Protein and Peptide Letters - Volume 30, Issue 1, 2023

Cold-induced RNA-binding protein (CIRP) and RNA-binding motif protein 3 (RBM3) have recently been reported to be involved in cold stress in mammals. These proteins are expressed at low levels in various normal cells, tissues, and organs but can be upregulated upon stimulation by multiple stressors. Studies have shown that CIRP and RBM3 are multifunctional RNA molecular chaperones with different biological functions in various physiological and pathophysiological processes, such as reproductive development, the inflammatory response, the immune response, nerve injury regulation, and tumorigenesis. This paper reviews recent studies on the structure, localization and correlation of CIRP and RBM3 with reproductive development and reproductive system diseases.

Necrotrophic phytopathogens pose a serious challenge to the productivity of several crops causing seedling damage, pre- and post-emergence damping-off and root rot thus reducing plant growth and yield. They are known to gain nutrition by secreting a diverse array of hydrolytic enzymes and thereby causing extensive host plant tissue maceration. Amongst the diverse hydrolases, proteases play a pivotal role in the necrotrophic mode of nutrition and thereby in determining pathogenic virulence. Host plants often counteract the necrotrophic proteolysis events by proteins (peptides), particularly through protease inhibitors (PIs). PIs play an important role in host innate immunity function by functioning as anti-metabolic proteins inhibiting the activity of phytopathogenic secretory proteases. Their abundance in plant storage organs explains their anti-nutritional interaction which stalls pathogenic invasion. PIs, therefore, constitute potential candidates that can be deployed as effective antimicrobials in agriculture, particularly against necrotrophic soil-borne pathogens. The present review traces the progress made in the identification of PIs from plants, and their inhibitory potential against necrotrophic phytopathogens and explores prospects of utilizing these molecules as effective anti-necrotrophic formulations for disease management.

Background: Wogonin, a natural flavonoid compound, represses cancer cell growth and induces cancer cell apoptosis in diverse malignancies. However, the function of Wogonin in lung cancer cells and its regulatory mechanism deserve to be identified. Methods: A549 and H460 cells were treated with Wogonin, and the cell growth, apoptosis, migration and invasion were measured by CCK-8 and EdU, flow cytometry and Transwell assays. The targeted genes of Wogonin and lung cancer were identified from the TCMSP and Genecards databases, respectively. The STRING database and Cytoscape software were used to establish a PPI network and screen hub genes. GO and KEGG analysis was conducted to explore the functions and signal pathways related to the hub genes. MMP1 expression in lung cancer was analyzed using the UALCAN databases, and GSEA was performed utilizing LinkedOmics. Gelatin zymography assay was used to detect MMP1 activity. MMP1 mRNA expression was detected by qRT-PCR. Besides, MMP1, p-AKT and c-Myc protein were detected by Western Blot assay. Results: Wogonin could suppress the proliferation, migration and invasion of A549 and H460 cells and induce apoptosis. GO and KEGG enrichment analysis revealed the hub genes were mostly enriched in re-entry into the mitotic cell cycle and apoptosis. The expression of MMP1 was markedly upregulated in lung squamous cell carcinoma, lung adenocarcinoma tissues, and lung cancer cell lines. Wogonin could significantly inhibit MMP1 expression and activity, and overexpression of MMP1 significantly reversed the effect of Wogonin on the malignant phenotypes of A549 and H460 cells. Wogonin inhibited the expression of p-AKT and c-Myc protein by regulating MMP1. Conclusion: Wogonin can repress lung cancer cells' growth and metastatic potential and promote cell apoptosis via repressing MMP1 expression and modulating PI3K/AKT signaling pathway.

Background: DNA helicases are unwinding enzymes that are essential for many cellular processes. Research has suggested that both the model microorganisms of a single chromosome and the model microorganisms of multiple chromosomes adopt DNA helicases encoded by chromosome I. Therefore, studying DNA helicases encoded by chromosome II may lay some foundation for understanding nucleic acid metabolism processes. Objective: To prove the existence of DNA helicase encoded by chromosome II and to reveal its difference compared to DNA helicase encoded by chromosome I. Methods: The DNA helicases of Pseudoalteromonas spongiae JCM 12884^T and Pseudoalteromonas tunicata DSM 14096^T were analyzed by sequence alignment and phylogenetic relationships with other known DNA helicases. Then, proteins of P. spongiae JCM 12884^T and P. tunicata DSM 14096^T were obtained by heterologous expression. N-terminal sequencing and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis were performed to confirm the form of proteins. A fluorescence resonance energy transfer (FRET) assay was used to measure the activity of helicases. Results: DnaB-pspo and DnaB-ptun belong to the same family, the PRK08840 superfamily, and form a branch with helicases encoded by chromosome I. YwqA-pspo and YwqA-ptun have similar domains and form another branch with helicases encoded by chromosome II. All four helicases have DNA unwinding activity. YwqA is more efficient than DnaB for DNA unwinding, especially YwqA-pspo, which is encoded by bidirectional replication chromosome II. Conclusion: This is the first study to show that the existence of a DNA helicase encoded by chromosome II, and DNA helicase encoded by chromosome II is more efficient than chromosome I for DNA unwinding.

