Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs

Targeting WEE1 kinase as a therapeutic strategy in ATIP3-deficient breast cancers

ATIP3-deficient breast cancers represent a subset of aggressive tumors with limited therapeutic options and poor prognosis. Here, we screened a panel of cell cycle kinase inhibitors to identify novel targets for these tumors. We show that loss of ATIP3 sensitizes breast cancer cells to WEE1 inhibition, resulting in aberrant mitoses characterized by detachment of centromere proteins from DNA and chromosome pulverization. This phenotype arises from excessive replication stress and DNA damage in S-phase, combined with premature mitotic entry driven by untimely CDK1 activation. Mechanistically, we identify DNA2 helicase/nuclease as a key mediator of chromosome pulverization. Importantly, the heightened sensitivity of ATIP3-deficient cells to WEE1 inhibition provides a strong rationale for clinical exploration of WEE1-targeted therapies. Furthermore, combining WEE1 and PKMYT1 inhibitors enhances therapeutic efficacy, offering a promising strategy for personalized treatment in ATIP3-deficient breast cancers.

Zmym2 Alters Expression of Key Craniofacial Genes

To identify novel Six1-interacting proteins, we previously screened the fly interactome for Sine oculis-binding partners whose orthologues are also expressed in Xenopus embryos. We identified a zinc-finger MYM-containing protein-Zmym2-based on its sequence similarity in a few domains also found in the Drosophila and vertebrate Sine oculis-binding proteins (Sobp). Because recent studies established Zmym2 as a transcriptional repressor that interacts with Six4 during renal development, herein we assessed whether it interacts with Six1, can modify Six1's transcriptional activity, and is involved in cranial neural crest or placode gene expression. Although during early development Zmym2 is expressed in many of the same tissues as Six1 and contains several domains also found in Sobp, we did not detect any interaction by co-immunoprecipitation and did not detect any effect on Six1 + Eya1 transcriptional activity in cultured cells. Nonetheless, increasing the level of Zmym2 in embryos resulted in broader expression domains of neural border, neural tube and neural crest genes, and smaller placode gene domains. These results suggest that although Zmym2 is unlikely to be a bone fide Six1 interacting protein, it appears to indirectly antagonize Six1 function during cranial placode development, promoting neural plate and neural crest gene expression.

Importin-alpha transports Norrin to the nucleus to promote proliferation and Notch signaling in glioblastoma stem cells

Norrin, a secreted protein encoded by NDP gene, is recognized for its established role as a paracrine canonical Frizzled-4/Wnt ligand that mediates angiogenesis and barrier function in the brain. However, emerging evidence suggests that Norrin possesses Frizzled-4-independent functions, notably impacting Notch activation and proliferation of cancer stem cells. We conducted a BioID protein-proximity screen to identify Norrin-interacting proteins. Surprisingly, a significant proportion of the proteins we identified were nuclear. Through comprehensive tagging and proximity ligation assays, we demonstrate that Norrin is transported to the nucleus through KPNA2 (member of the Importin-alpha family). Subsequently, we demonstrate that KPNA2 loss of function in patient-derived primary glioblastoma stem cells results in a nuclear to cytoplasmic shift of Norrin distribution, and a complete abrogation of its function in stimulating Notch signaling and cellular proliferation. These results indicate that Norrin is actively transported into the nucleus to regulate vital signaling pathways and cellular functions.

The ALX4 dimer structure provides insight into how disease alleles impact function

How homeodomain proteins gain sufficient DNA binding specificity to regulate diverse processes is a long-standing question. Here, we determine how the ALX4 Paired-like protein achieves DNA binding specificity for a TAAT-NNN-ATTA dimer site. We first show that ALX4 binds this motif independently of its co-factor, TWIST1, in cranial neural crest cells. Structural analysis identifies seven ALX4 residues that participate in dimer binding, many of which are conserved across the Paired-like family, but not other homeodomain proteins. Unexpectedly, the two ALX4 proteins within the dimer use distinct residues to form asymmetric protein-protein and protein-DNA interactions and mediate cooperativity. Moreover, we find that ALX4 cooperativity is required for transcriptional activation and that ALX4 disease variants cause distinct molecular defects that include loss of cooperativity. These findings provide insights into how Paired-like factors gain DNA specificity and show how disease variants can be stratified based on their molecular defects.

Decoding the Minimal Translation System of the Plasmodium falciparum Apicoplast: Essential tRNA-modifying Enzymes and Their Roles in Organelle Maintenance

Post-transcriptional tRNA modifications are essential for accurate and efficient protein translation across all organisms. The apicoplast organelle genome of Plasmodium falciparum contains a minimal set of 25 complete tRNA isotypes, making it an ideal model for studying minimal translational machinery. Efficient decoding of mRNA codons by this limited tRNA set depends on post-transcriptional modifications. In this study, we sought to define the minimal set of tRNA-modifying enzymes. Using comparative genomics and apicoplast protein localization prediction tools, we identified 16 nucleus-encoded tRNA-modifying enzymes predicted to localize to the apicoplast. Experimental studies confirmed apicoplast localization for 14 enzymes, including two with dual localization. Combining an apicoplast metabolic bypass parasite line with gene disruption tools, we disrupted 12 of the 14 apicoplast-localized enzymes. Six of these enzymes were found to be essential for parasite survival, and six were dispensable. All six essential enzymes are thought to catalyze modifications in the anticodon loop of tRNAs, and their deletions resulted in apicoplast disruption. Of the two genes refractory to deletion, one exhibited dual localization, suggesting essential functions outside the apicoplast. The other, which appears to localize solely to the apicoplast, may play an indispensable role that is not circumvented by our metabolic bypass. Our findings suggest the apicoplast translation system relies on a minimal set of tRNA modifications concentrated in the anticodon loop. This work advances our understanding of minimal translational machinery in reduced organelles, such as the apicoplast, with promising applications in synthetic biology.

SART1 uniquely localizes to spindle poles forming a SART1 cap and promotes spindle pole assembly

The nuclear protein squamous cell carcinoma antigen recognized by T cells 1 (SART1) has been associated with pre-mRNA splicing, but SART1 RNAi knockdown results also in defects in mitotic progression, centrosome biogenesis, and chromosome cohesion. The mitotic roles of SART1 have not been characterized in detail, and it remains unclear whether SART1 functions in mitosis directly or indirectly via pre-mRNA splicing. Here, we identify SART1 as a direct, mitosis-specific microtubule-associated protein. SART1 downregulation in human cells leads to spindle assembly defects with reduced microtubule dynamics, end-on attachment defects, and checkpoint activation, while microtubule dynamics remain unaffected in interphase. SART1 uniquely localizes to the distal surface of mitotic centrosomes along the spindle axis, forming a previously not described structure we refer to as SART1 cap. Immunoprecipitation of SART1 consistently identifies centrosomal proteins as interaction partners. Immunostaining of these shows that SART1 downregulation does not affect centriole duplication and centrosome accumulation of γ-tubulin but reduces the accumulation of selective pericentriolar material (PCM) proteins such as ninein. Depletion of SART1 from frog egg extracts disrupts spindle pole assembly around sperm nuclei and DNA-coated beads. Spindles formed around DNA-coated beads do not contain centrosomes but still recruit PCM proteins for spindle pole assembly. We finally show that the N-terminus of SART1 is its microtubule-binding region and is essential for spindle assembly. Our data unravel a unique localization of SART1 and its novel function to recruit selective PCM proteins for spindle pole assembly in centrosomal and acentrosomal spindle assembly.

Transport of DNA repair proteins to the cell nucleus by the classical nuclear importin pathway - a structural overview

DNA repair is a crucial biological process necessary to address damage caused by both endogenous and exogenous agents, with at least five major pathways recognized as central to this process. In several cancer types and other diseases, including neurodegenerative disorders, DNA repair mechanisms are often disrupted or dysregulated. Despite the diversity of these proteins and their roles, they all share the common requirement of being imported into the cell nucleus to perform their functions. Therefore, understanding the nuclear import of these proteins is essential for comprehending their roles in cellular processes. The first and best-characterized nuclear targeting signal is the classical nuclear localization sequence (NLS), recognized by importin-α (Impα). Several structural and affinity studies have been conducted on complexes formed between Impα and NLSs from DNA repair proteins, although these represent only a fraction of all known DNA repair proteins. These studies have significantly advanced our understanding of the nuclear import process of DNA repair proteins, often revealing unexpected results that challenge existing literature and computational predictions. Despite advances in computational, biochemical, and cellular assays, structural methods - particularly crystallography and in-solution biophysical approaches - continue to play a critical role in providing insights into molecular events operating in biological pathways. In this review, we aim to summarize experimental structural and affinity studies involving Impα and NLSs from DNA repair proteins, with the goal of furthering our understanding of the function of these essential proteins.

