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1.
Biol Res ; 57(1): 22, 2024 May 04.
Article En | MEDLINE | ID: mdl-38704609

BACKGROUND: Chromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors involved in chromatin dynamics at gene regulatory regions are general regulatory factors (GRFs). These factors contribute to establishment and maintenance of nucleosome-depleted regions (NDRs). These regions are populated by nucleosomes through histone deposition and nucleosome sliding, the latter catalyzed by a number of ATP-dependent chromatin remodeling complexes, including ISW1a. It has been observed that GRFs can act as barriers against nucleosome sliding towards NDRs. However, the relative ability of the different GRFs to hinder sliding activity is currently unknown. RESULTS: Considering this, we performed a comparative analysis for the main GRFs, with focus in their ability to modulate nucleosome sliding mediated by ISW1a. Among the GRFs tested in nucleosome remodeling assays, Rap1 was the only factor displaying the ability to hinder the activity of ISW1a. This effect requires location of the Rap1 cognate sequence on linker that becomes entry DNA in the nucleosome remodeling process. In addition, Rap1 was able to hinder nucleosome assembly in octamer transfer assays. Concurrently, Rap1 displayed the highest affinity for and longest dwell time from its target sequence, compared to the other GRFs tested. Consistently, through bioinformatics analyses of publicly available genome-wide data, we found that nucleosome occupancy and histone deposition in vivo are inversely correlated with the affinity of Rap1 for its target sequences in the genome. CONCLUSIONS: Our findings point to DNA binding affinity, residence time and location at particular translational positions relative to the nucleosome core as the key features of GRFs underlying their roles played in nucleosome sliding and assembly.


Chromatin Assembly and Disassembly , DNA-Binding Proteins , Nucleosomes , Nucleosomes/metabolism , Nucleosomes/genetics , Chromatin Assembly and Disassembly/physiology , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Histones/metabolism
2.
J Cell Biol ; 223(8)2024 Aug 05.
Article En | MEDLINE | ID: mdl-38709169

Histone H3 lysine36 dimethylation (H3K36me2) is generally distributed in the gene body and euchromatic intergenic regions. However, we found that H3K36me2 is enriched in pericentromeric heterochromatin in some mouse cell lines. We here revealed the mechanism of heterochromatin targeting of H3K36me2. Among several H3K36 methyltransferases, NSD2 was responsible for inducing heterochromatic H3K36me2. Depletion and overexpression analyses of NSD2-associating proteins revealed that NSD2 recruitment to heterochromatin was mediated through the imitation switch (ISWI) chromatin remodeling complexes, such as BAZ1B-SMARCA5 (WICH), which directly binds to AT-rich DNA via a BAZ1B domain-containing AT-hook-like motifs. The abundance and stoichiometry of NSD2, SMARCA5, and BAZ1B could determine the localization of H3K36me2 in different cell types. In mouse embryos, H3K36me2 heterochromatin localization was observed at the two- to four-cell stages, suggesting its physiological relevance.


Chromatin Assembly and Disassembly , Heterochromatin , Histone-Lysine N-Methyltransferase , Histones , Repressor Proteins , Animals , Humans , Mice , Adenosine Triphosphatases , Bromodomain Containing Proteins/genetics , Bromodomain Containing Proteins/metabolism , Centromere/metabolism , Centromere/genetics , Chromosomal Proteins, Non-Histone/metabolism , Chromosomal Proteins, Non-Histone/genetics , Heterochromatin/metabolism , Heterochromatin/genetics , Histone-Lysine N-Methyltransferase/metabolism , Histone-Lysine N-Methyltransferase/genetics , Histones/metabolism , Histones/genetics , Methylation , Repressor Proteins/metabolism , Repressor Proteins/genetics , Transcription Factors/metabolism , Transcription Factors/genetics
3.
J Nippon Med Sch ; 91(2): 140-145, 2024.
Article En | MEDLINE | ID: mdl-38777780

Moyamoya disease (MMD) is a cerebrovascular disorder that is predominantly observed in women of East Asian descent, and is characterized by progressive stenosis of the internal carotid artery, beginning in early childhood, and a distinctive network of collateral vessels known as "moyamoya vessels" in the basal ganglia. Additionally, a prevalent genetic variant found in most MMD cases is the p.R4810K polymorphism of RNF213 on chromosome 17q25.3. Recent studies have revealed that RNF213 mutations are associated not only with MMD, but also with other systemic vascular disorders, including intracranial atherosclerosis and systemic vascular abnormalities such as pulmonary artery stenosis and coronary artery diseases. Therefore, the concept of "RNF213-related vasculopathy" has been proposed. This review focuses on polymorphisms in the RNF213 gene and describes a wide range of clinical and genetic phenotypes associated with RNF213-related vasculopathy. The RNF213 gene has been suggested to play an important role in the pathogenesis of vascular diseases and developing new therapies. Therefore, further research and knowledge sharing through collaboration between clinicians and researchers are required.


