Non-redundant Protein Database Research Articles

Transcriptomic analysis of nitrogen metabolism pathways in Klebsiella aerogenes under nitrogen-rich conditions.

The acceleration of the nitrogen cycle and the nitrogen excess observed in some coastal waters has increased interest into understanding the biochemical and molecular basis of nitrogen metabolism in various microorganisms. To investigate nitrogen metabolism of a novel heterotrophic nitrification and aerobic denitrification bacterium Klebsiella aerogenes strain (B23) under nitrogen-rich conditions, we conducted physiological and transcriptomic high-throughput sequencing analyses on strain B23 cultured on potassium nitrate-free or potassium nitrate-rich media. Overall, K. aerogenes B23 assimilated 82.47% of the nitrate present into cellular nitrogen. Further, 1,195 differentially expressed genes were observed between K. aerogenes B23 cultured on potassium nitrate-free media and those cultured on potassium nitrate-rich media. Gene annotation and metabolic pathway analysis of the transcriptome were performed using a series of bioinformatics tools, including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Non-Redundant Protein Database annotation. Accordingly, the nitrogen metabolism pathway of K. aerogenes B23 was analyzed; overall, 39 genes were determined to be involved in this pathway. Differential expression analysis of the genes involved in the nitrogen metabolism pathway demonstrated that, compared to the control, FNR, NarK/14945, fdx, gshA, proB, proA, gapA, argH, artQ, artJ, artM, ArgR, GAT1, prmB, pyrG, glnS, and Ca1 were significantly upregulated in the nitrogen-treated K. aerogenes B23; these genes have been established to be involved in the regulation of nitrate, arginine, glutamate, and ammonia assimilation. Further, norV, norR, and narI were also upregulated in nitrogen-treated K. aerogenes B23; these genes are involved in the regulation of NO metabolism. These differential expression results are important for understanding the regulation process of key nitrogen metabolism enzyme genes in K. aerogenes B23. Therefore, this study establishes a solid foundation for further research into the expression regulation patterns of nitrogen metabolism-associated genes in K. aerogenes B23 under nitrogen-rich conditions; moreover, this research provides essential insight into how K. aerogenes B23 utilizes nutritional elements.

Exploring a GtfB-Type 4,6-α-Glucanotransferase to Synthesize the (α1 → 6) Linkages in Linear Chain and Branching Points from Amylose and Enhance the Functional Property of Granular Corn Starches.

Starch-converting α-glucanotransferases of glycoside hydrolase family 70 (GH70) are promising enzymatic tools for the production of diverse α-glucans with (potential) commercial applications in food and health and as biomaterials. In this study, a novel GtfB enzyme from Weissella confusa MBF8-1 was screened in the National Center for Biotechnology Information (NCBI) nonredundant protein database. The enzyme (named WcMBF8-1 GtfB) displayed high conservation in motifs I-IV with other GtfB enzymes but possessed unique variations in several substrate-binding residues. Structural characterizations of its α-glucan products revealed that WcMBF8-1 GtfB exhibited an atypical 4,6-α-glucanotransferase activity and was capable of catalyzing, by cleaving off (α1 → 4)-linkages in starch-like substrates and the synthesis of linear (α1 → 6) linkages and (α1 → 4,6) branching points. The product specificity enlarges the diversity of α-glucans and facilitates recognition of the determinants of the linkage specificity in GtfB enzymes. Furthermore, the contents of slowly digestible starch and resistant starch of granular corn starches, modified by WcMBF8-1 GtfB, increased by 6.7%, which suggested the potential value for the utilization of WcMBF8-1 GtfB to prepare "clean-label" starch ingredients with improved functional attributes.

