Protein Secondary Structure Research Articles

RNA editing-induced structural and functional adaptations of NAD9 in Triticum aestivum under drought stress

IntroductionMitochondria are essential organelles in eukaryotic cells, producing ATP through the electron transport chain to supply energy for cellular activities. Beyond energy production, mitochondria play crucial roles in cellular signaling, stress responses, and the regulation of reactive oxygen species. In plants, mitochondria are one of the keys to responding to environmental stresses which can significantly affect crop productivity, particularly in crops like wheat. RNA editing, a post-transcriptional RNA modification process in mitochondria, is linked to regulating these stress responses.MethodsThis study explores RNA editing patterns in the nad9 gene of wheat drought-tolerant (Giza168) and drought-sensitive (Gemmiza10) wheat cultivars under drought stress to understand plant adaptation mechanisms. RNA-seq data for these cultivars were analyzed using CLC Genomic Workbench to identify RNA editing sites in the nad9 gene, examining subsequent amino acid changes and predicting secondary structure modifications. These RNA editing sites were validated using qRT-PCR on drought-treated seedlings at 0, 2, and 12 hours post-treatment. Protein models were generated using AlphaFold, with functional predictions and structure verification conducted using various bioinformatics tools to investigate the effect of RNA editing on protein level.ResultsThe results showed significant RNA editing events, especially C-to-T conversions, in the nad9 gene across different drought exposure times. Giza168 had 22 editing sites, while Gemmiza10 had 19, with several showing significant differences between control and stress conditions. RNA editing influenced the NAD9 protein's secondary structure, particularly beta sheets, and 3D modeling highlighted the structural impacts of these edits. The N-terminal region of NAD9 contained important regulatory motifs, suggesting a complex regulatory environment.DiscussionThis study reveals key editing sites that differ between drought-tolerant and sensitive wheat cultivars, impacting NAD9 protein structures and highlighting the role of RNA editing in enhancing drought resilience. Additionally, the study suggests potential regulatory mechanisms, including phosphorylation and ubiquitination that influence mitochondrial stability and function.

The anti-fouling activity of solvothermally synthesized Nb2O5-coated Fe ship strip on optimal interactions at the targeted interfaces of barnacle attachments - An Insilico study

Abstract Fouling is a major issue occurring in water-going vessels, such as ships that cause increased surface roughness and drag resistance. The fouling organisms produce extracellular polymeric substances (EPS), which negatively impact water-going vessels. The settlement-inducing protein complex (SIPC) is a contact pheromone that promotes the gregarious settling of barnacle larvae (cyprids). The SIPC can be found in both adult barnacle cuticles and cyprids as transient adhesive secretions (footprints). The presence of SIPC in the footprints plays a critical role during the initial adhesion, which facilitates further settlement. The adsorption of of SIPC on Iron/Fe ship strip(FSS) surface was often found to be irreversible even after physical treatements. For the antifouling studies, Nb2O5 coated FSS were constructed and simulated to analyze the interaction of barnacles Aacp20K protein. For simulation studies, the homology model of barnacles Aacp20K protein is fabricated using the SWISS automated comparative modeling platform. The result of homology model showed a good 3D secondary structure of Aacp20K protein, especially 7q1y template protein. Adsorption location analysis results illustrate that the surface of the FSS coated with Nb2O5 film disfavour the binding of SIPC inhibiting the binding of barnacle cuticles and cyprids. For validating the simulation results, Nb2O5 nanostructure film was synthesized using a solvothermal process and characterized using XRD,SEM and EDS. Furthermore, the wetting behaviour was studied experimentally. The simulations and experimental results indicate Nb2O5-coated FSS as potent anti-fouling surfaces.

MIPPIS: protein–protein interaction site prediction network with multi-information fusion