Background: The antimicrobial peptides (AMPs) played a critical role in the innate immunity of the host and are considered natural sources illustrating a broad-spectrum antimicrobial activity with high specificity and low cytotoxicity. AMPs generally possess a net positive charge and have amphipathic structures. Thus, AMPs can bind and interact with negatively charged bacterial cell membranes, leading to destructive defects in biomembranes and ending in cell death. LL37 is the only human cathelicidin-derived antimicrobial peptide that shows a broad spectrum of antimicrobial activity. Materials and Methods: To determine the antibacterial efficiency of LL37 in a mouse model of systemic A. baumannii infection, LL37 corresponding gene was expressed in E. coli, purification and refolding situations were optimized. The antimicrobial performance of produced LL-37 against A. baumannii was evaluated in vitro via MIC and Time Kill assays, and its destructive effects on the bacterial cell were confirmed by SEM image. Results: The recombinant LL37 showed strong antibacterial function against A. baumannii at 1.5 μg/mL concentration. Time kill assay showed a sharp reduction of cell viability during the first period of exposure, and complete cell death was recorded after 40 min exposure. Conclusion: Furthermore, in vivo results represented a significant ability of LL37 in the treatment of systematic infected mouse models, and all infected mice receiving LL37 protein survived without no trace of bacteria in their blood samples.

Background: Thyroid cancer (THCA) is a common endocrine tumor. This study aims to identify the THCA-related key gene Fibronectin 1 (FN1) by bioinformatics methods and explore its function and regulatory mechanism. Methods: Gene Expression Omnibus database (GSE3678, GSE33630, and GSE53157 datasets) was searched for the analysis of differentially expressed genes (DEGs) in THCA tissues v.s. (normal tissues). The enrichment of DEGs was investigated by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathways using the DAVID database. Screening the hub gene was performed with the STRING database and Cytoscape software. The expression and survival analyses of these hub genes in THCA were studied with the Gene Expression Profiling Interactive Analysis database. LinkedOmics database was searched for the related signaling pathways regulated by FN1 in THCA. Real-time quantitative reverse transcriptase polymerase chain reaction was adopted to detect the mRNA expression of Fibromodulin, microfibril-associated protein 4, Osteoglycin, and FN1. The cell viability, growth, migration and aggressiveness were examined by Cell counting kit-8, 5-Ethynyl-2 ′- deoxyuridine assay, scratch assay, and Transwell assay. The expression levels of NF-ΚB signaling pathway-related proteins (p-IΚB-α, p-IKK-β, NF-ΚB p65) were detected by Western blot. Results: FN1 mRNA was up-regulated in THCA tissues and cell lines (MDA-T85 and MDA-T41). The high expression of FN1 is relevant to larger tumor diameters and lymph node metastasis in sufferers with THCA. Functional experiments showed that overexpression of FN1 in the MDA-T85 cell line promoted growth, migration and aggressiveness; knockdown of FN1 in MDA-T41 cells inhibited these malignant behaviors. In mechanism, FN1 promoted the expression levels of proteins related with NF-ΚB signaling pathway and activated NF-ΚB signaling pathway. Conclusion: FN1 is up-regulated in THCA and facilitates cell growth, migration and invasion by activating the NF-ΚB signaling pathway. FN1 will be a promising biomarker of THCA and may become a molecular target for THCA treatment.

Background: Interneural gap junctional coupling represents neural development that decreases during the postnatal period. The decrease of gap junction function coincides with the main period of chemical synapse creation and increment of synaptic activity during postnatal weeks 1 to 3. Methods: Here, we have assessed the role of chemical synapses on connexin (Cx) expression in neurons and glial cells of hippocampal and cortical neurons. We characterized the impact of NMDA receptors blockade on the expression of Cx36 and Cx43 proteins by western blot analysis in postnatal day (PND)14 and PND28. MK801 was injected subcutaneously from the first day of birth until 14 or 28 days, depending on the experimental groups. Saline was injected in the same volumes in the control group. Results: Early postnatal blockade of the NMDA subtype of glutamate receptors by the non-competitive antagonist dizocilpine maleate (MK801) arrested the developmental reduction in gap junctions during the initial postnatal weeks. Expression of Cx43 declined in PND28 compared to PND14 in visual cortex (VC) neurons. Also, we found that the expression of Cx36 and Cx43 augmented in the rats' VC in PND28 following the blockade of NMDA receptors. Expression of Cx36 declined in PND28 compared to PND14 in hippocampal neurons. Also, we found that the expression of Cx36 augmented in the rats' hippocampal neurons in PND14 and PND28 following a blockade of NMDA receptors. Conclusion: These results suggest that the postnatal enhancement in glutamatergic synaptic activity is associated with the loss of gap junctional connections and downregulation of Cx36 and Cx43 between developing neurons and glial cells.

