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1.
Nat Commun ; 15(1): 6641, 2024 Aug 05.
Article in English | MEDLINE | ID: mdl-39103378

ABSTRACT

DNA-protein crosslinks (DPCs) are toxic lesions that inhibit DNA related processes. Post-translational modifications (PTMs), including SUMOylation and ubiquitylation, play a central role in DPC resolution, but whether other PTMs are also involved remains elusive. Here, we identify a DPC repair pathway orchestrated by poly-ADP-ribosylation (PARylation). Using Xenopus egg extracts, we show that DPCs on single-stranded DNA gaps can be targeted for degradation via a replication-independent mechanism. During this process, DPCs are initially PARylated by PARP1 and subsequently ubiquitylated and degraded by the proteasome. Notably, PARP1-mediated DPC resolution is required for resolving topoisomerase 1-DNA cleavage complexes (TOP1ccs) induced by camptothecin. Using the Flp-nick system, we further reveal that in the absence of PARP1 activity, the TOP1cc-like lesion persists and induces replisome disassembly when encountered by a DNA replication fork. In summary, our work uncovers a PARP1-mediated DPC repair pathway that may underlie the synergistic toxicity between TOP1 poisons and PARP inhibitors.


Subject(s)
DNA Repair , DNA Replication , DNA Topoisomerases, Type I , Poly (ADP-Ribose) Polymerase-1 , Poly ADP Ribosylation , Animals , Poly (ADP-Ribose) Polymerase-1/metabolism , Poly (ADP-Ribose) Polymerase-1/genetics , DNA Topoisomerases, Type I/metabolism , Xenopus laevis , Ubiquitination , Humans , DNA/metabolism , DNA Damage , Camptothecin/pharmacology , Protein Processing, Post-Translational , DNA, Single-Stranded/metabolism , Xenopus Proteins/metabolism
2.
Mol Cell ; 84(16): 3026-3043.e11, 2024 Aug 22.
Article in English | MEDLINE | ID: mdl-39178838

ABSTRACT

Abasic sites are DNA lesions repaired by base excision repair. Cleavage of unrepaired abasic sites in single-stranded DNA (ssDNA) can lead to chromosomal breakage during DNA replication. How rupture of abasic DNA is prevented remains poorly understood. Here, using cryoelectron microscopy (cryo-EM), Xenopus laevis egg extracts, and human cells, we show that RAD51 nucleofilaments specifically recognize and protect abasic sites, which increase RAD51 association rate to DNA. In the absence of BRCA2 or RAD51, abasic sites accumulate as a result of DNA base methylation, oxidation, and deamination, inducing abasic ssDNA gaps that make replicating DNA fibers sensitive to APE1. RAD51 assembled on abasic DNA prevents abasic site cleavage by the MRE11-RAD50 complex, suppressing replication fork breakage triggered by an excess of abasic sites or POLθ polymerase inhibition. Our study highlights the critical role of BRCA2 and RAD51 in safeguarding against unrepaired abasic sites in DNA templates stemming from base alterations, ensuring genomic stability.


Subject(s)
BRCA2 Protein , DNA Damage , DNA Repair , DNA Replication , DNA, Single-Stranded , Rad51 Recombinase , Xenopus laevis , Humans , Rad51 Recombinase/metabolism , Rad51 Recombinase/genetics , BRCA2 Protein/genetics , BRCA2 Protein/metabolism , Animals , DNA, Single-Stranded/metabolism , DNA, Single-Stranded/genetics , Cryoelectron Microscopy , DNA Polymerase theta , DNA Methylation , DNA-Directed DNA Polymerase/metabolism , DNA-Directed DNA Polymerase/genetics , MRE11 Homologue Protein/metabolism , MRE11 Homologue Protein/genetics , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics
3.
Biol Open ; 13(8)2024 Aug 15.
Article in English | MEDLINE | ID: mdl-39162010

ABSTRACT

Collectively migrating Xenopus mesendoderm cells are arranged into leader and follower rows with distinct adhesive properties and protrusive behaviors. In vivo, leading row mesendoderm cells extend polarized protrusions and migrate along a fibronectin matrix assembled by blastocoel roof cells. Traction stresses generated at the leading row result in the pulling forward of attached follower row cells. Mesendoderm explants removed from embryos provide an experimentally tractable system for characterizing collective cell movements and behaviors, yet the cellular mechanisms responsible for this mode of migration remain elusive. We introduce a novel agent-based computational model of migrating mesendoderm in the Cellular-Potts computational framework to investigate the respective contributions of multiple parameters specific to the behaviors of leader and follower row cells. Sensitivity analyses identify cohesotaxis, tissue geometry, and cell intercalation as key parameters affecting the migration velocity of collectively migrating cells. The model predicts that cohesotaxis and tissue geometry in combination promote cooperative migration of leader cells resulting in increased migration velocity of the collective. Radial intercalation of cells towards the substrate is an additional mechanism contributing to an increase in migratory speed of the tissue. Model outcomes are validated experimentally using mesendoderm tissue explants.


