PubMed Health⌕ Search

Biomedical subjects

Peter Walter

Publications and source records attributed to Peter Walter.

35 records · Page 2Linked to original sources
PubMed2004

Genome-scale approaches for discovering novel nonconventional splicing substrates of the Ire1 nuclease.

BACKGROUND: The unfolded protein response (UPR) allows intracellular feedback regulation that adjusts the protein-folding capacity of the endoplasmic reticulum (ER) according to need. The signal from the ER lumen is transmitted by the ER-transmembrane kinase Ire1, which upon activation displays a site-specific endoribonuclease activity. Endonucleolytic cleavage of the intron from the HAC1 mRNA (encoding a UPR-specific transcription factor) is the first step in a nonconventional mRNA splicing pathway; the released exons are then joined by tRNA ligase. Because only the spliced mRNA is translated, splicing is the key regulatory step of the UPR. RESULTS: We developed methods to search for additional mRNA substrates of Ire1p in three independent lines of genome-wide analysis. These methods exploited the well characterized enzymology and genetics of the UPR and the yeast genome sequence in conjunction with microarray-based detection. Each method successfully identified HAC1 mRNA as a substrate according to three criteria: HAC1 mRNA is selectively cleaved in vitro by Ire1; the HAC1 mRNA sequence contains two predicted Ire1 cleavage sites; and HAC1 mRNA is selectively degraded in tRNA ligase mutant cells. CONCLUSION: Within the limits of detection, no other mRNA satisfies any of these criteria, suggesting that a unique nonconventional mRNA-processing mechanism has evolved solely for carrying out signal transduction between the ER and the nucleus. The approach described here, which combines biochemical and genetic 'fractionation' of mRNA with a novel application of cDNA microarrays, is generally applicable to the study of pathways in which RNA metabolism and alternative splicing have a regulatory role.

Alternative Splicing↗
PubMed2004

Unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry.

Among the methods used to unravel protein interaction surfaces, chemical cross-linking followed by identification of the cross-linked peptides by mass spectrometry has proven especially useful in dynamic and complex systems. During the signal recognition particle (SRP)-dependent targeting of proteins to the bacterial plasma membrane, the specific interaction between Ffh (the protein component of SRP) and FtsY (the SRP receptor) is known to be essential for the efficiency and fidelity of this process. In this work, we studied the Escherichia coli and Thermus aquaticus Ffh.FtsY complexes by using chemical cross-linking and tandem mass spectrometry to identify nine intermolecular cross-linked peptides. This information was used in conjunction with a previously undescribed model-building approach that combines geometric restraint optimization with macromolecular docking. The resulting model of the Ffh.FtsY complex is in good agreement with the crystal structure solved shortly thereafter. Intriguingly, four of the cross-linked pairs involve the M domain of Ffh, which is absent from the crystal structure, providing previously undocumented experimental evidence that the M domain is positioned in close proximity to the Ffh.FtsY interface in the complex.

Bacterial Proteins↗
PubMed2004

Gene recruitment of the activated INO1 locus to the nuclear membrane.

The spatial arrangement of chromatin within the nucleus can affect reactions that occur on the DNA and is likely to be regulated. Here we show that activation of INO1 occurs at the nuclear membrane and requires the integral membrane protein Scs2. Scs2 antagonizes the action of the transcriptional repressor Opi1 under conditions that induce the unfolded protein response (UPR) and, in turn, activate INO1. Whereas repressed INO1 localizes throughout the nucleoplasm, the gene is recruited to the nuclear periphery upon transcriptional activation. Recruitment requires the transcriptional activator Hac1, which is produced upon induction of the UPR, and is constitutive in a strain lacking Opi1. Artificial recruitment of INO1 to the nuclear membrane permits activation in the absence of Scs2, indicating that the intranuclear localization of a gene can profoundly influence its mechanism of activation. Gene recruitment to the nuclear periphery, therefore, is a dynamic process and appears to play an important regulatory role.

Basic Helix-Loop-Helix Proteins↗
PubMed2004

Mechanism of association and reciprocal activation of two GTPases.

