Protein Family Research Articles

TaWI12 may be involved in pistillody and leaf cracking in wheat

TaWI12 is a member of the wound-induced (WI) protein family, which has been implicated in plant stress responses and developmental processes. Wheat (Triticum aestivum L.) is a crucial staple crop upon which human sustenance relies. Consequently, investigating the developmental mechanisms of pistils and stamens in wheat is profoundly significant for enhancing wheat characteristics and boosting productivity. In this study, we cloned TaWI12, from common wheat and observed a significant resemblance among the three homoeologs of TaWI12. The open reading frames (ORFs) of TaWI12-4A, TaWI12-4B and TaWI12-4D were 408 bp, 417 bp and 417 bp, respectively, and encoded 135, 138 and 138 amino acids, respectively. The phylogenetic tree revealed a high degree of homology between the protein sequences of TaWI12 and the wound-induced proteins of Hordeum vulgare (KAI4994568) and Aegilops tauschii (XP_020196548). To clarify the characteristics and functions of TaWI12 homoeologs, we obtained transgenic positive plants of Arabidopsis thaliana and observed significant filament shortening and decrease. Simultaneously, we used the CRISPR/Cas9 system to generate mutant plants via the modification of three homoeologs of TaWI12 in wheat. We noticed two distinct phenotypic differences in the knockout mutant. First, we observed the different degrees of homologous conversion of stamens to pistils in the single mutant TaWI12-4D. Second, we observed leaf cracking in both the single mutant TaWI12-4A and the double mutants TaWI12-4A and TaWI12-4D. Our findings further revealed that TaWI12 plays an important role in flower development, which is important for revealing the molecular mechanisms of pistil and stamen development in wheat and has important application value for high-yield wheat breeding.

Organismal complexity strongly correlates with the number of protein families and domains

In the pregenomic era, scientists were puzzled by the observation that haploid genome size (the C-value) did not correlate well with organismal complexity. This phenomenon, called the "C-value paradox," is mostly explained by the fact that protein-coding genes occupy only a small fraction of eukaryotic genomes. When the first genome sequences became available, scientists were even more surprised by the fact that the number of genes (G-value) was also a poor predictor of complexity, which gave rise to the "G-value paradox." The proposed explanations usually invoke mechanisms that increase the information content of each individual gene (protein-protein interactions, intrinsic disorder, posttranslational modifications, alternative splicing, etc.). Less attention has been paid to mechanisms that increase the amount of genetic material but do not increase (or not to the same extent) the amount of information encoded in the genome, such as gene duplication and domain shuffling. Proteins belonging to the same family and/or sharing the same domains often carry out similar or even redundant functions. We thus hypothesized that an organism's number of different protein families and domains should be suitable predictors of organismal complexity. In agreement with our hypothesis, we observed that the number of protein families, clans, domains, and motifs increases from simple to progressively more complex organisms. In addition, these metrics correlate with the number of cell types better than and independently of the number of protein-coding genes and several previously proposed predictors of organismal complexity. Our observations have the potential to represent a resolution to the G-value paradox.

RNA recognition by minimal ProQ from Neisseria meningitidis.

Neisseria meningitidis minimal ProQ is a global RNA binding protein belonging to the family of FinO-domain proteins. The N. meningitidis ProQ consists only of the FinO domain accompanied by short N- and C-terminal extensions. To better understand how this minimal FinO-domain protein recognizes RNAs, we compared its binding to seven different natural RNA ligands of this protein. Next, two of these RNAs, rpmG-3' and AniS, were subject to further mutational studies. The data showed that N. meningitidis ProQ binds the lower part of the intrinsic transcription terminator hairpin, and that the single-stranded sequences on the 5' and 3' side of terminator stem are required for tight binding. However, the specific lengths of 5' and 3' RNA sequences required for optimal binding differed between the two RNAs. Additionally, our data show that the 2'-OH and 3'-OH groups of the 3' terminal ribose contribute to RNA binding by N. meningitidis ProQ. In summary, the minimal ProQ protein from N. meningitidis has generally similar requirements for RNA binding as the isolated FinO domains of other proteins of this family, but differs from them in detailed RNA features that are optimal for specific RNA recognition.