Whole-genome sequencing of a protease-producing strain isolated from fermented golden pompano and molecular docking of the protease to fish proteins

In fermented fish products, microorganisms catalyze protein degradation by secreting proteases, thereby altering the nutritional values of foods. In this study, we isolated a high proteinase-producing strain from fermented golden pompano (Trachinotus ovatus), and from the 16S rRNA, we identified the strain as Bacillus tropicus, which we named Bacillus tropicus MX-8. This strain could form a distinct proteolytic circle around the colony when plated on agar containing 3% skimmed milk powder and could grow under 0–5% salinity. Its protease significantly degraded fish proteins. Genome sequencing analysis revealed that the genome of B. tropicus MX-8 comprised one circular chromosome and three circular plasmids. A total of 27 genes encoding proteases, including a neutral protease and three serine proteases, were identified in the non-redundant protein database. Homology modeling showed that serine protease 2 had the best model quality and the highest sequence match. Molecular docking experiments revealed the presence of several amino acid active sites on serine protease 2. These active sites mainly rely on hydrogen bonding to interact with actin heavy chains and myosin to form complexes, which can promote further protein degradation. This study demonstrated that B. tropicus MX-8 has the potential to ferment fish, providing a theoretical basis for the production of rapidly fermented fish products.

Transcriptome analysis and identification of differentially expressed genes between early and mature ovarian stages in the female mantis shrimp (Harpiosquilla raphidea) using RNA-Seq

Harpiosquilla raphidea, the largest of the mantis shrimps, is a commercially important crustacean species widely distributed in many countries of the Pacific Ocean. However, no data are currently available regarding the molecular mechanisms that regulate reproduction in this species. To address this knowledge gap, we performed transcriptome sequencing (RNA-Seq) of previtellogenic and vitellogenic ovaries of female H. raphidea, and compared the expression patterns of transcripts from the two resulting libraries to identify genes involved in ovarian development. A total of 418,635,748 clean reads were retrieved after removing adapter sequences and filtering out low-quality data. The reads were assembled into 242,861 unigenes with an average length of 585.27 base pairs (bp) and an N50 of 829 bp. A search of all unigenes against the NR (non-redundant protein), SwissProt, KEGG, GO, and COG databases yielded 53,111; 25,460; 27,255; 26,793; and 3838 unigene matches, respectively). Of the 53,111 unigenes identified in the NR database, 30,441 could be functionally annotated, 59.49% of which were significantly matched with the transcripts of L. vannamei. A total of 13,867 full-length transcripts and 11,441 partial transcripts were retrieved. In addition, using all-unigenes as a reference, a total of 12,765 simple sequence repeats (SSRs) were identified. DESeq2 analysis identified a total of 962 differentially expressed genes (DEGs) between previtellogenic and vitellogenic ovaries, 456 of which were upregulated and 506 downregulated. Five unigenes were validated by quantitative real-time PCR (qPCR). The results of both the RNA-Seq and qPCR analysis revealed that the H. raphidea vitellogenin gene (HrVtg) was upregulated in vitellogenic ovaries. The open reading frame of HrVtg was found to be 7455 bp long, corresponding to a polypeptide of 2485 amino acids. The important functional genes and pathways identified here provide a valuable dataset for understanding the molecular mechanisms controlling ovarian development in H. raphidea.

Microbial Diversity in Children with Gastroenteritis in the Amazon Region of Brazil: Development and Validation of a Molecular Method for Complete Sequencing of Viral Genomes.

Metagenomic sequencing is a powerful tool that is widely used in laboratories worldwide for taxonomic characterization of microorganisms in clinical and environmental samples. In this study, we utilized metagenomics to investigate comprehensively the microbial diversity in fecal samples of children over a four-year period. Our methods were carefully designed to ensure accurate and reliable results. Validated and analyzed were metagenomic data obtained from sequencing 27 fecal samples from children under 10 years old with gastroenteritis over a four-year period (2012-2016). The fecal specimens were collected from patients who received care at public health facilities in the northern region of Brazil. Sequencing libraries were prepared from cDNA and sequenced on the Illumina HiSeq. Kraken-2 was utilized to classify bacterial taxonomy based on the 16S rRNA gene, using the Silva rRNA database. Additionally, the Diamond program was used for mapping to the non-redundant protein database (NR database). Phylogenomic analyses were conducted using Geneious R10 and MEGA X software, and Bayesian estimation of phylogeny was performed using the MrBayes program. The results indicate significant heterogeneity among norovirus strains, with evidence of recombination and point mutations. This study presents the first complete genome of parechovirus 8 in the region. Additionally, it describes the bacterial populations and bacteriophages present in feces, with a high abundance of Firmicutes and Proteobacteria, including an increased proportion of the Enterobacteriaceae family. The presented data demonstrate the genetic diversity of microbial populations and provide a comprehensive report on viral molecular characterization. These findings are relevant for genomic studies in gastrointestinal infections. The metagenomic approach is a powerful tool for investigating microbial diversity in children with gastroenteritis. However, further studies are imperative to conduct genomic analysis of identified bacterial strains and thoroughly analyze antimicrobial resistance genes.