Adenosine Triphosphatases , Moyamoya Disease , Mutation , Ubiquitin-Protein Ligases , Humans , Ubiquitin-Protein Ligases/genetics , Moyamoya Disease/genetics , Adenosine Triphosphatases/genetics , Vascular Diseases/genetics , Female , Polymorphism, Genetic , Phenotype , Male
4.
Nat Commun ; 15(1): 4358, 2024 May 22.
Article En | MEDLINE | ID: mdl-38778058

3C-based methods have significantly advanced our understanding of 3D genome organization. However, it remains a formidable task to precisely capture long-range chromosomal interactions between individual loci, such as those between promoters and distal enhancers. Here, we present Methyltransferase Targeting-based chromosome Architecture Capture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome in budding yeast with high resolution and sensitivity. MTAC detects hundreds of intra- and inter-chromosomal interactions within nucleosome-depleted regions (NDRs) that cannot be captured by 4C, Hi-C, or Micro-C. By applying MTAC to various viewpoints, we find that (1) most long-distance chromosomal interactions detected by MTAC reflect tethering by the nuclear pore complexes (NPCs), (2) genes co-regulated by methionine assemble into inter-chromosomal clusters near NPCs upon activation, (3) mediated by condensin, the mating locus forms a highly specific interaction with the recombination enhancer (RE) in a mating-type specific manner, and (4) correlation of MTAC signals among NDRs reveal spatial mixing and segregation of the genome. Overall, these results demonstrate MTAC as a powerful tool to resolve fine-scale long-distance chromosomal interactions and provide insights into the 3D genome organization.


Chromosomes, Fungal , DNA Methylation , Nucleosomes , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Nucleosomes/metabolism , Nucleosomes/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Chromosomes, Fungal/genetics , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae Proteins/metabolism , Chromosome Mapping/methods , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , Genome, Fungal , Promoter Regions, Genetic/genetics , Multiprotein Complexes/metabolism , Multiprotein Complexes/genetics , Nuclear Pore/metabolism , Nuclear Pore/genetics , Methyltransferases/metabolism , Methyltransferases/genetics
5.
Adv Tech Stand Neurosurg ; 49: 1-18, 2024.
Article En | MEDLINE | ID: mdl-38700677

Although the pathogenetic pathway of moyamoya disease (MMD) remains unknown, studies have indicated that variations in the RING finger protein RNF 213 is the strongest susceptible gene of MMD. In addition to the polymorphism of this gene, many circulating angiogenetic factors such as growth factors, vascular progenitor cells, inflammatory and immune mediators, angiogenesis related cytokines, as well as circulating proteins promoting intimal hyperplasia, excessive collateral formation, smooth muscle migration and atypical migration may also play critical roles in producing this disease. Identification of these circulating molecules biomarkers may be used for the early detection of this disease. In this chapter, how the hypothesized pathophysiology of these factors affect MMD and the interactive modulation between them are summarized.


Biomarkers , Moyamoya Disease , Ubiquitin-Protein Ligases , Moyamoya Disease/genetics , Moyamoya Disease/diagnosis , Humans , Biomarkers/metabolism , Biomarkers/blood , Ubiquitin-Protein Ligases/genetics , Adenosine Triphosphatases/genetics
6.
ACS Synth Biol ; 13(5): 1572-1581, 2024 May 17.
Article En | MEDLINE | ID: mdl-38717981

Inside cells, various biological systems work cooperatively for homeostasis and self-replication. These systems do not work independently as they compete for shared elements like ATP and NADH. However, it has been believed that such competition is not a problem in codependent biological systems such as the energy-supplying glycolysis and the energy-consuming translation system. In this study, we biochemically reconstituted the coupling system of glycolysis and translation using purified elements and found that the competition for ATP between glycolysis and protein synthesis interferes with their coupling. Both experiments and simulations revealed that this interference is derived from a metabolic tug-of-war between glycolysis and translation based on their reaction rates, which changes the threshold of the initial substrate concentration for the success coupling. By the metabolic tug-of-war, translation energized by strong glycolysis is facilitated by an exogenous ATPase, which normally inhibits translation. These findings provide chemical insights into the mechanism of competition among biological systems in living cells and provide a framework for the construction of synthetic metabolism in vitro.