S100A13-driven interaction between pancreatic adenocarcinoma cells and cancer-associated fibroblasts promotes tumor progression through calcium signaling

BackgroundCancer-associated fibroblasts (CAFs) are key components of the pancreatic adenocarcinoma (PAAD) tumor microenvironment (TME), where they promote tumor progression and metastasis through immunosuppressive functions. Although significant progress has been made in understanding the crosstalk between cancer cells and CAFs, many underlying mechanisms remain unclear. Recent studies have highlighted the importance of calcium signaling in enhancing interactions between tumor cells and the surrounding stroma, with the S100 family of proteins serving as important regulators. While the roles of some S100 proteins have been extensively studied, others, such as S100A13, remain less well understood.MethodsBioinformatic analysis was employed to predict the pathogenic potential of CAFs and S100A13. Stable S100A13 knockdown CAFs were generated using a short hairpin RNA system. Cellular viability and apoptosis rates were evaluated through CCK-8 and flow cytometry tests, respectively. Additionally, the wound healing and migration assays were conducted to assess the invasive and metastatic capabilities. Transcriptome analysis was conducted to identify differential gene expression and associated signaling pathways in PAAD cells derived from an indirect culture system. Furthermore, the protumoral role of S100A13 in PAAD was further verified using both 3D bioprinting and cell line-based xenograft tumor models.ResultsIn this study, we identified a strong association between S100A13, a calcium-binding protein, and CAFs in PAAD. Gene expression analysis revealed that S100A13 was highly expressed in CAFs and correlated with poor prognosis. Knockdown of S100A13 in CAFs reduced the metastatic potential of PAAD cells. In addition, S100A13 depletion impaired cell motility and calcium signaling pathways within the TME. Furthermore, silencing S100A13 in CAFs markedly slowed PAAD progression in both tumor spheroids and Balb/c nude mice.ConclusionsTogether, our findings underscore the critical role of CAFs-derived S100A13 in PAAD progression and suggest that targeting S100A13 may offer a promising therapeutic strategy for PAAD.

In silico screening and immunogenic features of putative tick cement protein PA107 from Ixodes ricinus tick.

Tick salivary proteins are crucial for efficient and successful tick feeding. Most of them are still uncharacterized, especially those involved in the formation of tick cement. Tick salivary protein PA107 is a putative cement protein, which is transcribed in salivary glands during the initial phase of tick feeding. It is a tick-unique protein, with homologs described in several tick genera. In this study, a detailed in silico analysis of its primary and tertiary structure was performed, along with the immunogenicity assessment for the PA107 protein from Ixodes ricinus species. The screening of the primary structure placed it to the glycine-rich protein family, revealing in parallel an overlapping 15mer at the C-terminus and borderline homology to non-tick proteins with antimicrobial activity. The analysis of tertiary structure revealed a high degree of intrinsic disorder for monomeric PA107, in contrast to highly ordered structures for different oligomeric states that might correlate with the putative role in the tick cement formation process. Regarding in silico PA107 immunogenicity inference, obtained results were inconclusive, which aligns with the in vitro findings showing definitely the lack of humoral response induction in experimentally infested rats and persons bitten by the I. ricinus ticks. The results represent new pieces of a huge puzzle depicting a complex tick-host relationship, but also identify PA107 as a possible compound of novel formulations to be used in biomedicine as bioadhesives, and as a target for new anti-tick strategies, by interfering with the cement cone formation and stability, i.e. tick attachment and feeding.

CCN5 suppresses injury-induced vascular restenosis by inhibiting smooth muscle cell proliferation and facilitating endothelial repair via thymosin β4 and Cd9 pathway.

Members of the CCN matricellular protein family are crucial in various biological processes. This study aimed to characterize vascular cell-specific effects of CCN5 on neointimal formation and its role in preventing in-stent restenosis (ISR) after percutaneous coronary intervention (PCI). Stent-implanted porcine coronary artery RNA-seq and mouse injury-induced femoral artery neointima single-cell RNA sequencing were performed. Plasma CCN5 levels were measured by enzyme-linked immunosorbent assay. Endothelial cell (EC)- and vascular smooth muscle cell (VSMC)-specific CCN5 loss-of-function and gain-of-function mice were generated. Mass spectrometry and co-immunoprecipitation were conducted to identify CCN5 interacting proteins. Additionally, CCN5 recombinant protein (CCN5rp)-coated stents were deployed to evaluate its anti-ISR effects in a porcine model. Plasma CCN5 levels were significantly reduced and correlated closely with the degree of restenosis in ISR patients. CCN5 expression was significantly decreased in VSMCs of stent-implanted porcine coronary segments and injured mouse femoral arteries, especially in synthetic VSMCs. In contrast, elevated CCN5 expression was observed in regenerating ECs of injured vessels. Endothelial cell- and VSMC-specific CCN5 deletion mice exhibited exacerbation of injury-induced neointimal hyperplasia, while CCN5 gain-of-function alleviated neointimal formation. Mechanistic studies identified thymosin β4 (Tβ4) as a CCN5 interacting protein in ECs and EC-CCN5 promoted injury repair through Tβ4 cleavage product Ac-SDKP. Also, CCN5rp promoted EC repair to suppress neointimal hyperplasia via interaction with Cd9 extracellular domain. Moreover, implantation with CCN5rp-coated stent significantly increased stent strut coverage with ECs, which suppressed neointimal formation and ultimately alleviated ISR. CCN5 exerts a dual protective effect on ISR by inhibiting VSMC proliferation and facilitating EC repair. CCN5rp-coated stent might be promising in the prevention of ISR after PCI.