Subject(s)
Cell Movement , Models, Biological , Xenopus , Animals , Xenopus/embryology , Mesoderm/cytology , Mesoderm/embryology , Cell Adhesion , Xenopus laevis/embryology , Computer Simulation
4.
FASEB J ; 38(16): e23883, 2024 Aug 31.
Article in English | MEDLINE | ID: mdl-39150825

ABSTRACT

Mutations in SCN4A gene encoding Nav1.4 channel α-subunit, are known to cause neuromuscular disorders such as myotonia or paralysis. Here, we study the effect of two amino acid replacements, K1302Q and G1306E, in the DIII-IV loop of the channel, corresponding to mutations found in patients with myotonia. We combine clinical, electrophysiological, and molecular modeling data to provide a holistic picture of the molecular mechanisms operating in mutant channels and eventually leading to pathology. We analyze the existing clinical data for patients with the K1302Q substitution, which was reported for adults with or without myotonia phenotypes, and report two new unrelated patients with the G1306E substitution, who presented with severe neonatal episodic laryngospasm and childhood-onset myotonia. We provide a functional analysis of the mutant channels by expressing Nav1.4 α-subunit in Xenopus oocytes in combination with ß1 subunit and recording sodium currents using two-electrode voltage clamp. The K1302Q variant exhibits abnormal voltage dependence of steady-state fast inactivation, being the likely cause of pathology. K1302Q does not lead to decelerated fast inactivation, unlike several other myotonic mutations such as G1306E. For both mutants, we observe increased window currents corresponding to a larger population of channels available for activation. To elaborate the structural rationale for our experimental data, we explore the contacts involving K/Q1302 and E1306 in the AlphaFold2 model of wild-type Nav1.4 and Monte Carlo-minimized models of mutant channels. Our data provide the missing evidence to support the classification of K1302Q variant as likely pathogenic and may be used by clinicians.


Subject(s)
Myotonia , NAV1.4 Voltage-Gated Sodium Channel , NAV1.4 Voltage-Gated Sodium Channel/genetics , NAV1.4 Voltage-Gated Sodium Channel/metabolism , Humans , Animals , Myotonia/genetics , Female , Xenopus laevis , Male , Mutation , Oocytes/metabolism , Adult , Amino Acid Substitution
5.
Commun Biol ; 7(1): 939, 2024 Aug 03.
Article in English | MEDLINE | ID: mdl-39097635

ABSTRACT

Monoterpenoid indole alkaloid (MIA) biosynthesis in Catharanthus roseus is a paragon of the spatiotemporal complexity achievable by plant specialized metabolism. Spanning a range of tissues, four cell types, and five cellular organelles, MIA metabolism is intricately regulated and organized. This high degree of metabolic differentiation requires inter-cellular and organellar transport, which remains understudied. Here, we have characterized a vacuolar importer of secologanin belonging to the multidrug and toxic compound extrusion (MATE) family, named CrMATE1. Phylogenetic analyses of MATEs suggested a role in alkaloid transport for CrMATE1, and in planta silencing in two varieties of C. roseus resulted in a shift in the secoiridoid and MIA profiles. Subcellular localization of CrMATE1 confirmed tonoplast localization. Biochemical characterization was conducted using the Xenopus laevis oocyte expression system to determine substrate range, directionality, and rate. We can confirm that CrMATE1 is a vacuolar importer of secologanin, translocating 1 mM of substrate within 25 min. The transporter displayed strict directionality and specificity for secologanin and did not accept other secoiridoid substrates. The unique substrate-specific activity of CrMATE1 showcases the utility of transporters as gatekeepers of pathway flux, mediating the balance between a defense arsenal and cellular homeostasis.