Endothelial lipase-binding peptides similar to netrin-1 inhibit hepatitis B virus infection

Hepatitis B virus (HBV) infects cells by attaching to heparan sulfate proteoglycans (HSPG) and Na+/taurocholate cotransporting polypeptide (NTCP). The endothelial lipase LIPG bridges HSPG and HBV, facilitating HBV attachment. From a randomized peptide expression library, we identified a short sequence binding to LIPG. This identified sequence closely resembled a sequence in the V domain of netrin-1, a protein known to bind heparin through its V domain. We designed two synthetic peptides based on this sequence and found that both synthetic peptides and netrin-1 suppressed HBV infection in chimeric mice with humanized livers and in primary hepatocytes isolated from them. The data reveal an antiviral function of the peptides and netrin-1 in HBV infection that is independent of LIPG lipase activity.

Nuclear-Localized BCKDK Facilitates Homologous Recombination Repair to Support Breast Cancer Progression and Therapy Resistance

Homologous recombination repair (HRR) is crucial for maintaining genomic stability by repairing DNA damage. Despite its importance, HRR's role in cancer progression is not fully elucidated. Here, this work shows that nuclear-localized branched-chain α-ketoacid dehydrogenase kinase (BCKDK) acts as a modulator of HRR, promoting cell resistance against DNA damage-inducing therapy in breast cancer. Mechanistically, this work demonstrates that BCKDK is localized in the nucleus and phosphorylates RNF8 at Ser157, preventing the ubiquitin-mediated degradation of RAD51, thereby facilitating HRR-mediated DNA repair under replication stress. Notably, aberrant expression of the BCKDK/p-RNF8/RAD51 axis correlates with breast cancer progression and poor patient survival. Furthermore, this work identifies a small molecule inhibitor of BCKDK, GSK180736A, that disrupts its HRR function and exhibits strong tumor suppression when combined with DNA damage-inducing drugs. Collectively, this study reveals a new role of BCKDK in regulating HRR, independent of its metabolic function, presenting it as a potential therapeutic target and predictive biomarker in breast cancer.

The membrane-associated β2e-subunit of voltage-gated calcium channels translocates to the nucleus and regulates gene expression

The β-subunit (Cavβ) is a central component of the voltage-gated calcium channel complex. It lacks transmembrane domains and exhibits both channel-related and non-related functions. Previous studies have shown that, in the absence of the Cavα1 pore-forming subunit, electrostatic interactions between the N-terminus of Cavβ2e and the plasma membrane mediate its anchoring to the cell surface. Here, we demonstrate that, upon phospholipase C activation, Cavβ2e dissociates from the plasma membrane and homogeneously distributes between the cytosol and the nucleus. Mutagenesis analysis identified critical residues in the N-terminus of the protein, including a stretch of positively charged amino acids and a dileucine motif, which serve as nuclear import and export signals, respectively. Fusion of the Cavβ2e N-terminus to a trimeric YFP chimeric construct shows that this segment suffices for nuclear shuttling. Thus, the N-terminus of Cavβ2e emerges as a regulatory hotspot region controlling the subcellular localization of the protein. Quantitative mass spectrometry analysis revealed that the heterologous expression of a nuclear-enriched Cavβ2e mutant regulates gene expression. Our findings demonstrate the presence of active nuclear localization signals in Cavβ2e that enables its nuclear targeting and regulation of protein expression. Furthermore, they establish the membrane-associated Cavβ2e as a novel signaling mediator within the phospholipase C cascade.

Unconventional receptor functions and location-biased signaling of the lactate GPCR in the nucleus

G-protein-coupled receptors (GPCRs) are virtually involved in every physiological process. However, mechanisms for their ability to regulate a vast array of different processes remain elusive. An unconventional functional modality could at least in part account for such diverse involvements but has yet to be explored. We found HCAR1, a multifunctional lactate GPCR, to localize at the nucleus and therein capable of initiating location-biased signaling notably nuclear-ERK and AKT. We discovered that nuclear HCAR1 (N-HCAR1) is directly involved in regulating diverse processes. Specifically, N-HCAR1 binds to protein complexes that are involved in promoting protein translation, ribosomal biogenesis, and DNA-damage repair. N-HCAR1 also interacts with chromatin remodelers to directly regulate gene expression. We show that N-HCAR1 displays a broader transcriptomic signature than its plasma membrane counterpart. Interestingly, exclusion of HCAR1 from the nucleus has the same effect as its complete cellular depletion on tumor growth and metastasis in vivo. These results reveal noncanonical functions for a cell nucleus-localized GPCR that are distinct from traditional receptor modalities and through which HCAR1 can participate in regulating various cellular processes.

On subcellular distribution of the zinc finger 469 protein (ZNF469) and observed discrepancy in the localization of endogenous and overexpressed ZNF469

The zinc finger 469 gene (ZNF469) is a single-exon gene predicted to encode a protein of 3953 amino acids. Despite pathogenic ZNF469 variants being associated with Brittle Cornea Syndrome (BCS), relatively little is known about ZNF469 beyond its participation in regulating the expression of genes encoding extracellular matrix proteins. In this study, we examined the expression and intracellular localization of ZNF469 in different cell lines. The level of ZNF469 mRNA varied from low levels in HEK293 cells to high levels in HeLa cells and primary fibroblasts. Antibodies against ZNF469 reacted among others with a protein of approximately 400 kDa in immunoblot analysis, which was mainly present in the insoluble fraction of the cytoplasm. Immunofluorescence analysis of interphase cells showed small cytoplasmic puncta and weak nuclear staining. In dividing HeLa cells, the antibodies recognized foci that also stained for proteasomes. In transfected cells, ZNF469 was observed mainly in foci resembling nuclear speckles in interphase and at the midbody during mitosis. The nuclear foci showed overlapping staining with proteasomes. In live cell imaging, liquid-like properties of the nuclear foci were recorded as they changed shape and position and occasionally fused with each other. During stress granule formation, cytoplasmic foci showed overlapping staining with G3BP1. Finally, in silico analysis revealed large intrinsically disordered regions with multiple low complexity domains in ZNF469. Our data indicate that ZNF469 forms aggregates possibly as biomolecular condensates when overexpressed. However, care must be taken when analyzing the intracellular distribution of ZNF469 due to the discrepancy in the localization of endogenous ZNF469 and overexpressed ZNF469 in transfected cells.

A Novel Hidden Protein p-414aa Encoded by circSETD2(14,15) Inhibits Vascular Remodeling

BACKGROUND

Phenotypic switching of vascular smooth muscle cells (VSMCs), leading to neointimal hyperplasia, is a fundamental cause of vascular remodeling diseases such as atherosclerosis and hypertension. Novel hidden proteins encoded by circular RNAs play crucial roles in disease progression, yet their involvement in vascular remodeling diseases has not been comprehensively studied. This study identifies a novel protein derived from a circular RNA in VSMCs and demonstrates its potential role in regulating vascular remodeling.

METHODS

Cell proliferation assays were performed to investigate the effects of circSETD2(14,15) on VSMC proliferation. Techniques such as vector construction, immunoprecipitation-mass spectrometry, and dual-luciferase reporter gene were used to confirm that circSETD2(14,15) encoded a novel protein, p-414aa. The interaction between p-414aa and HuR (human antigen R) was validated with techniques such as coimmunoprecipitation, mass spectrometry, and proximity ligation assay. Through experiments including RNA sequencing and RNA immunoprecipitation, the interaction between HuR and C-FOS (C-Fos proto-oncogene) mRNA was revealed. The role of p-414aa in neointimal hyperplasia was assessed with a carotid artery ligation model in male mice.

RESULTS

Overexpression of circSETD2(14,15) inhibits VSMC phenotypic switching. The novel protein p-414aa, encoded by circSETD2(14,15), interacts with HuR to reduce C-FOS mRNA stability, thereby suppressing VSMC proliferation and ultimately inhibiting neointimal hyperplasia in male mice.

CONCLUSIONS

We uncover a novel hidden protein derived from circSETD2(14,15), called p-414aa, that inhibits vascular remodeling. CircSETD2(14,15) and p-414aa may serve as potential therapeutic targets for vascular remodeling diseases.