The signal recognition particle (SRP) mediates the cotranslational targeting of nascent proteins to the eukaryotic endoplasmic reticulum membrane or the bacterial plasma membrane. During this process, two GTPases, one in SRP and one in the SRP receptor (named Ffh and FtsY in bacteria, respectively), form a complex in which both proteins reciprocally activate the GTPase reaction of one another. Here, we explore by site-directed mutagenesis the role of 45 conserved surface residues in the Ffh-FtsY interaction. Mutations of a large number of residues at the interface impair complex formation, supporting the importance of an extensive interaction surface. Surprisingly, even after a stable complex is formed, single mutations in FtsY can block the activation of GTP hydrolysis in both active sites. Thus, activation requires conformational changes across the interface that coordinate the positioning of catalytic residues in both GTPase sites. A distinct class of mutants exhibits half-site reactivity and thus allows us to further uncouple the activation of individual GTPases. Our dissection of the activation process suggests discrete conformational stages during formation of the active SRP*SRP receptor complex. Each stage provides a potential control point in the targeting reaction at which regulation by additional components can be exerted, thus ensuring the binding and release of cargo at the appropriate time.

Bacterial Proteins↗
PubMed2004

IRE1-independent gain control of the unfolded protein response.

Nonconventional splicing of the gene encoding the Hac1p transcription activator regulates the unfolded protein response (UPR) in Saccharomyces cerevisiae. This simple on/off switch contrasts with a more complex circuitry in higher eukaryotes. Here we show that a heretofore unrecognized pathway operates in yeast to regulate the transcription of HAC1. The resulting increase in Hac1p production, combined with the production or activation of a putative UPR modulatory factor, is necessary to qualitatively modify the cellular response in order to survive the inducing conditions. This parallel endoplasmic reticulum-to-nucleus signaling pathway thereby serves to modify the UPR-driven transcriptional program. The results suggest a surprising conservation among all eukaryotes of the ways by which the elements of the UPR signaling circuit are connected. We show that by adding an additional signaling element to the basic UPR circuit, a simple switch is transformed into a complex response.

Alternative Splicing↗
PubMed2004

Gcn4p and novel upstream activating sequences regulate targets of the unfolded protein response.

Eukaryotic cells respond to accumulation of unfolded proteins in the endoplasmic reticulum (ER) by activating the unfolded protein response (UPR), a signal transduction pathway that communicates between the ER and the nucleus. In yeast, a large set of UPR target genes has been experimentally determined, but the previously characterized unfolded protein response element (UPRE), an upstream activating sequence (UAS) found in the promoter of the UPR target gene KAR2, cannot account for the transcriptional regulation of most genes in this set. To address this puzzle, we analyzed the promoters of UPR target genes computationally, identifying as candidate UASs short sequences that are statistically overrepresented. We tested the most promising of these candidate UASs for biological activity, and identified two novel UPREs, which are necessary and sufficient for UPR activation of promoters. A genetic screen for activators of the novel motifs revealed that the transcription factor Gcn4p plays an essential and previously unrecognized role in the UPR: Gcn4p and its activator Gcn2p are required for induction of a majority of UPR target genes during ER stress. Both Hac1p and Gcn4p bind target gene promoters to stimulate transcriptional induction. Regulation of Gcn4p levels in response to changing physiological conditions may function as an additional means to modulate the UPR. The discovery of a role for Gcn4p in the yeast UPR reveals an additional level of complexity and demonstrates a surprising conservation of the signaling circuit between yeast and metazoan cells.

Amino Acid Motifs↗
PubMed2004

Visual outcome of patients with macular edema after pars plana vitrectomy and indocyanine green-assisted peeling of the internal limiting membrane.