Adenosine Triphosphate , Glycolysis , Protein Biosynthesis , Adenosine Triphosphate/metabolism , NAD/metabolism , Escherichia coli/metabolism , Escherichia coli/genetics , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics
7.
Acta Neuropathol ; 147(1): 86, 2024 May 17.
Article En | MEDLINE | ID: mdl-38758288

Dominantly inherited mutation D395G in the gene encoding valosin-containing protein causes vacuolar tauopathy, a type of behavioural-variant frontotemporal dementia, with marked vacuolation and abundant filamentous tau inclusions made of all six brain isoforms. Here we report that tau inclusions were concentrated in layers II/III of the frontotemporal cortex in a case of vacuolar tauopathy. By electron cryomicroscopy, tau filaments had the chronic traumatic encephalopathy (CTE) fold. Tau inclusions of vacuolar tauopathy share this cortical location and the tau fold with CTE, subacute sclerosing panencephalitis and amyotrophic lateral sclerosis/parkinsonism-dementia complex, which are believed to be environmentally induced. Vacuolar tauopathy is the first inherited disease with the CTE tau fold.


Chronic Traumatic Encephalopathy , Mutation , Tauopathies , Valosin Containing Protein , tau Proteins , Humans , Tauopathies/genetics , Tauopathies/pathology , Chronic Traumatic Encephalopathy/pathology , Chronic Traumatic Encephalopathy/genetics , tau Proteins/genetics , tau Proteins/metabolism , Valosin Containing Protein/genetics , Vacuoles/pathology , Vacuoles/ultrastructure , Male , Adenosine Triphosphatases/genetics , Cell Cycle Proteins/genetics , Middle Aged , Frontotemporal Dementia/genetics , Frontotemporal Dementia/pathology , Brain/pathology , Female
8.
Mol Cell ; 84(10): 1821-1823, 2024 May 16.
Article En | MEDLINE | ID: mdl-38759622

In this issue, Ji et al.1 show how a multipass membrane protein that initially inserts into the endoplasmic reticulum in a mostly inverted topology is post-translationally dislocated, re-inserted, and folded with the help of ATP13A1, a P-type ATPase.


Endoplasmic Reticulum , Membrane Proteins , Membrane Proteins/metabolism , Membrane Proteins/genetics , Membrane Proteins/chemistry , Endoplasmic Reticulum/metabolism , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , Protein Folding , Humans
9.
J Exp Clin Cancer Res ; 43(1): 139, 2024 May 09.
Article En | MEDLINE | ID: mdl-38725030

BACKGROUND: LncRNAs regulate tumorigenesis and development in a variety of cancers. We substantiate for the first time that LINC00606 is considerably expressed in glioblastoma (GBM) patient specimens and is linked with adverse prognosis. This suggests that LINC00606 may have the potential to regulate glioma genesis and progression, and that the biological functions and molecular mechanisms of LINC00606 in GBM remain largely unknown. METHODS: The expression of LINC00606 and ATP11B in glioma and normal brain tissues was evaluated by qPCR, and the biological functions of the LINC00606/miR-486-3p/TCF12/ATP11B axis in GBM were verified through a series of in vitro and in vivo experiments. The molecular mechanism of LINC00606 was elucidated by immunoblotting, FISH, RNA pulldown, CHIP-qPCR, and a dual-luciferase reporter assay. RESULTS: We demonstrated that LINC00606 promotes glioma cell proliferation, clonal expansion and migration, while reducing apoptosis levels. Mechanistically, on the one hand, LINC00606 can sponge miR-486-3p; the target gene TCF12 of miR-486-3p affects the transcriptional initiation of LINC00606, PTEN and KLLN. On the other hand, it can also regulate the PI3K/AKT signaling pathway to mediate glioma cell proliferation, migration and apoptosis by binding to ATP11B protein. CONCLUSIONS: Overall, the LINC00606/miR-486-3p/TCF12/ATP11B axis is involved in the regulation of GBM progression and plays a role in tumor regulation at transcriptional and post-transcriptional levels primarily through LINC00606 sponging miR-486-3p and targeted binding to ATP11B. Therefore, our research on the regulatory network LINC00606 could be a novel therapeutic strategy for the treatment of GBM.


