Direct neural induction and selective inhibition of mesoderm and epidermis inducers by Xnr3

Development ◽  
1997 ◽  
Vol 124 (2) ◽  
pp. 483-492 ◽  
Author(s):  
C.S. Hansen ◽  
C.D. Marion ◽  
K. Steele ◽  
S. George ◽  
W.C. Smith
Keyword(s):  
Family Members ◽  
Neural Induction ◽  
Structural Features ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Mesoderm Induction ◽  
Related Factors ◽  
Spemann's Organizer ◽  
Secreted Factors ◽  
C Terminus

During gastrulation in amphibians, secreted factors from Spemann's organizer act on dorsal ectoderm to induce the central nervous system. A number of secreted factors produced by Spemann's organizer have recently been identified. The TGFbeta family member Xnr3 is similar in amino acid sequence to the mouse factor nodal and is expressed in a restricted group of cells in the superficial layer of Spemann's organizer. Xnr3, unlike the related factors nodal, Xnr1 and Xnr2, lacks mesoderm-inducing activity. We report here that Xnr3 can directly induce neural tissue in Xenopus ectoderm explants (animal caps). Injection of animal caps with either Xnr3 RNA or plasmids induces the expression of the pan-neural genes NCAM and nrp1, as well as the anterior neural marker Cpl1. A growing body of evidence suggests that neural induction in Xenopus proceeds as the default in the absence of epidermis inducers. The best candidates for the endogenous epidermis inducers are BMP-4 and BMP-7. The neural inducing activity of Xnr3 can be inhibited by overexpression of BMP-4, as has been observed with the neural inducers noggin, chordin and follistatin. Furthermore, Xnr3 can block mesoderm induction by BMP-4 and activin, but not by Xnr2. The structural basis underlying the divergent activities of Xnr2 and Xnr3 was analyzed using site-directed mutagenesis. Mutations introduced to the conserved cysteine residues characteristic of the TGFbeta family were found to inactivate Xnr2, but not Xnr3. The most unique feature of Xnr3 is the absence of a conserved cysteine at the C terminus of the protein. This feature distinguishes Xnr3 from other TGFbeta family members, including Xnr2. However, we observed that changing the C terminus of Xnr3 to more closely resemble other TGFbeta family members did not significantly alter its activity, suggesting that other structural features of Xnr3 distinguish its biological activity from Xnr2.

XIPOU 2, a noggin-inducible gene, has direct neuralizing activity

Development ◽  
1995 ◽  
Vol 121 (3) ◽  
pp. 721-730 ◽  
Author(s):  
S.E. Witta ◽  
V.R. Agarwal ◽  
S.M. Sato
Keyword(s):  
Cell Fate ◽  
Neural Induction ◽  
Mesoderm Induction ◽  
Class Iii ◽  
Cell Stage ◽  
Neuronal Phenotype ◽  
Pou Domain ◽  
Spemann's Organizer ◽  
Stage Embryo ◽  
Synthetic Mrna

XIPOU 2, a member of the class III POU domain family, is expressed initially in Spemann's organizer, and later, in discrete regions of the developing nervous system in Xenopus laevis. XIPOU 2 may act downstream from initial neural induction events, since it is activated by the neural inducer, noggin. To determine if XIPOU 2 participates in the early events of neurogenesis, synthetic mRNA was microinjected into specific blastomeres of the 32-cell stage embryo. Misexpression of XIPOU 2 in the epidermis causes a direct switch in cell fate from an epidermal to a neuronal phenotype. In the absence of mesoderm induction, XIPOU 2 has the ability to induce a neuronal phenotype in uncommitted ectoderm. These data demonstrate the potential of XIPOU 2 to act as a master regulator of neurogenesis.

scholarly journals Structural Basis of Ubiquitin Recognition by the Ubiquitin-associated (UBA) Domain of the Ubiquitin Ligase EDD

2007 ◽  
Vol 282 (49) ◽  
pp. 35787-35795 ◽  
Author(s):  
Guennadi Kozlov ◽  
Long Nguyen ◽  
Tong Lin ◽  
Gregory De Crescenzo ◽  
Morag Park ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Titration Calorimetry ◽  
Polyubiquitin Chains ◽  
C Terminus ◽  
Damage Repair ◽  
The Family ◽  
Uba Domain ◽  
Ordered Water