PURPOSE: To evaluate the efficacy of inner limiting membrane (ILM) peeling in persistent macular edema. METHODS: This retrospective review analyzed a series of 23 eyes from 23 patients with persistent macular edema treated by pars plana vitrectomy (PPV) with indocyanine green (ICG)-assisted peeling of the ILM. Thirteen female and 10 male patients with a mean age of 57.2+/-15.6 (24-77) years underwent operation between May 2000 and October 2001. The main diagnoses were uveitis (anterior, intermediate, posterior and panuveitis) ( n=9), central retinal vein occlusion (CRVO) (n=4), diabetic retinopathy (DR) ( n=5), vitreoretinal traction syndrome ( n=2), and Irvine-Gass syndrome ( n=3). Nine eyes had undergone phacoemulsification (PE) previously and two eyes had been subjected to combined PE and ILM peeling. The eyes were tamponaded with gas (3), silicone oil (5) or air (11). In four cases no endotamponade was used. Improvement in visual acuity of 2 lines or more was regarded as significant. RESULTS: Visual acuity improved after 3 months in 9 of the 23 patients. After 6 months and at the follow-up, a significant improvement was found in 6/21 and 7/21 patients. This improvement was predominantly seen in patients with uveitis (5/9), or diabetic maculopathy (3/5); One patient with Irvine-Gass syndrome showed a significant reduction, one with vitreoretinal traction an improvement in visual acuity. The group of patients with CRVO showed no significant change during the follow-up. The choice of endotamponade did not alter the visual acuity outcome. CONCLUSIONS: Different patient groups respond differently to ILM peeling. Although overall significant visual acuity improvement was observed in only one third of all cases 12 months after ILM peeling for persistent macular edema, patients with uveitis and nonproliferative diabetic maculopathy demonstrated a benefit. The lack of long-term improvement in the majority of cases is in accordance with the hypothesis that ILM peeling may reduce the intraretinal edema, but does not affect the underlying mechanism causing macular edema. So far, only diabetics have shown improvement (still unproven) from ILM peeling, and this study provides no justification for extending the treatment to macular edema of other causes. Large-scale investigations are needed to evaluate the efficacy in certain diagnosis groups.

Adult↗
PubMed2004

Substrate twinning activates the signal recognition particle and its receptor.

Signal sequences target proteins for secretion from cells or for integration into cell membranes. As nascent proteins emerge from the ribosome, signal sequences are recognized by the signal recognition particle (SRP), which subsequently associates with its receptor (SR). In this complex, the SRP and SR stimulate each other's GTPase activity, and GTP hydrolysis ensures unidirectional targeting of cargo through a translocation pore in the membrane. To define the mechanism of reciprocal activation, we determined the 1.9 A structure of the complex formed between these two GTPases. The two partners form a quasi-two-fold symmetrical heterodimer. Biochemical analysis supports the importance of the extensive interaction surface. Complex formation aligns the two GTP molecules in a symmetrical, composite active site, and the 3'OH groups are essential for association, reciprocal activation and catalysis. This unique circle of twinned interactions is severed twice on hydrolysis, leading to complex dissociation after cargo delivery.

Amino Acid Sequence↗
PubMed2003

Bypassing a kinase activity with an ATP-competitive drug.

Unfolded proteins in the endoplasmic reticulum cause trans-autophosphorylation of the bifunctional transmembrane kinase Ire1, which induces its endoribonuclease activity. The endoribonuclease initiates nonconventional splicing of HAC1 messenger RNA to trigger the unfolded-protein response (UPR). We explored the role of Ire1's kinase domain by sensitizing it through site-directed mutagenesis to the ATP-competitive inhibitor 1NM-PP1. Paradoxically, rather than being inhibited by 1NM-PP1, drug-sensitized Ire1 mutants required 1NM-PP1 as a cofactor for activation. In the presence of 1NM-PP1, drug-sensitized Ire1 bypassed mutations that inactivate its kinase activity and induced a full UPR. Thus, rather than through phosphorylation per se, a conformational change in the kinase domain triggered by occupancy of the active site with a ligand leads to activation of all known downstream functions.

Adenosine Diphosphate↗
PubMed2003

Electro-oculographic findings after 360 degrees retinotomy and macular translocation for subfoveal choroidal neovascularisation in age-related macular degeneration.