Deep learning prioritizes cancer mutations that alter protein nucleocytoplasmic shuttling to drive tumorigenesis

Genetic variants can affect protein function by driving aberrant subcellular localization. However, comprehensive analysis of how mutations promote tumor progression by influencing nuclear localization is currently lacking. Here, we systematically characterize potential shuttling-attacking mutations (SAMs) across cancers through developing the deep learning model pSAM for the ab initio decoding of the sequence determinants of nucleocytoplasmic shuttling. Leveraging cancer mutations across 11 cancer types, we find that SAMs enrich functional genetic variations and critical genes in cancer. We experimentally validate a dozen SAMs, among which R14M in PTEN, P255L in CHFR, etc. are identified to disrupt the nuclear localization signals through interfering their interactions with importins. Further studies confirm that the nucleocytoplasmic shuttling altered by SAMs in PTEN and CHFR rewire the downstream signaling and eliminate their function of tumor suppression. Thus, this study will help to understand the molecular traits of nucleocytoplasmic shuttling and their dysfunctions mediated by genetic variants.

Cas9-mediated gene-editing frequency in microalgae is doubled by harnessing the interaction between importin α and phytopathogenic NLSs

Pathogen-derived nuclear localization signals (NLSs) enable vigorous nuclear invasion in the host by the virulence proteins harboring them. Herein, inspired by the robust nuclear import mechanism, we show that NLSs originating from the plant infection-associated Agrobacterium proteins VirD2 and VirE2 can be incorporated into the Cas9 system as efficient nuclear delivery enhancers, thereby improving the low gene-editing frequency in a model microalga, Chlamydomonas reinhardtii, caused by poor nuclear localization of the bulky nuclease. Prior to evaluation of the NLSs, IPA1 (Cre04.g215850) was first defined in the alga as the nuclear import-related importin alpha (Impα) that serves as a counterpart adaptor protein of the NLSs, based on extensive in silico analyses considering the protein's sequence, tertiary folding behavior, and structural basis when interacting with a well-studied SV40TAg NLS. Through precursive affinity explorations, we reproducibly found that the NLSs mediated the binding between the Cas9 and Impα with nM affinities and visually confirmed that the fusion of the NLSs strictly localized the peptide-bearing cargoes in the microalgal nucleus without compensating for their cleavage ability. When employed in a real-world application, the VirD2 NLS increases the mutation frequency (~1.12 × 10-5) over 2.4-fold compared to an archetypal SV40TAg NLS (~0.46 × 10-5) when fused with Cas9. We demonstrate the cross-species versatility of the Impα-dependent strategy by successfully applying it to an industrial alga, Chlorella Sp. HS2. This work, focused on affinity augmentation, provides insights into increasing the frequency of gene editing, which can be advantageously used in programmable mutagenesis with broad applicability.

Characterization of soybean vein necrosis virus (SVNV) proteins: Sequence analysis of field strains and comparison of localization patterns in differing cell types

Soybean vein necrosis virus (SVNV) is a persistent, propagative, ambisense single-stranded RNA virus in the genus Orthotospovirus, transmitted by Nehydatothrips variabilis. To understand SVNV in the field, 33 samples exhibiting symptoms of SVNV were collected. The N, NSs, and NSm open reading frames (ORFs) were sequenced, revealing amino acid mutations in each gene. The five open reading frames of the SVNV Tennessee strain (N, NSs, NSm, GN, and GC) were fused in frame to GFP for experimentation in both plant and insect cells. N and NSs localize in plants at the cell periphery and nucleus. NSm induces cell death in plant cells, but not in insect cells, where cytoplasmic localization is observed. GN and GC glycoproteins localize to the membranes and display increased cytoplasmic localization in insect cells. The findings of this study contribute to understanding the genes of SVNV and capture sequence changes that have occurred over the past fifteen years.

Enhanced kinase translocation reporters for simultaneous real-time measurement of PKA, ERK, and calcium

Kinase translocation reporters (KTRs) are powerful tools for single-cell measurement of time-integrated kinase activity but suffer from restricted dynamic range and limited sensitivity, particularly in neurons. To address these limitations, we developed enhanced KTRs (eKTRs) for PKA and extracellular signal-regulated kinase (ERK) by (i) increasing KTR size, which reduces the confounding effect of KTR diffusion through the nuclear pore and (ii) modulating the strength of the bipartite nuclear localization signal in their kinase sensor domains, to ensure that the relative distribution of the KTR between the nucleus and cytoplasmic is determined by active nuclear import, active nuclear export, and relative activity of their cognate kinase. The resultant sets of ePKA-KTRs and eERK-KTRs display high sensitivity, broad dynamic range, and cell type-specific tuning. Moreover, co-expression of optically separable ePKA-KTRs and eERK-KTRs allowed us to simultaneously monitor the activation and inhibition of PKA and ERK, together with calcium levels, in live cells. These eKTRs responded as expected to direct agonists and inhibitors, and also confirmed that crosstalk between the PKA and ERK pathways is highly unbalanced, with the activation of PKA suppressing ERK activity, while activation of ERK induces PKA activity. Taken together, our findings highlight the importance of KTR size and bipartite nuclear localization signal strength to KTR sensitivity and dynamic range, show that different cell types require different eKTRs, and identify ePKA-KTR1.4 and eERK-KTR1.2 as particularly well-suited for monitoring PKA and ERK in primary sensory neurons.

Antagonistic kinesin-14s within a single chromosomal drive haplotype

In maize, there are two meiotic drive systems that operate on large tandem repeat arrays called knobs that are found on chromosome arms. One meiotic drive haplotype, Abnormal chromosome 10 (Ab10), encodes two kinesin proteins that interact with two distinct tandem repeat arrays in a sequence-specific manner to confer meiotic drive. The kinesin KINDR associates with knob180 repeats while the kinesin TRKIN associates with TR-1 repeats. Prior data show that meiotic drive is conferred primarily by the KINDR/knob180 system, with the TRKIN/TR-1 system having little or no role. The second meiotic drive haplotype, K10L2, shows low levels of meiotic drive and only encodes the TRKIN/TR-1 system. Here we used long-read sequencing to assemble the K10L2 haplotype and showed that it has strong homology to an internal portion of the Ab10 haplotype. We also carried out CRISPR mutagenesis of Trkin to test the role of Trkin on Ab10 and K10L2. The data indicate that the Trkin gene on Ab10 does not improve drive or fitness but instead has a weak deleterious effect when paired with a normal chromosome 10. The deleterious effect is more severe when Ab10 is paired with K10L2: in this context functional Trkin on either chromosome nearly abolishes Ab10 drive. We modeled the effect of Trkin on Ab10 and found it should not persist in the population. We conclude that Trkin either confers an advantage to Ab10 in untested circumstances or that it is in the process of being purged from the Ab10 population.

Nuclear GTPSCS functions as a lactyl-CoA synthetase to promote histone lactylation and gliomagenesis

Histone lysine lactylation is a physiologically and pathologically relevant epigenetic pathway that can be stimulated by the Warburg effect-associated L-lactate. Nevertheless, the mechanism by which cells use L-lactate to generate lactyl-coenzyme A (CoA) and how this process is regulated remains unknown. Here, we report the identification of guanosine triphosphate (GTP)-specific SCS (GTPSCS) as a lactyl-CoA synthetase in the nucleus. The mechanism was elucidated through the crystallographic structure of GTPSCS in complex with L-lactate, followed by mutagenesis experiments. GTPSCS translocates into the nucleus and interacts with p300 to elevate histone lactylation but not succinylation. This process depends on a nuclear localization signal in the GTPSCS G1 subunit and acetylation at G2 subunit residue K73, which mediates the interaction with p300. GTPSCS/p300 collaboration synergistically regulates histone H3K18la and GDF15 expression, promoting glioma proliferation and radioresistance. GTPSCS represents the inaugural enzyme to catalyze lactyl-CoA synthesis for epigenetic histone lactylation and regulate oncogenic gene expression in glioma.

FoxO is required for neoblast differentiation during planarian regeneration

Stem cells are of great importance in the maintenance and regeneration of tissues, with Forkhead box O (FoxO) proteins emerging as pivotal regulators of their functions. However, the precise impact of FoxO proteins on stem cell behavior within regenerative environments remains ambiguous. Planarians, renowned for their abundance of adult stem cells (neoblasts), serve as an excellent model for investigating the dynamics of stem cells during regeneration. In this study, we identified DjfoxO, a conserved foxO gene in the planarian Dugesia japonica, and demonstrated its expression in neoblasts, with elevated levels detected in the regenerative blastema during the regeneration process. Using a FoxO inhibitor (AS1842856) together with RNA interference techniques, we demonstrated that inhibition of FoxO signaling in planarians hinders the regeneration of missing tissues, including the central nervous system, eyespots, anterior intestinal branches, and pharynx. It is noteworthy that the knockdown of DjfoxO does not significantly affect the mitotic activity of neoblasts. Conversely, it impedes the production of lineage-specific progenitors, potentially via modulation of the Erk pathway. These findings elucidate the instructive function of FoxO signaling in regulating stem cell differentiation and provide valuable insights into its potential for improving stem cell-based regenerative therapies.

