Arabidopsis GCP3-interacting protein 1/MOZART 1 is an integral component of the γ-tubulin-containing microtubule nucleating complex

Microtubules in eukaryotic cells are nucleated from ring-shaped complexes that contain γ-tubulin and a family of homologous γ-tubulin complex proteins (GCPs), but the subunit composition of the complexes can vary among fungi, animals and plants. Arabidopsis GCP3-interacting protein 1 (GIP1), a small protein with no homology to the GCP family, interacts with GCP3 in vitro, and is a plant homolog of vertebrate mitotic-spindle organizing protein associated with a ring of γ-tubulin 1 (MOZART1), a recently identified component of the γ-tubulin complex in human cell lines. In this study, we characterized two closely related Arabidopsis GIP1s: GIP1a and GIP1b. Single mutants of gip1a and gip1b were indistinguishable from wild-type plants, but their double mutant was embryonic lethal, and showed impaired development of male gametophytes. Functional fusions of GIP1a with green fluorescent protein (GFP) were used to purify GIP1a-containing complexes from Arabidopsis plants, which contained all the subunits (except NEDD1) previously identified in the Arabidopsis γ-tubulin complexes. GIP1a and GIP1b interacted specifically with Arabidopsis GCP3 in yeast. GFP-GIP1a labeled mitotic microtubule arrays in a pattern largely consistent with, but partly distinct from, the localization of the γ-tubulin complex containing GCP2 or GCP3 in planta. In interphase cortical arrays, the labeled complexes were preferentially recruited to existing microtubules, from which new microtubules were efficiently nucleated. However, in contrast to complexes labeled with tagged GCP2 or GCP3, their recruitment to cortical areas with no microtubules was rarely observed. These results indicate that GIP1/MOZART1 is an integral component of a subset of the Arabidopsis γ-tubulin complexes.     

Polar transmembrane-based amino acids in presenilin 1 are involved in endoplasmic reticulum localization, Pen2 protein binding, and γ-secretase complex stabilization

γ-Secretase is composed of the four membrane proteins presenilin, nicastrin, Pen2, and Aph1. These four proteins assemble in a coordinated and regulated manner into a high molecular weight complex. The subunits constitute a total of 19 transmembrane domains (TMD), with many carrying important amino acids involved in catalytic activity, interaction with other subunits, or in ER retention/retrieval of unassembled subunits. We here focus on TMD4 of presenilin 1 (PS1) and show that a number of polar amino acids are critical for γ-secretase assembly and function. An asparagine, a threonine, and an aspartate form a polar interface important for endoplasmic reticulum retention/retrieval. A single asparagine in TMD4 of PS1 is involved in a protein-protein interaction by binding to another asparagine in Pen2. Intriguingly, a charged aspartate in TMD4 is critical for γ-secretase activity, most likely by stabilizing the newly formed complex.     

CEP70 protein interacts with γ-tubulin to localize at the centrosome and is critical for mitotic spindle assembly

Deregulation of the mitotic spindle has been implicated in genomic instability, an important aspect of tumorigenesis and malignant transformation. To ensure the fidelity of chromosome transmission, the mitotic spindle is assembled by exquisite mechanisms and orchestrated by centrosomes in animal cells. Centrosomal proteins especially are thought to act coordinately to ensure accurate spindle formation, but the molecular details remain to be investigated. In this study, we report the molecular characterization and functional analysis of a novel centrosomal protein, Cep70. Our data show that Cep70 localizes to the centrosome throughout the cell cycle and binds to the key centrosomal component, γ-tubulin, through the peptide fragments that contain the coiled-coil domains. Our data further reveal that the centrosomal localization pattern of Cep70 is dependent on its interaction with γ-tubulin. Strikingly, Cep70 plays a significant role in the organization of both preexisting and nascent microtubules in interphase cells. In addition, Cep70 is necessary for the organization and orientation of the bipolar spindle during mitosis. These results thus report for the first time the identification of Cep70 as an important centrosomal protein that interacts with γ-tubulin and underscore its critical role in the regulation of mitotic spindle assembly.     

