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1.
J Neurol ; 270(9): 4276-4287, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37193796

ABSTRACT

BACKGROUND: The natural history of magnetic resonance imaging (MRI) in pre-ataxic stages of spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD) is not well known. We report cross-sectional and longitudinal data obtained at this stage. METHODS: Baseline (follow-up) observations included 32 (17) pre-ataxic carriers (SARA < 3) and 20 (12) related controls. The mutation length was used to estimate the time to onset (TimeTo) of gait ataxia. Clinical scales and MRIs were performed at baseline and after a median (IQR) of 30 (7) months. Cerebellar volumetries (ACAPULCO), deep gray-matter (T1-Multiatlas), cortical thickness (FreeSurfer), cervical spinal cord area (SCT) and white matter (DTI-Multiatlas) were assessed. Baseline differences between groups were described; variables that presented a p < 0.1 after Bonferroni correction were assessed longitudinally, using TimeTo and study time. For TimeTo strategy, corrections for age, sex and intracranial volume were done with Z-score progression. A significance level of 5% was adopted. RESULTS: SCT at C1 level distinguished pre-ataxic carriers from controls. DTI measures of the right inferior cerebellar peduncle (ICP), bilateral middle cerebellar peduncles (MCP) and bilateral medial lemniscus (ML), also distinguished pre-ataxic carriers from controls, and progressed over TimeTo, with effect sizes varying from 0.11 to 0.20, larger than those of the clinical scales. No MRI variable showed progression over study time. DISCUSSION: DTI parameters of the right ICP, left MCP and right ML were the best biomarkers for the pre-ataxic stage of SCA3/MJD. TimeTo is an interesting timescale, since it captured the longitudinal worsening of these structures.


Subject(s)
Machado-Joseph Disease , Spinocerebellar Ataxias , Humans , Machado-Joseph Disease/diagnostic imaging , Machado-Joseph Disease/genetics , Cross-Sectional Studies , Spinocerebellar Ataxias/pathology , Ataxia , Magnetic Resonance Imaging
2.
Mov Disord ; 38(1): 26-34, 2023 01.
Article in English | MEDLINE | ID: mdl-36129443

ABSTRACT

BACKGROUND: Little is known about preclinical stages of Machado-Joseph disease, a polyglutamine disorder characterized by progressive adult-onset ataxia. OBJECTIVE: We aimed to describe the longitudinal progression of clinical and oculomotor variables in the preataxic phase of disease. METHODS: Carriers and noncarriers were assessed at three visits. Preataxic carriers (Scale for Assessment and Rating of Ataxia score < 3) expected to start ataxia in ≤4 years were considered near onset (PAN). Progressions of ataxic and preataxic carriers, considering status at the end of the study, were described according to the start (or its prediction) of gait ataxia (TimeToAfterOnset) and according to the study time. RESULTS: A total of 35 ataxics, 38 preataxics, and 22 noncarriers were included. The "TimeToAfterOnset" timeline showed that Neurological Examination Scale for Spinocerebellar Ataxias (NESSCA; effect size, 0.09), Inventory of Non-Ataxia Symptoms (INAS0.07), and the vestibulo-ocular reflex gain (0.12) progressed in preataxic carriers, and that most slopes accelerate in PAN, turning similar to those of ataxics. In the study time, NESSCA (1.36) and vertical pursuit gain (1.17) significantly worsened in PAN, and 6 of 11 PANs converted to ataxia. For a clinical trial with 80% power and 2-year duration, 57 PANs are needed in each study arm to detect a 50% reduction in the conversion rate. CONCLUSIONS: NESSCA, INAS, vestibulo-ocular reflex, and vertical pursuit gains significantly worsened in the preataxic phase. The "TimeToAfterOnset" timeline unveiled that slopes of most variables are small in preataxics but increase and reach the ataxic slopes from 4 years before the onset of ataxia. For future trials in preataxic carriers, we recommend recruiting PANs and using the conversion rate as the primary outcome. © 2022 International Parkinson and Movement Disorder Society.