Background: There has been a large increase in the incidence of breast cancer (BC) among women. LINC00473 is a cancer-related lncRNA, participating in the progression of many cancers, but its role in the progression of BC awaits more elaboration. Methods: Quantitative real-time polymerase chain reaction (qRT-PCR) was used to quantify LINC00473, miR-424-5p, and cyclin E1 (CCNE1) mRNA expression levels in BC tissues and cells. Cell counting kit-8 (CCK-8) assay was employed to detect the cell viability; the cell migration and invasion abilities were evaluated by the Transwell assay. Western blot and immunohistochemistry (IHC) were adopted to study CCNE1 protein expression; dual-luciferase reporter assay was performed to clarify the targeting relationships among LINC00473, miR-424-5p, and CCNE1. Results: LINC00473 expression was elevated in BC tissues and cell lines, which was associated with lymph node metastasis and higher clinical stage of the patients with BC. LINC00473 proved to be a molecular sponge for miR-424-5p; LINC00473 knockdown impeded the growth, migration, invasion, and epithelial-mesenchymal transition of BC cells, while these effects were abolished by miR-424-5p inhibitors; miR-424-5p targeted CCNE1 to restrain its expression. LINC00473 positively regulated CCNE1 expression, and CCNE1 restoration counteracted the effects induced by LINC00473 knockdown in BC cells. Conclusion: LINC00473 facilitates the progression of BC through miR-424-5p/CCNE1 axis.

Background: Collagen has been widely utilized in tissue engineering, regenerative medicine and cosmetics. Collagen of low concentrations is frequently applied to reduce the production cost, while it may result in the loss of triple helical structure and bioactivity. CD and NMR techniques have enhanced our understanding of collagen triple helix, while they require high concentrations of collagen samples. Objective: We have systematically investigated the folding and unfolding features of collagen mimetic peptides at a broad variety of concentrations in order to decipher the role of the concentration in the triple helical stability. Methods: Peptide FAM-G(POG)10 was synthesized by the solid phase synthesis method. Fluorescence spectra of peptide FAM-G(POG)10 at different concentrations were recorded. The unfolding and folding profiles of peptide FAM-G(POG)10 with concentrations varying from 1 nM to 100 μM were examined. The effect of concentration on the folding and unfolding capability of peptide FAMG( POG)10 was investigated. Results: Fluorescence characterization of peptide FAM-G(POG)10 under widely varying concentrations from 1 nM to 100 μM has revealed that concentration played a critical role in the stability of collagen peptides. The two-phase pattern of the concentration-dependent folding and unfolding curves has for the first time demonstrated the presence of a critical concentration for the collagen peptide to trigger the complete folding of the triple helix and to maintain the triple helix structure. It is noteworthy that the triple helix structure of collagen peptides was very stable at μM-level concentrations from both the folding and unfolding perspectives. Conclusion: It has significantly contributed to our understanding of collagen triple helix stability at low and ultra-low concentrations, and provided valuable and practical guidelines for the preparation of collagen-based products.

Background: The body needs to maintain a firm balance between the inducers and inhibitors of angiogenesis, the process of proliferation of blood vessels from pre-existing ones. Human angiogenin (hAng), being a potent inducer of angiogenesis, is a cause of tumor cell proliferation, therefore its inhibition becomes a vital area of research. Aminoglycosides are linked ring systems consisting of amino sugars and an aminocyclitol ring and are in use in clinical practices for a long time. These compounds have found clinical uses as antibacterial agents that inhibit bacterial protein synthesis. Objective: Gentamycin C1, Kanamycin A, Neomycin B, Paromomycin I, and Streptomycin A are commonly used aminoglycoside antibiotics that have been used for the present study. Among these, Neomycin has reported inhibitory activity against angiogenin-induced angiogenesis on the chicken chorioallantoic membrane. This study focuses on the thermodynamic parameters involved in the interactions of these antibiotics with hAng. Methods: Agarose gel-based assay, Fluorescence quenching studies and Docking studies. Results: Anti-ribonucleolytic effect of the antibiotics was observed qualitatively using an agarose gelbased assay, which shows that Neomycin exhibits the most efficient inhibition of hAng. Fluorescence quenching studies at different temperatures, using Stern-Volmer and van’t Hoff equations provide information about the thermodynamics of binding, which furthermore highlights the higher binding constant of Neomycin. Docking studies showed that the antibiotics preferably interact with the nuclear translocation site, except Streptomycin, which shows affinity towards the ribonucleolytic site of the protein with very less affinity value. Conclusion: The study has shown the highly spontaneous formation of Neomycin-hAng complex, giving an exothermic reaction with increase in the degree of freedom of the protein-ligand complex.