TRMT1L-catalyzed m22G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress

tRNA modifications are critical for several aspects of their functions, including decoding, folding, and stability. Using a multifaceted approach encompassing eCLIP-seq and nanopore tRNA-seq, we show that the human tRNA methyltransferase TRMT1L interacts with the component of the Rix1 ribosome biogenesis complex and binds to the 28S rRNA as well as to a subset of tRNAs. Mechanistically, we demonstrate that TRMT1L is responsible for catalyzing N2,N2-dimethylguanosine (m22G) solely at position 27 of tRNA-Tyr-GUA. Surprisingly, TRMT1L depletion also impaired the deposition of 3-(3-amino-3-carboxypropyl) uridine (acp3U) and dihydrouridine on tRNA-Tyr-GUA, Cys-GCA, and Ala-CGC. TRMT1L knockout cells have a marked decrease in tRNA-Tyr-GUA levels, coinciding with a reduction in global translation rates and hypersensitivity to oxidative stress. Our results establish TRMT1L as the elusive methyltransferase catalyzing the m22G27 modification on tRNA Tyr, resolving a long-standing gap of knowledge and highlighting its potential role in a tRNA modification circuit crucial for translation regulation and stress response.

Regulatory dynamics of Sch9 in response to cytosolic acidification: From spatial reconfiguration to cellular adaptation to stresses

The regulation of cellular metabolism is crucial for cell survival, with Sch9 in Saccharomyces cerevisiae serving a key role as a substrate of TORC1. Sch9 localizes to the vacuolar membrane through binding to PI(3,5)P2, which is necessary for TORC1-dependent phosphorylation. This study demonstrates that cytosolic pH regulates Sch9 localization. Under stress conditions that induce cytosolic acidification, Sch9 detached from the vacuolar membrane. In vitro experiments confirmed that Sch9's affinity for PI(3,5)P2 is pH-dependent. This pH-dependent localization switch is essential for regulating the TORC1-Sch9 pathway. Impairment of the dissociation of Sch9 from the vacuolar membrane in response to cytosolic acidification resulted in the deficient induction of stress response gene expression and delayed the adaptive response to acetic acid stress. These findings indicate the importance of proper Sch9 localization for metabolic reprogramming and stress response in yeast cells.

Control of striatal circuit development by the chromatin regulator Zswim6

The pathophysiology of neurodevelopmental disorders involves vulnerable neural populations, including striatal circuitry, and convergent molecular nodes, including chromatin regulation and synapse function. Despite this, how epigenetic regulation regulates striatal development is understudied. Recurrent de novo mutations in Zswim6 are associated with intellectual disability and autism. We demonstrate that ZSWIM6 localizes to the nucleus where it associates with repressive chromatin regulators. Disruption of Zswim6 in ventral telencephalic progenitors leads to increased chromatin accessibility and transcriptional dysregulation. Ablating Zswim6 in either striatal direct or indirect pathway spiny projection neurons resulted in similar cell-autonomous changes in excitatory but not inhibitory synaptic transmission. Specifically, Zswim6 disruption altered the desensitization properties of AMPA receptors, leading to enhanced synaptic recruitment of SPNs, explaining SPN-subtype specific effects on activity and behavioral sub-structure. Last, adult deletion of Zswim6 identified a continuing role in the maintenance of mature striatal synapses. Together, we describe a mechanistic role for Zswim6 in the epigenetic control of striatal synaptic development.

Defining ortholog-specific UHRF1 inhibition by STELLA for cancer therapy

UHRF1 maintains DNA methylation by recruiting DNA methyltransferases to chromatin. In mouse, these dynamics are potently antagonized by a natural UHRF1 inhibitory protein STELLA, while the comparable effects of its human ortholog are insufficiently characterized, especially in cancer cells. Herein, we demonstrate that human STELLA (hSTELLA) is inadequate, while mouse STELLA (mSTELLA) is fully proficient in inhibiting the abnormal DNA methylation and oncogenic functions of UHRF1 in human cancer cells. Structural studies reveal a region of low sequence homology between these STELLA orthologs that allows mSTELLA but not hSTELLA to bind tightly and cooperatively to the essential histone-binding, linked tandem Tudor domain and plant homeodomain (TTD-PHD) of UHRF1, thus mediating ortholog-specific UHRF1 inhibition. For translating these findings to cancer therapy, we use a lipid nanoparticle (LNP)-mediated mRNA delivery approach in which the short mSTELLA, but not hSTELLA regions are required to reverse cancer-specific DNA hypermethylation and impair colorectal cancer tumorigenicity.

Homeodomain Involvement in Nuclear HOX Protein Homo- and Heterodimerization

HOX genes play essential roles in patterning the anteroposterior axis of animal embryos and in the formation of various organs. In mammals, there are 39 HOX genes organized into four clusters (HOXA-D) located on different chromosomes. In relationship with their orderly arrangement along the chromosomes, these genes show nested expression patterns which imply that embryonic territories co-express multiple HOX genes along the main body axis. Interactomic database entries, as well as a handful of publications, support that some HOX proteins can form homodimers or interact with other HOX proteins. However, the consequences of HOX protein interactions have been poorly investigated and remain largely elusive. In this study, we compiled a repository of all HOX-HOX interactions from available databases, and taking HOXA1, HOXA2, and HOXA5 as examples, we investigated the capacity of HOX proteins to form homo- and heterodimers. We revealed that while the DNA-binding domain, the homeodomain, is not necessary for HOXA1 homodimerization, the nuclear localization of the dimerization is dependent on the homeodomain, particularly the integrity of the third helix of HOXA1. Furthermore, we demonstrated that HOXA1 can influence the localization of HOXA1 when it is deprived of the homeodomain, increasing its abundance in the chromatin-containing fraction. Moreover, HOXA1 nuclear homodimerization occurs independently of the integrity of the hexapeptide and, consequently, of its well-known interactor, the homeodomain protein PBX. These results hint at a potential involvement of dimerization in the complex landscape of HOX regulatory mechanisms.

Exploring SERPINA3 as a neuroinflammatory modulator in Alzheimer's disease with sex and regional brain variations

SERPINA3, a serine protease inhibitor, is strongly associated with neuroinflammation, a typical condition of AD. Its expression is linked to microglial and astrocytic markers, suggesting it plays a significant role in modulating neuroinflammatory responses. In this study, we examined the SERPINA3 expression levels, along with CHI3L1, in various brain regions of AD patients and non-demented healthy controls (NDHC). Nineteen microarray datasets were analyzed, with brain samples stratified by sex and age from areas including the prefrontal cortex, occipital lobe, and cerebellum. Results showed that SERPINA3 was significantly highly expressed in AD patients compared to NDHCs only in males. Sex-specific differences were observed only in NDHCs, where females had higher SERPINA3 levels than males. ROC analysis suggested that SERPINA3 could be a strong marker for distinguishing AD in males but not females. In NDHCs, SERPINA3 expression correlated more strongly with age than in AD patients. In brain regions, SERPINA3 expression in NDHC females was higher across multiple areas, while in AD patients, this difference was limited to the prefrontal cortex. The most significant differences between NDHC and AD patients were found in the occipital and prefrontal regions. Furthermore, we identified a potential nuclear localization for SERPINA3, supported by immunohistochemistry analysis from The Human Protein Atlas. Correlation with neuropathological traits, including Clinical Dementia Rating (CDR) and Braak Neurofibrillary Tangle Score, showed positive significant associations between SERPINA3 and CDR in AD patients. Performing a docking analysis, we revealed an interaction region between SERPINA3 and CHI3L1 proteins, suggesting a potential role in AD. Tissue transcriptomic deconvolution analysis indicated a significant overlap between SERPINA3 expression and microglial/astrocytic signatures, suggesting that SERPINA3 plays a key role in modulating neuroinflammation in AD.

The StbHLH47 transcription factor negatively regulates drought tolerance in potato (Solanum tuberosum L.)