The essential β-barrel assembly machinery complex components BamD and BamA are required for autotransporter biogenesis

Autotransporter biogenesis is dependent upon BamA, a central component of the β-barrel assembly machinery (BAM) complex. In this report, we detail the role of the other BAM components (BamB-E). We identify the importance of BamD in autotransporter biogenesis and show that BamB, BamC, and BamE are not required.     

Mzt1/Tam4, a fission yeast MOZART1 homologue,is an essential component of the γ-tubulin complex and directly interacts with GCP3Alp6

In humans, MOZART1 plays an essential role in mitotic spindle formation as a component of the γ-tubulin ring complex. We report that the fission yeast homologue of MOZART1, Mzt1/Tam4, is located at microtubule-organizing centers (MTOCs) and coimmunoprecipitates with γ-tubulin Gtb1 from cell extracts. We show that mzt1/tam4 is an essential gene in fission yeast, encoding a 64–amino acid peptide, depletion of which leads to aberrant microtubule structure, including malformed mitotic spindles and impaired interphase microtubule array. Mzt1/Tam4 depletion also causes cytokinesis defects, suggesting a role of the γ-tubulin complex in the regulation of cytokinesis. Yeast two-hybrid analysis shows that Mzt1/Tam4 forms a complex with Alp6, a fission yeast homologue of γ-tubulin complex protein 3 (GCP3). Biophysical methods demonstrate that there is a direct interaction between recombinant Mzt1/Tam4 and the N-terminal region of GCP3^Alp6. Together our results suggest that Mzt1/Tam4 contributes to the MTOC function through regulation of GCP3^Alp6.     

The structural integrity of TDP-43 N-terminus is required for efficient aggregate entrapment and consequent loss of protein function

ABSTRACT. Nuclear factor TDP-43 has been shown to play a key role in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia, where TDP-43 aggregates accumulate in patient's affected neurons and this event can cause neuronal dysfunction. A major focus of today's research is to discover the critical factors that lead to TDP-43 aggregation and the consequences for neuronal metabolism. From a structural point of view, several lines of evidence point toward TDP-43 C-terminus as a key domain able to mediate this process. Regarding this region, we have recently described a novel cellular TDP-43 aggregation model based on 12 tandem repetitions of its 339-366 Q/N rich prion-like domain. In addition, we have shown and confirmed that a minimal TDP-43 construct constituted by the N and C-terminal regions, but lacking both RRM domains, induce aggregation of endogenous TDP-43 and leads to its total loss of function as seen by changes in the alternative splicing of endogenous genes. In this work, we further characterize this model and show the importance of the N-terminus structure in the loss of function process. In addition, from a biochemical point of view we report that, as shown in a previous version of this model (GFP 12×Q/N), the endogenous TDP-43 trapped in the aggregates undergoes the 2 most important post-translational modifications seen in pathological TDP-43 inclusions: ubiquitination and hyperphosphorylation.     

The structural integrity of TDP-43?N-terminus is required for efficient aggregate entrapment and consequent loss of protein function

ABSTRACT. Nuclear factor TDP-43 has been shown to play a key role in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia, where TDP-43 aggregates accumulate in patient''s affected neurons and this event can cause neuronal dysfunction. A major focus of today''s research is to discover the critical factors that lead to TDP-43 aggregation and the consequences for neuronal metabolism. From a structural point of view, several lines of evidence point toward TDP-43 C-terminus as a key domain able to mediate this process. Regarding this region, we have recently described a novel cellular TDP-43 aggregation model based on 12 tandem repetitions of its 339-366 Q/N rich prion-like domain. In addition, we have shown and confirmed that a minimal TDP-43 construct constituted by the N and C-terminal regions, but lacking both RRM domains, induce aggregation of endogenous TDP-43 and leads to its total loss of function as seen by changes in the alternative splicing of endogenous genes. In this work, we further characterize this model and show the importance of the N-terminus structure in the loss of function process. In addition, from a biochemical point of view we report that, as shown in a previous version of this model (GFP 12×Q/N), the endogenous TDP-43 trapped in the aggregates undergoes the 2 most important post-translational modifications seen in pathological TDP-43 inclusions: ubiquitination and hyperphosphorylation.     