BackgroundThe prediction of protein–protein interaction sites plays a crucial role in biochemical processes. Investigating the interaction between viruses and receptor proteins through biological techniques aids in understanding disease mechanisms and guides the development of corresponding drugs. While various methods have been proposed in the past, they often suffer from drawbacks such as long processing times, high costs, and low accuracy.ResultsAddressing these challenges, we propose a novel protein–protein interaction site prediction network based on multi-information fusion. In our approach, the initial amino acid features are depicted by the position-specific scoring matrix, hidden Markov model, dictionary of protein secondary structure, and one-hot encoding. Simultaneously, we adopt a multi-channel approach to extract deep-level amino acids features from different perspectives. The graph convolutional network channel effectively extracts spatial structural information. The bidirectional long short-term memory channel treats the amino acid sequence as natural language, capturing the protein’s primary structure information. The ProtT5 protein large language model channel outputs a more comprehensive amino acid embedding representation, providing a robust complement to the two aforementioned channels. Finally, the obtained amino acid features are fed into the prediction layer for the final prediction.ConclusionCompared with six protein structure-based methods and six protein sequence-based methods, our model achieves optimal performance across evaluation metrics, including accuracy, precision, F1, Matthews correlation coefficient, and area under the precision recall curve, which demonstrates the superiority of our model.

Identification of Laccase Family of Auricularia auricula-judae and Structural Prediction Using Alphafold

Laccase is an enzyme that plays an important role in fungi, including lignin degradation, stress defense, and formation of fruiting bodies. Auricularia auricula-judae is a white-rot fungus in the Basidiomycota phylum, capable of delignifying wood. In this study, seven genes belonging to the laccase family were identified through de novo sequencing, containing Cu-Oxidase, Cu-Oxidase_2, and Cu-Oxidase_3 domains. Subsequently, the physical characteristics, phylogenetic relationships, protein secondary structure, and tertiary structure of the laccase family (AaLac1–AaLac7) were analyzed. Prediction of N-glycosylation sites identified 2 to 10 sites in the laccase family, with AaLac7 having the highest number of sites at 10. Sequence alignment and analysis of the laccase family showed high consistency in signature sequences. Phylogenetic analysis confirmed the relationship among laccases within the family, with AaLac3–AaLac4 and AaLac5–AaLac6 being closely positioned on the tree, exhibiting high similarity in tertiary structure predictions. This study identified and analyzed laccase family genes in Auricularia auricula-judae using de novo sequencing, offering a simple method for identifying and analyzing the laccase family in organisms with unknown genetic information.

Inhibitory Mechanism of Apigenin, Quercetin, and Phloretin on α-Glucosidase

Flavonoids present promising potential as α-glucosidase inhibitors, with potential benefits in lowering blood glucose levels. In our previous study, apigenin, quercetin, and phloretin obtained from whole-grain highland barley demonstrated notable efficacy as α-glucosidase inhibitors. Therefore, in this study, we used enzyme kinetics, fluorescence spectroscopy, circular dichroism, and molecular docking to explore the interactions between apigenin, quercetin, and phloretin, and α-glucosidase. With the addition of three flavonoids, the inhibitory effect of all the flavonoids on α-glucosidase activity was reversible and exhibited a mixed-type pattern. Molecular docking analysis revealed that the three flavonoids predominantly bind to yeast-derived α-glucosidase mainly through hydrophobic interactions and van der Waals forces, whereas the interaction with human-derived α-glucosidase involved hydrophobic interactions. Further experiments revealed that the flavonoids quenched the fluorescence of α-glucosidase due to the complex formation between the flavonoids and α-glucosidase, leading to changes in the protein secondary structure and conformational changes, which was further supported by molecular dynamics simulations. These results provided insights into the mechanism of the flavonoid inhibition of α-glucosidase. These findings could promote the consumption of whole-grain highland barley and the development of hypoglycemic foods rich in flavonoids.

Monomer unfolding of a bacterial ESCRT-III superfamily member is coupled to oligomer disassembly.

The inner membrane associated protein of 30 kDa (IM30), a member of the endosomal sorting complex required for transport (ESCRT-III) superfamily, is crucially involved in the biogenesis and maintenance of thylakoid membranes in cyanobacteria and chloroplasts. In solution, IM30 assembles into various large oligomeric barrel- or tube-like structures, whereas upon membrane binding it forms large, flat carpet structures. Dynamic localization of the protein in solution, to membranes and changes of the oligomeric states are crucial for its in vivo function. ESCRT-III proteins are known to form oligomeric structures that are dynamically assembled from monomeric/smaller oligomeric proteins, and thus these smaller building blocks must be assembled sequentially in a highly orchestrated manner, a still poorly understood process. The impact of IM30 oligomerization on function remains difficult to study due to its high intrinsic tendency to homo-oligomerize. Here, we used molecular dynamics simulations to investigate the stability of individual helices in IM30 and identified unstable regions that may provide structural flexibility. Urea-mediated disassembly of the IM30 barrel structures was spectroscopically monitored, as well as changes in the protein's tertiary and secondary structure. The experimental data were finally compared to a three-state model that describes oligomer disassembly and monomer unfolding. In this study, we identified a highly stable conserved structural core of ESCRT-III proteins and discuss the advantages of having flexible intermediate structures and their putative relevance for ESCRT-III proteins.