Ectopic overexpression of Plasmodium falciparum DNA-/RNA-binding Alba proteins misregulates virulence gene homeostasis during asexual blood development.

Alba domain-containing proteins are ubiquitously found in archaea and eukaryotes. By binding to either DNA, RNA, or DNA:RNA hybrids, these proteins function in genome stabilization, chromatin organization, gene regulation, and/or translational modulation. In the malaria parasite Plasmodium falciparum, six Alba domain proteins PfAlba1-6 have been described, of which PfAlba1 has emerged as a "master regulator" of translation during parasite intra-erythrocytic development (IED). Given that a tight control of gene expression is especially important during IED, when malaria pathogenesis manifests, in this study, we focus on three other P. falciparum Albas, PfAlba2-4. Because genetic manipulation of the genomic loci of PfAlba2-4 was unsuccessful, we overexpressed each of these proteins from an episome under a strong constitutive promoter. We observed that PfAlba2 or PfAlba3 overexpression strongly reduced parasite growth and impacted IED stage transitions. In contrast, elevated levels of PfAlba4 were well-tolerated by the parasite. In keeping with this, differential gene expression analysis using RNA-seq of PfAlba2 or PfAlba3 overexpressing strains revealed a significant misregulation of mRNAs encoding virulence factors, such as those related to erythrocyte invasion; a general repression of var gene expression was also apparent. PfAlba4 overexpression, on the other hand, did not significantly perturb the steady-state transcriptome of IED stages and appeared to enhance var mRNA levels. Moreover, distinct sets of genes were targeted by each PfAlba for regulation. Taken together, this study highlights the nonredundant roles of PfAlba proteins in the P. falciparum IED, emphasizing their importance in subtelomeric chromatin biology and RNA regulation.IMPORTANCEThe malaria parasite Plasmodium falciparum tightly controls the expression of its genes at the epigenetic, transcriptional, post-transcriptional, and translational levels to synthesize essential proteins, including virulence factors, in a timely and spatially coordinated manner. A family of six proteins implicated in this process is called PfAlba, characterized by the presence of the DNA-, RNA- or DNA:RNA hybrid-binding Alba domain. To better understand the cellular pathways regulated by this protein family, we overexpressed three PfAlbas during P. falciparum intra-erythrocytic growth and found that high levels of PfAlba2 and PfAlba3 were detrimental to parasite development. This was accompanied by significant changes in the parasite's transcriptome, either with regards to mRNA steady-state levels or expression timing. PfAlba4 overexpression, on the other hand, was well-tolerated by the parasite. Overall, our results delineate specific pathways targeted by individual PfAlbas for regulation and link PfAlba2/PfAlba3 to mutually exclusive expression of the virulence-promoting surface antigen PfEMP1.

Transcriptional regulation of development by SMAX1-LIKE proteins, targets of strigolactone and karrikin/KAI2 ligand signaling.

SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE (SMXL) proteins comprise a family of plant growth regulators that includes downstream targets of the karrikin (KAR)/KAI2 ligand (KL) and strigolactone (SL) signaling pathways. Following the perception of KAR/KL or SL signals by α/β hydrolases, some types of SMXL proteins are polyubiquitinated by an E3 ubiquitin ligase complex containing the F-box protein MORE AXILLARY GROWTH2 (MAX2)/DWARF3 (D3), and proteolyzed. Because SMXL proteins interact with TOPLESS (TPL) and TPL-related (TPR) transcriptional corepressors, SMXL degradation initiates changes in gene expression. This simplified model of SMXL regulation and function in plants must now be revised in light of recent discoveries. It has become apparent that SMXL abundance is not regulated by KAR/KL or SL alone, and that some SMXL proteins are not regulated by MAX2/D3 at all. Therefore, SMXL proteins should be considered signaling hubs that integrate multiple cues. Here we review the current knowledge of how SMXL proteins impose transcriptional regulation of plant development and environmental responses. SMXL proteins can bind DNA directly and interact with transcriptional regulators from several protein families. Multiple mechanisms of downstream genetic control by SMXL proteins have been identified recently that do not involve the recruitment of TPL/TPR, expanding the paradigm of SMXL function.

Genome-wide analysis and characterization of TPD1 family proteins in pearl millet (Cenchrus americanus): Insights into reproductive regulation and phytohormone responses.

The Tapetum Determinant 1 (TPD1) family proteins are known to play a crucial role in the regulation of reproduction in plants, including Cenchrus americanus (pearl millet). However, members of TPD1 family proteins have not been fully identified. The current study aims to identify and characterize the TPD1 family proteins in Cenchrus americanus (L.) Morrone. Seven transmembrane proteins (from 127 to 172 aa) comprising TPD1 domain were identified via genome-wide mining. Analysis of gene expression during developmental stages revealed high expression of four CaTPD1s in reproductive organs. Treatment with phytohormones showed that the expression of CaTPD1s was repressed by hormone treatments except CaTPD1_Ch4.1 and CaTPD1_Ch4.3 which are highly expressed in response to brassinolide and auxin, respectively. Screening of cis-elements in the promoter of CaTPD1s revealed various cis-elements related to phytohormone regulation, wound response, abiotic stress defense, and light response. The phylogenetic tree revealed distinct clustering of CaTPD1_Ch6 and CaTPD1_Ch5 among the other CaTPD1s, which revealed close relationships with the orthologs from Arabidopsis and rice that are known to have a critical role in tapetum development and pollen and ovule production. Hence, this study affirms the role of the CaTPD1s genes in the growth and reproduction during pearl millet developmental stages.

The role of canopy family proteins: biological mechanism and disease function.

Canopy family proteins are highly sequence-conserved proteins with an N-terminal hydrophobic signal sequence, a unique pattern of six cysteine residues characteristic of the saposin-like proteins, and a C-terminal putative endoplasmic reticulum retention signal sequence. At present, the known canopy family proteins are canopy fibroblast growth factor signaling regulator 1 (CNPY1), CNPY2, CNPY3, and CNPY4. Despite similar structures, canopy family proteins regulate complex signal networks to participate in various biological processes. They are involved in a wide range of diseases, including angiogenesis, abnormal immune responses, neurodevelopmental disorders, and the development of tumors. Here, we summarized the biological processes and influence on the disease of every CNPY family protein to elucidate potential biomarkers and point out the direction for future in-depth research.

TMEM160 Promotes Tumor Growth in Lung Adenocarcinoma and Cervical Adenocarcinoma Cell Lines

The Chromosome-Centric Human Proteome Project (C-HPP) is an international initiative. It aims to create a protein list expressed in human cells by each chromosomal and mitochondrial DNA to enhance our understanding of disease mechanisms, akin to the gene list generated by the Human Genome Project. Transmembrane protein 160 (TMEM160) is a member of the transmembrane proteins (TMEM) family. TMEM proteins have been implicated in cancer-related processes, including cell proliferation, migration, epithelial-mesenchymal transition, metastasis, and resistance to chemotherapy and radiotherapy. This study aimed to investigate the role of TMEM160 in non-small cell lung cancer and cervical cancer using cell lines, clinical samples, and xenograft studies. Our findings demonstrated that TMEM160 knockdown decreased the proliferation of lung and cervical cancer cell lines. We observed that TMEM160 is localized in the nucleus and cytoplasm and dynamic localization during mitosis of cancer cells and discovered a novel interaction between TMEM160 and nuclear proteins such as NUP50. Furthermore, the TMEM160 interactome was enriched in processes associated with apical junctions, xenobiotic metabolism, glycolysis, epithelial-mesenchymal transition, reactive oxygen species, UV response DNA, the P53 pathway, and the mitotic spindle. This study provides an initial understanding of the function of TMEM160 in lung and cervical cancer progression and clarifies the need to continue investigating the participation of TMEM160 in these cancers.