BACKGROUND

Drought stress is a major environmental constraint affecting crop yields. Plants in agricultural and natural environments have developed various mechanisms to cope with drought stress. Identifying genes associated with drought stress tolerance in potato and elucidating their regulatory mechanisms is crucial for the breeding of new potato germplasms. The bHLH transcription factors involved play crucial roles not only in plant development and growth but also in responsesresponse to abiotic stress.

RESULTS

In this study, the StbHLH47 gene, which is highly expressed in potato leaves, was cloned and isolated. Subcellular localization assays revealed that the gene StbHLH47 performs transcriptional functions in the nucleus, as evidenced by increased malondialdehyde (MDA) content and relative conductivity under drought stress. These findings indicate that overexpressing plants are more sensitive to drought stress. Differential gene expression analysis of wild-type plants (WT) and plants overexpressing StbHLH47 (OE-StbHLH47) under drought stress revealed that the significantly differentially expressed genes were enriched in metabolic pathways, biosynthesis of various plant secondary metabolites, biosynthesis of metabolites, plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signalling pathway-plant, phenylpropanoid biosynthesis, and plant‒pathogen interactions. Among these pathways, the phenylalanine and abscisic acid (ABA) signal transduction pathways were enriched in a greater number of differentially expressed genes, and the expression trends of these differentially expressed genes (DEGs) were significantly different between WT and OE-StbHLH47. Therefore, it is speculated that StbHLH47 may regulate drought resistance mainly through these two pathways. Additionally, RT‒qPCR was used for fluorescence quantification of the expression of StNCED1 and StERD11, which are known for their drought resistance, and the results revealed that the expression levels were much lower in OE-StbHLH47 than in WT plants.

CONCLUSION

RNA-seq, RT‒qPCR, and physiological index analyses under drought conditions revealed that overexpression of the StbHLH47 gene increased the sensitivity of potato plants to drought stress, indicating that StbHLH47 negatively regulates drought tolerance in potato plants. In summary, our results indicate that StbHLH47 is a negative regulator of drought tolerance and provide a theoretical basis for further studies on the molecular mechanism involved.

Unveiling the Movement of RanBP1 During the Cell Cycle and Its Interaction with a Cyclin-Dependent Kinase (CDK) in Plants

In the Nicotiana tabacum flower development study, we identified SCI1 (Stigma/style Cell-cycle Inhibitor 1), a regulator of cell proliferation. SCI1 interacts with NtCDKG;2 (N. tabacum Cyclin-Dependent Kinase G;2), a homolog of human CDK11, which is responsible for RanGTP-dependent microtubule stabilization, regulating spindle assembly rate. In a Y2H screening of a cDNA library using NtCDKG;2 as bait, a RanBP1 (Ran-Binding Protein 1) was revealed as its interaction partner. RanBP1 is an essential regulatory protein of the RanGTPase system, contributing to the formation of the Ran gradient, which modulates different important cellular processes. RanBP1 is crucial in the nuclear import/export machinery during interphase and spindle checkpoint formation during cell division. These processes are well studied in animals, but very little is known about them in plants. We confirmed NtCDKG;2 and NtRanBP1 interaction by pairwise Y2H and characterized the localization of both proteins during plant cell division. We demonstrated the presence of NtRanBP1 in the cytoplasm during interphase and its nuclear arrest at mitosis onset. Meanwhile, we showed that NtCDKG;2 is localized in the mitotic spindle during cell division, indicating an analogous function to the human CDK11. We propose that the phosphorylation of the nuclear export signal at RanBP1 by NtCDKG;2 may be responsible for the reported nuclear arrest.

AXL-TBK1 driven AKT3 activation promotes metastasis

The receptor tyrosine kinase AXL promotes tumor progression, metastasis, and therapy resistance through the induction of epithelial-mesenchymal transition (EMT). Here, we found that activation of AXL resulted in the phosphorylation of TANK-binding kinase 1 (TBK1) and the downstream activation of AKT3 and Snail, a transcription factor critical for EMT. Mechanistically, we showed that TBK1 directly bound to and phosphorylated AKT3 in a manner dependent on the multiprotein complex mTORC1. Upon activation, AKT3 interacted with and promoted the nuclear accumulation of Snail, which led to increased EMT as assessed by marker abundance. In human pancreatic ductal adenocarcinoma tissue, nuclear AKT3 colocalized with Snail and correlated with worse clinical outcomes. Primary mouse pancreatic cancer cells deficient in AKT3 showed reduced metastatic spread in vivo, suggesting selective AKT3 inhibition as a potential therapeutic avenue for targeting EMT in aggressive cancers.

Identification and characterization of a Relish-type NF-κB, DvRelish, in Dermacentor variabilis in response to Rickettsia rickettsii infection

Ixodid ticks serve as hosts and transmission vectors for several obligate intracellular bacteria, including members of the spotted fever group (SFG) of Rickettsia. Although ticks generate an immune response to bacterial insults, many of the signaling molecules associated with the response and how they may contribute to vector competence for Rickettsia are undefined. In this study, we isolated a full-length dvrelish transcript from Dermacentor variabilis, which encoded a Relish-type NF-κB. The presence of a canonical Rel homology domain (RHD) consistent with NF-κB proteins suggested a role in tick immune response for DvRelish. The expression of DvRelish was confirmed in tick tissues and fluorescent microscopy of tick hemocytes indicated increased expression following infection with Rickettsia as compared to a non-tick-borne bacterial pathogen. To further determine the effect of dvRelish gene knockdown on rickettsial infection, we used RNA interference-mediated gene knockdown in D. variabilis and demonstrated that transcription of dvRelish was decreased after 24 h post-injection of siRNA. We then assessed the response of D. variabilis when exposed to Rickettsia rickettsii and determined that transcription of dvRelish was inversely associated with rickettsial loads at 48 h post-exposure. Further studies are required to broaden the understanding of differential immune responses in ticks to SFG Rickettsia infection and elucidate the role played by the arthropod immune system in vector competence.

Mapping of Nuclear Localization Signal in Secreted Liver-Specific Protein 2 of Plasmodium falciparum

The secretory proteome of Plasmodium exhibits differential spatial and functional activity within host cells. Plasmodium secretes proteins that translocate into the human host cell nucleus. Liver-specific protein 2 of Plasmodium falciparum (Pf-LISP2) shows nuclear accumulation in human hepatocytes during the late liver stage of malaria parasite development. However, the nuclear translocation mechanism for Pf-LISP2 remains largely uncharacterized. Here, we identified a classical bipartite nuclear localization signal (NLS) located in the C-terminal region of Pf-LISP2. Phylogenetic analysis revealed that this NLS is unique to Plasmodium falciparum and its close relative Plasmodium reichenowi, suggesting an evolutionary adaptation linked to their shared primate hosts. Functional assays confirmed the NLS's nuclear import activity, as fusion constructs of the Pf-LISP2 NLS with Pf-aldolase (Pf-aldolase-NLS-EGFP) localized exclusively to the nucleus of HepG2 cells. Mutation analysis of key lysine and arginine residues in the bipartite NLS demonstrated that the basic amino acid clusters are essential for nuclear localization. Importin-α/β interaction was found to be crucial for Pf-LISP2 nuclear transport, as coexpression of the NLS constructs with the importin-α/β inhibitor mCherry-Bimax2 significantly blocked nuclear translocation. Specific interactions between the lysine and arginine residues of Pf-LISP2's NLS and the conserved tryptophan and asparagine residues of human importin-α1 facilitate the cytosol-to-nuclear translocation of Pf-LISP2. Additionally, LISP2 lacks any nuclear export signal. These results provide new insights into the mechanisms of nuclear transport in Plasmodium falciparum, potentially contributing to the understanding of its pathogenicity and host-cell interactions during liver-stage infection.

Complete Genomes of DNA Viruses in Fecal Samples from Small Terrestrial Mammals in Spain

Viromics studies are allowing us to understand not only the enormous diversity of the virosphere, but also the potential threat posed by the emerging viruses. Regarding the latter, the main concern lies in monitoring the presence of RNA viruses, but the zoonotic potential of some DNA viruses, on which we have focused in the present study, should also be highlighted. For this purpose, we analyzed 160 fecal samples from 14 species of small terrestrial mammals, 9 of them belonging to the order Rodentia. This allowed us to identify a total of 25 complete or near-complete genomes belonging to the families Papillomaviridae, Polyomaviridae, Adenoviridae, Circoviridae, and Genomoviridae, 18 of which could be considered new species or types. Our results provide a significant increase in the number of complete genomes of DNA viruses of European origin with zoonotic potential in databases, which are at present under-represented compared to RNA viruses. In addition, the characterization of whole genomes is of relevance for the further study of the evolutionary forces governing virus adaptation, such as recombination, which may play an important role in cross-species transmission.

