Z-DNA binding protein 1 (ZBP1) is an innate immune sensor that recognizes Z-NAs, an atypical, left-handed nucleic acid structure produced during viral replication. This review contextualizes ZBP1 function within the spatiotemporal dynamics of the viral replication cycle, portraying it as a dynamic monitor rather than a static alarm. We discuss how the subcellular localization determines the signaling outcome (e.g., nuclear versus cytoplasmic sensing). Specifically, we discuss how ZBP1 functions as a dynamic molecular scaffold, where ligand-induced amyloid assembly concentrates downstream kinases to overcome cellular inhibition and initiate cell death. The review details ZBP1’s dual antiviral strategy, encompassing NF-κB-mediated inflammation and PANoptotic cell death, and the resulting co-evolutionary dynamics, characterized by viral countermeasures such as ‘signal masking’ seen in poxvirus E3 and ‘signal interception’ utilized by herpesvirus ICP6. Finally, the dual immunomodulatory role of ZBP1 in driving immunopathology is analyzed. This replication-centric perspective provides a theoretical foundation for developing precise, stage-based therapies targeting the ZBP1 pathway.

Programmed ribosomal frameshifting (PRF) is a translational mechanism that enables the ribosome to shift reading frames and access alternative coding sequences. PRF occurs naturally in a wide range of organisms, including viruses, bacteria, and eukaryotes, where it supports compact encoding and stoichiometric control of protein expression. Despite the great potential of PRF in synthetic circuit designs, a broader adoption of PRF in circuit designs has been hampered by rather strict sequence constraints and structural requirements. This work introduces a synthetic translational regulatory platform, protein-inducible ribosomal frameshifting (PIRF), by integrating aptamer-protein interactions with a - 1 PRF motif to enable regulated translation in Escherichia coli. PIRF modules respond to intracellular RNA-binding proteins such as PP7 and MS2, triggering frameshifting in a condition-dependent manner. PIRF could be used to program logic gate operations through frame-dependent translation and enable multilayered regulation in synthetic circuits. Further, the flexible PIRF designs enable reading frame-dependent control of fusion protein expression, protein aggregation, and periplasmic localization via strategic positioning of peptide tags and protein coding sequences. While PIRF enabled regulated frameshifting and could be flexibly reconfigured for a variety of circuits and applications, a measurable level of basal frameshifting was often observed, which may require additional strategies for further optimization in the future. Together, PIRF supports applications in programmable and logical control of downstream protein expression, including condition-dependent aggregation and regulated subcellular localization. PIRF provides a compact and genetically encoded strategy for programmable protein-level regulation, expanding the synthetic biology toolkit for translational control, biosensing and biotherapeutics.

The homeobox transcription factor (TF) superfamily includes the WUSCHEL-RELATED HOMEOBOX (WOX) family, which plays a critical role in adaptive plant growth. Specifically, WOX regulates stem growth in plants, with stems serving as the structural framework for laticifers in Euphorbia hirta. However, the number of WOX gene family members in the E. hirta genome has not been reported. In this study, we identified 14 EhWOX genes in E. hirta and characterized their physicochemical properties, chromosomal locations, phylogenetic relationships, conserved motifs, gene structures, promoter cis elements, gene ontology (GO) enrichment, tissue-specific expression patterns, and subcellular localization. Chromosomal mapping indicated their distribution across nine chromosomes. Phylogenetic analysis classified these genes into three evolutionary clades. Promoter cis-element analysis identified abundant light-responsive, hormone-responsive, and stress-responsive elements. GO enrichment suggested their broad involvement in diverse biological processes. Additionally, RNA-seq revealed high expression levels of EhWOX4-6 and EhWOX14 in stems. Furthermore, RT-qPCR confirmed tissue-specific expression in stems. Moreover, experimental evidence confirmed the subcellular localization and autoactivation capability of some WOX proteins that may be involved in stem development. Overall, this study provides a comprehensive characterization of the candidate EhWOX genes and provides a foundational resource for future functional investigations into their possible roles in stem and laticifer biology.

INAFM2, the human homolog of the Drosophila inaF, is a predicted membrane protein with no known function in vertebrates. Through an in vivo genome-wide transcriptional activation screen, we uncovered INAFM2 as a potent driver of metastasis, leading us to propose naming the vertebrate gene and its protein product ROME (Regulator of Metastasis). We discovered ROME's subcellular localization, posttranslational modifications, and transcriptional profiles related to its expression. ROME negatively regulates the canonical Wnt pathway by directly binding to beta-catenin. Blocking ROME expression in zebrafish embryos results in severe developmental defects and early mortality, which can be reversed by inhibiting the canonical Wnt pathway. Notably, we demonstrate that ROME expression regulates human cancer cell motility and invasion in vitro and metastasis in vivo in both zebrafish and immunodeficient mice via tail vein and orthotopic injection models. ROME-mediated increase in cancer cell intravasation is dependent on its direct interaction with vimentin. Further, we show that elevated ROME expression correlates with poorer patient survival in multiple human cancers. Taken together, this is the first report of the vertebrate ROME gene producing a biologically active plasma membrane glycoprotein that is critical for normal development and metastasis.