Subject(s)
Catharanthus , Plant Proteins , Secologanin Tryptamine Alkaloids , Vacuoles , Catharanthus/metabolism , Catharanthus/genetics , Plant Proteins/metabolism , Plant Proteins/genetics , Vacuoles/metabolism , Secologanin Tryptamine Alkaloids/metabolism , Animals , Phylogeny , Xenopus laevis/metabolism , Biological Transport , Oocytes/metabolism , Iridoid Glucosides
6.
Nat Commun ; 15(1): 6517, 2024 Aug 07.
Article in English | MEDLINE | ID: mdl-39112456

ABSTRACT

In response to DNA double-strand breaks or oxidative stress, ATM-dependent DNA damage response (DDR) is activated to maintain genome integrity. However, it remains elusive whether and how DNA single-strand breaks (SSBs) activate ATM. Here, we provide direct evidence in Xenopus egg extracts that ATM-mediated DDR is activated by a defined SSB structure. Our mechanistic studies reveal that APE1 promotes the SSB-induced ATM DDR through APE1 exonuclease activity and ATM recruitment to SSB sites. APE1 protein can form oligomers to activate the ATM DDR in Xenopus egg extracts in the absence of DNA and can directly stimulate ATM kinase activity in vitro. Our findings reveal distinct mechanisms of the ATM-dependent DDR activation by SSBs in eukaryotic systems and identify APE1 as a direct activator of ATM kinase.


Subject(s)
Ataxia Telangiectasia Mutated Proteins , DNA Breaks, Single-Stranded , DNA-(Apurinic or Apyrimidinic Site) Lyase , Signal Transduction , Ataxia Telangiectasia Mutated Proteins/metabolism , Ataxia Telangiectasia Mutated Proteins/genetics , Animals , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics , Xenopus Proteins/metabolism , Xenopus Proteins/genetics , Humans , Xenopus laevis , DNA Repair
7.
Nat Commun ; 15(1): 6659, 2024 Aug 22.
Article in English | MEDLINE | ID: mdl-39174502

ABSTRACT

Regeneration in many animals involves the formation of a blastema, which differentiates and organizes into the appropriate missing body parts. Although the mechanisms underlying blastema formation are often fundamental to regeneration biology, information on the cellular and molecular basis of blastema formation remains limited. Here, we focus on a fragmenting potworm (Enchytraeus japonensis), which can regenerate its whole body from small fragments. We find soxC and mmpReg as upregulated genes in the blastema. RNAi of soxC and mmpReg reduce the number of blastema cells, indicating that soxC and mmpReg promote blastema formation. Expression analyses show that soxC-expressing cells appear to gradually accumulate in blastema and constitute a large part of the blastema. Additionally, similar expression dynamics of SoxC orthologue genes in frog (Xenopus laevis) are found in the regeneration blastema of tadpole tail. Our findings provide insights into the cellular and molecular mechanisms underlying blastema formation across species.


Subject(s)
Regeneration , SOXC Transcription Factors , Animals , Regeneration/genetics , SOXC Transcription Factors/genetics , SOXC Transcription Factors/metabolism , Oligochaeta/genetics , Oligochaeta/physiology , Larva/genetics , RNA Interference , Xenopus laevis
8.
Mol Brain ; 17(1): 58, 2024 Aug 22.
Article in English | MEDLINE | ID: mdl-39175067

ABSTRACT

Protocadherin 19 (Pcdh19) is a homophilic cell adhesion molecule and is involved in a variety of neuronal functions. Here, we tested whether Pcdh19 has a regulatory role in axon guidance using the developing Xenopus retinotectal system. We performed targeted microinjections of a translation blocking antisense morpholino oligonucleotide to knock down the expression of Pcdh19 selectively in the central nervous system. Knocking down Pcdh19 expression resulted in navigational errors of retinal ganglion cell (RGC) axons specifically at the optic chiasm. Instead of projecting to the contralateral optic tectum, RGC axons in the Pcdh19-depleted embryo misprojected ipsilaterally. Although incorrectly delivered into the ipsilateral brain hemisphere, these axons correctly reached the optic tectum. These data suggest that Pcdh19 has a critical role in preventing mixing of RGC axons originating from the opposite eyes at the optic chiasm, highlighting the importance of cell adhesion in bundling of RGC axons.


