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1.
Nucleic Acids Res ; 49(20): 11491-11511, 2021 11 18.
Article in English | MEDLINE | ID: mdl-34648019

ABSTRACT

The eukaryotic initiation factor 3 (eIF3) complex is involved in every step of translation initiation, but there is limited understanding of its molecular functions. Here, we present a single particle electron cryomicroscopy (cryo-EM) reconstruction of yeast 48S ribosomal preinitiation complex (PIC) in an open conformation conducive to scanning, with core subunit eIF3b bound on the 40S interface near the decoding center in contact with the ternary complex eIF2·GTP·initiator tRNA. eIF3b is relocated together with eIF3i from their solvent interface locations observed in other PIC structures, with eIF3i lacking 40S contacts. Re-processing of micrographs of our previous 48S PIC in a closed state also suggests relocation of the entire eIF3b-3i-3g-3a-Cter module during the course of initiation. Genetic analysis indicates that high fidelity initiation depends on eIF3b interactions at the 40S subunit interface that promote the closed PIC conformation, or facilitate the relocation of eIF3b/eIF3i to the solvent interface, on start codon selection.


Subject(s)
Codon, Initiator , Eukaryotic Initiation Factor-3/chemistry , Fungal Proteins/chemistry , Peptide Chain Initiation, Translational , Ribosomes/ultrastructure , Cryoelectron Microscopy , Eukaryotic Initiation Factor-3/metabolism , Fungal Proteins/metabolism , Guanosine Triphosphate/chemistry , Guanosine Triphosphate/metabolism , Kluyveromyces , Molecular Dynamics Simulation , Protein Binding , RNA, Transfer/chemistry , RNA, Transfer/metabolism , Ribosomes/metabolism , Single Molecule Imaging
2.
J Inherit Metab Dis ; 43(4): 657-670, 2020 07.
Article in English | MEDLINE | ID: mdl-32017139

ABSTRACT

The bifunctional homooligomeric enzyme Δ1 -pyrroline-5-carboxylate synthetase (P5CS) and its encoding gene ALDH18A1 were associated with disease in 1998. Two siblings who presented paradoxical hyperammonemia (alleviated by protein), mental disability, short stature, cataracts, cutis laxa, and joint laxity, were found to carry biallelic ALDH18A1 mutations. They showed biochemical indications of decreased ornithine/proline synthesis, agreeing with the role of P5CS in the biosynthesis of these amino acids. Of 32 patients reported with this neurocutaneous syndrome, 21 familial ones hosted homozygous or compound heterozygous ALDH18A1 mutations, while 11 sporadic ones carried de novo heterozygous ALDH18A1 mutations. In 2015 to 2016, an upper motor neuron syndrome (spastic paraparesis/paraplegia SPG9) complicated with some traits of the neurocutaneous syndrome, although without report of cutis laxa, joint laxity, or herniae, was associated with monoallelic or biallelic ALDH18A1 mutations with, respectively, dominant and recessive inheritance. Of 50 SPG9 patients reported, 14 and 36 (34/2 familial/sporadic) carried, respectively, biallelic and monoallelic mutations. Thus, two neurocutaneous syndromes (recessive and dominant cutis laxa 3, abbreviated ARCL3A and ADCL3, respectively) and two SPG9 syndromes (recessive SPG9B and dominant SPG9A) are caused by essentially different spectra of ALDH18A1 mutations. On the bases of the clinical data (including our own prior patients' reports), the ALDH18A1 mutations spectra, and our knowledge on the P5CS protein, we conclude that the four syndromes share the same pathogenic mechanisms based on decreased P5CS function. Thus, these syndromes represent a continuum of increasing severity (SPG9A < SPG9B < ADCL3 ≤ ARCL3A) of the same disease, P5CS deficiency, in which the dominant mutations cause loss-of-function by dominant-negative mechanisms.


Subject(s)
Aldehyde Dehydrogenase/genetics , Bone and Bones/abnormalities , Cataract/genetics , Growth Disorders/genetics , Spastic Paraplegia, Hereditary/genetics , Aldehyde Dehydrogenase/deficiency , Humans , Mutation , Pedigree , Phenotype , Urea/metabolism
3.
World Neurosurg ; 135: e339-e349, 2020 Mar.
Article in English | MEDLINE | ID: mdl-31811967