Identification and functional characterization of the nuclear and nucleolar localization signals in the intrinsically disordered region of nucleomethylin

The nucleolar localization of proteins is regulated by specific signals directing their trafficking to nucleus and nucleolus. Here, we elucidate the mechanism underlying the nuclear and nucleolar localization of the nucleomethylin (NML) protein, focusing on its nuclear localization signals (NLSs) and nucleolar localization signal (NoLS). Using a combination of bioinformatic analysis and experimental validation, we identified two monopartite and one bipartite NLS motifs within NML. The combined presence of both monopartite NLSs significantly enhances nuclear localization of the protein, while specific basic amino acid clusters within the bipartite NLS are crucial for their functionality. We also reveal the functional role of the NLS-coupled NoLS motif in driving nucleolar localization of NML, which contains an arginine-rich motif essential for its function. The basic residues of the arginine-rich motif of NoLS of NML interacts with nucleophosmin 1 (NPM1), allowing the possible liquid-liquid phase separation and retention of NML in the nucleolus. Remarkably, the strong NoLS of NML can direct the nucleolar localization of a cytosolic protein, aldolase, emphasizing its potency. Overall, our findings provide insights into the combinatorial functioning of NLSs and NoLS in regulating the subcellular localization of NML, highlighting the intricate regulatory mechanisms governing its localization within the nucleus and nucleolus.

A lineage-specific protein network at the trypanosome nuclear envelope

The nuclear envelope (NE) separates translation and transcription and is the location of multiple functions, including chromatin organization and nucleocytoplasmic transport. The molecular basis for many of these functions have diverged between eukaryotic lineages. Trypanosoma brucei, a member of the early branching eukaryotic lineage Discoba, highlights many of these, including a distinct lamina and kinetochore composition. Here, we describe a cohort of proteins interacting with both the lamina and NPC, which we term lamina-associated proteins (LAPs). LAPs represent a diverse group of proteins, including two candidate NPC-anchoring pore membrane proteins (POMs) with architecture conserved with S. cerevisiae and H. sapiens, and additional peripheral components of the NPC. While many of the LAPs are Kinetoplastid specific, we also identified broadly conserved proteins, indicating an amalgam of divergence and conservation within the trypanosome NE proteome, highlighting the diversity of nuclear biology across the eukaryotes, increasing our understanding of eukaryotic and NPC evolution.

Identification of a Nuclear Localization Signal (NLS) in Human Transcription Elongation Factor ELL2

ELL2 is a transcription elongation factor suppressing transcriptional pausing of RNA polymerase II, thereby enhancing gene expression. In accordance with the nuclear localization of ELL2, the protein is supposed to carry out its function in promoting transcription in the nucleus. Yet, it is unknown whether ELL2 carries a nuclear localization signal (NLS). In this study, we identify the NLS of ELL2. In silico analysis resulted in prediction of a strong bipartite NLS with an exceptionally high score at amino acids 311-338 in the conserved region R1 of ELL2. Confocal laser scanning microscopy of a series of ELL2 truncation mutants and quantitative analysis of images verified the presence of R1 to be decisive for nuclear localization of ELL2 suggesting that the predicted NLS is accurate. Deletion of key basic amino acids within the putative NLS in silico and in vitro showed that K319, R320, and K333/K334 are crucial for ELL2's nuclear accumulation, thus confirming the predictions. The isolated ELL2-NLS was able to translocate an unrelated NLS-mapping system into the nucleus underlining the strength of the NLS. Taken together, we identified the NLS of ELL2 and mapped individual aa that are crucial for nuclear localization of ELL2.

A mitochondrial unfolded protein response-independent role of DVE-1 in longevity regulation

The special AT-rich sequence-binding (SATB) protein DVE-1 is widely recognized for its pivotal involvement in orchestrating the retrograde mitochondrial unfolded protein response (mitoUPR) in C. elegans. In our study of downstream factors contributing to lifespan extension in sensory ciliary mutants, we find that DVE-1 is crucial for this longevity effect independent of its canonical mitoUPR function. Additionally, DVE-1 also influences lifespan under conditions of dietary restriction and germline loss, again distinct from its role in mitoUPR. Mechanistically, while mitochondrial stress typically prompts nuclear accumulation of DVE-1 to initiate the transcriptional mitoUPR program, these long-lived mutants reduce DVE-1 nuclear accumulation, likely by enhancing its cytosolic translocation. This observation suggests a cytosolic role for DVE-1 in lifespan extension. Overall, our study implies that, in contrast to the more narrowly defined role of the mitoUPR-related transcription factor ATFS-1, DVE-1 may possess broader functions than previously recognized in modulating longevity and defending against stress.

Nuclear localization sequence of MoHTR1, a Magnaporthe oryzae effector, for transcriptional reprogramming of immunity genes in rice

Plant pathogens secrete nuclear effectors into the host nuclei to modulate the host immune system. Although several nuclear effectors of fungal pathogens have been recently reported, the molecular mechanism of NLS-associated transport vehicles of nuclear effectors and the roles of NLS in transcriptional reprogramming of host immunity genes remain enigmatic. We previously reported the MoHTR1, a nuclear effector of the rice blast fungus, Magnaporthe oryzae. MoHTR1 is translocated to rice nuclei but not in fungal nuclei. Here, we identify the core NLS (RxKK) responsible for MoHTR1's nuclear localization. MoHTR1 is translocated in the host nucleus through interaction with rice importin α. MoHTR1 NLS empowers it to translocate the cytoplasmic effectors of M. oryzae into rice nuclei. Furthermore, other nuclear effector candidates of the blast pathogen and rice proteins which have RxKK also exhibit nuclear localization, highlighting the crucial role of RxKK in this process. We also unveil the importance of SUMOylation in the stability of MoHTR1 and translocation of MoHTR1 to host nuclei. Moreover, MoHTR1 NLS is essential for the pathogenicity of M. oryzae by reprogramming immunity-associated genes in the host. Our findings provide insights into the significance of plant-specific NLS on fungal nuclear effectors and its role in plant-pathogen interactions.

Structural duality enables a single protein to act as a toxin-antidote pair for meiotic drive

In sexual reproduction, selfish genetic elements known as killer meiotic drivers (KMDs) bias inheritance by eliminating gametes that do not carry them. The selective killing behavior of most KMDs can be explained by a toxin-antidote model, where a toxin harms all gametes while an antidote provides resistance to the toxin in carriers. This study investigates whether and how the KMD element tdk1 in the fission yeast Schizosaccharomyces pombe deploys this strategy. Intriguingly, tdk1 relies on a single protein product, Tdk1, for both killing and resistance. We show that Tdk1 exists in a nontoxic tetrameric form during vegetative growth and meiosis but transforms into a distinct toxic form in spores. This toxic form acquires the ability to interact with the histone reader Bdf1 and assembles into supramolecular foci that disrupt mitosis in noncarriers after spore germination. In contrast, Tdk1 synthesized during germination of carrier spores is nontoxic and acts as an antidote, dismantling the preformed toxic Tdk1 assemblies. Replacement of the N-terminal region of Tdk1 with a tetramer-forming peptide reveals its dual roles in imposing an autoinhibited tetrameric conformation and facilitating the assembly of supramolecular foci when autoinhibition is released. Moreover, we successfully reconstituted a functional KMD element by combining a construct that exclusively expresses Tdk1 during meiosis ("toxin-only") with another construct that expresses Tdk1 specifically during germination ("antidote-only"). This work uncovers a remarkable example of a single protein employing structural duality to form a toxin-antidote pair, expanding our understanding of the mechanisms underlying toxin-antidote systems.

Arabidopsis ubiquitin ligase PUB41 positively regulates ABA-mediated seed dormancy and drought response

Seed germination is a tightly regulated, non-reversible developmental process, and it is crucial to prevent premature germination under conditions that may not allow the plant's life cycle to be completed. The plant hormone ABA is the key regulator of seed dormancy and inhibition of germination. ABA is also involved in the plant response to drought. Here we report on the involvement of Arabidopsis thaliana PUB41, encoding a U-BOX E3 ubiquitin ligase, in regulating ABA signaling, seed dormancy, germination, and drought resilience. AtPUB41 is expressed in most vegetative and reproductive tissues. AtPUB41 protein is localized in the cytosol and nucleus. pub41 T-DNA insertion mutants display reduced seed dormancy, and their germination is less inhibited by exogenous ABA than seeds of wild-type plants. pub41 mutant plants are also hypersensitive to drought. ABA induces AtPUB41 promoter activity and steady-state mRNA levels in the roots. Our data suggest that AtPUB41 is a positive regulator of ABA signaling.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-024-01526-6.