Subject(s)
Axon Guidance , Axons , Cadherins , Protocadherins , Retinal Ganglion Cells , Xenopus Proteins , Xenopus laevis , Animals , Cadherins/metabolism , Xenopus Proteins/metabolism , Xenopus Proteins/genetics , Retinal Ganglion Cells/metabolism , Xenopus laevis/embryology , Axons/metabolism , Retina/metabolism , Retina/embryology , Visual Pathways , Gene Knockdown Techniques , Optic Chiasm/embryology , Optic Chiasm/metabolism , Superior Colliculi/embryology , Superior Colliculi/metabolism , Gene Expression Regulation, Developmental
9.
Dev Comp Immunol ; 160: 105237, 2024 Nov.
Article in English | MEDLINE | ID: mdl-39103004

ABSTRACT

Historically, amphibians have been essential to our understanding of vertebrate biology and animal development. Because development from egg to tadpole to adult frog can be directly observed, amphibians contributed greatly to our understanding of not only vertebrate animal development but also the development of the immune system. The South African clawed frog (Xenopus laevis) has been key to many of these findings. For example, using Xenopus as a model, the comparative immunology community learned about the contribution of hematopoietic stem cells to development of the immune system and about the diversity of antibodies, B cells, T cells and antigen presenting cells. Amphibians offer many advantages as unique potential model systems to address questions about immune skin interactions, host responses to mycobacteria, the diverse functions of interferons, and immune and mucosal interactions. However, there are also many challenges to advance the research including the lack of specific reagents and well annotated genomes of diverse species. While much is known, many important questions remain. The aim of this short commentary is to look to the future of comparative immunology of amphibians as a group. By identifying some important questions or "information-deficit" areas of research, I hope to pique the interest of younger developing scientists and persuade funding agencies to continue to support comparative immunology studies including those of amphibians.


Subject(s)
Amphibians , Animals , Amphibians/immunology , Allergy and Immunology , Immune System/immunology , Xenopus laevis/immunology
10.
Cell Mol Life Sci ; 81(1): 332, 2024 Aug 07.
Article in English | MEDLINE | ID: mdl-39110172

ABSTRACT

Drug modulation of the α7 acetylcholine receptor has emerged as a therapeutic strategy for neurological, neurodegenerative, and inflammatory disorders. α7 is a homo-pentamer containing topographically distinct sites for agonists, calcium, and drug modulators with each type of site present in five copies. However, functional relationships between agonist, calcium, and drug modulator sites remain poorly understood. To investigate these relationships, we manipulated the number of agonist binding sites, and monitored potentiation of ACh-elicited single-channel currents through α7 receptors by PNU-120596 (PNU) both in the presence and absence of calcium. When ACh is present alone, it elicits brief, sub-millisecond channel openings, however when ACh is present with PNU it elicits long clusters of potentiated openings. In receptors harboring five agonist binding sites, PNU potentiates regardless of the presence or absence of calcium, whereas in receptors harboring one agonist binding site, PNU potentiates in the presence but not the absence of calcium. By varying the numbers of agonist and calcium binding sites we show that PNU potentiation of α7 depends on a balance between agonist occupancy of the orthosteric sites and calcium occupancy of the allosteric sites. The findings suggest that in the local cellular environment, fluctuations in the concentrations of neurotransmitter and calcium may alter this balance and modulate the ability of PNU to potentiate α7.


Subject(s)
Calcium , alpha7 Nicotinic Acetylcholine Receptor , alpha7 Nicotinic Acetylcholine Receptor/metabolism , alpha7 Nicotinic Acetylcholine Receptor/agonists , Binding Sites , Calcium/metabolism , Humans , Animals , Phenylurea Compounds/pharmacology , Phenylurea Compounds/metabolism , Acetylcholine/metabolism , Acetylcholine/pharmacology , HEK293 Cells , Xenopus laevis , Nicotinic Agonists/pharmacology , Nicotinic Agonists/metabolism , Isoxazoles
11.
Cell Mol Life Sci ; 81(1): 337, 2024 Aug 09.
Article in English | MEDLINE | ID: mdl-39120784

ABSTRACT

The α9α10 nicotinic cholinergic receptor (nAChR) is a ligand-gated pentameric cation-permeable ion channel that mediates synaptic transmission between descending efferent neurons and mechanosensory inner ear hair cells. When expressed in heterologous systems, α9 and α10 subunits can assemble into functional homomeric α9 and heteromeric α9α10 receptors. One of the differential properties between these nAChRs is the modulation of their ACh-evoked responses by extracellular calcium (Ca2+). While α9 nAChRs responses are blocked by Ca2+, ACh-evoked currents through α9α10 nAChRs are potentiated by Ca2+ in the micromolar range and blocked at millimolar concentrations. Using chimeric and mutant subunits, together with electrophysiological recordings under two-electrode voltage-clamp, we show that the TM2-TM3 loop of the rat α10 subunit contains key structural determinants responsible for the potentiation of the α9α10 nAChR by extracellular Ca2+. Moreover, molecular dynamics simulations reveal that the TM2-TM3 loop of α10 does not contribute to the Ca2+ potentiation phenotype through the formation of novel Ca2+ binding sites not present in the α9 receptor. These results suggest that the TM2-TM3 loop of α10 might act as a control element that facilitates the intramolecular rearrangements that follow ACh-evoked α9α10 nAChRs gating in response to local and transient changes of extracellular Ca2+ concentration. This finding might pave the way for the future rational design of drugs that target α9α10 nAChRs as otoprotectants.