ABSTRACT

OBJECTIVES: Since the introduction of endovascular treatment for cerebral aneurysms, hospitals in which subarachnoid hemorrhage is treated show different availability and/or preferences towards both treatment modalities. The main aim is to evaluate the clinical and angiographic results according to the hospital's treatment preferences applied. METHODS: This study was conducted based on use of the subarachnoid hemorrhage database of the Vascular Pathology Group of the Spanish Neurosurgery Society. Centers were classified into 3 subtypes according to an index in the relationship between endovascular and surgical treatment as: endovascular preference, high endovascular preference, and elevated surgical preference. The clinical results and angiographic results were evaluated among the 3 treatment strategies. RESULTS: From November 2004 to December 2017, 4282 subarachnoid hemorrhage patients were selected for the study: 630 (14.7%) patients from centers with surgical preference, 2766 (64.6%) from centers with endovascular preference, and 886 (20.7%) from centers with high endovascular preference. The surgical preference group obtained the best angiographic results associated with a greater complete exclusion (odds ratio: 1.359; 95% confidence interval: 1.025-1.801; P = 0.033). The surgical preference subgroup obtained the best outcome at discharge (65.45%), followed by the high endovascular preference group (61.5%) and the endovascular preference group (57.8%) (odds ratio: 1.359; 95% confidence interval: 1.025-1.801; P = 0.033). CONCLUSIONS: In Spain, there is significant variability in aneurysm exclusion treatment in aneurysmal subarachnoid hemorrhage. Surgical centers offer better results for both surgical and endovascular patients. A multidisciplinary approach and the maintenance of an elevated quality of surgical competence could be responsible for these results.


Subject(s)
Endovascular Procedures , Intracranial Aneurysm/surgery , Neurosurgical Procedures , Subarachnoid Hemorrhage/surgery , Adult , Aged , Databases, Factual , Endovascular Procedures/methods , Female , Humans , Male , Middle Aged , Neurosurgical Procedures/methods , Surgical Instruments , Treatment Outcome
4.
Neurocirugía (Soc. Luso-Esp. Neurocir.) ; 30(5): 215-221, sept.-oct. 2019. graf
Article in Spanish | IBECS | ID: ibc-183874

ABSTRACT

Introducción: El tratamiento de elección para la mayor parte de los adenomas hipofisarios es su resección quirúrgica por vía transesfenoidal. Las fístulas posquirúrgicas de líquido cefalorraquídeo (LCR) constituyen una de las complicaciones más características y potencialmente graves de este tratamiento. Su incidencia es variable para las principales series publicadas en la literatura, con un rango del 0,5 al 15%. Objetivos: El objetivo principal de nuestro trabajo fue establecer la incidencia de fístulas de LCR tras cirugía transesfenoidal en una muestra de 302 intervenciones realizadas en pacientes afectos de adenomas hipofisarios en el Hospital Universitario de la Ribera y por un mismo equipo quirúrgico. Como objetivos secundarios se plantearon: conocer las características diferenciales entre pacientes con y sin fístulas posquirúrgicas de LCR, detectar factores de riesgo para su desarrollo, valorar la relación entre la técnica de cierre de la silla turca y la aparición de fístulas posquirúrgicas de LCR y valorar las diferentes pautas de tratamiento de la complicación. Métodos: Se realizó un estudio descriptivo retrospectivo basado en una revisión sistemática de 302 casos de adenomas hipofisarios intervenidos en nuestro centro a través de una vía de abordaje transesfenoidal entre los años 1999 y 2017. Resultados y conclusiones: La incidencia de fístulas posquirúrgicas de LCR en nuestra serie fue del 2,3% (concordante con la descrita en series amplias previamente publicadas). La aparición de una fístula intraoperatoria de LCR se correlacionó con dos variables del estudio: macroadenomas y tumores con extensión supraselar (p<0,005). Esta correlación no existió para fístulas posquirúrgicas. Sí fue posible establecer una relación estadísticamente significativa entre la aparición de fístulas intraoperatorias y posquirúrgicas de LCR (p<0,005). La baja incidencia de fístulas posquirúrgicas de LCR tras cirugía transesfenoidal de adenomas hipofisarios en nuestra casuística no permitió identificar factores de riesgo para su desarrollo


Introduction: Transsphenoidal surgical removal is the preferred treatment of most pituitary adenomas. Postoperative cerebrospinal fluid (CSF) leakage is the leading cause of morbidity after this procedure, with an incidence rate that varies from 0,5-15% in the main published series. Objectives: The primary objective of this study was to establish the incidence of postoperative CSF leakage in a sample of surgeries performed at the University Hospital of La Ribera by the same surgical team. The secondary objectives were to: ascertain the distinctive features between patients with and without postoperative CSF leakage, identify risk factors for their development, evaluate the relationship between the surgical technique for closing the sella turcica and the onset of postoperative CSF leakage and evaluate different treatment regimens for this complication. Methods: The data of 302 consecutive transsphenoidal surgical procedures for pituitary adenoma removal which were performed between 1999 and 2017 were retrospectively reviewed. Results and conclusions: The incidence of postoperative CSF leakage in our series was 2,3% (in accordance with similar published studies). It was possible to correlate intraoperative CSF leakage with two variables: pituitary macroadenoma and tumors with suprasellar extension (P<.005). This correlation did not exist for postoperative CSF leakage. We found a statistically significant correlation between intraoperative and postoperative CSF leakage (P<.005). Due to the low incidence of postoperative CSF leakage in our series, it was not possible to identify risk factors for its development