AI-assisted structural consensus-proteome prediction of human monkeypox viruses isolated within a year after the 2022 multi-country outbreak.

The monkeypox virus (MPX) belongs to the Orthopoxvirus genus of the Poxviridae family, is endemic in parts of Africa and causes a disease in humans similar to smallpox. The most recent outbreak of MPX is already affecting 110 countries, with 86,956 confirmed cases since May 2022 and has consequently become a focus of interest. In particular, a molecular understanding of the virus is essential to study infection processes and pathogen-host interactions, predict tropism changes, or guide drug development and drug discovery as well as vaccine development or vaccine adaptation at a very early stage. Herein, we present a study of the structural proteome of the currently circulating MPX: Our consensus analysis of 3,713 genome sequences sampled within a year after the outbreak revealed 10,580 characteristic candidate open reading frames (ORFs). A search in the non-redundant protein database reduced the number of suspected ORFs to 1,079, of which 210 are representative proteins in typical MPX reference genomes. This should serve as a collection of putative proteins within the currently spreading MPX, a compound of information that could support timely drug discovery, mutational analyses, and vaccine development. We, herein, present the so far most comprehensive structural proteome by providing atomistic 3D models of 210 proteins, generated with three state-of-the-art structure prediction methods, including a mutational analysis of the proteome, with a particular focus on the drug-binding sites of tecovirimat and brincidofovir. IMPORTANCE The 2022 outbreak of the monkeypox virus already involves, by April 2023, 110 countries with 86,956 confirmed cases and 119 deaths. Understanding an emerging disease on a molecular level is essential to study infection processes and eventually guide drug discovery at an early stage. To support this, we provide the so far most comprehensive structural proteome of the monkeypox virus, which includes 210 structural models, each computed with three state-of-the-art structure prediction methods. Instead of building on a single-genome sequence, we generated our models from a consensus of 3,713 high-quality genome sequences sampled from patients within 1 year of the outbreak. Therefore, we present an average structural proteome of the currently isolated viruses, including mutational analyses with a special focus on drug-binding sites. Continuing dynamic mutation monitoring within the structural proteome presented here is essential to timely predict possible physiological changes in the evolving virus.

The Draft Genome of the "Golden Tide" Seaweed, Sargassum horneri: Characterization and Comparative Analysis.

Sargassum horneri, a prevalent species of brown algae found along the coast of the northwest Pacific Ocean, holds significant importance as a valuable source of bioactive compounds. However, its rapid growth can lead to the formation of a destructive "golden tide", causing severe damage to the local economy and coastal ecosystems. In this study, we carried out de novo whole-genome sequencing of S. horneri using next-generation sequencing to unravel the genetic information of this alga. By utilizing a reference-guided de novo assembly pipeline with a closely related species, we successfully established a final assembled genome with a total length of 385 Mb. Repetitive sequences made up approximately 30.6% of this genome. Among the identified putative genes, around 87.03% showed homology with entries in the NCBI non-redundant protein database, with Ectocarpus siliculosus being the most closely related species for approximately one-third of these genes. One gene encoding an alkaline phosphatase family protein was found to exhibit positive selection, which could give a clue for the formation of S. horneri golden tides. Additionally, we characterized putative genes involved in fucoidan biosynthesis metabolism, a significant pathway in S. horneri. This study represents the first genome-wide characterization of a S. horneri species, providing crucial insights for future investigations, such as ecological genomic analyses.