An augmented transformer model trained on protein family specific variant data leads to improved prediction of variants of uncertain significance.

Variants of uncertain significance (VUS) represent variants that lack sufficient evidence to be confidently associated with a disease, thus posing a challenge in the interpretation of genetic testing results. Here we report an improved method for predicting the VUS of Arylsulfatase A (ARSA) gene as part of the Critical Assessment of Genome Interpretation challenge (CAGI6). Our method uses a transfer learning approach that leverages a pre-trained protein language model to predict the impact of mutations on the activity of the ARSA enzyme, whose deficiency is known to cause a rare genetic disorder, metachromatic leukodystrophy. Our innovative framework combines zero-shot log odds scores and embeddings from the ESM, an evolutionary scale model as features for training a supervised model on gene variants functionally related to the ARSA gene. The zero-shot log odds score feature captures the generic properties of the proteins learned due to its pre-training on millions of sequences in the UniProt data, while the ESM embeddings for the proteins in the ARSA family capture features specific to the family. We also tested our approach on another enzyme, N-acetyl-glucosaminidase (NAGLU), that belongs to the same superfamily as ARSA. Our results demonstrate that the performance of our family models (augmented ESM models) is either comparable or better than the ESM models. The ARSA model compares favorably with the majority of state-of-the-art predictors on area under precision and recall curve (AUPRC) performance metric. However, the NAGLU model outperforms all pathogenicity predictors evaluated in this study on AUPRC metric. The improved AUPRC has relevance in a diagnostic setting where variant prioritization generally entails identifying a small number of pathogenic variants from a larger number of benign variants. Our results also indicate that genes that have sparse or no experimental variant impact data, the family variant data can serve as a proxy training data for making accurate predictions. Attention analysis of active sites and binding sites in ARSA and NAGLU proteins shed light on probable mechanisms of pathogenicity for positions that are highly attended.

Pyroptosis: A Novel Therapeutic Target for Bioactive Compounds in Human Disease Treatment? A Narrative Review

Background/Objectives: Bioactive compounds possess the ability to maintain health and improve diseases by regulating inflammation and cell death processes. Pyroptosis is programmed cell death related to inflammation and exerts a critical role in the development and progression of different types of diseases. This narrative review aims to investigate and discuss the effects of dietary bioactive compounds on pyroptosis in different common human pathologies, such as inflammatory disease, bacterial infection, injury disease, cancer, diabetes and heart disease, etc. Method: Studies published in the major databases until December 2024 in English were considered, for a total of 50 papers. Results: The current evidence demonstrated that the bioactive compounds are able to regulate the pyroptosis process by modulating different inflammasome sensors (NLRP1, NLRP3, and AIM2), caspase family proteins (caspase-1, caspase-3, and caspase-11), and gasdermins (GSDMD and GSDME) in many pathological conditions related to inflammation, including cancer and cardiovascular diseases. Conclusions: Bioactive compounds have powerful potential to be the candidate drug for pyroptosis modulation in inflammatory diseases, even if more clinical studies are needed to confirm the effects and establish efficient doses for humans.

TRIM29 reverses lenvatinib resistance in liver cancer cells by ubiquitinating and degrading YBX1 to inhibit the PI3K/AKT pathway.

Sorafenib and lenvatinib are frontline treatments for advanced hepatocellular carcinoma (HCC). While lenvatinib surpasses sorafenib in efficacy and tolerability, resistance remains a significant clinical challenge. Recent research highlights the potential of TRIM family proteins in modulating lenvatinib resistance in HCC, necessitating a deeper understanding of their specific mechanisms. In this study, we screened TRIM family genes differentially expressed in lenvatinib-resistant cells using the GEO database, verifying their expression through qRT-PCR and identifying TRIM29 as a key target. Clinical samples were analyzed to assess TRIM29 expression, clinical significance, and its correlation with lenvatinib treatment efficacy. Stable TRIM29 overexpression in SK-Hep1 and LM3 cells was confirmed by Western blotting. The impact of TRIM29 on lenvatinib sensitivity in liver cancer cells was evaluated using colony formation assays, CCK8, flow cytometry, and in vivo experiments. Transcriptome sequencing, mass spectrometry, and co-immunoprecipitation (CO-IP) were employed to elucidate TRIM29's regulatory mechanisms. Results from the GEO database indicated significant upregulation of TRIM29, TRIM50, TRIM31, and TRIM9 in HUH7-resistant cells, with qRT-PCR confirming TRIM29 as markedly upregulated. In 112 liver cancer patients clinical samples, TRIM29 expression was significantly higher in patients with stable disease or partial response to lenvatinib compared to those with disease progression. High TRIM29 expression was associated with longer overall survival and recurrence-free periods in HCC patients. Mechanistic studies revealed that TRIM29 enhances lenvatinib sensitivity by degrading YBX1 through ubiquitination, thereby inhibiting the PI3K/AKT signaling pathway and reversing resistance. These findings suggest that TRIM29 is a promising therapeutic target for overcoming lenvatinib resistance in HCC. CONCLUSION: TRIM29 degrades YBX1 through ubiquitination, thereby inhibiting the PI3K/AKT signaling pathway and reversing lenvatinib resistance in HCC. TRIM29 can serve as an independent prognostic indicator of survival and recurrence in HCC patients, and it may provide new avenues for developing innovative treatment strategies for HCC.