Subject(s)
Humans , Fistula/surgery , Cerebrospinal Fluid , Adenoma/complications , Adenoma/surgery , Pituitary Neoplasms/complications , Pituitary Neoplasms/surgery , Postoperative Complications , Risk Factors , Retrospective Studies , Neurosurgical Procedures , Sphenoid Bone/surgery
5.
Neurocirugia (Astur : Engl Ed) ; 30(5): 215-221, 2019.
Article in English, Spanish | MEDLINE | ID: mdl-31130305

ABSTRACT

INTRODUCTION: Transsphenoidal surgical removal is the preferred treatment of most pituitary adenomas. Postoperative cerebrospinal fluid (CSF) leakage is the leading cause of morbidity after this procedure, with an incidence rate that varies from 0,5-15% in the main published series. OBJECTIVES: The primary objective of this study was to establish the incidence of postoperative CSF leakage in a sample of surgeries performed at the University Hospital of La Ribera by the same surgical team. The secondary objectives were to: ascertain the distinctive features between patients with and without postoperative CSF leakage, identify risk factors for their development, evaluate the relationship between the surgical technique for closing the sella turcica and the onset of postoperative CSF leakage and evaluate different treatment regimens for this complication. METHODS: The data of 302 consecutive transsphenoidal surgical procedures for pituitary adenoma removal which were performed between 1999 and 2017 were retrospectively reviewed. RESULTS AND CONCLUSIONS: The incidence of postoperative CSF leakage in our series was 2,3% (in accordance with similar published studies). It was possible to correlate intraoperative CSF leakage with two variables: pituitary macroadenoma and tumors with suprasellar extension (P<.005). This correlation did not exist for postoperative CSF leakage. We found a statistically significant correlation between intraoperative and postoperative CSF leakage (P<.005). Due to the low incidence of postoperative CSF leakage in our series, it was not possible to identify risk factors for its development.


Subject(s)
Adenoma/surgery , Cerebrospinal Fluid Leak/etiology , Hypophysectomy/adverse effects , Intraoperative Complications/etiology , Pituitary Neoplasms/surgery , Postoperative Complications/etiology , Adenoma/diagnostic imaging , Adenoma/pathology , Adenoma/radiotherapy , Adolescent , Adult , Aged , Aged, 80 and over , Cerebrospinal Fluid Leak/epidemiology , Cerebrospinal Fluid Rhinorrhea/etiology , Combined Modality Therapy , Cranial Irradiation , Female , Humans , Incidence , Intraoperative Complications/epidemiology , Male , Middle Aged , Neoplasm Invasiveness/pathology , Pituitary Neoplasms/diagnostic imaging , Pituitary Neoplasms/pathology , Pituitary Neoplasms/radiotherapy , Postoperative Complications/epidemiology , Reoperation , Sella Turcica/pathology , Sphenoid Sinus/pathology , Young Adult
6.
Cell ; 167(1): 133-144.e13, 2016 Sep 22.
Article in English | MEDLINE | ID: mdl-27662086

ABSTRACT

In bacterial translational initiation, three initiation factors (IFs 1-3) enable the selection of initiator tRNA and the start codon in the P site of the 30S ribosomal subunit. Here, we report 11 single-particle cryo-electron microscopy (cryoEM) reconstructions of the complex of bacterial 30S subunit with initiator tRNA, mRNA, and IFs 1-3, representing different steps along the initiation pathway. IF1 provides key anchoring points for IF2 and IF3, thereby enhancing their activities. IF2 positions a domain in an extended conformation appropriate for capturing the formylmethionyl moiety charged on tRNA. IF3 and tRNA undergo large conformational changes to facilitate the accommodation of the formylmethionyl-tRNA (fMet-tRNA(fMet)) into the P site for start codon recognition.