Glioblastoma , MicroRNAs , RNA, Long Noncoding , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , Glioblastoma/genetics , Glioblastoma/metabolism , Glioblastoma/pathology , RNA, Long Noncoding/genetics , RNA, Long Noncoding/metabolism , Animals , Mice , Disease Progression , Cell Line, Tumor , Cell Proliferation , Brain Neoplasms/genetics , Brain Neoplasms/metabolism , Brain Neoplasms/pathology , Male , Female , Gene Expression Regulation, Neoplastic , Cell Movement , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , Mice, Nude , Apoptosis
10.
BMC Biol ; 22(1): 105, 2024 May 03.
Article En | MEDLINE | ID: mdl-38702628

BACKGROUND: Histone H3K4 tri-methylation (H3K4me3) catalyzed by Set1/COMPASS, is a prominent epigenetic mark found in promoter-proximal regions of actively transcribed genes. H3K4me3 relies on prior monoubiquitination at the histone H2B (H2Bub) by Rad6 and Bre1. Swd2/Cps35, a Set1/COMPASS component, has been proposed as a key player in facilitating H2Bub-dependent H3K4me3. However, a more comprehensive investigation regarding the relationship among Rad6, Swd2, and Set1 is required to further understand the mechanisms and functions of the H3K4 methylation. RESULTS: We investigated the genome-wide occupancy patterns of Rad6, Swd2, and Set1 under various genetic conditions, aiming to clarify the roles of Set1 and Rad6 for occupancy of Swd2. Swd2 peaks appear on both the 5' region and 3' region of genes, which are overlapped with its tightly bound two complexes, Set1 and cleavage and polyadenylation factor (CPF), respectively. In the absence of Rad6/H2Bub, Set1 predominantly localized to the 5' region of genes, while Swd2 lost all the chromatin binding. However, in the absence of Set1, Swd2 occupancy near the 5' region was impaired and rather increased in the 3' region. CONCLUSIONS: This study highlights that the catalytic activity of Rad6 is essential for all the ways of Swd2's binding to the transcribed genes and Set1 redistributes the Swd2 to the 5' region for accomplishments of H3K4me3 in the genome-wide level.


Histone-Lysine N-Methyltransferase , Histones , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Histones/metabolism , Histones/genetics , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/metabolism , Histone-Lysine N-Methyltransferase/metabolism , Histone-Lysine N-Methyltransferase/genetics , Methylation , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , Ubiquitin-Conjugating Enzymes/metabolism , Ubiquitin-Conjugating Enzymes/genetics
11.
Commun Biol ; 7(1): 533, 2024 May 06.
Article En | MEDLINE | ID: mdl-38710747

Insect wing development is a fascinating and intricate process that involves the regulation of wing size through cell proliferation and apoptosis. In this study, we find that Ter94, an AAA-ATPase, is essential for proper wing size dependently on its ATPase activity. Loss of Ter94 enables the suppression of Hippo target genes. When Ter94 is depleted, it results in reduced wing size and increased apoptosis, which can be rescued by inhibiting the Hippo pathway. Biochemical experiments reveal that Ter94 reciprocally binds to Mer, a critical upstream component of the Hippo pathway, and disrupts its interaction with Ex and Kib. This disruption prevents the formation of the Ex-Mer-Kib complex, ultimately leading to the inactivation of the Hippo pathway and promoting proper wing development. Finally, we show that hVCP, the human homolog of Ter94, is able to substitute for Ter94 in modulating Drosophila wing size, underscoring their functional conservation. In conclusion, Ter94 plays a positive role in regulating wing size by interfering with the Ex-Mer-Kib complex, which results in the suppression of the Hippo pathway.


Drosophila Proteins , Drosophila melanogaster , Membrane Proteins , Protein Serine-Threonine Kinases , Signal Transduction , Tumor Suppressor Proteins , Wings, Animal , Animals , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , Apoptosis , Drosophila/genetics , Drosophila/growth & development , Drosophila/metabolism , Drosophila melanogaster/genetics , Drosophila melanogaster/growth & development , Drosophila melanogaster/metabolism , Drosophila Proteins/metabolism , Drosophila Proteins/genetics , Gene Expression Regulation, Developmental , Intracellular Signaling Peptides and Proteins/metabolism , Intracellular Signaling Peptides and Proteins/genetics , Neurofibromin 2/metabolism , Neurofibromin 2/genetics , Protein Serine-Threonine Kinases/metabolism , Protein Serine-Threonine Kinases/genetics , Wings, Animal/growth & development , Wings, Animal/metabolism
12.
J Med Chem ; 67(10): 8186-8200, 2024 May 23.
Article En | MEDLINE | ID: mdl-38733345

The ATPase family AAA+ domain containing 2 (ATAD2) protein and its paralog ATAD2B have a C-terminal bromodomain (BRD) that functions as a reader of acetylated lysine residues on histone proteins. Using a structure-function approach, we investigated the ability of the ATAD2/B BRDs to select acetylated lysine among multiple histone post-translational modifications. The ATAD2B BRD can bind acetylated histone ligands that also contain adjacent methylation or phosphorylation marks, while the presence of these modifications significantly weakened the acetyllysine binding activity of the ATAD2 BRD. Our structural studies provide mechanistic insights into how ATAD2/B BRD-binding pocket residues coordinate the acetyllysine group in the context of adjacent post-translational modifications. Furthermore, we investigated how sequence changes in amino acids of the histone ligands impact the recognition of an adjacent acetyllysine residue. Our study highlights how the interplay between multiple combinations of histone modifications influences the reader activity of the ATAD2/B BRDs, resulting in distinct binding modes.