NCRD: A non-redundant comprehensive database for detecting antibiotic resistance genes

Antibiotic resistance genes (ARGs) are emerging pollutants present in various environments. Identifying ARGs has become a growing concern in recent years. Several databases, including the Antibiotic Resistance Genes Database (ARDB), Comprehensive Antibiotic Resistance Database (CARD), and Structured Antibiotic Resistance Genes (SARG), have been applied to detect ARGs. However, these databases have limitations, which hinder the comprehensive profiling of ARGs in environmental samples. To address these issues, we constructed a non-redundant antibiotic resistance genes database (NRD) by consolidating sequences from ARDB, CARD, and SARG. We identified the homologous proteins of NRD from Non-redundant Protein Database (NR) and the Protein DataBank Database (PDB) and clustered them to establish a non-redundant comprehensive antibiotic resistance genes database (NCRD) with similarities of 100% (NCRD100) and 95% (NCRD95). To demonstrate the advantages of NCRD, we compared it with other databases by using metagenome datasets. Results revealed its strong ability in detecting potential ARGs.

First Report of Banana mild mosaic virus Infecting Banana in China.

Banana (Musa spp.) is an important fruit in tropical and subtropical regions and an essential food crop in some developing countries. China has a long history of banana cultivation and ranks second in global banana production, with a planting area exceeding 11 million hectares (FAOSTAT, 2023). Banana mild mosaic virus (BanMMV) is a flexuous filamentous virus infecting bananas and a banmivirus in the Betaflexiviridae family. Its infection often results in symptomless plants of Musa spp., and the virus has a worldwide distribution, which can explain its high prevalence (Kumar et al., 2015). BanMMV infection often causes transitory symptoms, such as mild chlorotic streaks and mosaics, on young leaves (Thomas, 2015). The mixed infection of BanMMV with other banana-infecting viruses such as banana streak viruses (BSV) and cucumber mosaic virus (CMV), can exacerbate the mosaic symptoms of BanMMV (Fidan et al., 2019). In October 2021, we collected twenty-six leaf samples of suspected viral disease of bananas from four cities (Huizhou, Qingyuan, Zhanjiang, and Yangjiang) in Guangdong province, two cities (Hekou and Jinghong) in Yunnan province, two cities (Yulin and Wuming) in Guangxi Zhuang autonomous region. After fully mixing these infected samples, we divided them into two pools and sent them to Shanghai Biotechnology Corporation (China) for metatranscriptome sequencing. Each sample contained about 5 g of leaves in total. Zymo-Seq RiboFree Total RNA Library Prep Kit (Zymo Research, USA) was used for ribosomal RNA depletion and library preparations. Illumina sequencing (Illumina NovaSeq 6000) was carried out by Shanghai Biotechnology Corporation (China). Paired-end (150 bp) sequencing of the RNA library was performed on an Illumina HiSeq 2000/2500 platform. Clean reads were assembled by a metagenomic de novo assembly using the CLC Genomics Workbench (version: 6.0.4). Then the non-redundant protein database in the National Center for Biotechnology Information (NCBI) was used for BLASTx annotation. A total of 79,528 contigs were generated from the clean reads (68,878,162) through de novo assembly. A contig of 7265 nucleotides (nts) showed the highest nucleotide sequence identity (90.08%) to the genome of BanMMV isolate EM4-2 (GenBank accession no. OL826745.1). We designed specific primers according to the BanMMV CP gene (Table S1), tested the twenty-six leaf samples collected from the above-mentioned eight cities, and found that only one sample of Fenjiao (Musa ABB Pisang Awak) in Guangzhou city was infected with this virus. The symptoms of banana leaves containing BanMMV were slight chlorosis and yellowing of leaf edges (Fig. S1). We failed to detect other banana viruses, such as BSV, CMV, and banana bunchy top virus (BBTV) in the BanMMV-infected banana leaves. RNA from the infected leaves was extracted, and the assembled contig was confirmed by overlapping PCR amplification across the whole sequence (Table S1). All ambiguous regions were amplified by PCR and RACE, and the products were subjected to Sanger sequencing. The complete genome of the virus candidate was 7310 nts in length, excluding the poly (A) tail. The sequence was deposited in GenBank under accession number ON227268 (isolate BanMMV-GZ from Guangzhou). A schematic representation of the genome organization of BanMMV-GZ is shown in Fig. S2. Its genome has five open reading frames (ORF) encoding RNA-dependent RNA polymerase (RdRp), three triple gene block proteins necessary for cell-to-cell movement (TGBp1 to TGBp3) and a coat protein (CP), similar to other BanMMV isolates (Kondo et al., 2021). Phylogenetic analyses of the complete nt sequence of the full genome and RdRp gene using the neighbor-joining (NJ) method also clearly placed the BanMMV-GZ firmly within all isolates of BanMMV (Fig. S3). To our knowledge, this is the first report of BanMMV infecting bananas in China, extending the geographical range of this viral disease around the world. Accordingly, larger-scale BanMMV investigations must be conducted to determine the distribution and prevalence of BanMMV in China.