EDD (or HYD) is an E3 ubiquitin ligase in the family of HECT (homologous to E6-AP C terminus) ligases. EDD contains an N-terminal ubiquitin-associated (UBA) domain, which is present in a variety of proteins involved in ubiquitin-mediated processes. Here, we use isothermal titration calorimetry (ITC), NMR titrations, and pull-down assays to show that the EDD UBA domain binds ubiquitin. The 1.85Å crystal structure of the complex with ubiquitin reveals the structural basis of ubiquitin recognition by UBA helices α1 and α3. The structure shows a larger number of intermolecular hydrogen bonds than observed in previous UBA/ubiquitin complexes. Two of these involve ordered water molecules. The functional importance of residues at the UBA/ubiquitin interface was confirmed using site-directed mutagenesis. Surface plasmon resonance (SPR) measurements show that the EDD UBA domain does not have a strong preference for polyubiquitin chains over monoubiquitin. This suggests that EDD binds to monoubiquitinated proteins, which is consistent with its involvement in DNA damage repair pathways.

The cleavage stage origin of Spemann's Organizer: analysis of the movements of blastomere clones before and during gastrulation in Xenopus

Development ◽  
1994 ◽  
Vol 120 (5) ◽  
pp. 1179-1189 ◽  
Author(s):  
D.V. Bauer ◽  
S. Huang ◽  
S.A. Moody
Keyword(s):  
Neural Induction ◽  
Axis Formation ◽  
Mesoderm Induction ◽  
Animal Pole ◽  
Genetic Manipulations ◽  
Spemann's Organizer ◽  
History Of ◽  
Clonal Origin ◽  
The Relationship ◽  
Early Gastrula

Recent investigations into the roles of early regulatory genes, especially those resulting from mesoderm induction or first expressed in the gastrula, reveal a need to elucidate the developmental history of the cells in which their transcripts are expressed. Although fates both of the early blastomeres and of regions of the gastrula have been mapped, the relationship between the two sets of fate maps is not clear and the clonal origin of the regions of the stage 10 embryo are not known. We mapped the positions of each blastomere clone during several late blastula and early gastrula stages to show where and when these clones move. We found that the dorsal animal clone (A1) begins to move away from the animal pole at stage 8, and the dorsal animal marginal clone (B1) leaves the animal cap by stage 9. The ventral animal clones (A4 and B4) spread into the dorsal animal cap region as the dorsal clones recede. At stage 10, the ventral animal clones extend across the entire dorsal animal cap. These changes in the blastomere constituents of the animal cap during epiboly may contribute to the changing capacity of the cap to respond to inductive growth factors. Pregastrulation movements of clones also result in the B1 clone occupying the vegetal marginal zone to become the primary progenitor of the dorsal lip of the blastopore (Spemann's Organizer). This report provides the fundamental descriptions of clone locations during the important periods of axis formation, mesoderm induction and neural induction. These will be useful for the correct targeting of genetic manipulations of early regulatory events.

scholarly journals The crystal structure of phosphorylated MAPK13 reveals common structural features and differences in p38 MAPK family activation

2015 ◽  
Vol 71 (4) ◽  
pp. 790-799 ◽  
Author(s):  
Zeynep Yurtsever ◽  
Suzanne M. Scheaffer ◽  
Arthur G. Romero ◽  
Michael J. Holtzman ◽  
Tom J. Brett
Keyword(s):  
Family Member ◽  
P38 Mapk ◽  
Map Kinases ◽  
Sequence Similarity ◽  
Family Members ◽  
Structural Features ◽  
P38 Map Kinase ◽  
Structural Basis ◽  
Structure Based Drug Design ◽  
Specific Inhibitors

The p38 MAP kinases (p38 MAPKs) represent an important family centrally involved in mediating extracellular signaling. Recent studies indicate that family members such as MAPK13 (p38δ) display a selective cellular and tissue expression and are therefore involved in specific diseases. Detailed structural studies of all p38 MAPK family members are crucial for the design of specific inhibitors. In order to facilitate such ventures, the structure of MAPK13 was determined in both the inactive (unphosphorylated; MAPK13) and active (dual phosphorylated; MAPK13/pTpY) forms. Here, the first preparation, crystallization and structure determination of MAPK13/pTpY are presented and the structure is compared with the previously reported structure of MAPK13 in order to facilitate studies for structure-based drug design. A comprehensive analysis of inactiveversusactive structures for the p38 MAPK family is also presented. It is found that MAPK13 undergoes a larger interlobe configurational rearrangement upon activation compared with MAPK14. Surprisingly, the analysis of activated p38 MAPK structures (MAP12/pTpY, MAPK13/pTpY and MAPK14/pTpY) reveals that, despite a high degree of sequence similarity, different side chains are used to coordinate the phosphorylated residues. There are also differences in the rearrangement of the hinge region that occur in MAPK14 compared with MAPK13 which would affect inhibitor binding. A thorough examination of all of the active (phosphorylated) and inactive (unphosphorylated) p38 MAPK family member structures was performed to reveal a common structural basis of activation for the p38 MAP kinase family and to identify structural differences that may be exploited for developing family member-specific inhibitors.