Subject(s)
Calcium , Receptors, Nicotinic , Animals , Rats , Acetylcholine/metabolism , Acetylcholine/pharmacology , Amino Acid Sequence , Binding Sites , Calcium/metabolism , Molecular Dynamics Simulation , Patch-Clamp Techniques , Protein Subunits/metabolism , Protein Subunits/genetics , Receptors, Nicotinic/metabolism , Receptors, Nicotinic/genetics , Receptors, Nicotinic/chemistry , Xenopus laevis
12.
Nat Commun ; 15(1): 5782, 2024 Jul 10.
Article in English | MEDLINE | ID: mdl-38987269

ABSTRACT

Self-regenerating trigger waves can spread rapidly through the crowded cytoplasm without diminishing in amplitude or speed, providing consistent, reliable, long-range communication. The macromolecular concentration of the cytoplasm varies in response to physiological and environmental fluctuations, raising the question of how or if trigger waves can robustly operate in the face of such fluctuations. Using Xenopus extracts, we find that mitotic and apoptotic trigger wave speeds are remarkably invariant. We derive a model that accounts for this robustness and for the eventual slowing at extremely high and low cytoplasmic concentrations. The model implies that the positive and negative effects of cytoplasmic concentration (increased reactant concentration vs. increased viscosity) are nearly precisely balanced. Accordingly, artificially maintaining a constant cytoplasmic viscosity during dilution abrogates this robustness. The robustness in trigger wave speeds may contribute to the reliability of the extremely rapid embryonic cell cycle.


Subject(s)
Cytoplasm , Mitosis , Xenopus laevis , Animals , Cytoplasm/metabolism , Apoptosis , Viscosity , Cell Extracts/chemistry , Models, Biological , Xenopus , Cell Cycle
13.
J Mech Behav Biomed Mater ; 157: 106648, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38996625

ABSTRACT

Mechanical properties are essential for the biological activities of cells, and they have been shown to be affected by diseases. Therefore, accurate mechanical characterization is important for studying the cell lifecycle, cell-cell interactions, and disease diagnosis. While the cytoskeleton and actin cortex are typically the primary structural stiffness contributors in most live cells, oocytes possess an additional extracellular layer known as the vitelline membrane (VM), or envelope, which can significantly impact their overall mechanical properties. In this study, we utilized nanoindentation via an atomic force microscope to measure the Young's modulus of Xenopus laevis oocytes at different force setpoints and explored the influence of the VM by conducting measurements on oocytes with the membrane removed. The findings revealed that the removal of VM led to a significant decrease in the apparent Young's modulus of the oocytes, highlighting the pivotal role of the VM as the main structural component responsible for the oocyte's shape and stiffness. Furthermore, the mechanical behavior of VM was investigated through finite element (FE) simulations of the nanoindentation process. FE simulations with the VM Young's modulus in the range 20-60 MPa resulted in force-displacement curves that closely resemble experimental in terms of shape and maximum force for a given indentation depth.


Subject(s)
Elastic Modulus , Mechanical Phenomena , Microscopy, Atomic Force , Oocytes , Xenopus laevis , Animals , Oocytes/cytology , Biomechanical Phenomena , Finite Element Analysis , Mechanical Tests , Materials Testing
14.
Elife ; 122024 Jul 31.
Article in English | MEDLINE | ID: mdl-39082933

ABSTRACT

Global amphibian declines are compounded by deadly disease outbreaks caused by the chytrid fungus, Batrachochytrium dendrobatidis (Bd). Much has been learned about the roles of amphibian skin-produced antimicrobial components and microbiomes in controlling Bd, yet almost nothing is known about the roles of skin-resident immune cells in anti-Bd defenses. Mammalian mast cells reside within and serve as key immune sentinels in barrier tissues like skin. Accordingly, we investigated the roles of Xenopus laevis frog mast cells during Bd infections. Our findings indicate that enrichment of X. laevis skin mast cells confers anti-Bd protection and ameliorates the inflammation-associated skin damage caused by Bd infection. This includes a significant reduction in infiltration of Bd-infected skin by neutrophils, promoting mucin content within cutaneous mucus glands, and preventing Bd-mediated changes to skin microbiomes. Mammalian mast cells are known for their production of the pleiotropic interleukin-4 (IL4) cytokine and our findings suggest that the X. laevis IL4 plays a key role in manifesting the effects seen following cutaneous mast cell enrichment. Together, this work underscores the importance of amphibian skin-resident immune cells in anti-Bd defenses and illuminates a novel avenue for investigating amphibian host-chytrid pathogen interactions.