ATPases Associated with Diverse Cellular Activities , DNA-Binding Proteins , Histones , Lysine , Histones/metabolism , Histones/chemistry , ATPases Associated with Diverse Cellular Activities/metabolism , ATPases Associated with Diverse Cellular Activities/chemistry , Humans , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/chemistry , Lysine/metabolism , Lysine/chemistry , Acetylation , Protein Processing, Post-Translational , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/chemistry , Protein Binding , Protein Domains , Models, Molecular , Binding Sites
13.
Stroke ; 55(6): 1699-1706, 2024 Jun.
Article En | MEDLINE | ID: mdl-38690664

Systemic vasculopathy has occasionally been reported in cases of moyamoya disease (MMD). Since the pathological relationship between moyamoya vasculopathy (MMV) and moyamoya-related systemic vasculopathy (MMRSV) remains unclear, it was examined herein by a review of histopathologic studies in consideration of clinicopathological and genetic viewpoints. Although luminal stenosis was a common finding in MMV and MMRSV, histopathologic findings of vascular remodeling markedly differed. MMV showed intimal hyperplasia, marked medial atrophy, and redundant tortuosity of the internal elastic lamina, with outer diameter narrowing called negative remodeling. MMRSV showed hyperplasia, mainly in the intima and sometimes in the media, with disrupted stratification of the internal elastic lamina. Systemic vasculopathy has also been observed in patients with non-MMD carrying the RNF213 (ring finger protein 213) mutation, leading to the concept of RNF213 vasculopathy. RNF213 vasculopathy in patients with non-MMD was histopathologically similar to MMRSV. Cases of MMRSV have sometimes been diagnosed with fibromuscular dysplasia. Fibromuscular dysplasia is similar to MMD not only in the histopathologic findings of MMRSV but also from clinicopathological and genetic viewpoints. The significant histopathologic difference between MMV and MMRSV may be attributed to a difference in the original vascular wall structure and its resistance to pathological stress between the intracranial and systemic arteries. To understand the pathogeneses of MMD and MMRSV, a broader perspective that includes RNF213 vasculopathy and fibromuscular dysplasia as well as an examination of the 2- or multiple-hit theory consisting of genetic factors, vascular structural conditions, and vascular environmental factors, such as blood immune cells and hemodynamics, are needed.


Moyamoya Disease , Ubiquitin-Protein Ligases , Moyamoya Disease/genetics , Moyamoya Disease/pathology , Humans , Ubiquitin-Protein Ligases/genetics , Adenosine Triphosphatases/genetics , Mutation , Fibromuscular Dysplasia/genetics , Fibromuscular Dysplasia/pathology , Fibromuscular Dysplasia/complications
14.
Sci Adv ; 10(18): eadl6082, 2024 May 03.
Article En | MEDLINE | ID: mdl-38701207

The AAA+-ATPase valosin-containing protein (VCP; also called p97 or Cdc48), a major protein unfolding machinery with a variety of essential functions, localizes to different subcellular compartments where it has different functions. However, the processes regulating the distribution of VCP between the cytosol and nucleus are not understood. Here, we identified p37 (also called UBXN2B) as a major factor regulating VCP nucleocytoplasmic shuttling. p37-dependent VCP localization was crucial for local cytosolic VCP functions, such as autophagy, and nuclear functions in DNA damage repair. Mutations in VCP causing multisystem proteinopathy enhanced its association with p37, leading to decreased nuclear localization of VCP, which enhanced susceptibility to DNA damage accumulation. Both VCP localization and DNA damage susceptibility in cells with such mutations were normalized by lowering p37 levels. Thus, we uncovered a mechanism by which VCP nucleocytoplasmic distribution is fine-tuned, providing a means for VCP to respond appropriately to local needs.