More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases.

Mobilized colistin resistance genes (mcr) may confer resistance to the last-resort antimicrobial colistin and can often be transmitted horizontally. mcr encode phosphoethanolamine transferases (PET), which are closely related to chromosomally encoded, intrinsic lipid modification PET (i-PET; e.g., EptA, EptB, CptA). To gain insight into the evolution of mcr within the context of i-PET, we identified 69,814 MCR-like proteins present across 256 bacterial genera (obtained by querying known MCR family representatives against the National Center for Biotechnology Information [NCBI] non-redundant protein database via protein BLAST). We subsequently identified 125 putative novel mcr-like genes, which were located on the same contig as (i) ≥1 plasmid replicon and (ii) ≥1 additional antimicrobial resistance gene (obtained by querying the PlasmidFinder database and NCBI's National Database of Antibiotic Resistant Organisms, respectively, via nucleotide BLAST). At 80% amino acid identity, these putative novel MCR-like proteins formed 13 clusters, five of which represented putative novel MCR families. Sequence similarity and a maximum likelihood phylogeny of mcr, putative novel mcr-like, and ipet genes indicated that sequence similarity was insufficient to discriminate mcr from ipet genes. A mixed-effect model of evolution (MEME) indicated that site- and branch-specific positive selection played a role in the evolution of alleles within the mcr-2 and mcr-9 families. MEME suggested that positive selection played a role in the diversification of several residues in structurally important regions, including (i) a bridging region that connects the membrane-bound and catalytic periplasmic domains, and (ii) a periplasmic loop juxtaposing the substrate entry tunnel. Moreover, eptA and mcr were localized within different genomic contexts. Canonical eptA genes were typically chromosomally encoded in an operon with a two-component regulatory system or adjacent to a TetR-type regulator. Conversely, mcr were represented by single-gene operons or adjacent to pap2 and dgkA, which encode a PAP2 family lipid A phosphatase and diacylglycerol kinase, respectively. Our data suggest that eptA can give rise to "colistin resistance genes" through various mechanisms, including mobilization, selection, and diversification of genomic context and regulatory pathways. These mechanisms likely altered gene expression levels and enzyme activity, allowing bona fide eptA to evolve to function in colistin resistance.

