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Background: Global public health is seriously threatened by the escalating issue of antimicrobial resistance (AMR). Antimicrobial peptides (AMPs), pivotal components of the innate immune system, have emerged as a potent solution to AMR due to their therapeutic potential. Employing computational methodologies for the prompt recognition of these antimicrobial peptides indeed unlocks fresh perspectives, thereby potentially revolutionizing antimicrobial drug development. Methods: In this study, we have developed a model named as deepAMPNet. This model, which leverages graph neural networks, excels at the swift identification of AMPs. It employs structures of antimicrobial peptides predicted by AlphaFold2, encodes residue-level features through a bi-directional long short-term memory (Bi-LSTM) protein language model, and constructs adjacency matrices anchored on amino acids' contact maps. Results: In a comparative study with other state-of-the-art AMP predictors on two external independent test datasets, deepAMPNet outperformed in accuracy. Furthermore, in terms of commonly accepted evaluation matrices such as AUC, Mcc, sensitivity, and specificity, deepAMPNet achieved the highest or highly comparable performances against other predictors. Conclusion: deepAMPNet interweaves both structural and sequence information of AMPs, stands as a high-performance identification model that propels the evolution and design in antimicrobial peptide pharmaceuticals. The data and code utilized in this study can be accessed at https://github.com/Iseeu233/deepAMPNet. [ABSTRACT FROM AUTHOR]

The CCT (CO, COL and TOC1) gene family has been elucidated to be involved in the functional differentiation of the products in various plant species, but their specific mechanisms are poorly understood. In the present investigation, we conducted a genome-wide identification and phylogenetic analysis of CCT genes from microalgae to legumes. A total of 700 non-redundant members of the CCT gene family from 30 species were identified through a homology search. Phylogenetic clustering with Arabidopsis and domain conservation analysis categorized the CCT genes into three families. Multiple sequence alignment showed that the CCT domain contains important amino acid residues, and each CCT protein contains 24 conserved motifs, as demonstrated by the motif analysis. Whole-genome/segment duplication, as well as tandem duplication, are considered to be the driving forces in the evolutionary trajectory of plant species. This comprehensive investigation into the proliferation of the CCT gene family unveils the evolutionary dynamics whereby WGD/segment duplication is the predominant mechanism contributing to the expansion of the CCT genes. Meanwhile, the examination of the gene expression patterns revealed that the expression patterns of CCT genes vary in different tissues and at different developmental stages of plants, with high expression in leaves, which is consistent with the molecular regulation of flowering in photosynthesis by CCT. Based on the protein–protein interaction analysis of CCT genes in model plants, we propose that the CCT gene family synergistically regulates plant development and flowering with light-signaling factors (PHYs and PIFs) and MYB family transcription factors. Understanding the CCT gene family's molecular evolution enables targeted gene manipulation for enhanced plant traits, including optimized flowering and stress resistance. [ABSTRACT FROM AUTHOR]

Light-harvesting chlorophyll a/b-binding (LHC) superfamily proteins play a vital role in photosynthesis. Although the physiological and biochemical functions of LHC genes have been well-characterized, the structural evolution and functional differentiation of the products need to be further studied. In this paper, we report the genome-wide identification and phylogenetic analysis of LHC genes in photosynthetic organisms. A total of 1222 non-redundant members of the LHC family were identified from 42 species. According to the phylogenetic clustering of their homologues with Arabidopsis thaliana, they can be divided into four subfamilies. In the subsequent evolution of land plants, a whole-genome replication (WGD) event was the driving force for the evolution and expansion of the LHC superfamily, with its copy numbers rapidly increasing in angiosperms. The selection pressure of photosystem II sub-unit S (PsbS) and ferrochelatase (FCII) families were higher than other subfamilies. In addition, the transcriptional expression profiles of LHC gene family members in different tissues and their expression patterns under exogenous abiotic stress conditions significantly differed, and the LHC genes are highly expressed in mature leaves, which is consistent with the conclusion that LHC is mainly involved in the capture and transmission of light energy in photosynthesis. According to the expression pattern and copy number of LHC genes in land plants, we propose different evolutionary trajectories in this gene family. This study provides a basis for understanding the molecular evolutionary characteristics and evolution patterns of plant LHCs. [ABSTRACT FROM AUTHOR]