Post-translational modifications (PTMs) of key transcription factors constitute important switches that shape protein function and, consequently, signal transduction and cellular responses. Seed germination and seedling establishment are complex traits regulated by PTMs, which converge on key molecular devices such as the bZIP transcription factor ABI5. The latter represents a molecular hub in the abscisic acid (ABA) signaling pathway, which represses seed germination and seedling establishment. ABI5 is post-translationally modified by nitric oxide (NO) through Cys153-specific S-nitrosylation (SNO), leading to its degradation. Despite the physiological effects of redox-sensitive proteins, the specificity and molecular mechanisms underlying this type of regulation during seed germination and post-germination developmental checkpoints remain unknown. Here we show the effect of the redox environment on the formation of ABI5 complexes, emphasizing the relevance of Cys153. In addition, the mutation of this key residue and the phosphorylation status influence the subcellular localization of ABI5. Recent research points to the reversibility of redox-mediated modifications through the action of redoxins. We establish an enzymatic system underlying the reversibility of SNO mediated by thioredoxin h5 (TRXh5). Furthermore, seeds overexpressing the redoxins ROXY10 and ROXY21 show a dysregulation in germination and in the accumulation of the ABI5 protein. These results provide a physiological link between redox regulation and the ABA signaling pathway through the control of ABI5, which is crucial for a successful seedling establishment.

Heat stress (HS) is a growing environmental factor impacting the growth and medicinal value of plateau medicinal plants due to global climate change. Plant heat shock factors (HSFs) are key transcriptional regulators in HS responses, yet the mechanisms of HSFs in plateau medicinal plants remain largely unexplored. In this study, we identified 17 HSF genes from the plateau medicinal plant Fritillaria cirrhosa D.Don. All FcHSF members were divided into two different phylogenetic groups. Moreover, the distribution of conserved motifs among these genes reveals subfamily-specific divergence. PCR-based cloning was further used to amplify two transcript variants of FcHSFA1, designated as FcHSFA1a and FcHSFA1b, which display distinct tandem repeat configurations at their C-termini regions. Both variants were upregulated under HS, with FcHSFA1b showing higher expression. Subcellular localization showed both variants in the nucleus and cytoplasm of tobacco epidermal cells. FcHSFA1b exhibited stronger transcriptional activation activity than FcHSFA1a in yeast cells. Overexpression of both variants in tobacco enhanced HS-related gene expression, increased peroxidase activity and chlorophyll content, and thereby improved thermotolerance. These findings suggest that FcHSFA1 variants contribute to heat tolerance, with distinct transcriptional responses, offering strategies to enhance basal thermotolerance in F. cirrhosa.

A positive feedback loop between the lncRNA TaHTMAR and TaHGSNAT is essential for thermo-sensitive male fertility in wheat.

Nannochloropsis is an industrially relevant marine microalga with exceptional potential as a chassis for sunlight-driven CO2 valorization. However, its broad application in synthetic biology has been constrained by the lack of a standardized and modular genetic toolbox. Here, we report the development of a comprehensive Modular Cloning (MoClo) toolkit for Nannochloropsis, based on Golden Gate assembly and a standard syntax. The toolkit comprises 91 domesticated genetic parts spanning promoters, signal peptides, selectable markers, reporter genes, tags and terminators. A large subset of these parts, including several not previously evaluated in Nannochloropsis, was functionally validated, enabling convenient and reliable transformant selection, immunodetection, and subcellular localization. To demonstrate the utility of the toolkit for multi-gene pathway engineering, modularly assembled keto-carotenoid biosynthetic pathways were introduced into Nannochloropsis, leading to substantial accumulation of canthaxanthin (4.5mgg-1) or astaxanthin (2.8mgg-1). Collectively, this flexible and expandable MoClo toolkit establishes a standardized foundation for synthetic biology in Nannochloropsis, enables rapid design-build-test cycles for multi-gene constructs, and advances the use of industrial microalga for sustainable, CO2-based production of value-added biochemicals.

Paracellular transport is the primary pathway for the intact absorption of the egg white-derived peptide QIGLF. This study aimed to explore the paracellular absorption process of QIGLF in Caco-2 cells using 4D-FastDIA proteomics. A total of 147 differentially expressed proteins (DEPs) were identified. Gene Ontology enrichment analysis revealed that key DEPs, including GRHL2, ECT2, and MARVELD2 involved in apical junction assembly and tight junctions, as well as ARHGEF18 and EphA2 in the plasma membrane, participate in regulating the paracellular absorption of QIGLF. KEGG pathway analysis further indicated that Toll-like receptors and nuclear factor-kappa B-signaling pathways, along with the phosphatidylinositol signaling system, were closely associated with this absorption process. Altogether, the findings of this study demonstrate that QIGLF may alter the expression or subcellular localization of tight junction proteins through these signaling pathways, thereby modulating intestinal tight junction permeability and facilitating its paracellular absorption.

