Using FIBexDB for In-Depth Analysis of Flax Lectin Gene Expression in Response to Fusarium oxysporum Infection

Plant proteins with lectin domains play an essential role in plant immunity modulation, but among a plurality of lectins recruited by plants, only a few members have been functionally characterized. For the analysis of flax lectin gene expression, we used FIBexDB, which includes an efficient algorithm for flax gene expression analysis combining gene clustering and coexpression network analysis. We analyzed the lectin gene expression in various flax tissues, including root tips infected with Fusarium oxysporum. Two pools of lectin genes were revealed: downregulated and upregulated during the infection. Lectins with suppressed gene expression are associated with protein biosynthesis (Calreticulin family), cell wall biosynthesis (galactose-binding lectin family) and cytoskeleton functioning (Malectin family). Among the upregulated lectin genes were those encoding lectins from the Hevein, Nictaba, and GNA families. The main participants from each group are discussed. A list of lectin genes, the expression of which can determine the resistance of flax, is proposed, for example, the genes encoding amaranthins. We demonstrate that FIBexDB is an efficient tool both for the visualization of data, and for searching for the general patterns of lectin genes that may play an essential role in normal plant development and defense.

Computational identification of 4-carboxyglutamate sites to supplement physiological studies using deep learning

In biological systems, Glutamic acid is a crucial amino acid which is used in protein biosynthesis. Carboxylation of glutamic acid is a significant post-translational modification which plays important role in blood coagulation by activating prothrombin to thrombin. Contrariwise, 4-carboxy-glutamate is also found to be involved in diseases including plaque atherosclerosis, osteoporosis, mineralized heart valves, bone resorption and serves as biomarker for onset of these diseases. Owing to the pathophysiological significance of 4-carboxyglutamate, its identification is important to better understand pathophysiological systems. The wet lab identification of prospective 4-carboxyglutamate sites is costly, laborious and time consuming due to inherent difficulties of in-vivo, ex-vivo and in vitro experiments. To supplement these experiments, we proposed, implemented, and evaluated a different approach to develop 4-carboxyglutamate site predictors using pseudo amino acid compositions (PseAAC) and deep neural networks (DNNs). Our approach does not require any feature extraction and employs deep neural networks to learn feature representation of peptide sequences and performing classification thereof. Proposed approach is validated using standard performance evaluation metrics. Among different deep neural networks, convolutional neural network-based predictor achieved best scores on independent dataset with accuracy of 94.7%, AuC score of 0.91 and F1-score of 0.874 which shows the promise of proposed approach. The iCarboxE-Deep server is deployed at https://share.streamlit.io/sheraz-n/carboxyglutamate/app.py.

Multitalented Synthetic Antimicrobial Peptides and Their Antibacterial, Antifungal and Antiviral Mechanisms

Despite the great strides in healthcare during the last century, some challenges still remained unanswered. The development of multi-drug resistant bacteria, the alarming growth of fungal infections, the emerging/re-emerging of viral diseases are yet a worldwide threat. Since the discovery of natural antimicrobial peptides able to broadly hit several pathogens, peptide-based therapeutics have been under the lenses of the researchers. This review aims to focus on synthetic peptides and elucidate their multifaceted mechanisms of action as antiviral, antibacterial and antifungal agents. Antimicrobial peptides generally affect highly preserved structures, e.g., the phospholipid membrane via pore formation or other constitutive targets like peptidoglycans in Gram-negative and Gram-positive bacteria, and glucan in the fungal cell wall. Additionally, some peptides are particularly active on biofilm destabilizing the microbial communities. They can also act intracellularly, e.g., on protein biosynthesis or DNA replication. Their intracellular properties are extended upon viral infection since peptides can influence several steps along the virus life cycle starting from viral receptor-cell interaction to the budding. Besides their mode of action, improvements in manufacturing to increase their half-life and performances are also taken into consideration together with advantages and impairments in the clinical usage. Thus far, the progress of new synthetic peptide-based approaches is making them a promising tool to counteract emerging infections.