scholarly journals Structural basis for substrate binding and specificity of a sodium/alanine symporter AgcS

2018 ◽  
Author(s):  
Jinming Ma ◽  
Hsiang-Ting Lei ◽  
Francis E. Reyes ◽  
Silvia Sanchez-Martinez ◽  
Maen Sarhan ◽  
...  
Keyword(s):  
Organic Molecules ◽  
Substrate Binding ◽  
Structural Features ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Substrate Selectivity ◽  
Methanococcus Maripaludis ◽  
Functional Studies ◽  
Stereo Selectivity ◽  
Key Residues

AbstractThe amino acid, polyamine, and organocation (APC) superfamily is the second largest superfamily of membrane proteins forming secondary transporters that move a range of organic molecules across the cell membrane. Each transporter in APC superfamily is specific for a unique sub-set of substrates, even if they possess a similar structural fold. The mechanism of substrate selectivity remains, by and large, elusive. Here we report two crystal structures of an APC member from Methanococcus maripaludis, the alanine or glycine:cation symporter (AgcS), with L- or D-alanine bound. Structural analysis combined with site-directed mutagenesis and functional studies inform on substrate binding, specificity, and modulation of the AgcS family and reveal key structural features that allow this transporter to accommodate glycine and alanine while excluding all other amino acids. Mutation of key residues in the substrate binding site expand the selectivity to include valine and leucine. Moreover, as a transporter that binds both enantiomers of alanine, the present structures provide an unprecedented opportunity to gain insights into the mechanism of stereo-selectivity in APC transporters.

scholarly journals Structural basis for substrate binding and specificity of a sodium–alanine symporter AgcS

2019 ◽  
Vol 116 (6) ◽  
pp. 2086-2090 ◽  
Author(s):  
Jinming Ma ◽  
Hsiang-Ting Lei ◽  
Francis E. Reyes ◽  
Silvia Sanchez-Martinez ◽  
Maen F. Sarhan ◽  
...  
Keyword(s):  
Organic Molecules ◽  
Substrate Binding ◽  
Structural Features ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Directed Mutagenesis ◽  
Substrate Selectivity ◽  
Methanococcus Maripaludis ◽  
Functional Studies ◽  
Key Residues

The amino acid, polyamine, and organocation (APC) superfamily is the second largest superfamily of membrane proteins forming secondary transporters that move a range of organic molecules across the cell membrane. Each transporter in the APC superfamily is specific for a unique subset of substrates, even if they possess a similar structural fold. The mechanism of substrate selectivity remains, by and large, elusive. Here, we report two crystal structures of an APC member fromMethanococcus maripaludis, the alanine or glycine:cation symporter (AgcS), withl- ord-alanine bound. Structural analysis combined with site-directed mutagenesis and functional studies inform on substrate binding, specificity, and modulation of the AgcS family and reveal key structural features that allow this transporter to accommodate glycine and alanine while excluding all other amino acids. Mutation of key residues in the substrate binding site expand the selectivity to include valine and leucine. These studies provide initial insights into substrate selectivity in AgcS symporters.

scholarly journals Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhiwen Liu ◽  
Fanglong Zhao ◽  
Boyang Zhao ◽  
Jie Yang ◽  
Joseph Ferrara ◽  
...  
Keyword(s):  
High Resolution ◽  
Organic Synthesis ◽  
Indole Alkaloids ◽  
Site Directed Mutagenesis ◽  
Structural Basis ◽  
Directed Mutagenesis ◽  
Computational Studies ◽  
X Ray ◽  
Evolutionary Branch ◽  
Catalytic Mechanisms

AbstractPrenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.

scholarly journals Structural basis for the functional properties of the P2X7 receptor for extracellular ATP

2021 ◽  
Author(s):  
Lin-Hua Jiang ◽  
Emily A. Caseley ◽  
Steve P. Muench ◽  
Sébastien Roger
Keyword(s):  
Functional Properties ◽  
P2x7 Receptor ◽  
Site Directed Mutagenesis ◽  
P2x Receptor ◽  
Structural Basis ◽  
Structure Characteristic ◽  
Purinergic Signalling ◽  
Directed Mutagenesis ◽  
Important Mediator ◽  
Receptor Family