Spectroscopic Studies on Maillard Reactions of Peanut Ara h 2.01 With Respective Reducing Sugars and Their Impacts on Ara h 2.01 Allergenicity.

The effects of the Maillard reactions of peanut Ara h 2.01 with respective glucose and xylose on its conformation and allergenicity were investigated. Circular dichroism (CD) spectral studies showed that short-term heating alone with reducing sugars did not change protein secondary structures, but after undergoing Maillard reactions, its secondary structures changed with some α-helices being transformed into β-sheets and random coils. Fluorescence spectral studies indicated that as temperature increased, protein became loose and extended induced by the reducing sugars. Long heat treatment at higher temperature caused protein collapse with the extrusion of its internal water molecules, which was hindered partially by the reducing sugars that entered the protein in Maillard reaction. Resonance light scattering (RLS) spectra confirmed that more xylose molecules entered protein due to its stronger interaction with the protein after Maillard reactions. ELISA assays exhibited that heat treatment at 100°C led to some allergenic epitopes being embedded inside protein molecules due to protein collapse and that partial epitopes were covered by the reducing sugars after Maillard reaction, resulting in decreases in its allergenicity. Also, xylose reduced the allergenicity of protein more efficiently owing to the stronger interaction between them. All above experimental results were explained reasonably by bioinformatic analysis and molecular docking.

Sludge dewaterability improvement in microbial fuel cell powered electro-Fenton system (MFCⓅEFs) coupled with chitosan quaternary ammonium salt

As improved and expanded wastewater treatment facilities, sludge dewatering is the essential process and major challenge due to the complex and abundant organic matter. Microbial fuel cell powered electro-Fenton system (MFCⓅEFs) has been demonstrated to generate •OH and destroy hydrophilic extracellular polymeric substances (EPS) as an improved method of high efficiency and low energy consumption. Nevertheless, the smaller particle size of the treated sludge and the release of partial organic matter into the supernatant can affect the sludge-water separation process. Chitosan quaternary ammonium salt (CQAS) as a renewable and biodegradability cationic coagulant can be involved in the follow-up treatment. The sludge after combined treatment exhibited better dewaterability, where the water content of sludge cake (WCSC), capillary suction time (CST), and specific resistance filtration (SRF) were 61.21%, 15.6 s, and 1.02×1012 m/kg (26.47%, 80.72% and 84.28% reduction), respectively. The oxidation of the MFCⓅEFs destroyed the cellular and EPS structure and the bridging flocculation and charge neutralization of CQAS caused the fine particles to squeeze each other. The combined treatment fully reduced the content of negative charge and hydrophilic substances on the surface, which affected the intensity change of N-H bond and altered the protein secondary structure to make it looser, thus releasing more bound water while improving aggregation characteristics. Overall, combined treatment can significantly improve sludge dewaterability and owns operational advantages of high efficiency, low energy and consumption, safety, and non-toxicity.

A strategy for improving the mechanical properties of silk fibers through the combination of genetic manipulation and zinc ion crosslinking

Silk fiber is generally considered an excellent biological material due to its good biocompatibility, morphological plasticity and biodegradability. Previously, the construction of silkworm silk gland bioreactors based on the piggyBac transposon has been optimized. However, the inserted exogenous genes have problems such as position uncertainty, and expression is not strictly controlled. Here, we applied transcription activator-like effector nuclease (TALEN)-mediated homology-directed repair (HDR) to precisely insert histidine-rich cuticular protein (CP) into silkworm Sericin1 (Ser1) gene. The Ser1-CP fusion protein was successfully secreted into cocoon shell. Subsequently, based on the metal coordination ability of the histidine imidazole group, we crosslinked cocoon with metal ions in vitro. In this strategy, the mechanical properties of the fused silk fibers with crosslinked Zn2+ improved, and the maximum breaking stress of the crosslinked Zn2+-fused silk fibers was 23.5 % greater than that of the wild-type fibers. Analysis of the secondary structure of the silk protein showed that the fused silk fibers crosslinked with Zn2+ had more β-sheet structures. This study pioneered a method of improving the mechanical properties of silk fibers by crosslinking metal ions with fused exogenous proteins and expanded the application value of silk gland bioreactors in the development of novel biomaterials.