Subject(s)
Codon, Initiator , Peptide Chain Initiation, Translational , Prokaryotic Initiation Factor-3/chemistry , RNA, Messenger/chemistry , RNA, Transfer, Met/chemistry , Ribosome Subunits, Small, Bacterial/chemistry , Thermus thermophilus/metabolism , Cryoelectron Microscopy , Crystallography , Protein Conformation , Thermus thermophilus/genetics
7.
Neurocir.-Soc. Luso-Esp. Neurocir ; 27(4): 199-203, jul.-ago. 2016. ilus
Article in English | IBECS | ID: ibc-153754

ABSTRACT

Arterial supply and venous drainage at the foramen magnum is variable. Two main forms of clinical presentation, intracranial and spinal, can be differentiated when a dural arteriovenous fistula (DAVF) is found at this level. We describe a case of a 68-year-old patient with a progressive paraparesis, diagnosed of dural arteriovenous fistula located at the posterior lip of foramen magnum. We review, in this setting, the vascular radiological anatomy of those fistulas and its important correlation with neurologic clinical symptoms


El aporte arterial y el drenaje venoso en el agujero magno son variables. Dos formas principales de presentación clínica, intracraneal y medular pueden ser diferenciadas en las fístulas durales arteriovenosas encontradas a este nivel. Se presenta el caso de un paciente de 68 años que, tras un cuadro de paraparesia progresiva, se diagnostica de una fístula dural arteriovenosa dural localizada en el borde posterior del agujero magno. A propósito de este caso se revisa la anatomía radiológica y vascular de estas fístulas y su importante correlación con los síntomas neurológicos


Subject(s)
Humans , Male , Aged , Arteriovenous Fistula/diagnosis , Foramen Magnum/physiopathology , Spinal Cord Diseases/diagnosis , Drainage , Diagnosis, Differential
8.
Neurocirugia (Astur) ; 27(4): 199-203, 2016.
Article in English | MEDLINE | ID: mdl-26949168

ABSTRACT

Arterial supply and venous drainage at the foramen magnum is variable. Two main forms of clinical presentation, intracranial and spinal, can be differentiated when a dural arteriovenous fistula (DAVF) is found at this level. We describe a case of a 68-year-old patient with a progressive paraparesis, diagnosed of dural arteriovenous fistula located at the posterior lip of foramen magnum. We review, in this setting, the vascular radiological anatomy of those fistulas and its important correlation with neurologic clinical symptoms.


Subject(s)
Central Nervous System Vascular Malformations , Foramen Magnum , Aged , Central Nervous System Vascular Malformations/diagnosis , Central Nervous System Vascular Malformations/therapy , Humans , Male
9.
Mol Cell ; 59(3): 399-412, 2015 Aug 06.
Article in English | MEDLINE | ID: mdl-26212456

ABSTRACT

Translation initiation in eukaryotes begins with the formation of a pre-initiation complex (PIC) containing the 40S ribosomal subunit, eIF1, eIF1A, eIF3, ternary complex (eIF2-GTP-Met-tRNAi), and eIF5. The PIC, in an open conformation, attaches to the 5' end of the mRNA and scans to locate the start codon, whereupon it closes to arrest scanning. We present single particle cryo-electron microscopy (cryo-EM) reconstructions of 48S PICs from yeast in these open and closed states, at 6.0 Å and 4.9 Å, respectively. These reconstructions show eIF2ß as well as a configuration of eIF3 that appears to encircle the 40S, occupying part of the subunit interface. Comparison of the complexes reveals a large conformational change in the 40S head from an open mRNA latch conformation to a closed one that constricts the mRNA entry channel and narrows the P site to enclose tRNAi, thus elucidating key events in start codon recognition.


Subject(s)
Eukaryotic Initiation Factors/chemistry , Eukaryotic Initiation Factors/metabolism , Kluyveromyces/metabolism , RNA, Messenger/metabolism , RNA, Transfer/metabolism , Saccharomyces cerevisiae/metabolism , Binding Sites , Cryoelectron Microscopy , Kluyveromyces/chemistry , Models, Molecular , Peptide Chain Initiation, Translational , Protein Binding , Protein Conformation , Protein Multimerization , RNA, Fungal/metabolism , Ribosome Subunits, Small, Eukaryotic/chemistry , Ribosome Subunits, Small, Eukaryotic/metabolism , Saccharomyces cerevisiae/chemistry
10.
Cell ; 159(3): 597-607, 2014 Oct 23.
Article in English | MEDLINE | ID: mdl-25417110

ABSTRACT

During eukaryotic translation initiation, initiator tRNA does not insert fully into the P decoding site on the 40S ribosomal subunit. This conformation (POUT) is compatible with scanning mRNA for the AUG start codon. Base pairing with AUG is thought to promote isomerization to a more stable conformation (PIN) that arrests scanning and promotes dissociation of eIF1 from the 40S subunit. Here, we present a cryoEM reconstruction of a yeast preinitiation complex at 4.0 Å resolution with initiator tRNA in the PIN state, prior to eIF1 release. The structure reveals stabilization of the codon-anticodon duplex by the N-terminal tail of eIF1A, changes in the structure of eIF1 likely instrumental in its subsequent release, and changes in the conformation of eIF2. The mRNA traverses the entire mRNA cleft and makes connections to the regulatory domain of eIF2?, eIF1A, and ribosomal elements that allow recognition of context nucleotides surrounding the AUG codon.