Genome sequencing, assembly, and characterization of Pichia fermentans Z9Y-3 as a non-Saccharomyces yeast with aroma enhancing potential

Pichia fermentans is an important non-Saccharomyces yeast applied in mixed fermentation to enhance fruity and floral traits of wine aroma. In this study, genome sequencing of P. fermentans Z9Y-3 was performed using the PacBio single-molecule real-time sequencing platform, and was further assembled using MECAT. The sequenced genes are annotated by non-redundant protein (Nr), Gene Ontology (GO), Cluster of Orthologous Groups of proteins (COG), Kyoto Encyclopedia of Genes and Genomes (KEGG) and carbohydrate-active enzymes (CAZymes) database. Results indicated that the genome size was about 13.5 Mb with 42.09% GC content and 4730 protein coding genes. The 95.90% genes were annotated to the non-redundant protein (Nr) database, and then annotated to GO database. The 62.64% genes annotated to the COG database revealed 25 functional groups. The 58.22% genes annotated to the KEGG database revealed 5 groups. The 586 genes were annotated to CAZymes, in which two genes bglH and bglC encoding beta-glucosidase were found and further analyzed its motifs. A terpene and a nonribosomal peptides like secondary metabolic gene clusters were predicted using antiSMASH 7.0.0. This study benefits us to understand physiological and biochemical behavior of P. fermentans Z9Y-3 at a molecular level to better use P. fermentans Z9Y-3 in aroma enhancing winemaking.

Phosphorylation of SiRAV1 at Ser31 regulates the SiCAT expression to enhance salt tolerance in Setaria italica

Salinity severely affects plant growth and development. Thus, it is crucial to identify the genes functioning in salt stress response and unravel the mechanism by which plants against salt stress. This study used the phosphoproteomic assay and found that 123 of the 4 000 quantitative analyzed phosphopeptides were induced by salt stress. The functional annotation of the non-redundant protein database (NR) showed 23 differentially expressed transcription factors, including a phosphopeptide covering the Serine 31 in the RAV (related to ABI3/VP1) transcription factor (named SiRAV1). SiRAV1 was located in the nucleus. Phenotypic and physiological analysis showed that overexpressing SiRAV1 in foxtail millet enhanced salt tolerance and alleviated the salt-induced increases of H2O2 accumulation, malondialdehyde (MDA) content, and percent of electrolyte leakage. Further analysis showed that SiRAV1 positively regulated SiCAT expression to modulate the catalase (CAT) activity by directly binding to the SiCAT promoter in vivo and in vitro. Moreover, we found that phosphorylation of SiRAV1 at the Ser31 site positively regulated salt tolerance in foxtail millet via enhancing its binding ability to SiCAT promoter but did not affect its subcellular localization. Overall, our results define a mechanism for SiRAV1 function in salt response where salt-triggered phosphorylation of SiRAV1 at Ser31 enhances its binding ability to SiCAT promoter, and the increased SiCAT expression contributes to salt tolerance in foxtail millet.

Genome Sequence Resource for Colletotrichum gloeosporioides, an Important Pathogenic Fungus Causing Anthracnose of Dioscorea alata.

Anthracose disease is one of the most important diseases of Dioscorea alata and many other food yams, which is caused by Colletotrichum gloeosporioides fugus from the Glomerellaceae family of the Sordariomycetes class. In the present study, a C. gloeosporioides starin named CgDa01 was isolated from D. alata, and its genome was sequenced based on Oxford Nanopore technology (ONT) and the Illumina sequencing platform. The high-quality genome of CgDa01 was assembled with a 62.78 Mb genome size and 15,845 predicted protein-coding genes. The proteins of predicted genes were annotated using multiple public databases, including the nonredundant protein database, the InterProScan databases, and Kyoto Encyclopedia of Genes and Genomes. Among the annotated protein-coding genes, 55 were predicted as potential virulence genes by the fungal virulence factor database. The C. gloeosporioides CgDa01 genome assembly described in this study can serve as a resource for better understanding the pathogenic mechanism of C. gloeosporioides on yam hosts.

Genome Sequence Resource of Ustilago crameri, a Fungal Pathogen Causing Millet Smut Disease of Foxtail Millet.

Genome Sequence Resource of Ustilago crameri, a Fungal Pathogen Causing Millet Smut Disease of Foxtail Millet.