Research on the spoilage potential and metabolic patterns of specific spoilage bacteria in grouper (Epinephelus lanceolatus) during cold storage

Pseudomonas fragi and Serratia liquefaciens are key spoilage microorganisms in aerobically packed groupers during cold storage. Spoilage bacteria were inoculated into fillets to investigate their spoilage potential. The results showed that P. fragi had stronger degradation activity, and the P. fragi inoculated group had higher total volatile basic nitrogen (TVB-N) and K values, lower water holding capacity (WHC), and textural qualities. The P. fragi inoculated group had higher levels of carbonyl groups and lower levels of sulfhydryl groups, indicating higher levels of protein oxidation. The secondary and tertiary structure of myofibrillar protein (MP), scanning electron microscopy, and low-field nuclear magnetic resonance (LF-NMR) analyses showed that P. fragi degraded myofibrils more and induced water loss from the muscle. Metabolomics analyses indicated that purine metabolism and glycine, serine, and threonine metabolism were important pathways associated with P. fragi spoilage; linoleic acid metabolism and β-alanine metabolism were important pathways for S. liquefaciens spoilage.

Effect of Succinylation on Oxidation–Aggregation of Low-Density Lipoprotein and Formation of Off-Flavors in Heated Egg Yolks

This study examined the effect of succinylation on protein oxidation–aggregation and the formation of off-flavors in heated egg yolks (EYs). The sensory evaluation, content of volatile compounds, stability of low-density lipoprotein (LDL) particles, and oxidation of lipid and protein at six levels of succinylated EY (0.25%, 0.5%, 1%, 2%, 5%, and 10%, w/w) were determined. The results showed that the succinylated thermal EY’s concentration of volatiles and off-flavors was reduced. Oil exudation and lipid and protein oxidation decreased with the improved succinylation degree. Succinylation also reduced the LDL particle size and changed the secondary structure (decreased the β-sheets and increased the α-helices) of protein in LDL particles. Meanwhile, succinylation could effectively change the thermal oxidation–aggregation of LDL protein by introducing succinyl groups with negative charges, thus increasing the stability of LDL particles in succinylated EY during heating. These results further revealed the relationship between the oxidation–aggregation of LDL and the formation of off-flavors in heated EY. These results also help improve the flavor quality of heat-treated EY and expands the application scope of egg products.

From Zebrafish To Humans: In Silico Comparative Study of RAD50 Sequences

DNA damage, particularly the occurrence of DNA double-strand breaks (DSBs), presents a significant hazard to the integrity and viability of cells. Improper repair of DSBs can result in chromosomal alterations, oncogenic changes, or cell demise. The MRE11-RAD50-NBS1 (MRN) complex plays a crucial role in DNA repair and signaling under the Ataxia Telangiectasia Mutated (ATM) kinase regulation. In this study, we employed comprehensive computational techniques to analyze the structure of RAD50 in Danio rerio (Zebrafish), utilized as a model organism. Additionally, we conducted in silico assessments of RAD50 from both Zebrafish and humans, comparing their characteristics. The substantial sequence resemblance between DrRAD50 and HsRAD50 suggests that DrRAD50 could potentially serve as a valuable model for HsRAD50. However, it is important to acknowledge that sequence similarity alone does not necessarily imply functional equivalence. Further functional studies are needed to confirm the extent of their functional similarities. By examining the secondary and tertiary protein structures of RAD50, we observed a notable likeness between Zebrafish and Human RAD50 proteins. In silico analysis demonstrated that the sequence of RAD50 in zebrafish shares 70% similarity with the human RAD50 protein.