The carbohydrate-binding domain of overexpressed STBD1 is important for its stability and protein–protein interactions

STBD1 (starch-binding domain-containing protein 1) belongs to the CBM20 (family 20 carbohydrate binding module) group of proteins, and is implicated in glycogen metabolism and autophagy. However, very little is known about its regulation or interacting partners. Here, we show that the CBM20 of STBD1 is crucial for its stability and ability to interact with glycogen-associated proteins. Mutation of a conserved tryptophan residue (W293) in this domain abolished the ability of STBD1 to bind to the carbohydrate amylose. Compared with the WT (wild-type) protein, this mutant exhibited rapid degradation that was rescued upon inhibition of the proteasome. Furthermore, STBD1 undergoes ubiquitination when expressed in COS cells, and requires the N-terminus for this process. In contrast, inhibition of autophagy did not significantly affect protein stability. In overexpression experiments, we discovered that STBD1 interacts with several glycogen-associated proteins, such as GS (glycogen synthase), GDE (glycogen debranching enzyme) and Laforin. Importantly, the W293 mutant of STBD1 was unable to do so, suggesting an additional role for the CBM20 domain in protein–protein interactions. In HepG2 hepatoma cells, overexpressed STBD1 could associate with endogenous GS. This binding increased during glycogenolysis, suggesting that glycogen is not required to bridge this interaction. Taken together, our results have uncovered new insights into the regulation and binding partners of STBD1.     

The chromosomal localization of human β-galactosidase revisited: a locus for β-galactosidase on human chromosome 3 and for its protective protein on human chromosome 22

Summary A series of man-Chinese hamster and man-mouse somatic cell hybrids was investigated to study the localization of the genes coding for the human lysosomal enzyme -galactosidase (EC 3.2.1.23) and for its protective protein. Using a monoclonal antibody, raised against human placental -galactosidase, it was observed that the structural locus for the -galactosidase polypeptide is located on chromosome 3. The nature of the involvement of chromosome 22 in the expression of human -galactosidase was elucidated by metabolic labelling of the hybrids with radioactive amino acids, immunoprecipitation with monoclonal and polyclonal antibodies against -galactosidase, followed by analysis via gel electrophoresis and fluorography.The data show that the presence of chromosome 22 coincides with the presence of a 32 kd protein. This polypeptide, the protective protein was previously shown to be intimately associated with human -galactosidase. In addition, the protective protein was found to be essential for the in vivo stability of -galactosidase by aggregating -galactosidase monomers into high molecular weight multimes. Both chromosome 3 and 22 are therefore necessary to obtain normal levels og -galactosidase activity in human cells.     

p24 family type 1 transmembrane proteins are required for insulin biosynthesis and secretion in pancreatic β-cells

The p24 protein family have multiple functions in protein transport in the early secretory pathway. In this study we examined the role of p24 proteins in insulin transport. Several members were detected in insulinoma cell lines and rat islets and expression levels positively correlated with insulin abundance, particularly for p24δ1 and p24β1. Knocking down p24δ1 in insulinoma cell lines, which also resulted in the concomitant knock-down of other family members, impaired glucose-stimulated insulin secretion, decreased total cellular insulin content and reduced proinsulin biosynthesis. There was no effect on overall protein biosynthesis or ER stress. These results suggest that p24δ1 and possibly other p24 family proteins are required for normal insulin biosynthesis and subsequent secretion in pancreatic β-cells.     

ßFTZ-F1 and Matrix metalloproteinase 2 are required for fat-body remodeling in Drosophila

During metamorphosis, holometabolous insects eliminate obsolete larval tissues via programmed cell death. In contrast, tissues required for further development are retained and often remodeled to meet the needs of the adult fly. The larval fat body is involved in fueling metamorphosis, and thus it escapes cell death and is instead remodeled during prepupal development. The molecular mechanisms by which the fat body escapes programmed cell death have not yet been described, but it has been established that fat-body remodeling requires 20-hydroxyecdysone (20E) signaling. We have determined that 20E signaling is required within the fat body for the cell-shape changes and cell detachment that are characteristic of fat-body remodeling. We demonstrate that the nuclear hormone receptor ßFTZ-F1 is a key modulator of 20E hormonal induction of fat body remodeling and Matrix metalloproteinase 2 (MMP2) expression in the fat body. We show that induction of MMP2 expression in the fat body requires 20E signaling, and that MMP2 is necessary and sufficient to induce fat-body remodeling.     