Subject(s)
Eukaryotic Initiation Factors/metabolism , Kluyveromyces/metabolism , Peptide Chain Initiation, Translational , Saccharomyces cerevisiae/metabolism , Base Sequence , Codon, Initiator , Cryoelectron Microscopy , Models, Molecular , Molecular Sequence Data , RNA, Transfer/metabolism , Ribosomes/metabolism , Sequence Alignment
11.
Biomed Res Int ; 2014: 207974, 2014.
Article in English | MEDLINE | ID: mdl-24971317

ABSTRACT

BACKGROUND: The introduction of fluorescence-guided resection allows a better identification of tumor tissue and its more radical resection. We describe our experience with a modified exoscope to detect 5 ALA-induced fluorescence in neuronavigation-guided brain surgery or biopsy of malignant brain tumors. METHODS: Thirty-eight patients with a suspected preoperative diagnosis of high-grade astrocytoma were included. We used a neuronavigation device and a high-definition exoscope system with a built-in filter to detect 5-ALA fluorescence in all cases. Thirty patients underwent craniotomy with tumor resection and 8 underwent frameless stereotactic brain biopsy. RESULTS: Histopathological diagnosis confirmed the presence of high-grade gliomas in 34 patients. Total resection was achieved in 23 cases and subtotal in 7. No relevant complications related to the administration of 5-ALA were detected. CONCLUSIONS: The use of the exoscope in 5-ALA fluorescence-guided tumor surgery has twofold implications: during brain tumor surgery it can be considered a valuable tool to achieve a more radical resection of the lesion, and when applied to a biopsy of a suspected brain high-grade glioma, it decreases the possibility of a negative biopsy.


Subject(s)
Aminolevulinic Acid/chemistry , Astrocytoma/surgery , Brain Neoplasms/surgery , Glioma/surgery , Neuronavigation/methods , Adult , Aged , Biopsy/methods , Female , Fluorescence , Humans , Male , Middle Aged , Young Adult
12.
Science ; 343(6178): 1485-1489, 2014 Mar 28.
Article in English | MEDLINE | ID: mdl-24675956

ABSTRACT

Mitochondria have specialized ribosomes that have diverged from their bacterial and cytoplasmic counterparts. We have solved the structure of the yeast mitoribosomal large subunit using single-particle cryo-electron microscopy. The resolution of 3.2 angstroms enabled a nearly complete atomic model to be built de novo and refined, including 39 proteins, 13 of which are unique to mitochondria, as well as expansion segments of mitoribosomal RNA. The structure reveals a new exit tunnel path and architecture, unique elements of the E site, and a putative membrane docking site.


Subject(s)
Mitochondria/ultrastructure , Ribosome Subunits, Large, Eukaryotic/ultrastructure , Saccharomyces cerevisiae/ultrastructure , Cryoelectron Microscopy , Mitochondrial Proteins/chemistry , Nucleic Acid Conformation , RNA, Ribosomal/chemistry , RNA, Transfer/chemistry , Ribosome Subunits, Large, Eukaryotic/chemistry
13.
Acta Neurochir (Wien) ; 156(4): 653-60, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24468884

ABSTRACT

BACKGROUND: Fluorescence-guided microsurgical resections of high-grade gliomas using 5-aminolevulinic acid (5-ALA) is superior to conventional microsurgery. An optical device, usually a modified microscope, is needed for these procedures. However, an exoscope may be implemented for fluorescence techniques. We present the use of an exoscope to perform tumor resection guided by 5-ALA fluorescence in 21 consecutive patients with high-grade glioma and two neuronavigation-guided biopsies. METHODS: Twenty-three patients underwent operations. Tumor volume and localization were quantified with pre- and postoperative volumetric MRI in non-biopsy cases. RESULTS: In non-biopsy cases, the age range was 20 to 79 years, with a median of 56 (interquartile range = 45-66). Histological analysis indicated that 14 had glioblastoma multiforme, 2 grade-III oligodendrogliomas and 1 anaplastic astrocytoma, 3 metastases and 1 low-grade astrocytoma. Total resection was achieved in 15 cases; subtotal resection was performed in 5 patients. The result was partial resection in one case. There was no perioperative mortality. The median fluorescence intensity, on a scale of 1-5, was 4.5 in the GBM group (IQR = 4-5), 3 (IQR = 2.5-3.5) in anaplastic glioma, and 2.5 (IQR = 2.25-2.75) for oligodendrogliomas. Of the three metastases, one showed fluorescence level 4. As for the two biopsy cases, one was anaplastic astrocytoma and one glioblastoma multiforme. The samples obtained were fluorescent in both cases. CONCLUSIONS: An exoscope can be also used for fluorescence-guided surgery with 5-aminolevulinic acid (5-ALA) and neuronavigation-guided biopsy. With an important advantage of low cost, this allows the surgeon to perform collaborative surgeries and adds agility to the procedure.