A comprehensive and single-use foot-and-mouth disease sero-surveillance prototype employing rationally designed multiple viral antigens

Foot-and-mouth disease (FMD) is a great havoc in agri-business-based countries like Bangladesh, for which existing detection system limits the identification and differentiation of serotypes. In this study, an engineered platform was introduced incorporating serotype-specific FMDV VP1 (structural), serotype-independent VP2 (structural) and 3AB (non-structural) proteins for holistic detection. VP1 sequences were engineered combining sequences of BAN/TA/Dh-301/2016 (serotype O), BAN/CH/Sa-304/2016 (serotype A) and BAN/DH/Sa-318/2016 (serotype Asia1). Consensus 3AB sequence was constructed from the selected prevalent viral genomes. Both VP1 and 3AB along with designed VP2 sequences were optimized for codon usage bias, stable mRNA, secondary and tertiary protein structure. Proteins were synthesized in pET-21a ( +) plasmid vector followed by transformation of Escherichia coli BL21(DE3) and IPTG-induced- expression. The western blot analysis of engineered proteins showed that purified VP1 prominently bound to anti-VP1 antibodies in vaccinated sera, whereas 3AB and VP2 bound anti-3AB and anti-VP2 antibodies, respectively from infected cattle sera, all previously collected during epidemiological investigation. Furthermore, dot blot hybridization confirmed efficient antibody capture ability of the membrane-immobilized proteins. This holistic diagnostic platform justifies a comprehensive prototype diagnostic kit that would be cost-effective and efficient for serotype specific and non-specific FMDV sero-surveillance.

Novel insights into fouling mechanisms in anaerobic acidification membrane bioreactor: The leading role of pH value

Anaerobic acidification membrane bioreactors (AAMBRs) have recently emerged as effective systems for recovering volatile fatty acids (VFAs) from municipal wastewater. However, membrane fouling remains a critical challenge, with its underlying mechanisms not yet fully understood. Given its importance in inhibiting methanogenic bacteria and stabilizing VFAs production, this study explores the direct and indirect effects of pH on membrane fouling mechanisms in AAMBRs. The results demonstrated that compared to pH 7, the fouling potential of anaerobic sludge was significantly higher at pH levels of 5 and 10 owing to a decrease of sludge floc size and an increase of soluble microbial products (SMP) especially proteins. Analytical techniques such as confocal laser scanning microscopy (CLSM), fourier transform infrared spectroscopy (FTIR), and fluorescence excitation-emission matrix (F-EEM) analyses revealed a substantial increase in organic foulants particularly proteins on the membrane surface at pH levels of 5 and 10. Circular dichroism (CD) spectroscopy further indicated a significant change in protein secondary structure, specifically an increase in α-helix content under extreme pH conditions. Furthermore, the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory indicated that elevated protein concentrations enhance the adhesion of sludge and SMP to membrane surfaces. Insights from the Flory-Huggins theory demonstrated that variations in protein structure significantly contribute to increased filtration resistance within the gel layer. Both experimental data and theoretical models underscore the dual role of pH in optimizing VFAs production and managing membrane fouling, offering insights for enhancing AAMBR performance and mitigating fouling issues.

ILMCNet: A Deep Neural Network Model That Uses PLM to Process Features and Employs CRF to Predict Protein Secondary Structure.

Protein secondary structure prediction (PSSP) is a critical task in computational biology, pivotal for understanding protein function and advancing medical diagnostics. Recently, approaches that integrate multiple amino acid sequence features have gained significant attention in PSSP research. We aim to automatically extract additional features represented by evolutionary information from a large number of sequences while simultaneously incorporating positional information for more comprehensive sequence features. Additionally, we consider the interdependence between secondary structures during the prediction stage. To this end, we propose a deep neural network model, ILMCNet, which utilizes a language model and Conditional Random Field (CRF). Protein language models (PLMs) pre-trained on sequences from multiple large databases can provide sequence features that incorporate evolutionary information. ILMCNet uses positional encoding to ensure that the input features include positional information. To better utilize these features, we propose a hybrid network architecture that employs a Transformer Encoder to enhance features and integrates a feature extraction module combining a Convolutional Neural Network (CNN) with a Bidirectional Long Short-Term Memory Network (BiLSTM). This design enables deep extraction of localized features while capturing global bidirectional information. In the prediction stage, ILMCNet employs CRF to capture the interdependencies between secondary structures. Experimental results on benchmark datasets such as CB513, TS115, NEW364, CASP11, and CASP12 demonstrate that the prediction performance of our method surpasses that of comparable approaches. This study proposes a new approach to PSSP research and is expected to play an important role in other protein-related research fields, such as protein tertiary structure prediction.