The PucC protein of Rhodobacter capsulatus mitigates an inhibitory effect of light-harvesting 2 α and β proteins on light-harvesting complex 1

Rhodobacter capsulatus contains lhaA and pucC genes that have been implicated in light-harvesting complex 1 and 2 (LH1 and LH2) assembly. The proteins encoded by these genes, and homologues in other photosynthetic organisms, have been classified as the bacteriochlorophyll delivery (BCD) family of the major facilitator superfamily. A new BCD family phylogenetic tree reveals that several PucC, LhaA and Orf428-related sequences each form separate clusters, while plant and cyanobacterial homologues cluster more distantly. The PucC protein is encoded in the pucBACDE superoperon which also codes for LH2 α (PucA) and β (PucB) proteins. PucC was previously shown to be necessary for formation of LH2. This article gives evidence indicating that PucC has a shepherding activity that keeps the homologous α and β proteins of LH1 and LH2 apart, allowing LH1 to assemble properly. This shepherding function was indicated by a 62% reduction in LH1 levels in ΔLHII strains carrying plasmids encoding pucBA along with a C-terminally truncated pucC gene. More severe reductions in LH1 were seen when the truncated pucC gene was co-expressed in the presence of C-terminal PucC::PhoA fusion proteins. It appears that interaction between truncated PucC::PhoA fusion proteins and the truncated PucC protein disrupts LH1 assembly, pointing towards a PucC dimeric or multimeric functional unit.     

Intact MDM2 E3 ligase activity is required for the cytosolic localization and function of β-arrestin2

β-arrestins are well known for their roles in desensitization and sequestration of G protein-coupled receptors. Unlike β-arrestin1, β-arrestin2 exhibits a predominant cytoplasmic distribution at steady state. However, the mechanism and functional significance underlying the regulation of β-arrestin2 subcellular localization remains undefined. Here we report that the subcellular localization and function of β-arrestin2 is tightly regulated by Mdm2 E3 ligase activity. Inhibition of Mdm2 E3 ligase activity either by expressing Mdm2 RING finger mutants or using specific Mdm2 E3 ligase inhibitor is sufficient to stabilize the Mdm2/β-arrestin2 complex and cause abnormal nuclear localization of β-arrestin2. Next we demonstrate that lysine residues at position 11 and 12 of β-arrestin2 are required for the interaction between Mdm2 RING finger mutant H457S (Mdm2(H457S)) and β-arrestin2, mutation of which prevents Mdm2(H457S)/β-arrestin2 interaction and subsequent nuclear localization of β-arrestin2. Finally, β-arrestin2-dependent signalings, such as receptor internalization and extracellular signal-regulated protein kinase activation, are found to be impaired once the β-arrestin2 is sequestered in the nuclei by Mdm2(H457S). Our findings depict the essential role of Mdm2 E3 ligase activity in determining β-arrestin2 subcellular localization and corresponding signaling.     

Co-suppression of synthesis of major α-kafirin sub-class together with γ-kafirin-1 and γ-kafirin-2 required for substantially improved protein digestibility in transgenic sorghum

Key message

Co-suppressing major kafirin sub-classes is fundamental to improved protein digestibility and nutritional value of sorghum. The improvement is linked to an irregularly invaginated phenotype of protein bodies.

Abstract

The combined suppression of only two genes, γ kafirin-1 (25 kDa) and γ-kafirin-2 (50 kDa), significantly increases sorghum kafirin in vitro digestibility. Co-suppression of a third gene, α-kafirin A1 (25 kDa), in addition to the two genes increases the digestibility further. The high-digestibility trait has previously only been obtained either through the co-suppression of six kafirin genes (α-A1, 25 kDa; α-B1, 19 kDa; α-B2, 22 kDa; γ-kaf1, 27 kDa; γ-kaf 2, 50 kDa; and δ-kaf 2, 18 kDa) or through random chemical-induced mutations (for example, the high protein digestibility mutant). We present further evidence that suppressing just three of these genes alters kafirin protein cross-linking and protein body microstructure to an irregularly invaginated phenotype. The irregular invaginations are consistent with high pepsin enzyme accessibility and hence high digestibility. The approach we adopted towards increasing sorghum protein digestibility appears to be an effective tool in improving the status of sorghum as a principal supplier of energy and protein in poor communities residing in marginal agro-ecological zones of Africa.     