Subject(s)
Brain Neoplasms/surgery , Glioma/surgery , Microscopy, Fluorescence/methods , Microsurgery/methods , Neuronavigation/methods , Adult , Aged , Aminolevulinic Acid , Astrocytoma/pathology , Astrocytoma/surgery , Biopsy , Brain Neoplasms/pathology , Female , Fluorescent Dyes , Glioblastoma/pathology , Glioblastoma/surgery , Glioma/pathology , Humans , Male , Middle Aged , Oligodendroglioma/pathology , Oligodendroglioma/surgery , Retrospective Studies , Treatment Outcome
14.
Proc Natl Acad Sci U S A ; 107(35): 15397-402, 2010 Aug 31.
Article in English | MEDLINE | ID: mdl-20716687

ABSTRACT

PII, an ancient and widespread signaling protein, transduces nitrogen/carbon/energy abundance signals through interactions with target proteins. We clarify structurally how PII regulates gene expression mediated by the transcription factor NtcA, the global nitrogen regulator of cyanobacteria, shedding light on NtcA structure and function and on how NtcA is activated by 2-oxoglutarate (2OG) and coactivated by the nonenzymatic PII target, protein PipX. We determine for the cyanobacteria Synechococcus elongatus the crystal structures of the PII-PipX and PipX-NtcA complexes and of NtcA in active and inactive conformations (respective resolutions, 3.2, 2.25, 2.3, and 3.05 A). The structures and the conclusions derived from them are consistent with the results of present and prior site-directed mutagenesis and functional studies. A tudor-like domain (TLD) makes up most of the PipX structure and mediates virtually all the contacts of PipX with PII and NtcA. In the PII-PipX complex, one PII trimer sequesters the TLDs of three PipX molecules between its body and its extended T loops, preventing PipX activation of NtcA. Changes in T loop conformation triggered by 2OG explain PII-PipX dissociation when 2OG is bound. The structure of active dimeric NtcA closely resembles that of the active cAMP receptor protein (CRP). This strongly suggests that with these proteins DNA binding, transcription activation, and allosteric regulation occur by common mechanisms, although the effectors are different. The PipX-NtcA complex consists of one active NtcA dimer and two PipX monomers. PipX coactivates NtcA by stabilizing its active conformation and by possibly helping recruit RNA polymerase but not by providing extra DNA contacts.


Subject(s)
Bacterial Proteins/chemistry , DNA-Binding Proteins/chemistry , PII Nitrogen Regulatory Proteins/chemistry , Transcription Factors/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Binding Sites/genetics , Crystallization , Crystallography, X-Ray , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Electrophoresis, Polyacrylamide Gel , Ketoglutaric Acids/pharmacology , Kinetics , Models, Molecular , Mutagenesis, Site-Directed , Mutation , PII Nitrogen Regulatory Proteins/genetics , PII Nitrogen Regulatory Proteins/metabolism , Protein Binding , Protein Conformation , Protein Multimerization , Protein Structure, Tertiary , Structure-Activity Relationship , Surface Plasmon Resonance , Synechococcus/genetics , Synechococcus/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Transcription, Genetic/drug effects , Two-Hybrid System Techniques
15.
Curr Opin Struct Biol ; 18(6): 673-81, 2008 Dec.
Article in English | MEDLINE | ID: mdl-19013524

ABSTRACT

When nitrogen is abundant, prokaryotic and eukaryotic oxygen-producing photosynthetic organisms store nitrogen as arginine, by relieving feedback inhibition of the arginine biosynthesis controlling enzyme, N-acetylglutamate kinase (NAGK). The signalling protein PII, an ancient and widely distributed nitrogen/carbon/ADP/ATP sensor, mediates feedback inhibition relief of NAGK by binding to this enzyme. PII phosphorylation or PII binding of ADP or 2-oxoglutarate prevents PII-NAGK complex formation. Crystal structures of NAGK, cyanobacterial and plant PII and corresponding PII-NAGK complexes have been recently determined. In these complexes, two polar PII trimers sandwich one ring-like NAGK hexamer. Each PII subunit contacts one NAGK subunit, triggering a symmetry-restricted narrowing of the NAGK ring, with concomitant adoption by the arginine sites of a low-affinity conformation.