TaLBD1, a LOB Transcription Factor Gene In T. Aestivum, Improves Plant N Starvation Adaptation Via Modulating N Acquisition-Associated Processes

Members of transcription factor (TF) families contribute largely to plant N starvation tolerance by regulating downstream stress defensive genes. In this study, we characterized TaLBD1, a Lateral Organ Boundary (LOB) TF gene in T. aestivum, in regulating plant low-N stress adaptation. TaLBD1 harbors the conserved domains specified by plant LOB proteins, targeting onto nucleus after endoplasmic reticulum (ER) assortment. The TaLBD1 transcripts were response sensitively to N starvation (NS) signaling, showing to be gradually upregulated in aerial and root tissues over a 27-h NS condition. The N. tabacum lines overexpressing TaLBD1 improved phenotype, root system architecture (RSA) establishment, biomass, and N contents of plants under NS treatment. The nitrate transporter gene NtNRT2.4 and PIN-FORMED gene NtPIN6 significantly upregulated in expression in NS-challenged lines; knockdown expression of NtNRT2.4 decreased N uptake and that of NtPIN6 alleviated RSA establishment relative to WT. These results validate the function of NRT and PIN genes in regulating plant N uptake and RSA behavior. RNA-seq analyses revealed that a quantity of genes modify expression in N-deprived lines overexpressing TaLBD1, which enriched into functional groups of signal transduction, transcription, protein biosynthesis, primary or secondary metabolism, and stress defensiveness. These findings suggested that the TaLBD1-improved NS adaptation attributes largely to its role in transcriptionally regulating NRT and PIN genes as well as in modulating those functional in various biological processes. TaLBD1 is a crucial regulator in plant N starvation tolerance and valuable target for molecular breeding high N use efficiency (NUE) crop cultivars.

Translational control in cell ageing: an update

Cellular ageing is one of the main drivers of organismal ageing and holds keys towards improving the longevity and quality of the extended life. Elucidating mechanisms underlying the emergence of the aged cells as well as their altered responses to the environment will help understanding the evolutionarily defined longevity preferences across species with different strategies of survival. Much is understood about the role of alterations in the DNA, including many epigenetic modifications such as methylation, in relation to the aged cell phenotype. While transcriptomes of the aged cells are beginning to be better-characterised, their translational responses remain under active investigation. Many of the translationally controlled homeostatic pathways are centred around mitigation of DNA damage, cell stress response and regulation of the proliferative potential of the cells, and thus are critical for the aged cell function. Translation profiling-type studies have boosted the opportunities in discovering the function of protein biosynthesis control and are starting to be applied to the aged cells. Here, we provide a summary of the current knowledge about translational mechanisms considered to be commonly altered in the aged cells, including the integrated stress response-, mechanistic target of Rapamycin- and elongation factor 2 kinase-mediated pathways. We enlist and discuss findings of the recent works that use broad profiling-type approaches to investigate the age-related translational pathways. We outline the limitations of the methods and the remaining unknowns in the established ageing-associated translation mechanisms, and flag translational mechanisms with high prospective importance in ageing, for future studies.

FDH Knockout and TsFDH Transformation Led to Enhanced Growth Rate of Escherichia Coli

Background:Increased Atmospheric CO2 to over 400 ppm has prompted global climate irregularities. Reducing the released CO2 from biotechnological processes could remediate these phenomena. In this study, we sought to find a solution to reduce the amount of CO2 in the process of growth and reproduction by preventing the conversion of formic acid into CO2.Results:The (bio)chemical conversion of formic acid to CO2 is a key reaction. Therefore, we compared the growth of BL21, being a subfamily of K12, alongside two strains in which two different genes related to the formate metabolism were deleted, in complex and simple media. Experimental results were entirely consistent with metabolic predictions. Subsequently, the knockout bacteria grew more efficiently than BL21. Interestingly, TsFDH, a formate dehydrogenase with the tendency of converting CO2 to formate, increased the growth of all strains compared with cells without the TsFDH. Most mutants grew in a simple medium containing glycerol, which showed that glycerol is the preferred carbon source compared to glucose for the growth of E. coli. Conclusion:These results explain the reasons for the inconsistency of predictions in previous metabolic models that declared glycerol as a suitable carbon source for the growth of E. coli but failed to achieve it in practice. To conduct a more mechanistic evaluation of our observations, RNA sequencing data analysis was conducted on an E. coli RNA-seq dataset. The gene expression correlation outcome revealed the increased expression levels of several genes related to protein biosynthesis and glycerol degradation as a possible explanation of our observations.