Subject(s)
Batrachochytrium , Mast Cells , Skin , Xenopus laevis , Animals , Mast Cells/immunology , Mast Cells/microbiology , Mast Cells/metabolism , Xenopus laevis/microbiology , Xenopus laevis/immunology , Skin/microbiology , Skin/immunology , Mycoses/immunology , Mycoses/veterinary , Mycoses/microbiology , Microbiota
15.
PLoS One ; 19(7): e0293852, 2024.
Article in English | MEDLINE | ID: mdl-39083515

ABSTRACT

The zinc finger and BTB domain-containing 11 gene (zbtb11) is expressed in the Xenopus anterior neuroectoderm, but the molecular nature of the Zbtb11 protein during embryonic development remains to be elucidated. Here, we show the role of Zbtb11 in anterior patterning of the neuroectoderm and the cooperative action with the transcription factor Otx2. Both overexpression and knockdown of zbtb11 caused similar phenotypes: expanded expression of the posterior gene gbx2 in the neural plate, and later microcephaly with reduced eyes, suggesting that a proper level of zbtb11 expression is necessary for normal patterning of the neuroectoderm, including eye formation. Co-immunoprecipitation assays showed that Zbtb11 formed a complex with itself and with a phosphomimetic and repressive form of Otx2, suggesting that Zbtb11 forms a dimer or oligomer and interacts with Otx2 in a phosphorylation-dependent manner. Reporter analysis further showed that Zbtb11 enhanced the activity of the phosphomimetic Otx2 to repress a silencer element of the posterior gene meis3. These data suggest that Zbtb11 coordinates with phosphorylated Otx2 to specify the anterior neuroectoderm by repressing posterior genes.


Subject(s)
Gene Expression Regulation, Developmental , Neural Plate , Otx Transcription Factors , Xenopus Proteins , Animals , Otx Transcription Factors/metabolism , Otx Transcription Factors/genetics , Xenopus Proteins/genetics , Xenopus Proteins/metabolism , Neural Plate/metabolism , Neural Plate/embryology , Xenopus laevis , Protein Binding , Phosphorylation , Body Patterning/genetics
16.
Nature ; 631(8021): 678-685, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38961301

ABSTRACT

Pericentric heterochromatin is a critical component of chromosomes marked by histone H3 K9 (H3K9) methylation1-3. However, what recruits H3K9-specific histone methyltransferases to pericentric regions in vertebrates remains unclear4, as does why pericentric regions in different species share the same H3K9 methylation mark despite lacking highly conserved DNA sequences2,5. Here we show that zinc-finger proteins ZNF512 and ZNF512B specifically localize at pericentric regions through direct DNA binding. Notably, both ZNF512 and ZNF512B are sufficient to initiate de novo heterochromatin formation at ectopically targeted repetitive regions and pericentric regions, as they directly recruit SUV39H1 and SUV39H2 (SUV39H) to catalyse H3K9 methylation. SUV39H2 makes a greater contribution to H3K9 trimethylation, whereas SUV39H1 seems to contribute more to silencing, probably owing to its preferential association with HP1 proteins. ZNF512 and ZNF512B from different species can specifically target pericentric regions of other vertebrates, because the atypical long linker residues between the zinc-fingers of ZNF512 and ZNF512B offer flexibility in recognition of non-consecutively organized three-nucleotide triplets targeted by each zinc-finger. This study addresses two long-standing questions: how constitutive heterochromatin is initiated and how seemingly variable pericentric sequences are targeted by the same set of conserved machinery in vertebrates.