PURPOSE: To evaluate potential electro-oculographic changes after 360 degrees retinotomy and macular translocation for subfoveal choroidal neovascularisation in patients with age-related macular degeneration (AMD) in a randomised comparative (self-controlled) trial. METHODS: A consecutive series of 30 patients suffering from subfoveal choroidal neovascularisation secondary to age-related macular degeneration underwent 360 degrees retinotomy and macular translocation. The EOG served as the main parameter of the study and was recorded 1 day prior to the translocation surgery and no earlier than 21 days after the silicone oil removal. RESULTS: Postoperatively, a statistically significant decrease in mean dark trough by 64% was found for treated eyes (P<0.001). The mean dark trough of the fellow eye remained stable after surgery (P=0.33). The postoperative difference between the treated und untreated eyes proved to be statistically significant (P<0.001). The Arden ratio remained stable in the treated and untreated eyes with mean values of 204% (P=0.81) and 213% (P=0.18), respectively. A significant correlation between the reduction of the dark trough and the visual acuity at the 1-year follow-up was found. CONCLUSIONS: A persistent decrease in the corneofundal potential is associated with 360 degrees retinotomy and macular translocation for exudative AMD. This indicates a substantial postoperative malfunction of retinal pigment epithelial cells and an impaired photoreceptor regeneration. The impeded recovery of the RPE-photoreceptor complex can be interpreted as the result of the surgical trauma on the basis of prediseased RPE. A severe postoperative decrease in dark trough forecasts an incomplete recovery of visual acuity.

Choroidal Neovascularization↗
PubMed2003

Induced nucleotide specificity in a GTPase.

In signal-recognition particle (SRP)-dependent protein targeting to the bacterial plasma membrane, two GTPases, Ffh (a subunit of the bacterial SRP) and FtsY (the bacterial SRP receptor), act as GTPase activating proteins for one another. The molecular mechanism of this reciprocal GTPase activation is poorly understood. In this work, we show that, unlike other GTPases, free FtsY exhibits only low preference for GTP over other nucleotides. On formation of the SRP.FtsY complex, however, the nucleotide specificity of FtsY is enhanced 10(3)-fold. Thus, interactions with SRP must induce conformational changes that directly affect the FtsY GTP-binding site: in response to SRP binding, FtsY switches from a nonspecific "open" state to a "closed" state that provides discrimination between cognate and noncognate nucleotides. We propose that this conformational change leads to more accurate positioning of the nucleotide and thus could contribute to activation of FtsY's GTPase activity by a novel mechanism.

Bacterial Proteins↗
PubMed2003

Intermediate uveitis in childhood preceding the diagnosis of multiple sclerosis: a 13-year follow-up.

PURPOSE: An association between multiple sclerosis during childhood and uveitis is exceptionally rare. This is a report of a female patient who presented at the age of 8 years with bilateral intermediate uveitis and whose final diagnosis of multiple sclerosis was made at age 21 years. DESIGN: Case report. METHOD: Retrospective chart review of a 13-year follow-up history. RESULTS: Over 10 years our patient was treated systemically and underwent bilateral vitrectomy to reduce permanent side effects. Owing to good visual function and low inflammatory signs, systemic therapy was stopped. Multiple sclerosis was diagnosed at the age of 21, after a 13-year history of uveitis and after 3 years without medication. CONCLUSIONS: In the constellation of uveitis in childhood and later diagnosis of multiple sclerosis, the outlined therapy provided good functional results. Moreover, it may have delayed the manifestation of the underlying disease for 13 years.

Azathioprine↗
PubMed2003

The effect of membrane differential filtration on the colloid osmotic pressure in patients with age-related macular degeneration: significance to visual function?

To investigate the effect of membrane differential filtration (MDF) on plasma colloid osmotic pressure (COP) and visual functions in age-related geographic macular degeneration (AMD). Ten consecutive patients with non-exudative AMD underwent one MDF cycle. Primary endpoint was COP. Secondary endpoints were visual acuity and the mean defect of visual field. The COP was markedly reduced after one MDF cycle by 23.9% (P = 0.001). Compared with the baseline examination, visual acuity and the mean defect of visual field improved significantly after MDF. A significant positive correlation was found between the improvement in visual field and the decrease in COP (Pearson's coefficient = 0.65; P = 0.04). Membrane differential filtration lowers plasma colloid osmotic pressure in patients with non-exudative AMD. Based on the observation that visual field and COP are correlated, one may hope for a means to improve decreased central retinal function in eyes with geographic AMD by modulation of COP plasma level.

Female↗
PubMed2002

Structural basis for mobility in the 1.1 A crystal structure of the NG domain of Thermus aquaticus Ffh.