Subject(s)
Arginine/metabolism , Nitrogen/metabolism , Phosphotransferases (Carboxyl Group Acceptor)/chemistry , Phosphotransferases (Carboxyl Group Acceptor)/metabolism , Allosteric Regulation , Animals , Arabidopsis/enzymology , Arabidopsis Proteins/chemistry , Arabidopsis Proteins/metabolism , Arginine/chemistry , Models, Molecular , Protein Binding , Protein Interaction Domains and Motifs , Signal Transduction , Synechococcus/enzymology
16.
Proc Natl Acad Sci U S A ; 104(45): 17644-9, 2007 Nov 06.
Article in English | MEDLINE | ID: mdl-17959776

ABSTRACT

Photosynthetic organisms can store nitrogen by synthesizing arginine, and, therefore, feedback inhibition of arginine synthesis must be relieved in these organisms when nitrogen is abundant. This relief is accomplished by the binding of the PII signal transduction protein to acetylglutamate kinase (NAGK), the controlling enzyme of arginine synthesis. Here, we describe the crystal structure of the complex between NAGK and PII of Synechococcus elongatus, at 2.75-A resolution. We prove the physiological relevance of the observed interactions by site-directed mutagenesis and functional studies. The complex consists of two polar PII trimers sandwiching one ring-like hexameric NAGK (a trimer of dimers) with the threefold axes of these molecules aligned. The binding of PII favors a narrow ring conformation of the NAGK hexamer that is associated with arginine sites having low affinity for this inhibitor. Each PII subunit contacts one NAGK subunit only. The contacts map in the inner circumference of the NAGK ring and involve two surfaces of the PII subunit. One surface is on the PII body and interacts with the C-domain of the NAGK subunit, helping widen the arginine site found on the other side of this domain. The other surface is at the distal region of a protruding large loop (T-loop) that presents a novel compact shape. This loop is inserted in the interdomain crevice of the NAGK subunit, contacting mainly the N-domain, and playing key roles in anchoring PII on NAGK, in activating NAGK, and in complex formation regulation by MgATP, ADP, 2-oxoglutarate, and by phosphorylation of serine-49.


Subject(s)
Arginine/metabolism , PII Nitrogen Regulatory Proteins/chemistry , PII Nitrogen Regulatory Proteins/metabolism , Phosphotransferases (Carboxyl Group Acceptor)/chemistry , Phosphotransferases (Carboxyl Group Acceptor)/metabolism , Synechococcus/enzymology , Thermotoga maritima/enzymology , Arginine/chemistry , Bacterial Proteins/chemistry , Bacterial Proteins/metabolism , Binding Sites , Crystallography, X-Ray , Cyanobacteria/chemistry , Cyanobacteria/metabolism , Homeostasis , Models, Molecular , Nitrogen/metabolism , Protein Conformation , Protein Subunits/chemistry , Protein Subunits/metabolism
17.
J Bacteriol ; 189(4): 1254-65, 2007 Feb.
Article in English | MEDLINE | ID: mdl-17028272

ABSTRACT

Enterococcus faecalis makes ATP from agmatine in three steps catalyzed by agmatine deiminase (AgDI), putrescine transcarbamylase (PTC), and carbamate kinase (CK). An antiporter exchanges putrescine for agmatine. We have cloned the E. faecalis ef0732 and ef0734 genes of the reported gene cluster for agmatine catabolism, overexpressed them in Escherichia coli, purified the products, characterized them functionally as PTC and AgDI, and crystallized and X-ray diffracted them. The 1.65-Angstroms-resolution structure of AgDI forming a covalent adduct with an agmatine-derived amidine reactional intermediate is described. We provide definitive identification of the gene cluster for agmatine catabolism and confirm that ornithine is a genuine but poor PTC substrate, suggesting that PTC (found here to be trimeric) evolved from ornithine transcarbamylase. N-(Phosphonoacetyl)-putrescine was prepared and shown to strongly (K(i) = 10 nM) and selectively inhibit PTC and to improve PTC crystallization. We find that E. faecalis AgDI, which is committed to ATP generation, closely resembles the AgDIs involved in making polyamines, suggesting the recruitment of a polyamine-synthesizing AgDI into the AgDI pathway. The arginine deiminase (ADI) pathway of arginine catabolism probably supplied the genes for PTC and CK but not those for the agmatine/putrescine antiporter, and thus the AgDI and ADI pathways are not related by a single "en bloc" duplication event. The AgDI crystal structure reveals a tetramer with a five-blade propeller subunit fold, proves that AgDI closely resembles ADI despite a lack of sequence identity, and explains substrate affinity, selectivity, and Cys357-mediated-covalent catalysis. A three-tongued agmatine-triggered gating opens or blocks access to the active center.