Subject(s)
Centromere , Evolution, Molecular , Heterochromatin , Histone-Lysine N-Methyltransferase , Histones , Nucleotide Motifs , Animals , Humans , Mice , Centromere/genetics , Centromere/metabolism , Chickens , Chromobox Protein Homolog 5 , Gene Silencing , Heterochromatin/metabolism , Heterochromatin/chemistry , Heterochromatin/genetics , Histone-Lysine N-Methyltransferase/metabolism , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/chemistry , Histones/metabolism , Histones/chemistry , Lancelets , Methylation , Petromyzon , Repressor Proteins/metabolism , Repressor Proteins/chemistry , Repressor Proteins/genetics , Snakes , Xenopus laevis , Zebrafish , Zinc Fingers
17.
Nature ; 632(8023): 209-217, 2024 Aug.
Article in English | MEDLINE | ID: mdl-39085540

ABSTRACT

Glutamate transmission and activation of ionotropic glutamate receptors are the fundamental means by which neurons control their excitability and neuroplasticity1. The N-methyl-D-aspartate receptor (NMDAR) is unique among all ligand-gated channels, requiring two ligands-glutamate and glycine-for activation. These receptors function as heterotetrameric ion channels, with the channel opening dependent on the simultaneous binding of glycine and glutamate to the extracellular ligand-binding domains (LBDs) of the GluN1 and GluN2 subunits, respectively2,3. The exact molecular mechanism for channel gating by the two ligands has been unclear, particularly without structures representing the open channel and apo states. Here we show that the channel gate opening requires tension in the linker connecting the LBD and transmembrane domain (TMD) and rotation of the extracellular domain relative to the TMD. Using electron cryomicroscopy, we captured the structure of the GluN1-GluN2B (GluN1-2B) NMDAR in its open state bound to a positive allosteric modulator. This process rotates and bends the pore-forming helices in GluN1 and GluN2B, altering the symmetry of the TMD channel from pseudofourfold to twofold. Structures of GluN1-2B NMDAR in apo and single-liganded states showed that binding of either glycine or glutamate alone leads to distinct GluN1-2B dimer arrangements but insufficient tension in the LBD-TMD linker for channel opening. This mechanistic framework identifies a key determinant for channel gating and a potential pharmacological strategy for modulating NMDAR activity.


Subject(s)
Glutamic Acid , Glycine , Ion Channel Gating , Receptors, N-Methyl-D-Aspartate , Animals , Rats , Allosteric Regulation , Cryoelectron Microscopy , Glutamic Acid/metabolism , Glycine/metabolism , Ligands , Models, Molecular , Oocytes/metabolism , Protein Domains , Protein Multimerization , Protein Subunits/metabolism , Protein Subunits/chemistry , Receptors, N-Methyl-D-Aspartate/chemistry , Receptors, N-Methyl-D-Aspartate/metabolism , Receptors, N-Methyl-D-Aspartate/ultrastructure , Rotation , Xenopus laevis
18.
Int J Biol Macromol ; 275(Pt 2): 133692, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38972657

ABSTRACT

Bombus terrestris are efficient pollinators in forestry and agriculture, with higher cold tolerance than other bees. Yet, their cold tolerance mechanism remains unclear. Aquaporins (AQPs) function as cell membrane proteins facilitating rapid water flow, aiding in osmoregulation. Recent studies highlight the importance of insect AQPs in dehydration and cold stress. Comparative transcriptome analysis of B. terrestris under cold stress revealed up-regulation of four AQPs, indicating their potential role in cold tolerance. Seven AQPs-Eglp1, Eglp2, Eglp3, DRIP, PRIP, Bib, and AQP12L-have been identified in B. terrestris. These are widely expressed in various tissues, particularly in the alimentary canal and Malpighian tubules. Functional analysis of BterAQPs in the Xenopus laevis oocytes expressing system showed distinct water and glycerol selectivity, with BterDrip exhibiting the highest water permeability. Molecular modeling of BterDrip revealed six transmembrane domains, two NPA motifs, and an ar/R constriction region (Phe131, His256, Ser265, and Arg271), likely contributing to its water selectivity. Silencing BterDRIP accelerated mortality in B. terrestris under cold stress, highlighting the crucial role of BterDRIP in their cold tolerance and providing a molecular mechanism for their cold adaptation.