Nuclear localization of Arabidopsis HD-Zip IV transcription factor GLABRA2 is driven by importin α

GLABRA2 (GL2), a class IV homeodomain leucine-zipper (HD-Zip IV) transcription factor from Arabidopsis, is a developmental regulator of specialized cell types in the epidermis. GL2 contains a monopartite nuclear localization sequence (NLS) that is conserved in most HD-Zip IV members across the plants. We demonstrate that NLS mutations affect nuclear transport and result in a loss-of-function phenotypes. NLS fusions to enhanced yellow fluorescent protein (EYFP) show that it is sufficient for nuclear localization in roots and trichomes. Despite partial overlap of the NLS with the homeodomain, genetic dissection indicates that nuclear localization and DNA binding are separable functions. Affinity purification of GL2 from plants followed by MS-based proteomics identified importin α (IMPα) isoforms as potential GL2 interactors. NLS structural prediction and molecular docking studies with IMPα-3 revealed major interacting residues. Cytosolic yeast two-hybrid assays and co-immunoprecipitation experiments with recombinant proteins verified NLS-dependent interactions between GL2 and several IMPα isoforms. IMPα triple mutants (impα-1,2,3) exhibit abnormal trichome formation and defects in GL2 nuclear localization in trichomes, consistent with tissue-specific and redundant functions of IMPα isoforms. Taken together, our findings provide mechanistic evidence for IMPα-dependent nuclear localization of GL2 in Arabidopsis, a process that is critical for cell type differentiation of the epidermis.

Genome-wide identification of CAMTA genes and their expression dependence on light and calcium signaling during seedling growth and development in mung bean

BACKGROUND

Calmodulin-binding transcription activator (CAMTA) is comprised of a group of transcription factors and plays an important role in the Ca2+ signaling pathway, mediating various molecular responses via interactions with other transcription factors and binding to the promoter region of specific genes. Mung beans (Vigna radiata) are one of the most commonly consumed commodities in Asia. To date, CAMTA proteins have not been characterized in this important crop plant.

RESULTS

Eight paralogous VrCAMTA genes were identified and found to be distributed on five of the 11 chromosomes. The proteins possessed CG-1 DNA-binding domains with bipartite NLS signals, ankyrin domains, CaM-binding IQ motifs, and CaM-binding domain (CaMBD). The 2 kb upstream regions of VrCAMTA genes contained sequence motifs of abscisic acid-responsive elements (ABRE) and ethylene-responsive elements (ERE), and binding sites for transcription factors of the bZIP and bHLH domains. Analysis of RNA-seq data from a public repository revealed ubiquitous expression of the VrCAMTA genes, as VrCAMTA1 was expressed at the highest level in seedling leaves, whereas VrCAMTA8 was expressed at the lowest level, which agreed with the RT-qPCR analysis performed on the first true leaves. On day four after leaf emergence, all VrCAMTA genes were upregulated, with VrCAMTA1 exhibiting the highest degree of upregulation. In darkness on day 4, upregulation was not observed in most VrCAMTA genes, except VrCAMTA7, for which a low degree of upregulation was found, whereas no difference was found in VrCAMTA8 expression between light and dark conditions. Treatment with calcium ionophores enhanced VrCAMTA expression under light and/or dark conditions at different times after leaf emergence, suggesting that calcium signaling is involved in the light-induced upregulation of VrCAMTA gene expression.

CONCLUSIONS

The expression dependence of nearly all VrCAMTA genes on light and calcium signaling suggests their possible differential but likely complementary roles during the early stages of mung bean growth and development.

TRMT1L-catalyzed m2 2G27 on tyrosine tRNA is required for efficient mRNA translation and cell survival under oxidative stress

tRNA modifications are critical for several aspects of their functions, including decoding, folding, and stability. Using a multifaceted approach encompassing eCLIP-seq and Nanopore tRNA-seq, we show that the human tRNA methyltransferase TRMT1L interacts with component of the Rix1 ribosome biogenesis complex and binds to the 28S rRNA, as well as to a subset of tRNAs. Mechanistically, we demonstrate that TRMT1L is responsible for catalyzing m2 2G solely at position 27 of tRNA-Tyr-GUA. Surprisingly, TRMT1L depletion also impaired the deposition of acp3U and dihydrouridine on tRNA-Tyr-GUA, Cys-GCA, and Ala-CGC. TRMT1L knockout cells have a marked decrease in tRNA-Tyr-GUA levels, coinciding with a reduction in global translation rates and hypersensitivity to oxidative stress. Our results establish TRMT1L as the elusive methyltransferase catalyzing the m2 2G27 modification on tRNA Tyr, resolving a long-standing gap of knowledge and highlighting its potential role in a tRNA modification circuit crucial for translation regulation and stress response.

Enhanced kinase translocation reporters for simultaneous real-time measurement of PKA, ERK, and Ca2

Kinase translocation reporters (KTRs) are powerful tools for single-cell measurement of time-integrated kinase activity but suffer from restricted dynamic range and limited sensitivity, particularly in neurons. To address these limitations, we developed enhanced KTRs (eKTRs) for protein kinase A (PKA) and extracellular signal-regulated kinase (ERK) that display high sensitivity, rapid response kinetics, broad dynamic range, cell type-specific tuning, and an ability to detect PKA and ERK activity in primary sensory neurons. Moreover, co-expression of optically separable eKTRs for PKA and ERK revealed the kinetics of expected and unexpected crosstalk between PKA, ERK, protein kinase C, and calcium signaling pathways, demonstrating the utility of eKTRs for live cell monitoring of diverse and interacting signaling pathways. These results open the door to improved live-cell and in vivo measurements of key signaling pathways in neurons, while at the same time demonstrating the importance of KTR size and NLS strength to KTR dynamics.

Amelioration of nonalcoholic fatty liver disease by inhibiting the deubiquitylating enzyme RPN11

Nonalcoholic fatty liver disease (NAFLD), including its more severe manifestation nonalcoholic steatohepatitis (NASH), is a global public health challenge. Here, we explore the role of deubiquitinating enzyme RPN11 in NAFLD and NASH. Hepatocyte-specific RPN11 knockout mice are protected from diet-induced liver steatosis, insulin resistance, and steatohepatitis. Mechanistically, RPN11 deubiquitinates and stabilizes METTL3 to enhance the m6A modification and expression of acyl-coenzyme A (CoA) synthetase short-chain family member 3 (ACSS3), which generates propionyl-CoA to upregulate lipid metabolism genes via histone propionylation. The RPN11-METTL3-ACSS3-histone propionylation pathway is activated in the livers of patients with NAFLD. Pharmacological inhibition of RPN11 by Capzimin ameliorated NAFLD, NASH, and related metabolic disorders in mice and reduced lipid contents in human hepatocytes cultured in 2D and 3D. These results demonstrate that RPN11 is a novel regulator of NAFLD/NASH and that suppressing RPN11 has therapeutic potential for the treatment.

Protective role of cytosolic prion protein against virus infection in prion-infected cells

Production of the amyloidogenic prion protein, PrPSc, which forms infectious protein aggregates, or prions, is a key pathogenic event in prion diseases. Functional prion-like protein aggregations, such as the mitochondrial adaptor protein MAVS and the inflammasome component protein ASC, have been identified to play a protective role in viral infections in mammalian cells. In this study, to investigate if PrPSc could play a functional role against external stimuli, we infected prion-infected cells with a neurotropic influenza A virus strain, IAV/WSN. We found that prion-infected cells were highly resistant to IAV/WSN infection. In these cells, NF-κB nuclear translocation was disturbed; therefore, mitochondrial superoxide dismutase (mtSOD) expression was suppressed, and mitochondrial reactive oxygen species (mtROS) was increased. The elevated mtROS subsequently activated NLRP3 inflammasomes, leading to the suppression of IAV/WSN-induced necroptosis. We also found that prion-infected cells accumulated a portion of PrP molecules in the cytosol, and that the N-terminal potential nuclear translocation signal of PrP impeded NF-κB nuclear translocation. These results suggest that PrPSc might play a functional role in protection against viral infections by stimulating the NLRP3 inflammasome-dependent antivirus mechanism through the cytosolic PrP-mediated disturbance of NF-κB nuclear translocation, which leads to suppression of mtSOD expression and consequently upregulation of the NLRP3 inflammasome activator mtROS.