Gαs serves as the prototypical signal transducer for G-protein-coupled receptors (GPCRs) and is the heterotrimeric G protein most frequently mutated in cancer. The classical view of the plasma membrane as the only cellular location where GPCR signal transduction occurs has been challenged by evidence suggesting that Gs also signals from intracellular compartments. However, progress on this topic has stalled because of insufficient approaches with adequate spatiotemporal resolution. Here we describe genetically encoded probes and cell-penetrating compounds that block the effector-binding site of active Gαs in cells to prevent signal propagation at discrete subcellular locations, at user-specified times and across diverse experimental conditions. Using these tools, we show direct evidence of Gαs-mediated signaling on intracellular organelles, unique spatiotemporal features of signaling by Gαs oncomutants and specific regulation of physiologically relevant responses in cardiac or immune cells. These findings pave the way to harnessing the spatiotemporal modulation of Gs signaling and its untapped therapeutic potential.

Transcription factors (TFs) are ubiquitously distributed in plants and play pivotal roles in regulating plant growth and development. The present study aims to elucidate the function of transcription factors (TFs) in highland barley’s response to selenium stress. The results show that 89, 218, 141, 92, 23, and 34 genes were identified from the bHLH, MYB, NAC, WRKY, GATA, and HSF families, respectively. We analyzed the physicochemical properties of the transcription factor family, including amino acid number and molecular weight, theoretical PI, instability index, hydrophilicity index, and subcellular location. The majority of proteins encoded by these gene families are hydrophilic and predominantly localized in the nucleus. Structural analysis demonstrates that each family contains conserved motifs and domains. Most bHLH genes, such as KAE8811666.1 and KAE8789390.1, contain bHLH_SF superfamily domains. 45 MYB genes possess the myb_SHAQKYF domain. Most NAC genes possess typical NAM domains. Most WRKY proteins showed the WRKY superfamily domain. The 22 members of GATA possess the ZnF_GATA domain. HSF gene family showed that 24 gene family members contained HSF domains. Systematic evolutionary analysis indicates that the bHLH and NAC families can each be divided into nine subfamilies, while the remaining four families are categorized into five to eight subfamilies, respectively. Based on transcriptome data, under low selenium treatment, 56.25%, 76%, 67.39%, 47.37%, 50%, and 56.25% of the genes belonging to the bHLH, MYB, NAC, WRKY, GATA, and HSF transcription factor families were significantly upregulated, respectively. In contrast, under high selenium treatment, the proportions of upregulated genes in these families were 81.25%, 80%, 65.22%, 63.16%, 75%, and 75%, respectively. Additionally, qRT-PCR results were consistent with the trends of the transcriptome expression data, corroborating the reliability and accuracy of the transcriptomic findings. These results elucidate the molecular characteristics and response patterns of six transcription factor families to selenium stress in highland barley, laying a foundation for further in-depth research on the functions of transcription factors in highland barley plants.

ProtLoc-GRPO: Cell line-specific subcellular localization prediction using a graph-based model and reinforcement learning.

Eukaryotic cells consist of various organelles, each responsible for specific biological processes, making the understanding of protein subcellular localization essential for determining their potential functions. However, the rapid polar growth of pollen tubes requires careful consideration of organelle trafficking when analyzing subcellular localization in related studies. Fluorescence-tagged organelle markers have shown limited utility for studying pollen during the reproductive stage. In this study, we developed pollen-specific fluorescent marker sets for organelles and other cell structures using the promoter of the OsTAPE gene, which is highly expressed in mature pollen and pollen tubes of rice (Oryza sativa L.). These marker sets enable the visualization of cell membranes, nuclei, endoplasmic reticulum, Golgi apparatus, prevacuolar compartments, and filamentous actin by tagging fluorescent proteins (FP) at the amino N-terminal end. Specifically designed to accommodate the rapid tube elongation of rice pollen, this system offers a valuable resource for gene function research and colocalization analysis, helping to elucidate the pollen tube elongation process. This study expands the potential for using fluorescent labeling in monocotyledonous plants like rice during reproductive stages, facilitating gene function studies under varying environmental conditions through subcellular localization analysis in growing pollen tubes.

MdARF18-like, a member of Auxin response factor gene family, promotes adventitious root elongation in apple.

The TET/5hmC mediated epigenetic landscape in glioma: From molecular mechanisms to therapeutic targeting and future perspectives.

Localization, trafficking, and signaling of trace amine-associated receptor 2 in mouse neuroblastoma cells.

Protein CoAlation is regulated by and integrated with growth factor signalling and the cellular antioxidant response.

Genome-wide identification of scavenger receptor family genes in Octopus sinensis and their immune response to PGN, poly I:C, and Vibrio parahaemolyticus.

RIPK2/STAT3 signaling axis drives lung cancer metastasis through SNAIL activation: Molecular mechanisms and clinical implications.

Osmotic stress suppresses osteogenic differentiation by inhibiting nuclear translocation of YAP via perinuclear actin accumulation.