Subject(s)
Machado-Joseph Disease , Spinocerebellar Ataxias , Adult , Humans , Machado-Joseph Disease/diagnosis , Machado-Joseph Disease/genetics , Eye Movements , Spinocerebellar Ataxias/diagnosis , Spinocerebellar Ataxias/genetics , Heterozygote , Severity of Illness Index , Disease Progression
3.
Sci Adv ; 8(43): eabp8085, 2022 Oct 28.
Article in English | MEDLINE | ID: mdl-36306355

ABSTRACT

Mammalian genomes are a battleground for genetic conflict between repetitive elements and KRAB-zinc finger proteins (KZFPs). We asked whether KZFPs can regulate cell fate by using ZFP819, which targets a satellite DNA array, ZP3AR. ZP3AR coats megabase regions of chromosome 7 encompassing genes encoding ZSCAN4, a master transcription factor of totipotency. Depleting ZFP819 in mouse embryonic stem cells (mESCs) causes them to transition to a 2-cell (2C)-like state, whereby the ZP3AR array switches from a poised to an active enhancer state. This is accompanied by a global erosion of heterochromatin roadblocks, which we link to decreased SETDB1 stability. These events result in transcription of active LINE-1 elements and impaired differentiation. In summary, ZFP819 and TRIM28 partner up to close chromatin across Zscan4, to promote exit from totipotency. We propose that satellite DNAs may control developmental fate transitions by barcoding and switching off master transcription factor genes.


Subject(s)
DNA, Satellite , Repressor Proteins , Animals , Mice , DNA, Satellite/genetics , Mammals/genetics , Oligonucleotide Array Sequence Analysis , Repressor Proteins/metabolism , Transcription Factors/genetics , Chromosomes
4.
Cerebellum ; 21(2): 297-305, 2022 Apr.
Article in English | MEDLINE | ID: mdl-34231179

ABSTRACT

Although health-related quality of life (HRQoL) has been increasingly valued in healthcare and in clinical trials, there is scarce information about it in spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD). This study describes the HRQoL results obtained from ataxic SCA3/MJD subjects, and their non-ataxic offspring included in the BIGPRO (Biomarkers and genetic modifiers in a study of presymptomatic and symptomatic SCA3/MJD carriers) study. Demographic data, clinical scales, and HRQoL instruments EQ-5D-3L and SF-36 were collected. Subjects at 50% risk were genotyped in a double-blind manner. The time left until the onset of the disease was estimated for mutation carriers with a SARA < 3 and combined with disease duration of ataxic subjects (TimeToAfterOnset). Analyses were performed using PASW Statistics version 18.0, R version 4.0.0, and G*Power 3.1, and p < 0.05 was considered statistically significant. Twenty-three ataxic carriers, 33 pre-ataxic carriers, and 21 controls were enrolled. Significant differences between ataxic carriers and controls were seen in EQ-VAS, EQ-5D Index, and in some domains of EQ-5D-3L and SF-36. EQ-5D Index showed the best effect size between ataxic and controls (Cohen's d = 2.423). Stepwise changes were seen in pre-ataxic subjects, although not statistically significant. TimeToAfterOnset correlated with EQ-5D Index, EQ-VAS, and SF-36 Physical functioning, Role Physical, Pain, and General Health. EQ-5D Index and EQ-VAS correlated with clinical scales in the ataxic group. These results suggest that HRQoL worsens among carriers since pre-ataxic stages and that they might encompass the underlying disease process. In this cohort, SF-36 Physical Functioning, SF-36 General health, and especially EQ-5D Index and EQ-VAS were the best HRQoL instruments to be used as ancillary evidence to support biological and social meanings for future interventions.


Subject(s)
Machado-Joseph Disease , Spinocerebellar Ataxias , Double-Blind Method , Humans , Machado-Joseph Disease/genetics , Quality of Life , Spinocerebellar Ataxias/genetics , Surveys and Questionnaires
5.
Mov Disord ; 36(4): 985-994, 2021 04.
Article in English | MEDLINE | ID: mdl-33438269