Subject(s)
Aquaporins , Animals , Aquaporins/genetics , Aquaporins/chemistry , Aquaporins/metabolism , Water/chemistry , Water/metabolism , Xenopus laevis , Models, Molecular , Oocytes/metabolism , Structure-Activity Relationship , Cold-Shock Response , Phylogeny , Amino Acid Sequence , Insect Proteins/genetics , Insect Proteins/metabolism , Insect Proteins/chemistry
19.
PLoS One ; 19(7): e0299179, 2024.
Article in English | MEDLINE | ID: mdl-39028705

ABSTRACT

The African claw-toed frog, Xenopus laevis, is a well-established laboratory model for the biology of vertebrate oogenesis, fertilisation, and development at embryonic, larval, and metamorphic stages. For ovulation, X. laevis females are usually injected with chorionic gonadotropin, whereupon they lay typically hundreds to thousands of eggs in a day. After being rested for a minimum of three months, animals are re-used. The literature suggests that adult females can lay much larger numbers of eggs in a short period. Here, we compared the standard "single ovulation" protocol with a "double ovulation" protocol, in which females were ovulated, then re-ovulated after seven days and then rested for three months before re-use. We quantified egg number, fertilisation rate (development to cleavage stage), and corticosterone secretion rate as a measure of stress response for the two protocol groups over seven 3-month cycles. We found no differences in egg number-per-ovulation or egg quality between the groups and no long-term changes in any measures over the 21-month trial period. Corticosterone secretion was elevated by ovulation, similarly for the single ovulation as for the first ovulation in the double-ovulation protocol, but more highly for the second ovulation (to a level comparable to that seen following shipment) in the latter. However, both groups exhibited the same baseline secretion rates by the time of the subsequent cycle. Double ovulation is thus transiently more stressful/demanding than single ovulation but within the levels routinely experienced by laboratory X. laevis. Noting that "stress hormone" corticosterone/cortisol secretion is linked to physiological processes, such as ovulation, that are not necessarily harmful to the individual, we suggest that the benefits of a doubling in egg yield-per-cycle per animal without loss of egg quality or signs of acute or long-term harm may outweigh the relatively modest and transient corticosterone elevation we observed. The double ovulation protocol therefore represents a potential new standard practice for promoting the "3Rs" (animal use reduction, refinement and replacement) mission for Xenopus research.


Subject(s)
Corticosterone , Fertilization , Ovulation , Xenopus laevis , Animals , Female , Ovulation/physiology , Corticosterone/metabolism , Ovum , Chorionic Gonadotropin/administration & dosage
20.
Proc Natl Acad Sci U S A ; 121(28): e2408346121, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38968117

ABSTRACT

Xenopus embryos provide a favorable material to dissect the sequential steps that lead to dorsal-ventral (D-V) and anterior-posterior (A-P) cell differentiation. Here, we analyze the signaling pathways involved in this process using loss-of-function and gain-of-function approaches. The initial step was provided by Hwa, a transmembrane protein that robustly activates early ß-catenin signaling when microinjected into the ventral side of the embryo leading to complete twinned axes. The following step was the activation of Xenopus Nodal-related growth factors, which could rescue the depletion of ß-catenin and were themselves blocked by the extracellular Nodal antagonists Cerberus-Short and Lefty. During gastrulation, the Spemann-Mangold organizer secretes a cocktail of growth factor antagonists, of which the BMP antagonists Chordin and Noggin could rescue simultaneously D-V and A-P tissues in ß-catenin-depleted embryos. Surprisingly, this rescue occurred in the absence of any ß-catenin transcriptional activity as measured by ß-catenin activated Luciferase reporters. The Wnt antagonist Dickkopf (Dkk1) strongly synergized with the early Hwa signal by inhibiting late Wnt signals. Depletion of Sizzled (Szl), an antagonist of the Tolloid chordinase, was epistatic over the Hwa and Dkk1 synergy. BMP4 mRNA injection blocked Hwa-induced ectopic axes, and Dkk1 inhibited BMP signaling late, but not early, during gastrulation. Several unexpected findings were made, e.g., well-patterned complete embryonic axes are induced by Chordin or Nodal in ß-catenin knockdown embryos, dorsalization by Lithium chloride (LiCl) is mediated by Nodals, Dkk1 exerts its anteriorizing and dorsalizing effects by regulating late BMP signaling, and the Dkk1 phenotype requires Szl.


Subject(s)
Body Patterning , Intercellular Signaling Peptides and Proteins , Signal Transduction , Xenopus Proteins , beta Catenin , Animals , Body Patterning/genetics , Xenopus Proteins/metabolism , Xenopus Proteins/genetics , beta Catenin/metabolism , beta Catenin/genetics , Intercellular Signaling Peptides and Proteins/metabolism , Intercellular Signaling Peptides and Proteins/genetics , Xenopus laevis/embryology , Gene Expression Regulation, Developmental , Gastrulation , Nodal Protein/metabolism , Nodal Protein/genetics , Embryo, Nonmammalian/metabolism , Embryo, Nonmammalian/embryology , Organizers, Embryonic/metabolism , Glycoproteins
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