Signaling components of the 1α,25(OH)2D3-dependent Pdia3 receptor complex are required for Wnt5a calcium-dependent signaling

Wnt5a and 1α,25(OH)₂D₃ are important regulators of endochondral ossification. In osteoblasts and growth plate chondrocytes, 1α,25(OH)₂D₃ initiates rapid effects via its membrane-associated receptor protein disulfide isomerase A3 (Pdia3) in caveolae, activating phospholipase A₂ (PLA₂)-activating protein (PLAA), calcium/calmodulin-dependent protein kinase II (CaMKII), and PLA₂, resulting in protein kinase C (PKC) activation. Wnt5a initiates its calcium-dependent effects via intracellular calcium release, activating PKC and CaMKII. We investigated the requirement for components of the Pdia3 receptor complex in Wnt5a calcium-dependent signaling. We determined that Wnt5a signals through a CaMKII/PLA₂/PGE₂/PKC cascade. Silencing or blocking Pdia3, PLAA, or vitamin D receptor (VDR), and inhibition of calmodulin (CaM), CaMKII, or PLA₂ inhibited Wnt5a-induced PKC activity. Wnt5a activated PKC in caveolin-1-silenced cells, but methyl-beta-cyclodextrin reduced its stimulatory effect. 1α,25(OH)₂D₃ reduced stimulatory effects of Wnt5a on PKC in a dose-dependent manner. In contrast, Wnt5a had a biphasic effect on 1α,25(OH)₂D₃-stimulated PKC activation; 50 ng/ml Wnt5a caused a 2-fold increase in 1α,25(OH)₂D₃-stimulated PKC but higher Wnt5a concentrations reduced 1α,25(OH)₂D₃-stimulated PKC activation. Western blots showed that Wnt receptors Frizzled2 (FZD2) and Frizzled5 (FZD5), and receptor tyrosine kinase-like orphan receptor 2 (ROR2) were localized to caveolae. Blocking ROR2, but not FZD2 or FZD5, abolished the stimulatory effects of 1α,25(OH)₂D₃ on PKC and CaMKII. 1α,25(OH)₂D₃ membrane receptor complex components (Pdia3, PLAA, caveolin-1, CaM) interacted with Wnt5a receptors/co-receptors (ROR2, FZD2, FZD5) in immunoprecipitation studies, interactions that changed with either 1α,25(OH)₂D₃ or Wnt5a treatment. This study demonstrates that 1α,25(OH)₂D₃ and Wnt5a mediate their effects via similar receptor components and suggests that these pathways may interact.     

The Center for Optimized Structural Studies (COSS) platform for automation in cloning,expression, and purification of single proteins and protein–protein complexes

Expression in Escherichia coli represents the simplest and most cost effective means for the production of recombinant proteins. This is a routine task in structural biology and biochemistry where milligrams of the target protein are required in high purity and monodispersity. To achieve these criteria, the user often needs to screen several constructs in different expression and purification conditions in parallel. We describe a pipeline, implemented in the Center for Optimized Structural Studies, that enables the systematic screening of expression and purification conditions for recombinant proteins and relies on a series of logical decisions. We first use bioinformatics tools to design a series of protein fragments, which we clone in parallel, and subsequently screen in small scale for optimal expression and purification conditions. Based on a scoring system that assesses soluble expression, we then select the top ranking targets for large-scale purification. In the establishment of our pipeline, emphasis was put on streamlining the processes such that it can be easily but not necessarily automatized. In a typical run of about 2 weeks, we are able to prepare and perform small-scale expression screens for 20–100 different constructs followed by large-scale purification of at least 4–6 proteins. The major advantage of our approach is its flexibility, which allows for easy adoption, either partially or entirely, by any average hypothesis driven laboratory in a manual or robot-assisted manner.