Subject(s)
Agmatine/metabolism , Carboxyl and Carbamoyl Transferases/metabolism , Enterococcus faecalis/genetics , Enterococcus faecalis/metabolism , Hydrolases/metabolism , Multigene Family , Binding Sites , Carboxyl and Carbamoyl Transferases/genetics , Catalysis , Gene Expression Regulation, Bacterial , Gene Expression Regulation, Enzymologic , Hydrolases/genetics , Models, Molecular , Oligoribonucleotides , Protein Conformation , Protein Folding , Recombinant Proteins , Substrate Specificity
18.
J Bacteriol ; 186(18): 6142-9, 2004 Sep.
Article in English | MEDLINE | ID: mdl-15342584

ABSTRACT

To help clarify the control of arginine synthesis in Thermotoga maritima, the putative gene (argB) for N-acetyl-L-glutamate kinase (NAGK) from this microorganism was cloned and overexpressed, and the resulting protein was purified and shown to be a highly thermostable and specific NAGK that is potently and selectively inhibited by arginine. Therefore, NAGK is in T. maritima the feedback control point of arginine synthesis, a process that in this organism involves acetyl group recycling and appears not to involve classical acetylglutamate synthase. The inhibition of NAGK by arginine was found to be pH independent and to depend sigmoidally on the concentration of arginine, with a Hill coefficient (N) of approximately 4, and the 50% inhibitory arginine concentration (I0.5) was shown to increase with temperature, approaching above 65 degrees C the I0.50 observed at 37 degrees C with the mesophilic NAGK of Pseudomonas aeruginosa (the best-studied arginine-inhibitable NAGK). At 75 degrees C, the inhibition by arginine of T. maritima NAGK was due to a large increase in the Km for acetylglutamate triggered by the inhibitor, but at 37 degrees C arginine also substantially decreased the Vmax of the enzyme. The NAGKs of T. maritima and P. aeruginosa behaved in gel filtration as hexamers, justifying the sigmoidicity and high Hill coefficient of arginine inhibition, and arginine or the substrates failed to disaggregate these enzymes. In contrast, Escherichia coli NAGK is not inhibited by arginine and is dimeric, and thus the hexameric architecture may be an important determinant of arginine sensitivity. Potential thermostability determinants of T. maritima NAGK are also discussed.


Subject(s)
Arginine/biosynthesis , Phosphotransferases (Carboxyl Group Acceptor)/metabolism , Thermotoga maritima/enzymology , Thermotoga maritima/metabolism , Arginine/pharmacology , Chromatography, Gel , Cloning, Molecular , Coenzymes/pharmacology , Enzyme Inhibitors/pharmacology , Enzyme Stability , Escherichia coli/enzymology , Hydrogen-Ion Concentration , Phosphotransferases (Carboxyl Group Acceptor)/genetics , Protein Subunits , Pseudomonas aeruginosa/enzymology , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Substrate Specificity , Temperature
19.
NMR Biomed ; 17(4): 191-205, 2004 Jun.
Article in English | MEDLINE | ID: mdl-15229932

ABSTRACT

High-resolution magic angle spinning (HR-MAS) one- and two-dimensional 1H and 13C nuclear magnetic resonance (NMR) spectroscopy has been used to study intact glioblastoma (GBM) brain tumour tissue. The results were compared with in vitro chemical extract and in vivo spectra. The resolution of 1H one-dimensional, 1H TOCSY and 13C HSQC HR-MAS spectra is comparable to that obtained on perchloric extracts. 13C HSQC HR-MAS spectra have been particularly useful for the identification of 37 different metabolites in intact biopsy tumours, excluding water and DSS components. To our knowledge, this is the most detailed assignment of biochemical compounds obtained in intact human tissue, in particular in brain tumour tissue. Tissue degradation during the recording of the NMR experiment was avoided by keeping the sample at a temperature of 4 degrees C. Detailed metabolical compositions of 10 GBM (six primary, two secondary and two unclassified) were obtained. A good correlation between ex vivo and in vivo MRS has been found.


Subject(s)
Biomarkers/metabolism , Brain Neoplasms/diagnosis , Brain Neoplasms/metabolism , Glioblastoma/diagnosis , Glioblastoma/metabolism , Neoplasm Proteins/metabolism , Nuclear Magnetic Resonance, Biomolecular/methods , Adult , Aged , Carbon Isotopes , Female , Humans , Magnetic Resonance Spectroscopy/methods , Male , Middle Aged , Protons , Statistics as Topic
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