Transcriptome Analysis of a Wild Eggplant Germplasm M239 in Response to Verticillium dahliae Infection

In this study, wild eggplant germplasm No. M239, which is highly susceptible to Verticillium wilt, was used as the experimental material. The physiological and biochemical indices (SOD, PAL, MDA and soluble protein) of M239 roots were measured at different times (0, 12, 24, 36, 48, 60 and 72 h) post inoculation with Verticillium dahliae, and the key time points for the M239 response to Verticillium wilt infection were screened. Then, RNA-Seq technology was used to screen the differentially expressed genes (DEGs) in M239 roots at 0, 12 and 48 h post-inoculation (hpi). The transcriptional results of M239 were also compared with those resistance genes from some reported wild relative Solanum species (S. sisymbriifolium and S. aculeatissimum). Then some DEGs were chosen for validation by qRT–PCR. The results showed that 12 and 48 hpi were the turning points in the changes in all physiological and biochemical indices. A total of 6,783 DEGs were identified by RNA-Seq, including 6,141 DEGs (3,046 upregulated and 3,095 downregulated) at the M_12 h vs. M_0 h, 1,903 DEGs (792 upregulated and 1,111 downregulated) at M_48 h vs. M_12 h, and 1,261 DEGs that appeared simultaneously in both stages. KEGG enrichment analysis showed that there were 5 metabolic pathways enriched from DEGs, which were mostly related to primary metabolism, such as glycolysis, amino acid and ribosome biogenesis. Compared with the NCBI non-redundant protein (NR) database, one Ve2 homologous gene and 8 PR protein-related genes were screened. Transcription factor analysis showed that there were a large number of DEGs, such as MYB, AP2-EREBP, bHLH, NAC and Orphans in the two stages. Compared with the reported Verticillium wilt-resistant wild eggplant species, it was found that there were fewer genes and enriched metabolic pathways in the M239 response to Verticillium wilt infection, and it also lacked the response of some known key resistance genes. These results proved that the above resistance genes and metabolic pathways played a key role in the wild eggplant response to V. dahliae infection.

Transcriptomic Identification and Expression Profile Analysis of Odorant-Degrading Enzymes from the Asian Corn Borer Moth, Ostrinia furnacalis.

The Asian corn borer moth Ostrinia furnacalis is an important lepidopteran pest of maize in Asia. Odorant-degrading enzymes (ODEs), including carboxylesterases (CCEs), glutathione S-transferases (GSTs), cytochrome P450s (CYPs), UDP-glycosyltransferases (UGTs), and aldehyde oxidases (AOXs), are responsible for rapid inactivation of odorant signals in the insect antennae. In this study, we performed a transcriptome assembly for the antennae of O. furnacalis to identify putative ODE genes. Transcriptome sequencing revealed 35,056 unigenes, and 21,012 (59.94%) of these were annotated by searching against the reference sequences in the NCBI non-redundant (NR) protein database. For functional classification, these unigenes were subjected to Gene Ontology (GO), Eukaryotic Orthologous Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations. We identified 79 genes encoding putative ODEs: 19 CCEs, 17 GSTs, 24 CYPs, 13 UGTs, and 6 AOXs. BLASTX best hit results indicated that these genes shared quite high amino acid identities with their respective orthologs from other lepidopteran species. Reverse transcription-quantitative PCR showed that OfurCCE2, OfurCCE5, and OfurCCE18 were enriched in male antennae, while OfurCCE7 and OfurCCE10 were enriched in female antennae. OfurCCE14 and OfurCCE15 were expressed at near-equal amounts in the antennae of both sexes. Our findings establish a solid foundation for future studies aimed at understanding the olfactory functions of these genes in O. furnacalis.

Trypanosoma evansi RoTat 1.2 variant surface antigen mimotopes selected by panning of the random peptide phage-display library against monoclonal antibodies.