Adaptor Proteins, Signal Transducing , Cell Nucleus , Cytosol , Valosin Containing Protein , Valosin Containing Protein/metabolism , Valosin Containing Protein/genetics , Humans , Cytosol/metabolism , Cell Nucleus/metabolism , Mutation , Active Transport, Cell Nucleus , DNA Damage , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , Cell Cycle Proteins/metabolism , Cell Cycle Proteins/genetics , Protein Transport , Nuclear Proteins/metabolism , Nuclear Proteins/genetics , DNA Repair , Autophagy , Protein Binding , HEK293 Cells
15.
EMBO Rep ; 25(5): 2239-2257, 2024 May.
Article En | MEDLINE | ID: mdl-38632376

The PIWI-interacting RNA (piRNA) pathway plays a crucial role in silencing transposons in the germline. piRNA-guided target cleavage by PIWI proteins triggers the biogenesis of new piRNAs from the cleaved RNA fragments. This process, known as the ping-pong cycle, is mediated by the two PIWI proteins, Siwi and BmAgo3, in silkworms. However, the detailed molecular mechanism of the ping-pong cycle remains largely unclear. Here, we show that Spindle-E (Spn-E), a putative ATP-dependent RNA helicase, is essential for BmAgo3-dependent production of Siwi-bound piRNAs in the ping-pong cycle and that this function of Spn-E requires its ATPase activity. Moreover, Spn-E acts to suppress homotypic Siwi-Siwi ping-pong, but this function of Spn-E is independent of its ATPase activity. These results highlight the dual role of Spn-E in facilitating proper heterotypic ping-pong in silkworms.


Bombyx , RNA, Small Interfering , Bombyx/genetics , Bombyx/metabolism , Animals , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , Insect Proteins/genetics , Insect Proteins/metabolism , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , RNA Helicases/metabolism , RNA Helicases/genetics , Argonaute Proteins/metabolism , Argonaute Proteins/genetics , Piwi-Interacting RNA
16.
Proc Natl Acad Sci U S A ; 121(18): e2319205121, 2024 Apr 30.
Article En | MEDLINE | ID: mdl-38652748

The ParABS system is crucial for the faithful segregation and inheritance of many bacterial chromosomes and low-copy-number plasmids. However, despite extensive research, the spatiotemporal dynamics of the ATPase ParA and its connection to the dynamics and positioning of the ParB-coated cargo have remained unclear. In this study, we utilize high-throughput imaging, quantitative data analysis, and computational modeling to explore the in vivo dynamics of ParA and its interaction with ParB-coated plasmids and the nucleoid. As previously observed, we find that F-plasmid ParA undergoes collective migrations ("flips") between cell halves multiple times per cell cycle. We reveal that a constricting nucleoid is required for these migrations and that they are triggered by a plasmid crossing into the cell half with greater ParA. Using simulations, we show that these dynamics can be explained by the combination of nucleoid constriction and cooperative ParA binding to the DNA, in line with the behavior of other ParA proteins. We further show that these ParA flips act to equally partition plasmids between the two lobes of the constricted nucleoid and are therefore important for plasmid stability, especially in fast growth conditions for which the nucleoid constricts early in the cell cycle. Overall, our work identifies a second mode of action of the ParABS system and deepens our understanding of how this important segregation system functions.


Escherichia coli , Plasmids , Plasmids/metabolism , Plasmids/genetics , Escherichia coli/genetics , Escherichia coli/metabolism , Escherichia coli Proteins/metabolism , Escherichia coli Proteins/genetics , Chromosomes, Bacterial/metabolism , Chromosomes, Bacterial/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , Chromosome Segregation , DNA Primase/metabolism , DNA Primase/genetics , DNA, Bacterial/genetics , DNA, Bacterial/metabolism
17.
Expert Opin Ther Pat ; 34(3): 159-169, 2024 Mar.
Article En | MEDLINE | ID: mdl-38578210

INTRODUCTION: The multi-subunit SWI/SNF chromatin remodeling complex is a key epigenetic regulator for many cellular processes, and several subunits are found to be mutated in human cancers. The inactivating mutations of SMARCA4, the ATPase subunit of the complex, result in cellular dependency on the paralog SMARCA2 for survival. This observed synthetic lethal relationship posits targeting SMARCA2 in SMARCA4-deficient settings as an attractive therapeutic target in oncology. AREAS COVERED: This review covers patent literature disclosed during the 2019-30 June 2023 period which claim ATPase inhibitors and PROTAC degraders that bind to the ATPase domain of SMARCA2 and/or SMARCA4. A total of 16 documents from 6 applicants are presented. EXPERT OPINION: The demonstration of cellular dependence on SMARCA2 ATPase activity in SMARCA4-deficient settings has prompted substantial research toward SMARCA2-targeting therapies. Although selectively targeting the ATPase domain of SMARCA2 is viewed as challenging, several ATPase inhibitor scaffolds have been disclosed within the last five years. Most early compounds are weakly selective, but these efforts have culminated in the first dual SMARCA2/SMARCA4 ATPase inhibitor to enter clinical trials. Data from the ongoing clinical trials, as well as continued advancement of SMARCA2-selective ATPase inhibitors, are anticipated to significantly impact the field of therapies, targeting SMARCA4-deficient tumors.