The NG domain of the prokaryotic signal recognition protein Ffh is a two-domain GTPase that comprises part of the prokaryotic signal recognition particle (SRP) that functions in co-translational targeting of proteins to the membrane. The interface between the N and G domains includes two highly conserved sequence motifs and is adjacent in sequence and structure to one of the conserved GTPase signature motifs. Previous structural studies have shown that the relative orientation of the two domains is dynamic. The N domain of Ffh has been proposed to function in regulating the nucleotide-binding interactions of the G domain. However, biochemical studies suggest a more complex role for the domain in integrating communication between signal sequence recognition and interaction with receptor. Here, we report the structure of the apo NG GTPase of Ffh from Thermus aquaticus refined at 1.10 A resolution. Although the G domain is very well ordered in this structure, the N domain is less well ordered, reflecting the dynamic relationship between the two domains previously inferred. We demonstrate that the anisotropic displacement parameters directly visualize the underlying mobility between the two domains, and present a detailed structural analysis of the packing of the residues, including the critical alpha4 helix, that comprise the interface. Our data allows us to propose a structural explanation for the functional significance of sequence elements conserved at the N/G interface.

Bacterial Proteins↗
PubMed2002

Translocation of lipid-linked oligosaccharides across the ER membrane requires Rft1 protein.

N-linked glycosylation of proteins in eukaryotic cells follows a highly conserved pathway. The tetradecasaccharide substrate (Glc3Man9GlcNAc2) is first assembled at the membrane of the endoplasmic reticulum (ER) as a dolichylpyrophosphate (Dol-PP)-linked intermediate, and then transferred to nascent polypeptide chains in the lumen of the ER. The assembly of the oligosaccharide starts on the cytoplasmic side of the ER membrane with the synthesis of a Man5GlcNAc2-PP-Dol intermediate. This lipid-linked intermediate is then translocated across the membrane so that the oligosaccharides face the lumen of the ER, where the biosynthesis of Glc3Man9GlcNAc2-PP-Dol continues to completion. The fully assembled oligosaccharide is transferred to selected asparagine residues of target proteins. The transmembrane movement of lipid-linked Man5GlcNAc2 oligosaccharide is of fundamental importance in this biosynthetic pathway, and similar processes involving phospholipids and glycolipids are essential in all types of cells. The process is predicted to be catalysed by proteins, termed flippases, which to date have remained elusive. Here we provide evidence that yeast RFT1 encodes an evolutionarily conserved protein required for the translocation of Man5GlcNAc2-PP-Dol from the cytoplasmic to the lumenal leaflet of the ER membrane.

Asparagine↗
PubMed2002

Macular translocation with 360 degrees retinotomy for exudative age-related macular degeneration.

BACKGROUND: Macular rotation surgery comprises surgical extraction of choroidal neovascular membranes in age-related macular degeneration (AMD) and translocation of the foveal neural retina over adjacent retinal pigment epithelium. OBJECTIVE: To determine whether macular translocation with 360 degrees retinotomy can stabilize and/or improve visual acuity in patients with subfoveal choroidal neovascularization (CNV) secondary to AMD. DESIGN: This study consisted of a standardized surgical procedure on a series of 90 consecutive patients and follow-up examinations at fixed intervals for 12 months. PARTICIPANTS: All patients in this study had experienced recent visual loss resulting from subfoveal CNV caused by AMD. Twenty-six patients had major macular subretinal hemorrhage, 39 patients had occult subfoveal CNV, and 25 patients had classic subfoveal CNV. METHODS: Macular translocation surgery was performed between 1997 and 1999. The patients were examined preoperatively and at 3, 6, and 12 months postoperatively, including visual acuity, microperimetry, angiography, and orthoptic assessment. RESULTS: Visual acuity increased by 15 or more letters in 24 patients, remained stable in 37 patients, and deteriorated by 15 or more letters in 29 patients at 12 months postoperatively. A secondary procedure was necessary in 17 patients because of severe complications; proliferative vitreoretinopathy was observed in 17 eyes, macular pucker in 5 eyes, and macular hole in 1 patient. CONCLUSION: Macular translocation is a technically demanding surgical procedure. Although the procedure has a high rate of surgical and postoperative complications, the functional and anatomical results appear to be promising for selected patients with subfoveal CNV secondary to AMD.

Aged↗