AbstractThe P2X7 receptor, originally known as the P2Z receptor due to its distinctive functional properties, has a structure characteristic of the ATP-gated ion channel P2X receptor family. The P2X7 receptor is an important mediator of ATP-induced purinergic signalling and is involved the pathogenesis of numerous conditions as well as in the regulation of diverse physiological functions. Functional characterisations, in conjunction with site-directed mutagenesis, molecular modelling, and, recently, structural determination, have provided significant insights into the structure–function relationships of the P2X7 receptor. This review discusses the current understanding of the structural basis for the functional properties of the P2X7 receptor.

scholarly journals Structural basis for distinct inflammasome complex assembly by human NLRP1 and CARD8

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Qin Gong ◽  
Kim Robinson ◽  
Chenrui Xu ◽  
Phuong Thao Huynh ◽  
Kelvin Han Chung Chong ◽  
...  
Keyword(s):  
Cell Death ◽  
Inner Core ◽  
Inflammatory Diseases ◽  
Structural Features ◽  
Structural Basis ◽  
Cultured Human Cells ◽  
Structural Insight ◽  
Sensor Proteins ◽  
Insight Into

AbstractNod-like receptor (NLR) proteins activate pyroptotic cell death and IL-1 driven inflammation by assembling and activating the inflammasome complex. Closely related sensor proteins NLRP1 and CARD8 undergo unique auto-proteolysis-dependent activation and are implicated in auto-inflammatory diseases; however, their mechanisms of activation are not understood. Here we report the structural basis of how the activating domains (FIINDUPA-CARD) of NLRP1 and CARD8 self-oligomerize to assemble distinct inflammasome complexes. Recombinant FIINDUPA-CARD of NLRP1 forms a two-layered filament, with an inner core of oligomerized CARD surrounded by an outer ring of FIINDUPA. Biochemically, self-assembled NLRP1-CARD filaments are sufficient to drive ASC speck formation in cultured human cells—a process that is greatly enhanced by NLRP1-FIINDUPA which forms oligomers in vitro. The cryo-EM structures of NLRP1-CARD and CARD8-CARD filaments, solved here at 3.7 Å, uncover unique structural features that enable NLRP1 and CARD8 to discriminate between ASC and pro-caspase-1. In summary, our findings provide structural insight into the mechanisms of activation for human NLRP1 and CARD8 and reveal how highly specific signaling can be achieved by heterotypic CARD interactions within the inflammasome complexes.

scholarly journals The C Terminus of Foamy Retrovirus Gag Contains Determinants for Encapsidation of Pol Protein into Virions

2008 ◽  
Vol 82 (21) ◽  
pp. 10803-10810 ◽  
Author(s):  
Eun-Gyung Lee ◽  
Maxine L. Linial
Keyword(s):  
Site Directed Mutagenesis ◽  
Rna Packaging ◽  
Interaction Domain ◽  
Virus Particles ◽  
Charged Amino Acids ◽  
C Terminus ◽  
Foamy Viruses ◽  
Substitution Mutations ◽  
Gag Assembly ◽  
Positively Charged

ABSTRACT Foamy viruses (FV) differ from orthoretroviruses in many aspects of their replication cycle. A major difference is in the mode of Pol expression, regulation, and encapsidation into virions. Orthoretroviruses synthesize Pol as a Gag-Pol fusion protein so that Pol is encapsidated into virus particles through Gag assembly domains. However, as FV express Pol independently of Gag from a spliced mRNA, packaging occurs through a distinct mechanism. FV genomic RNA contains cis-acting sequences that are required for Pol packaging, suggesting that Pol binds to RNA for its encapsidation. However, it is not known whether Gag is directly involved in Pol packaging. Previously our laboratory showed that sequences flanking the three glycine-arginine-rich (GR) boxes at the C terminus of FV Gag contain domains important for RNA packaging and Pol expression, cleavage, and packaging. We have now shown that both deletion and substitution mutations in the first GR box (GR1) prevented neither the assembly of particles with wild-type density nor packaging of RNA genomes but led to a defect in Pol packaging. Site-directed mutagenesis of GR1 indicated that the clustered positively charged amino acids in GR1 play important roles in Pol packaging. Our results suggest that GR1 contains a Pol interaction domain and that a Gag-Pol complex is formed and binds to RNA for incorporation into virions.

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