bims-micpro 2025-05-04 papers

J Hazard Mater. 2025 Apr 27. pii: S0304-3894(25)01335-4. [Epub ahead of print]494 138420

MIR408-encoded peptide, miPEP408, regulates cadmium stress response through sulfur assimilation pathway.

Ravi Shankar Kumar, Tapasya Datta, Hiteshwari Sinha, Prabodh Kumar Trivedi.

Small peptides encoded by pri-miRNAs (miPEPs), have been identified as significant plant growth and development regulators. However, their roles in plant-environment interactions and heavy metal stress response remain largely unexplored. Here, we demonstrate that Arabidopsis MIR408-encoded peptide (miPEP408) plays a significant role in cadmium (Cd) stress response by modulating the sulfur assimilation pathway. Using a combination of exogenous synthetic peptide assays, CRISPR/Cas9-mediated knockout mutants (miPEP408CR), and overexpression lines (miPEP408OX), we analyzed phenotypic and molecular levels to elucidate the function of miPEP408 under Cd stress. Our results suggest that miPEP408 regulates miR408 expression and its targets in response to Cd exposure. Plants treated with exogenous miPEP408 or overexpressing miPEP408 exhibited reduced glutathione (GSH) levels, suppression of sulfur assimilation pathway genes, and heightened sensitivity to Cd. miPEP408CR plants showed enhanced GSH levels, upregulation of sulfur assimilation genes, and improved Cd detoxification. Furthermore, miPEP408 influenced the expression of Cd transporters and Cd accumulation in plants. In conclusion, this study establishes miPEP408 as a key regulator of Cd stress response in Arabidopsis, functioning through modulation of the sulfur assimilation pathway and metal transporter gene expression. These findings underscore the indispensable role of miPEPs in enhancing plant resilience to heavy metal stress.

Keywords: CRISPR; Cadmium; GSH; Genome-editing; Heavy metal; MiPEPs; Sulfur assimilation pathway

DOI: https://doi.org/10.1016/j.jhazmat.2025.138420

PLoS One. 2025 ;20(4): e0320314

SORFPP: Enhancing rich sequence-driven information to identify SEPs based on fused framework on validation datasets.

Hongqi Feng, Qi Nie, Sen Yang.

BACKGROUND: Genome sequencing has enabled us to find functional peptides encoded by short open read frames (sORFs) in long non-coding RNAs (lncRNAs). sORFs-encoded peptides (SEPs) regulate gene expression, signaling, and so on and have significant roles, unlike common peptides. Various computational methods have been proposed. However, there is a lack of contributive features and effective models. Therefore, a high-throughput computational method to predict SEPs is needed.
RESULTS: We propose a computational method, SORFPP, to predict SEPs by mining feature information from multiple perspectives in an experimentally validated dataset from TranLnc. SORFPP fully extracts SEP sequence information using the protein language model ESM-2 and curated traditional encoding, including QSOrder, k-mer, etc. SORFPP uses CatBoost to solve the sparsity problem of traditional encoding. SORFPP also analyzes ESM-2 pre-training characterization information with the Self-attention model. Finally, an ensemble learning framework combines the two models and their results are fed into Logistic Regression model for accurate and robust predictions. For comparison, SORFPP outperforms other state-of-the-art models in Matthew correlation coefficient by 12.2%-24.2% on three benchmark datasets.
CONCLUSION: Integrating the ensemble learning strategy with contributive traditional features and the protein language encoding methods shows better performance. Datasets and codes are accessible at https://doi.org/10.6084/m9.figshare.28079897 and http://111.229.198.94:5000/.

DOI: https://doi.org/10.1371/journal.pone.0320314

Antioxidants (Basel). 2025 Apr 19. pii: 493. [Epub ahead of print]14(4):

Cell-Permeable Microprotein from Panax Ginseng Protects Against Doxorubicin-Induced Oxidative Stress and Cardiotoxicity.

Bamaprasad Dutta, Shining Loo, Antony Kam, Xiaoliang Wang, Na Wei, Kathy Qian Luo, Chuan-Fa Liu, James P Tam.

(1) Background: Doxorubicin (DOX) is a frontline chemotherapeutic, but its side-effects from oxidative stress, leading to cardiotoxicity, pose significant challenges to its clinical use. We recently discovered a novel family of proteolysis-resistant, cystine-dense, and cell-penetrating microproteins from Panax ginseng that we term ginsentides. Ginsentides, such as the 31-residue TP1, coordinate multiple biological systems to prevent vascular dysfunction and endoplasmic reticulum stress induced by internal and external stressors. (2) Methods: We assessed the protective effects of ginsentide TP1 on DOX-induced cardiotoxicity using both in vitro functional studies on H9c2 cardiomyocytes and in vivo animal models by zebrafish and ICR mouse models. In these models, we examined oxidative stress, apoptosis, intracellular calcium levels, mitochondrial function, inflammatory responses, and cardiac function. (3) Results: We show that ginsentide TP1 protects against DOX-induced cytotoxicity in the mitochondria-rich H9c2 cardiomyocytes and reduces myocardial injury in zebrafish and mice by mitigating oxidative stress, inflammation, calcium, and mitochondrial dysfunction, as well as apoptosis-mediated cell death. Importantly, TP1 preserves cellular homeostasis without compromising the anticancer potency of DOX in breast cancer cells. (4) Conclusions: our findings highlight a specific antioxidative function of ginsentide TP1 in managing DOX-induced cardiotoxicity during cancer treatment and provide a promising lead for developing cardioprotective peptides and microproteins against oxidative stress.

Keywords: antioxidation; cardioprotective adjuvant; cysteine-rich peptide; doxorubicin-induced cardiotoxicity; ginsentide; microprotein; oxidative stress

DOI: https://doi.org/10.3390/antiox14040493

Anal Chem. 2025 Apr 30.

Ultrafiltration-Enhanced Cross-Linking Mass Spectrometry for Comprehensive Analysis of Low Molecular Weight Protein Cross-Links.

Beirong Zhang, Zhou Gong, Bowen Zhong, Zhen Liang, Yukui Zhang, Qun Zhao, Lihua Zhang.

Low molecular weight (LMW) proteins are crucial for cellular functions, including transcription, translation, immune response, and homeostasis. However, their small size and limited lysine residues pose significant challenges in cross-linking mass spectrometry (XL-MS), resulting in low cross-linking efficiency and difficulty detecting protein interactions. To address these issues, we developed an ultrafiltration membrane-aided size exclusion chromatography (UF-SEC) strategy. By utilizing ultrafiltration membranes with progressively smaller pore sizes (ranging from 0.45 μm to 10 kDa), this method selectively removes high molecular weight proteins, enriching cross-linked LMW protein complexes and enhancing the sensitivity and specificity of XL-MS. Compared to traditional high-pH reversed-phase or strong cation exchange fractionation methods, UF-SEC provides better complementarity at the protein level with peptide fractionation methods, offering a more effective solution for identifying LMW protein complexes. Using UF-SEC, we constructed a comprehensive protein interaction network for LMW proteins (defined as <20 kDa), identifying 234 protein-protein interactions involving 77 proteins, accounting for 47.8% of the entire interaction network. This approach not only provides cross-linking distance restraints for intracellular complexes of LMW proteins but also enables scalable cross-linking evidence for PPIs, revealing potential functions such as microprotein generation from noncoding RNAs. Therefore, UF-SEC significantly enhances the capability of XL-MS to investigate LMW protein complexes, offering a powerful tool to deepen our understanding of the roles of small but crucial proteins in cellular biology.

DOI: https://doi.org/10.1021/acs.analchem.5c00331