Mimotope peptides of native antigens are valuable for diverse applications such as diagnostics, therapeutics and modern vaccine design. Here, we report for the first time the selection and identification of peptide mimotopes of Trypanosoma evansi RoTat 1.2 variant surface glycoprotein (VSG) for their potential uses in surra diagnostics and multi-epitope vaccine research. First, we produced the mouse monoclonal antibodies (mAbs), designated as 2E11 (IgG1) and 1C2 (IgG1), against the antigens in T. evansi RoTat 1.2 lysates. We then used 2E11 mAb to immunoprecipitate the target antigen. The immunoprecipitated antigen was then identified to be the VSG by mass spectrometry. Both 2E11 and 1C2 mAbs reacted with the VSG in immunoblots. The surface plasmon resonance immunosensors developed with both the mAbs detected VSG in the parasite lysates as well as in the rodent sera. Further, the mAbs were biotinylated and used in three rounds of panning to select peptide mimotopes from the random peptide phage display library (PhD-12; New England Biolabs, USA). The phage clones selected against each mAb were amplified and tested by phage capture ELISA for specificity. The peptide coding regions of the selected phages were sequenced and the protein blast search of the deduced amino acid sequences was performed by accessing the non-redundant protein database at https://blast.ncbi.nlm.nih.gov/. The conformational B epitope prediction of the selected mimotope sequences was done by using 3D Pepitope algorithms accessed at: http://pepitope.tau.ac.il/. The potential applications of the selected mimotopes in surra diagnostics and research are being explored.

Genome Sequence Resource of Albifimbria verrucaria Causing the Leaf Spot Disease of the Spinach Plant Spinacia oleracea.

Genome Sequence Resource of Albifimbria verrucaria Causing the Leaf Spot Disease of the Spinach Plant Spinacia oleracea.

Whole-Genome Sequencing of a Potential Ester-Synthesizing Bacterium Isolated from Fermented Golden Pomfret and Identification of Its Lipase Encoding Genes.

Microbial ester synthases are regarded as valuable catalysts in the food industry. Here, one strain of Acinetobacter venetianus with ester synthase-production capacity, SCSMX-3, was isolated from traditional fermented golden pomfret. It exhibited good growth in mesophilic, low salt, and slightly alkaline environments. The ester synthase produced by SCSMX-3 displayed maximum activity at pH 8.0 and 35 °C. Genome sequencing revealed that the strain contains one circular chromosome of 336313 bp and two circular plasmids (plasmid A-14424 bp and plasmid B-11249 bp). Six CRISPR structures enhance the genomic stability of SCSMX-3 and provide the opportunity to create new functional strains. Gene function analysis indicated that SCSMX-3 produces the necessary enzymes for survival under different conditions and for flavor substance synthesis. Furthermore, 49 genes encoding enzymes associated with lipid metabolism, including three triacylglycerol lipases and two esterases, were identified through the NCBI Non-Redundant Protein Database. The lipase encoded by gene0302 belongs to the GX group and the abH15.02 (Burkholderia cepacia lipase) homolog of the abH15 superfamily. Our results shed light on the genomic diversity of and lipid metabolism in A. venetianus isolated from fermented golden pomfret, laying a foundation for the exploration of new ester synthases to improve the flavor of fermented fish products.

Whole-genome sequencing and functional analysis of a novel chitin-degrading strain Rhodococcus sp. 11-3

Chitin is the second most abundant polysaccharide in nature. Therefore, how to utilize the resource is an important issue. Rhodococcus sp. 11-3 is a strain with high chitin deacetylase (CDA) activity. In the present study, we used a combined Illumina and PacBio sequencing strategy to assemble the whole genome sequence of this strain. The genome of Rhodococcus sp. 11-3 was 5,627,661 bp in size and contained 5983 coding genes, of which 5983, 4040, 4648, 4914, 4174, 2350, and 173 genes were annotated in the Non-Redundant Protein Database (NR), Swiss-Prot, Pfam, Clusters of Orthologous Groups of proteins (COG), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-active enzymes (CAZymes) databases, respectively. The genome was annotated to a chitin deacetylase gene (RhoCDA) and a chitinase gene (RhoChi). They were not very similar to the previously reported chitin deacetylase and chitinase. This made it possible to investigate the genes associated with chitin degradation and would provide an important reference for subsequent gene cloning, functional research, development and application. Therefore, the Rhodococcus sp. 11-3 strain has great potential in the development of chitin resources.