Lentiavidins: Novel avidin-like proteins with low isoelectric points from shiitake mushroom (Lentinula edodes)

Genome-Wide Identification, Expression and Stress Analysis of the GRAS Gene Family in Phoebe bournei

GRAS genes are important transcriptional regulators in plants that govern plant growth and development through enhancing plant hormones, biosynthesis, and signaling pathways. Drought and other abiotic factors may influence the defenses and growth of Phoebe bournei, which is a superb timber source for the construction industry and building exquisite furniture. Although genome-wide identification of the GRAS gene family has been completed in many species, that of most woody plants, particularly P. bournei, has not yet begun. We performed a genome-wide investigation of 56 PbGRAS genes, which are unequally distributed across 12 chromosomes. They are divided into nine subclades. Furthermore, these 56 PbGRAS genes have a substantial number of components related to abiotic stress responses or phytohormone transmission. Analysis using qRT-PCR showed that the expression of four PbGRAS genes, namely PbGRAS7, PbGRAS10, PbGRAS14 and PbGRAS16, was differentially increased in response to drought, salt and temperature stresses, respectively. We hypothesize that they may help P. bournei to successfully resist harsh environmental disturbances. In this work, we conducted a comprehensive survey of the GRAS gene family in P. bournei plants, and the results provide an extensive and preliminary resource for further clarification of the molecular mechanisms of the GRAS gene family in P. bournei in response to abiotic stresses and forestry improvement.

Metal organic framework encapsulated tamavidin-Gluc reporter: application in COVID-19 spike antigen bioluminescent immunoassay

Enzyme linked immunosorbent assay (ELISA) is one of the most utilized serological methods to diagnose and identify etiologic agents of many infectious diseases and other physiologically important analytes. ELISA can be used either alone or adjunct to other diagnostic methods such as molecular arrays, and other serological techniques. Most ELISA assays utilize reagents that are proteinaceous in nature, which are not very stable and require cold-chain transport systems. Development of a desirable immunoassay requires stability of reagents used and its ability to be stored at room temperature without sacrificing the activity of the reagents or the protein of interest. Metal organic frameworks (MOFs) are a rapidly emerging and evolving class of porous polymeric materials used in a variety of biosensor applications. In this study, we introduce the use of MOFs to stabilize a universal reporter fusion protein, specifically, avidin-like protein (Tam-avidin2) and the small bioluminescent protein Gaussia luciferase (Gluc) forming the fusion reporter, tamavidin2-Gluc (TA2-Gluc). This fusion protein serves as a universal reporter for any assays that utilize biotin-avidin binding strategy. Using SARS-CoV2 S1 spike antigen as the model target antigen, we demonstrated that encapsulation of TA2-Gluc fusion protein using a nano-porous material, zeolitic imidazolate framework-8 (ZIF-8), allows us to store and preserve this reporter protein at room temperature for over 6 months and use it as a reporter for an ELISA assay. Our optimized assay was validated demonstrating a 0.26 μg mL-1 limit of detection, high reproducibility of assay over days, detection of spiked non-virulent SARS-COV2 pseudovirus in real sample matrix, and detection in real COVID-19 infected individuals. This result can lead to the utilization of our TA2-Gluc fusion protein reporter with other assays and potentially in diagnostic technologies in a point-of-care setting.

Genome-wide identification, expression and salt stress tolerance analysis of the GRAS transcription factor family in Betula platyphylla

The GRAS gene family is a plant-specific family of transcription factors and play a vital role in many plant growth processes and abiotic stress responses. Nevertheless, the functions of the GRAS gene family in woody plants, especially in Betula platyphylla (birch), are hardly known. In this study, we performed a genome-wide analysis of 40 BpGRAS genes (BpGRASs) and identified typical GRAS domains of most BpGRASs. The BpGRASs were unevenly distributed on 14 chromosomes of birch and the phylogenetic analysis of six species facilitated the clustering of 265 GRAS proteins into 17 subfamilies. We observed that closely related GRAS homologs had similar conserved motifs according to motif analysis. Besides, an analysis of the expression patterns of 26 BpGRASs showed that most BpGRASs were highly expressed in the leaves and responded to salt stress. Six BpGRASs were selected for cis-acting element analysis because of their significant upregulation under salt treatment, indicating that many elements were involved in the response to abiotic stress. This result further confirmed that these BpGRASs might participate in response to abiotic stress. Transiently transfected birch plants with transiently overexpressed 6 BpGRASs and RNAi-silenced 6 BpGRASs were generated for gain- and loss-of-function analysis, respectively. In addition, overexpression of BpGRAS34 showed phenotype resistant to salt stress, decreased the cell death and enhanced the reactive oxygen species (ROS) scavenging capabilities and proline content under salt treatment, consistent with the results in transiently transformed birch plants. This study is a systematic analysis of the GRAS gene family in birch plants, and the results provide insight into the molecular mechanism of the GRAS gene family responding to abiotic stress in birch plants.

Genome-Wide Identification and Stage-Specific Expression Profile Analysis Reveal the Function of Ribosomal Proteins for Oogenesis of Spodoptera litura

Ribosomal proteins (Rps) are indispensable in ribosome biogenesis and protein synthesis, which tightly correlate with cell growth and proliferation in different physiological processes across species. Up to now, genes coding for Rps have been identified and studied in many species, however, their information still remains elusive in many insect species, especially in Spodoptera litura. In this study, 81 Rp genes were identified from S. litura genome and were mapped to their positions on the chromosomes. In addition, their physical and chemical properties, gene structure, phylogenetic relationships, targeted microRNAs were also analyzed. Gene ontology analysis disclosed that Rp genes were closely associated with processes related to ribosome biosynthesis, proteins translation processing, molecular binding activities. The quantitative real-time PCR (qRT-PCR) revealed expression profiles of Rp genes varied in different stages of oogenesis, and found that most Rp genes accumulated in previtellogenesis stage. This study described the comprehensive genome-wide analysis of Rp gene family in agricultural pests, which provided foundation for further characterizing the roles of Rps in oogenesis of insects, and some Rp genes may further serve as targets for innovative pest control.