Promising LOX proteins for cartilage- targeting osteoarthritis therapy.

Osteoarthritis (OA) is the most affected joint disease worldwide, touching millions of people every year. It is caused by a progressive degeneration of articular cartilage, causing pain and limited mobility. Among the pathways involved in cartilage homeostasis, "LOX" proteins (referring to three distinct protein families, very often confused in the literature) play a prominent role. The lipoxygenase enzyme family is involved in the inflammatory process of OA by inducing the production of several pro-inflammatory leukotrienes. Lectin-like oxidized low-density lipoprotein family are receptors located at the surface of chondrocytes, which interact with their ligand, ox-LDL, activating several catabolic pathways involved in OA pathophysiology. Finally, lysyl oxidase and lysyl oxidase-like are enzymes expressed intracellularly in chondrocytes cytoplasm involved in elastin biosynthesis and collagen cross-linking in cartilage extracellular matrix. EMA and FDA have yet approved no drugs targeting the LOX proteins. In particular, lysyl oxidase-like 2 is considered today as a new promising target for OA modifying therapy. This review clarifies the main role of different LOX proteins involved in the progression of OA. Some potential LOX inhibitor strategies for drug development in advanced OA therapy, particularly for local intraarticular delivery, were listed and discussed for each target type. This review, therefore, proposes promising strategies for future drug development in OA treatment.

Genome-Wide Characterization and Expression Profiling of YTH Domain-Containing RNA-Binding Protein Family in Taxus chinensis

N6-methyladenosine (m6A), the most common internal RNA modification in eukaryotes, plays a vital role in post-transcriptional regulation. The YT521-B homology (YTH) domain plays a pivotal role in the methylation-dependent recognition of m6A. In this study, we performed an in-depth analysis of the YTH domain-containing RNA-binding protein family in Taxus chinensis (T. chinensis), a species renowned for its rich content of taxol, a significant compound in cancer therapy. We identified and analyzed six YTH domain-containing proteins in T. chinensis, elucidating their phylogenetic relationships, conserved domain, gene structures, conserved motifs, and chromosomal locations. The prion-like domain analyses provided insights into their potential functions in liquid–liquid phase separation and mRNA metabolism. Quantitative tissue analysis revealed TcYTH1 as the most highly expressed gene among the six TcYTH members. Additionally, we investigated the expression profiles of TcYTH genes under various stress conditions, such as high light, ABA, and PEG treatments. The expression levels of all TcYTH genes changed significantly under stress, revealing their involvement in stress response mechanisms. Our research provides novel insights into the YTH genes family in T. chinensis, emphasizing their potential roles in growth regulation and stress tolerance. The identification and analysis of these genes lay the groundwork for future studies on their functional roles in plant biology.

Mina53 catalyzes arginine demethylation of p53 to promote tumor growth.

Arginine methylation is a common post-translational modification that plays critical roles in many biological processes. However, the existence of arginine demethylases that remove the modification has not been fully established. Here, we report that Myc-induced nuclear antigen 53 (Mina53), a member of the jumonji C (JmjC) protein family, is an arginine demethylase. Mina53 catalyzes the removal of asymmetric dimethylation at arginine 337 of p53. Mina53-mediated demethylation reduces p53 stability and oligomerization and alters chromatin modifications at the gene promoter, thereby suppressing p53-mediated transcriptional activation and cell-cycle arrest. Mina53 represses p53-dependent tumor suppression both in mouse xenografts and spontaneous tumor models. Moreover, downregulation of p53-mediated gene expression is observed in several types of cancer with elevated expression of Mina53. Thus, our study reveals a regulatory mechanism of p53 homeostasis and activity and, more broadly, defines a paradigm for dynamic arginine methylation in controlling important biological functions.

Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools.

In silico functional annotation of proteins is crucial to narrowing the sequencing-accelerated gap in our understanding of protein activities. Numerous function annotation methods exist, and their ranks have been growing, particularly so with the recent deep learning-based developments. However, it is unclear if these tools are truly predictive. As we are not aware of any methods that can identify new terms in functional ontologies, we ask if they can, at least, identify molecular functions of proteins that are non-homologous to or far-removed from known protein families. Here, we explore the potential and limitations of the existing methods in predicting molecular functions of thousands of such proteins. Lacking the "ground truth" functional annotations, we transformed the assessment of function prediction into evaluation of functional similarity of protein pairs that likely share function but are unlike any of the currently functionally annotated sequences. Notably, our approach transcends the limitations of functional annotation vocabularies, providing a means to assess different-ontology annotation methods. We find that most existing methods are limited to identifying functional similarity of homologous sequences and fail to predict function of proteins lacking reference. Curiously, despite their seemingly unlimited by-homology scope, deep learning methods also have trouble capturing the functional signal encoded in protein sequence. We believe that our work will inspire the development of a new generation of methods that push boundaries and promote exploration and discovery in the molecular function domain. Supplementary data are available at Bioinformatics online.

CSE-8, a filamentous fungus-specific Shr3-like chaperone, facilitates endoplasmic reticulum exit of chitin synthase CHS-3 (class I) in Neurospora crassa

Chitin is a crucial structural polysaccharide in fungal cell walls, essential for maintaining cellular plasticity and integrity. Its synthesis is orchestrated by chitin synthases (CHS), a major family of transmembrane proteins. In Saccharomyces cerevisiae, the cargo receptor Chs7, belonging to the Shr3-like chaperone family, plays a pivotal role in the exit of Chs3 from the endoplasmic reticulum (ER) and its subsequent activity in the plasma membrane (PM). However, the auxiliary machinery responsible for CHS trafficking in filamentous fungi remains poorly understood. The Neurospora crassa genome encodes two orthologues of Chs7: chitin synthase export (CSE) proteins CSE-7 (NCU05720) and CSE-8 (NCU01814), both of which are highly conserved among filamentous fungi. In contrast, yeast forms only possess a single copy CHS export receptor. Previous research highlighted the crucial role of CSE-7 in the localization of CHS-4 at sites of cell wall synthesis, including the Spitzenkörper (SPK) and septa. In this study, CSE-8 was identified as an export protein for CHS-3 (class I). In the Δcse-8 knockout strain of N. crassa, CHS-3-GFP fluorescence was absent from the SPK or septa, indicating that CSE-8 is required for the exit of CHS-3 from the ER. Additionally, sexual development was disrupted in the Δcse-8 strain, with 20% of perithecia from homozygous crosses exhibiting two ostioles. A Δcse-7;Δcse-8 double mutant strain showed reduced N-acetylglucosamine (GlcNAc) content and decreased radial growth. Furthermore, the loss of cell polarity and the changes in subcellular distribution of CSE-8-GFP and CHS-3-GFP observed in hyphae under ER stress induced by the addition of tunicamycin and dithiothreitol reinforce the hypothesis that CSE-8 functions as an ER protein. The current evidence suggests that the biogenesis of CHS exclusive to filamentous fungi may involve pathways independent of CSE-mediated receptors.

What is known and unknown about the role of neuroendocrine genes Ptprn and Ptprn2

The protein tyrosine phosphatase receptors N and N2 are encoded by the Ptprn and Ptprn2 genes expressed in neuroendocrine cells of the hypothalamus, pituitary gland, and diffuse neuroendocrine system, including the pancreas, lung, and intestine. Unlike other members of the protein tyrosine phosphatase receptor family, PTPRN and PTPRN2 lack protein tyrosine phosphatase activity due to mutation of two residues in their intracellular catalytic domains. However, during evolution these proteins acquired new cellular roles beyond tyrosine dephosphorylation in the centralized and diffuse neuroendocrine systems. Here we discuss the current understanding and lack of information about the actions of these proteins, focusing on neuroendocrine cells of the hypothalamus, pituitary, and pancreas.