IMPORTANCE

Cytosolic PrP has been detected in prion-infected cells and suggested to be involved in the neurotoxicity of prions. Here, we also detected cytosolic PrP in prion-infected cells. We further found that the nuclear translocation of NF-κB was disturbed in prion-infected cells and that the N-terminal potential nuclear translocation signal of PrP expressed in the cytosol disturbed the nuclear translocation of NF-κB. Thus, the N-terminal nuclear translocation signal of cytosolic PrP might play a role in prion neurotoxicity. Prion-like protein aggregates in other protein misfolding disorders, including Alzheimer's disease were reported to play a protective role against various environmental stimuli. We here showed that prion-infected cells were partially resistant to IAV/WSN infection due to the cytosolic PrP-mediated disturbance of the nuclear translocation of NF-κB, which consequently activated NLRP3 inflammasomes after IAV/WSN infection. It is thus possible that prions could also play a protective role in viral infections.

A UTP3-dependent nucleolar translocation pathway facilitates pre-rRNA 5'ETS processing

The ribosome small subunit (SSU) is assembled by the SSU processome which contains approximately 70 non-ribosomal protein factors. Whilst the biochemical mechanisms of the SSU processome in 18S rRNA processing and maturation have been extensively studied, how SSU processome components enter the nucleolus has yet to be systematically investigated. Here, in examining the nucleolar localization of 50 human SSU processome components, we found that UTP3, together with another 24 proteins, enter the nucleolus autonomously. For the remaining 25 proteins we found that UTP3/SAS10 assists the nucleolar localization of five proteins (MPP10, UTP25, EMG1 and the two UTP-B components UTP12 and UTP13), likely through its interaction with nuclear importin α. This 'ferrying' function of UTP3 was then confirmed as conserved in the zebrafish. We also found that knockdown of human UTP3 impairs cleavage at the A0-site while loss-of-function of either utp3/sas10 or utp13/tbl3 in zebrafish causes the accumulation of aberrantly processed 5'ETS products, which highlights the crucial role of UTP3 in mediating 5'ETS processing. Mechanistically, we found that UTP3 facilitates the degradation of processed 5'ETS by recruiting the RNA exosome component EXOSC10 to the nucleolus. These findings lay the groundwork for studying the mechanism of cytoplasm-to-nucleolus trafficking of SSU processome components.

ADBP-1 regulates ADR-2 nuclear localization to control editing substrate selection

Adenosine-to-inosine (A-to-I) RNA editing, catalyzed by ADAR enzymes, is a prevalent and conserved RNA modification. While A-to-I RNA editing is essential in mammals, in Caenorhabditis elegans, it is not, making them invaluable for RNA editing research. In C. elegans, ADR-2 is the sole catalytic A-to-I editing enzyme, and ADR-1 is an RNA editing regulator. ADAR localization is well-studied in humans but not well-established in C. elegans. In this study, we examine the cellular and tissue-specific localization of ADR-2. We show that while ADR-2 is present in most cells in the embryo, at later developmental stages, its expression is both tissue- and cell-type-specific. Additionally, both ADARs are mainly in the nucleus. ADR-2 is adjacent to the chromosomes during the cell cycle. We show that the nuclear localization of endogenous ADR-2 depends on ADBP-1, not ADR-1. In adbp-1 mutant worms, ADR-2 is mislocalized, while ADR-1 is not, leading to decreased editing levels and de-novo editing, mostly in exons, suggesting that ADR-2 is also functional in the cytoplasm. Besides, mutated ADBP-1 affects gene expression. Furthermore, we show that ADR-2 targets adenosines with different surrounding nucleotides in exons and introns. Our findings indicate that ADR-2 cellular localization is highly regulated and affects its function.

KLF12 interacts with TRIM27 to affect cisplatin resistance and cancer metastasis in esophageal squamous cell carcinoma by regulating L1CAM expression

Krüppel-like factor 12 (KLF12) has been characterized as a transcriptional repressor, and previous studies have unveiled its roles in angiogenesis, neural tube defect, and natural killer (NK) cell proliferation. However, the contribution of KLF12 to cancer treatment remains undefined. Here, we show that KLF12 is downregulated in various cancer types, and KLF12 downregulation promotes cisplatin resistance and cancer metastasis in esophageal squamous cell carcinoma (ESCC). Mechanistically, KLF12 binds to the promoters of L1 Cell Adhesion Molecule (L1CAM) and represses its expression. Depletion of L1CAM abrogates cisplatin resistance and cancer metastasis caused by KLF12 loss. Moreover, the E3 ubiquitin ligase tripartite motif-containing 27 (TRIM27) binds to the N-terminal region of KLF12 and ubiquitinates KLF12 at K326 via K33-linked polyubiquitination. Notably, TRIM27 depletion enhances the transcriptional activity of KLF12 and consequently inhibits L1CAM expression. Overall, our study elucidated a novel regulatory mechanism involving TRIM27, KLF12 and L1CAM, which plays a substantial role in cisplatin resistance and cancer metastasis in ESCC. Targeting these genes could be a promising approach for ESCC treatment.

Lysine methyltransferase 2 plays a key role in the encystation process in the parasite Giardia lamblia

Histone post-translational modifications are extensively studied for their role in regulating gene transcription and cellular environmental adaptation. Research into these modifications has recently begun in the protozoan parasite Giardia lamblia, focusing on histone-modifying enzymes and specific post-translational changes. In the transformation from the trophozoite to the cyst form in the life cycle of this parasite, significant morphological and genetic alterations occur, culminating in the synthesis of cyst wall proteins responsible for forming the protective cyst wall. It has been previously demonstrated that histone deacetylation is required during encystation and that the enzyme lysine methyltransferase 1 is involved in the upregulation of encystation. Our study aims to extend the analysis to lysine methyltransferase 2 (GlKMT2) function. For this, two constructs were generated: one that downregulate the expression of GLKMT2 via antisense (glkmt2-as transgenic cells) and the other overexpressing GlKMT2 (glkmt2-ha transgenic cells). We found that the glktm2-as transgenic cells showed an arrest in progress at the late encystation stage. Consequently, the number of cysts produced was lower than that of the control cells. On the other hand, we found that the overexpression of GlKMT2 acts as a negative mutant of the enzyme. In this way, these glktm2-ha transgenic cells showed the same behavior during growth and encystation as glkmt2-as transgenic cells. This interplay between different enzymes acting during encystation reveals the complex process behind the differentiation of the parasite. Understanding how these enzymes play their role during the encystation of the parasite would allow the design of inhibitors to control the parasite.

A Combined Transcriptomic and Proteomic Analysis of Monkeypox Virus A23 Protein on HEK293T Cells

Monkeypox virus (MPXV) is a cross-kingdom pathogen infecting both humans and wildlife, which poses a significant health risk to the public. Although MPXV attracts broad attention, there is a lack of adequate studies to elucidate pathogenic mechanisms associated with viral infections. In this study, a high-throughput RNA sequencing (RNA-seq) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach was used to explore the transcriptional and metabolic responses of MPXV A23 protein to HEK293T cells. The protein-protein interactions and signaling pathways were conducted by GO and KEGG analyses. The localization of A23 protein in HEK293T cells was detected by immunofluorescence. A total of 648 differentially expressed genes (DEGs) were identified in cells by RNA-Seq, including 314 upregulated genes and 334 downregulated genes. Additionally, liquid chromatography-tandem mass spectrometry (LC-MS/MS) detected 115 cellular proteins that interact with the A23 proteins. Transcriptomic sequencing analysis revealed that transfection of MPXV A23 protein modulated genes primarily associated with cellular apoptosis and DNA damage repair. Proteomic analysis indicated that this protein primarily interacted with host ribosomal proteins and histones. Following the identification of the nuclear localization sequence RKKR within the A23 protein, a truncated mutant A23ΔRKKR was constructed to investigate the subcellular localization of A23 protein. The wild-type A23 protein exhibits a significantly higher nuclear-to-cytoplasmic ratio, exceeding 1.5, in contrast to the mutant A23ΔRKKR, which has a ratio of approximately 1. Immunofluorescence assays showed that the A23 protein was mainly localized in the nucleus. The integration of transcriptomics and proteomics analysis provides a comprehensive understanding of the interaction between MPXV A23 protein and the host. Our findings highlight the potential role of this enzyme in suppressing host antiviral immune responses and modulating host gene expression.