Ischemic stroke susceptibility associated with ALPK1 single nucleotide polymorphisms by inhibiting URAT1 in uric acid hemostasis

ObjectivesIschemic stroke (IS) prevalence rising annually, the necessity of discovering non-interventional genetic influences is progressing. Single nucleotide polymorphism (SNP) plays a pivotal role in stable inheritance of disease susceptibility. Based on the relationship between Alpha- Kinase 1 (ALPK1) and traditional IS risk factors especially hyperuricemia, our study investigated the association and function of ALPK1 SNPs with IS susceptibility. MethodsA case-control study of 1539 patients and 933 controls from northeast China was conducted. Genotyping information of ALPK1 rs2074379 and rs2074388 was collected. Four types of plasmids including rs2074379/rs2074388 G/G, A/G, G/A, and A/A were transfected into 293T cells to observe ALPK1 and SLC22A12 expression. Possible ALPK1 structures of different SNPs were predicted online. ResultsGenotype GG (OR = 1.371, CI = 1.029–1.828, P = 0.031) and GA (OR = 1.326, CI = 1.110–1.584, P = 0.002) of rs2074379 and GA of rs2074388 (OR = 1.359, CI = 1.137–1.624, P = 0.001) were found significantly susceptible to IS, with G allele on sites to be a risk allele. Rs2074379 had a multiplicative interaction with hyperuricemia (OR = 1.637, CI = 1.157–2.315, P = 0.005). Uric acid levels differed in genotypes (P < 0.001). The expression of ALPK1 (P < 0.01) and SLC22A12 in membrane urate transporter 1 (URAT1) protein (P < 0.05) functionally changed with G allele on either site. With glycine changing into aspartic acid at rs2074388, the protein secondary structure changed, but the ALPK1 protein subtype remained still. ConclusionsALPK1 rs2074379 and rs2074388 SNPs were functionally associated with IS susceptibility. The wild allele progressed IS risk probably by reducing ALPK1 expression and inhibiting URAT1 raising the uric acid level, contributing to further exploration of pathogenetic mechanisms of stroke.Chinese Clinical Trial Registration number: ChiCTR-COC-17013559.

Functional characteristics and molecular structural modification of plant proteins. Review

Protein preparations from plant raw materials are widely used in the food industry as improvers, replacers or enrichers for products. However, their functional properties, as a rule, are less pronounced than those of proteins of animal origin. The aim of the review is to analyze and summarize the results of investigations dedicated to studying and characterizing the main functional properties of plant proteins (hydration, solubility, water binding capacity, fat binding capacity and gel-forming capacity, stability of emulsions, foams, rheological properties, texturization) and their modification. The objects of the research were scientific publications, most of which were published in 2017–2024. Functional properties of proteins were characterized; their dependence on the nature and variety of crop, methods of extraction, technological factors of processing and methods of modification was revealed. The search and selection of papers were carried out in the bibliographic databases eLIBRARY.RU, RSCI, Google Scholar, Scopus, Web of Science, Elsevier, and PubMed. Data analysis was performed with their systematization, generalization, intermediate conclusions and general conclusion. The special attention was paid to chemical, physical, physico-chemical and enzymatic methods for modification of protein properties, their advantages and disadvantages, as well as the interrelation of structural and physico-chemical features of proteins with their functional properties. The main regularities were revealed for an effect of modification methods on the secondary and tertiary structures of proteins, surface hydrophobicity, the ratio from fractions, aggregation, denaturation and biological activity obtained by the modern methods of investigations (IR‑spectroscopy, fluorescent microscopy, SDS-PAGE, circular dichroism, spectrophotometry and so on). It has been concluded that it is necessary to carry out further investigations aimed to studying interrelation of molecular structural features of proteins with indicators of functionality and regularities of their behavior in food systems due to an increase in the production of protein preparations from alternative raw materials (pea, chickpea, sunflower, kidney bean, rice and others). Based on the revealed and newly obtained theoretical information, the targeted modification and regulation of properties of protein ingredients for production of high-quality foods are possible.

Cloning and Expression Analysis of ATG8 (Autophagy-Related 8) Gene Family in Solanaceae.