Antineoplastic Agents , DNA Helicases , Molecular Targeted Therapy , Neoplasms , Nuclear Proteins , Patents as Topic , Transcription Factors , Humans , Transcription Factors/metabolism , Transcription Factors/antagonists & inhibitors , Transcription Factors/genetics , Neoplasms/drug therapy , Neoplasms/pathology , Neoplasms/genetics , Nuclear Proteins/metabolism , Nuclear Proteins/antagonists & inhibitors , Nuclear Proteins/genetics , Antineoplastic Agents/pharmacology , DNA Helicases/metabolism , DNA Helicases/antagonists & inhibitors , DNA Helicases/genetics , Animals , Synthetic Lethal Mutations , Mutation , Adenosine Triphosphatases/metabolism
18.
Appl Environ Microbiol ; 90(5): e0041824, 2024 May 21.
Article En | MEDLINE | ID: mdl-38624198

Cyclic di-GMP (c-di-GMP) is a crucial signaling molecule found extensively in bacteria, involved in the regulation of various physiological and biochemical processes such as biofilm formation, motility, and pathogenicity through binding to downstream receptors. However, the structural dissimilarity of c-di-GMP receptor proteins has hindered the discovery of many such proteins. In this study, we identified LspE, a homologous protein of the type II secretion system (T2SS) ATPase GspE in Lysobacter enzymogenes, as a receptor protein for c-di-GMP. We identified the more conservative c-di-GMP binding amino acid residues as K358 and T359, which differ from the previous reports, indicating that GspE proteins may represent a class of c-di-GMP receptor proteins. Additionally, we found that LspE in L. enzymogenes also possesses a novel role in regulating the production of the antifungal antibiotic HSAF. Further investigations revealed the critical involvement of both ATPase activity and c-di-GMP binding in LspE-mediated regulation of HSAF (Heat-Stable Antifungal Factor) production, with c-di-GMP binding having no impact on LspE's ATPase activity. This suggests that the control of HSAF production by LspE encompasses two distinct processes: c-di-GMP binding and the inherent ATPase activity of LspE. Overall, our study unraveled a new function for the conventional protein GspE of the T2SS as a c-di-GMP receptor protein and shed light on its role in regulating antibiotic production.IMPORTANCEThe c-di-GMP signaling pathway in bacteria is highly intricate. The identification and functional characterization of novel receptor proteins have posed a significant challenge in c-di-GMP research. The type II secretion system (T2SS) is a well-studied secretion system in bacteria. In this study, our findings revealed the ATPase GspE protein of the T2SS as a class of c-di-GMP receptor protein. Notably, we discovered its novel function in regulating the production of antifungal antibiotic HSAF in Lysobacter enzymogenes. Given that GspE may be a conserved c-di-GMP receptor protein, it is worthwhile for researchers to reevaluate its functional roles and mechanisms across diverse bacterial species.


Adenosine Triphosphatases , Bacterial Proteins , Cyclic GMP , Lysobacter , Cyclic GMP/analogs & derivatives , Cyclic GMP/metabolism , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , Lysobacter/metabolism , Lysobacter/genetics , Lysobacter/enzymology , Type II Secretion Systems/metabolism , Type II Secretion Systems/genetics , Anti-Bacterial Agents/metabolism , Gene Expression Regulation, Bacterial , Antifungal Agents/metabolism
19.
Asian Pac J Cancer Prev ; 25(4): 1411-1417, 2024 Apr 01.
Article En | MEDLINE | ID: mdl-38680002