Comparative Proteomic Analysis within the Developmental Stages of the Mushroom White Hypsizygus marmoreus

(1) Background: The white Hypsizygus marmoreus is a popular edible mushroom in East Asia markets. Research on the systematic investigation of the protein expression changes in the cultivation process of this mushroom are few. (2) Methods: Label-free LC-MS/MS quantitative proteomics analysis technique was adopted to obtain the protein expression profiles of six groups of samples collected in different growth stages. A total of 3468 proteins were identified. The UpSetR plot analysis, Pearson correlation coefficient (PCC) analysis, and principal component (PC) analysis were performed to reveal the correlation among the six groups of samples. The differentially expressed proteins (DEPs) were organised by One-way ANOVA test and divided into four clusters. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed to divide the DEPs into different metabolic processes and pathways in each cluster. (3) Results: The DEPs in cluster 1 are of the highest abundance in the mycelium and are mainly involved in protein biosynthesis, biosynthesis of cofactors, lipid metabolism, spliceosome, cell cycle regulation, and MAPK signaling pathway. The DEPs in cluster 2 are enriched in the stem and are mainly associated with protein biosynthesis, biosynthesis of cofactors, carbon, and energy metabolism. The DEPs in cluster 3 are highly expressed in the primordia and unmatured fruiting bodies and are related to amino acids metabolism, carbon and carbohydrate metabolism, protein biosynthesis and processing, biosynthesis of cofactors, cell cycle regulation, MAPK signaling pathway, ubiquitin-mediated proteolysis, and proteasome. The DEPs in cluster 4 are of the highest abundance in the cap and are mainly associated with spliceosome, endocytosis, nucleocytoplasmic transport, protein processing, oxidative phosphorylation, biosynthesis of cofactors, amino acids metabolism, and lipid metabolism. (4) Conclusions: This research reports the proteome analysis of different developmental stages during the cultivation of the commercially relevant edible fungi the white H. marmoreus. In the mycelium stage, most of the DEPs are associated with cell proliferation, signal response, and mycelium growth. In the primordia and unmatured fruiting bodies stage, the DEPs are mainly involved in biomass increase, cell proliferation, signal response, and differentiation. In the mature fruiting body stage, the DEPs in the stem are largely associated with cell elongation and increase in biomass, and most of the DEPs in the cap are mainly related to pileus expansion. Several carbohydrate-active enzymes, transcription factors, heat shock proteins, and some DEPs involved in MAPK and cAMP signaling pathways were determined. These proteins might play vital roles in metabolic processes and activities. This research can add value to the understanding of mechanisms concerning mushroom development during commercial production.

Human Telomerase RNA Protein Encoded by Telomerase RNA is Involved in Metabolic Responses

Cell proliferation is associated with increased energy and nutrients consumption. Metabolism switch from oxidative phosphorylation to glycolysis and telomerase activity are induced during stimulation of proliferation, such as tumorigenesis, immune cell activation, and stem cell differentiation, among others. Telomerase RNA is one of the core components of the telomerase complex and participates in survival mechanisms that are activated under stress conditions. Human telomerase RNA protein (hTERP) is encoded by telomerase RNA and has been recently shown to be involved in autophagy regulation. In this study, we demonstrated the role of hTERP in the modulation of signaling pathways regulating autophagy, protein biosynthesis, and cell proliferation. The AMPK signaling pathway was affected in cells deficient of hTERP and when hTERP was overexpressed. The appearance of hTERP is important for metabolism switching associated with the accelerated proliferation of cells in healthy and pathological processes. These findings demonstrate the connection between telomerase RNA biogenesis and function and signaling pathways.