Influence of Endogenous Factors of Food Matrices on Avidin—Biotin Immunoassays for the Detection of Bacitracin and Colistin in Food

(Strept)avidin–biotin technology is frequently used in immunoassay systems to improve their analytical properties. It is known from clinical practice that many (strept)avidin–biotin-based tests provide false results when analyzing patient samples with a high content of endogenous biotin. No specific investigation has been carried out regarding possible interferences from avidin (AVI) and biotin (B₇) contained in food matrices in (strept)avidin–biotin-based immunoanalytical systems for food safety. Two kinds of competitive ELISAs for bacitracin (BT) and colistin (COL) determination in food matrices were developed based on conventional hapten–protein coating conjugates and biotinylated BT and COL bound to immobilized streptavidin (SAV). Coating SAV–B₇–BT and SAV–B₇–COL complexes-based ELISAs provided 2- and 15-times better sensitivity in BT and COL determination, corresponding to 0.6 and 0.3 ng/mL, respectively. Simultaneously with the determination of the main analytes, these kinds of tests were used as competitive assays for the assessment of AVI or B₇ content up to 10 and 1 ng/mL, respectively, in food matrices (egg, infant milk formulas enriched with B₇, chicken and beef liver). Matrix-free experiments with AVI/B₇-enriched solutions showed distortion of the standard curves, indicating that these ingredients interfere with the adequate quantification of analytes. Summarizing the experience of the present study, it is recommended to avoid immunoassays based on avidin–biotin interactions when analyzing biosamples containing these endogenous factors or enriched with B₇.

Genome-Wide Identification, Transcript Profiling and Bioinformatic Analyses of GRAS Transcription Factor Genes in Rice

Our group has previously identified the activation of a GRAS transcription factor (TF) gene in the gain-of-function mutant population developed through activation tagging in rice (in an indica rice variety, BPT 5204) that was screened for water use efficiency. This family of GRAS transcription factors has been well known for their diverse roles in gibberellin signaling, light responses, root development, gametogenesis etc. Recent studies indicated their role in biotic and abiotic responses as well. Although this family of TFs received significant attention, not many genes were identified specifically for their roles in mediating stress tolerance in rice. Only OsGRAS23 (here named as OsGRAS22) was reported to code for a TF that induced drought tolerance in rice. In the present study, we have analyzed the expression patterns of rice GRAS TF genes under abiotic (NaCl and ABA treatments) and biotic (leaf samples infected with pathogens, Xanthomonas oryzae pv. oryzae that causes bacterial leaf blight and Rhizoctonia solani that causes sheath blight) stress conditions. In addition, their expression patterns were also analyzed in 13 different developmental stages. We studied their spatio-temporal regulation and correlated them with the in-silico studies. Fully annotated genomic sequences available in rice database have enabled us to study the protein properties, ligand interactions, domain analysis and presence of cis-regulatory elements through the bioinformatic approach. Most of the genes were induced immediately after the onset of stress particularly in the roots of ABA treated plants. OsGRAS39 was found to be a highly expressive gene under sheath blight infection and both abiotic stress treatments while OsGRAS8, OsSHR1 and OsSLR1 were also responsive. Our earlier activation tagging based functional characterization followed by the genome-wide characterization of the GRAS gene family members in the present study clearly show that they are highly appropriate candidate genes for manipulating stress tolerance in rice and other crop plants.

Genome-Wide Identification and Comprehensive Expression Profiling of Ribosomal Protein Small Subunit (RPS) Genes and their Comparative Analysis with the Large Subunit (RPL) Genes in Rice

Ribosomal proteins (RPs) are indispensable in ribosome biogenesis and protein synthesis, and play a crucial role in diverse developmental processes. Our previous studies on Ribosomal Protein Large subunit (RPL) genes provided insights into their stress responsive roles in rice. In the present study, we have explored the developmental and stress regulated expression patterns of Ribosomal Protein Small (RPS) subunit genes for their differential expression in a spatiotemporal and stress dependent manner. We have also performed an in silico analysis of gene structure, cis-elements in upstream regulatory regions, protein properties and phylogeny. Expression studies of the 34 RPS genes in 13 different tissues of rice covering major growth and developmental stages revealed that their expression was substantially elevated, mostly in shoots and leaves indicating their possible involvement in the development of vegetative organs. The majority of the RPS genes have manifested significant expression under all abiotic stress treatments with ABA, PEG, NaCl, and H2O2. Infection with important rice pathogens, Xanthomonas oryzae pv. oryzae (Xoo) and Rhizoctonia solani also induced the up-regulation of several of the RPS genes. RPS4, 13a, 18a, and 4a have shown higher transcript levels under all the abiotic stresses, whereas, RPS4 is up-regulated in both the biotic stress treatments. The information obtained from the present investigation would be useful in appreciating the possible stress-regulatory attributes of the genes coding for rice ribosomal small subunit proteins apart from their functions as house-keeping proteins. A detailed functional analysis of independent genes is required to study their roles in stress tolerance and generating stress- tolerant crops.