BACKGROUND: Hepatocellular carcinoma (HCC) is the fourth most prevalent type of cancer in Egypt and the sixth globally. Most patients with HCC are typically diagnosed during the advanced stages of the disease due to the absence of biomarkers for early detection. Consequently, these patients miss the optimal timeframe for receiving therapy. OBJECTIVE: we aimed to assess the circular RNA SMARCA5 level and SMARCA5 mRNA gene expression as a potential biomarker for early detection of HCC. METHODS: The present study utilized a case-control design comprising 159 participants. Participants were selected from both inpatient and outpatient hepatology and gastroenterology clinics at the National Liver Institute Hospital, Menoufia University. They were evenly distributed among three groups: Group I: 53 control subjects, Group II: 53 HCV cirrhotic patients, and Group III: 53 HCC patients. Tumor staging was done using BCLC staging system. Each patient underwent a thorough clinical examination, radiological examination, complete history taking, and serum Alpha-fetoprotein (AFP) assessment and detection of circular RNASMARCA5 and SMARCA5mRNA gene sutilizing quantitative real-time polymerase chain reaction. RESULTS: Statistically substantial differences were observed in the examined groups in terms of AFP, SMARCA5, and CircSMARCA5 (P-value = 0.001, 0.001 & 0.001). CircSMARCA5 and SMARCA5mRNA were markedly down regulated in the HCC group compared to HCV cirrhotic patients and controls. ROC analysis for early HCC diagnosis demonstrated that the CircSMARCA5 area under the curve (AUC) at cut-off point 4.55 yielded a specificity of 83.8% and sensitivity of 91.7%. The AUC for AFP at a cut-off point of 515ng/ml yielded a specificity of 89.2% and a sensitivity of 91.3%. CONCLUSION: CircSMARCA5 has the potential to be a more sensitive predictor of HCC disease compared to AFP.


Biomarkers, Tumor , Carcinoma, Hepatocellular , Liver Neoplasms , RNA, Circular , Female , Humans , Male , Middle Aged , Adenosine Triphosphatases , alpha-Fetoproteins/metabolism , alpha-Fetoproteins/analysis , Biomarkers, Tumor/genetics , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/diagnosis , Carcinoma, Hepatocellular/virology , Carcinoma, Hepatocellular/pathology , Case-Control Studies , Chromosomal Proteins, Non-Histone/genetics , Egypt , Follow-Up Studies , Liver Neoplasms/genetics , Liver Neoplasms/pathology , Liver Neoplasms/diagnosis , Prognosis , RNA, Circular/genetics , RNA, Messenger/genetics , ROC Curve
20.
mBio ; 15(5): e0285023, 2024 May 08.
Article En | MEDLINE | ID: mdl-38564676

Condensin I is a pentameric complex that regulates the mitotic chromosome assembly in eukaryotes. The kleisin subunit CAP-H of the condensin I complex acts as a linchpin to maintain the structural integrity and loading of this complex on mitotic chromosomes. This complex is present in all eukaryotes and has recently been identified in Plasmodium spp. However, how this complex is assembled and whether the kleisin subunit is critical for this complex in these parasites are yet to be explored. To examine the role of PfCAP-H during cell division within erythrocytes, we generated an inducible PfCAP-H knockout parasite. We find that PfCAP-H is dynamically expressed during mitosis with the peak expression at the metaphase plate. PfCAP-H interacts with PfCAP-G and is a non-SMC member of the condensin I complex. Notably, the absence of PfCAP-H does not alter the expression of PfCAP-G but affects its localization at the mitotic chromosomes. While mitotic spindle assembly is intact in PfCAP-H-deficient parasites, duplicated centrosomes remain clustered over the mass of unsegmented nuclei with failed karyokinesis. This failure leads to the formation of an abnormal nuclear mass, while cytokinesis occurs normally. Altogether, our data suggest that PfCAP-H plays a crucial role in maintaining the structural integrity of the condensin I complex on the mitotic chromosomes and is essential for the asexual development of malarial parasites. IMPORTANCE: Mitosis is a fundamental process for Plasmodium parasites, which plays a vital role in their survival within two distinct hosts-human and Anopheles mosquitoes. Despite its great significance, our comprehension of mitosis and its regulation remains limited. In eukaryotes, mitosis is regulated by one of the pivotal complexes known as condensin complexes. The condensin complexes are responsible for chromosome condensation, ensuring the faithful distribution of genetic material to daughter cells. While condensin complexes have recently been identified in Plasmodium spp., our understanding of how this complex is assembled and its precise functions during the blood stage development of Plasmodium falciparum remains largely unexplored. In this study, we investigate the role of a central protein, PfCAP-H, during the blood stage development of P. falciparum. Our findings reveal that PfCAP-H is essential and plays a pivotal role in upholding the structure of condensin I and facilitating karyokinesis.


Adenosine Triphosphatases , DNA-Binding Proteins , Mitosis , Multiprotein Complexes , Plasmodium falciparum , Protozoan Proteins , Multiprotein Complexes/metabolism , Multiprotein Complexes/genetics , Plasmodium falciparum/genetics , Plasmodium falciparum/metabolism , Plasmodium falciparum/physiology , Plasmodium falciparum/growth & development , Adenosine Triphosphatases/metabolism , Adenosine Triphosphatases/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Protozoan Proteins/metabolism , Protozoan Proteins/genetics , Erythrocytes/parasitology , Gene Knockout Techniques , Humans
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