vaccine administration and exerted NNV-neutralizing effects. The efficacy tests revealed that the relative percent survival (RPS) of LAE antigen formulated with adjuvant was above 72% and LAE vaccine was effective for preventing NNV infection in giant grouper. This study is the first to develop an NNV vaccine by using epitope repeats, which provided effective protection to giant grouper against virus infection. The LAE construct can be used as a vaccine design platform against various pathogenic diseases.

Genetic characterization and modification of a bioethanol-producing yeast strain.

Yeast Saccharomyces cerevisiae strains isolated from different sources generally show extensive genetic and phenotypic diversity. Understanding how genomic variations influence phenotypes is important for developing strategies with improved economic traits. The diploid S. cerevisiae strain NY1308 is used for cellulosic bioethanol production. Whole genome sequencing identified an extensive amount of single nucleotide variations and small insertions/deletions in the genome of NY1308 compared with the S288c genome. Gene annotation of the assembled NY1308 genome showed that 43 unique genes are absent in the S288c genome. Phylogenetic analysis suggested most of the unique genes were obtained through horizontal gene transfer from other species. RNA-Seq revealed that some unique genes were not functional in NY1308 due to unidentified intron sequences. During bioethanol fermentation, NY1308 tends to flocculate when certain inhibitors (derived from the pretreatment of cellulosic feedstock) are present in the fermentation medium. qRT-PCR and genetic manipulation confirmed that the novel gene, NYn43, contributed to the flocculation ability of NY1308. Deletion of NYn43 resulted in a faster fermentation rate for NY1308. This work disclosed the genetic characterization of a bioethanol-producing S. cerevisiae strain and provided a useful paradigm showing how the genetic diversity of the yeast population would facilitate the personalized development of desirable traits.

Crystal Structures of a Piscine Betanodavirus: Mechanisms of Capsid Assembly and Viral Infection.

Betanodaviruses cause massive mortality in marine fish species with viral nervous necrosis. The structure of a T = 3 Grouper nervous necrosis virus-like particle (GNNV-LP) is determined by the ab initio method with non-crystallographic symmetry averaging at 3.6 Å resolution. Each capsid protein (CP) shows three major domains: (i) the N-terminal arm, an inter-subunit extension at the inner surface; (ii) the shell domain (S-domain), a jelly-roll structure; and (iii) the protrusion domain (P-domain) formed by three-fold trimeric protrusions. In addition, we have determined structures of the T = 1 subviral particles (SVPs) of (i) the delta-P-domain mutant (residues 35-217) at 3.1 Å resolution; and (ii) the N-ARM deletion mutant (residues 35-338) at 7 Å resolution; and (iii) the structure of the individual P-domain (residues 214-338) at 1.2 Å resolution. The P-domain reveals a novel DxD motif asymmetrically coordinating two Ca2+ ions, and seems to play a prominent role in the calcium-mediated trimerization of the GNNV CPs during the initial capsid assembly process. The flexible N-ARM (N-terminal arginine-rich motif) appears to serve as a molecular switch for T = 1 or T = 3 assembly. Finally, we find that polyethylene glycol, which is incorporated into the P-domain during the crystallization process, enhances GNNV infection. The present structural studies together with the biological assays enhance our understanding of the role of the P-domain of GNNV in the capsid assembly and viral infection by this betanodavirus.