The autophagy-related gene family ATG8 (Autophagy-related 8) plays an important role in plant growth, development, and stress response. In this study, 15 ATG8 gene family sequences were amplified from Solanaceae, namely tobacco, tomato, and pepper, using RT-PCR to evaluate their basic properties, protein structure, and function, as well as the role of ATG8 in autophagy. The physicochemical properties, the predicted secondary and tertiary protein structures, subcellular localisation, gene structures, conserved motifs, and phylogenetic relationships of the ATG8 genes were analysed using bioinformatic techniques, and their expression patterns under sericin-induced plant disease resistance were investigated by RT-qPCR. The lengths of these proteins ranged from 79 to 120 aa, while their predicted molecular weights and isoelectric points (PI) ranged from 9283.62 to 13,778.74 and 6.32 to 11.44, respectively. The majority of the proteins were localised in the nucleus or chloroplasts. Conserved protein motifs and various cis-regulatory elements in the protein, with a wide range of related functions, were identified. The ATG8 gene family members showed expression changes after treatment with osthole, which induces disease resistance in tobacco, tomato, and pepper. These findings provide a foundation for further analyses of the ATG8 gene family in Solanaceae and the mechanism underlying the response to adverse conditions.

Magnetic field improves the quality of frozen tilapia fillets by decreasing the ice crystals during freezing process

SummaryIn this study, the alternating magnetic field (AMF) with frequency of 50, 100, 150, 200 and 250 Hz at magnetic field intensity of 5 mT was used to assist the freezing of tilapia fillets, with no magnetic field (NMF) as a control group. The evaluation of thawed tilapia fillets encompassed an assessment of freezing curve, texture, microstructure, moisture state and protein structure, followed by a subsequent analysis of their correlation. The findings showed that the application of a magnetic field during the freezing process yielded favourable outcomes in enhancing the overall quality of tilapia fillets. Among them, 200 Hz had the best effect. Under the condition, the frozen tilapia fillets assisted by magnetic field showed the shortest freezing time, the least decrease in hardness and elasticity and the best chewiness after thawing. The size of the ice crystals generated during freezing was small and uniform, and the fractal dimension of the frozen sections was the highest. Muscle tissue was the least damaged, which led to the improvement of its water‐holding capacity. Magnetic field‐assisted freezing was found to maintain the α‐helix and β‐sheet in the secondary structure of proteins. The correlation analysis showed that cohesion, elasticity, fractal dimension, FD, A2, A22 and β‐turn were closely related to the quality changes of tilapia fillets after magnetic field treatment.

Translation of Mutant Repetitive Genomic Sequences in Hirsutella sinensis and Changes in the Secondary Structures and Functional Specifications of the Encoded Proteins.

Multiple repetitive sequences of authentic genes commonly exist in fungal genomes. AT-biased genotypes of Ophiocordyceps sinensis have been hypothesized as repetitive pseudogenes in the genome of Hirsutella sinensis (GC-biased Genotype #1 of O. sinensis) and are generated through repeat-induced point mutation (RIP), which is charactered by cytosine-to-thymine and guanine-to-adenine transitions, concurrent epigenetic methylation, and dysfunctionality. This multilocus study examined repetitive sequences in the H. sinensis genome and transcriptome using a bioinformatic approach and revealed that 8.2% of the authentic genes had repetitive copies, including various allelic insertions/deletions, transversions, and transitions. The transcripts for the repetitive sequences, regardless of the decreases, increases, or bidirectional changes in the AT content, were identified in the H. sinensis transcriptome, resulting in changes in the secondary protein structure and functional specification. Multiple repetitive internal transcribed spacer (ITS) copies containing multiple insertion/deletion and transversion alleles in the genome of H. sinensis were GC-biased and were theoretically not generated through RIP mutagenesis. The repetitive ITS copies were genetically and phylogenetically distinct from the AT-biased O. sinensis genotypes that possess multiple transition alleles. The sequences of Genotypes #2-17 of O. sinensis, both GC- and AT-biased, were absent from the H. sinensis genome, belong to the interindividual fungi, and differentially occur in different compartments of the natural Cordyceps sinensis insect-fungi complex, which contains >90 fungal species from >37 genera. Metatranscriptomic analyses of natural C. sinensis revealed the transcriptional silencing of 5.8S genes in all C. sinensis-colonizing fungi in natural settings, including H. sinensis and other genotypes of O. sinensis. Thus, AT-biased genotypes of O. sinensis might have evolved through advanced evolutionary mechanisms, not through RIP mutagenesis, in parallel with GC-biased Genotype #1 of H. sinensis from a common genetic ancestor over the long course of evolution.