ABSTRACT

BACKGROUND: The pathological burden of spinocerebellar ataxia type 3, also known as Machado-Joseph disease (SCA3/MJD), accumulates before the beginning of symptoms. Our study aims at validating biomarkers for disease progression since pre-ataxic periods. We report on baseline findings of clinical scales and oculomotor neurophysiology. METHODS: Ataxic (Scale for the Assessment and Rating of Ataxia > 2.5) and at 50% risk subjects were included. The latter were subdivided into noncarriers, pre-ataxic carriers near (PAN), or pre-ataxic carriers far from (PAFF) ataxia onset (AO), with 4 years from the predicted age at onset being the cutoff. The subjects were assessed by Neurological Examination Score for Spinocerebellar Ataxia (NESSCA), International Cooperative Ataxia Rating Scale (ICARS), Inventory of Non-Ataxic Signs (INAScount), Composite Cerebellar Functions Score and SCA Functional Index, and video-oculography, including the regression slope of vestibulo-ocular reflex gain (VORr), main sequence of volitional and reflexive vertical saccades, slow-phase velocity of central and gaze-evoked (SPV-GE) nystagmus, and vertical pursuit gain. Correction for multiple comparisons was performed; the threshold for statistical significance was P < 0.05. RESULTS: A total of 35 ataxic, 14 PAN, 24 PAFF, and 22 noncarriers were included. All variables showed significant differences between groups and correlated to time to onset or time after onset, among all 73 SCA3/MJD carriers; none significantly changed with age in controls. NESSCA, ICARS, INAScount, VORr, main sequence of volitional saccades, and SPV-GE not only distinguished PAN from controls but also correlated with time left to AO. CONCLUSIONS: Clinical scales and video-oculography variables were already altered in pre-ataxic SCA3/MJD carriers and worsened with time. NESSCA, ICARS, INAScount, VORr, main sequence of vertical volitional saccades, and SPV-GE are good candidates to measure preclinical changes in SCA3/MJD. © 2021 International Parkinson and Movement Disorder Society.


Subject(s)
Machado-Joseph Disease , Spinocerebellar Ataxias , Disease Progression , Eye Movements , Heterozygote , Humans
6.
Genet Mol Biol ; 42(1 suppl 1): 297-304, 2019.
Article in English | MEDLINE | ID: mdl-30985857

ABSTRACT

In 1990, the first Teratogen Information Service in Brazil (SIAT) was implemented in the Medical Genetics Service at Hospital de Clinicas de Porto Alegre. SIAT is a free-to-use information service both to health professionals and the general population, especially to women who are pregnant or planning pregnancy. The main objective of this paper is to present the activities of SIAT in its initial years (1990-2006), compared to those in the last decade (2007-2017). In addition we review the scientific contribution of SIAT in the field of human teratogenesis. Since 1990, SIAT received 10,533 calls. Use of medications were the main reason for concern, accounting for 74% of all questions, followed by other chemical exposures (occupational, cosmetics, environmental), and maternal infectious diseases. Among its main contributions to scientific knowledge was the collaboration for the identification of two new human teratogens: misoprostol in the 1990s and Zika virus in 2015/16. In conclusion, SIAT is still evolving, as is the Medical Genetics Service that hosts it. Through its 27 years of existence more than 300 undergraduate and graduate students have rotated at SIAT. Presently, SIAT is expanding the research to experimental teratogenesis and to investigation of molecular mechanisms of teratogens.

7.
Epigenetics Chromatin ; 11(1): 7, 2018 02 26.
Article in English | MEDLINE | ID: mdl-29482634

ABSTRACT

BACKGROUND: The KZFP/KAP1 (KRAB zinc finger proteins/KRAB-associated protein 1) system plays a central role in repressing transposable elements (TEs) and maintaining parent-of-origin DNA methylation at imprinting control regions (ICRs) during the wave of genome-wide reprogramming that precedes implantation. In naïve murine embryonic stem cells (mESCs), the genome is maintained highly hypomethylated by a combination of TET-mediated active demethylation and lack of de novo methylation, yet KAP1 is tethered by sequence-specific KZFPs to ICRs and TEs where it recruits histone and DNA methyltransferases to impose heterochromatin formation and DNA methylation. RESULTS: Here, upon removing either KAP1 or the cognate KZFP, we observed rapid TET2-dependent accumulation of 5hmC at both ICRs and TEs. In the absence of the KZFP/KAP1 complex, ICRs lost heterochromatic histone marks and underwent both active and passive DNA demethylation. For KAP1-bound TEs, 5mC hydroxylation correlated with transcriptional reactivation. Using RNA-seq, we further compared the expression profiles of TEs upon Kap1 removal in wild-type, Dnmt and Tet triple knockout mESCs. While we found that KAP1 represents the main effector of TEs repression in all three settings, we could additionally identify specific groups of TEs further controlled by DNA methylation. Furthermore, we observed that in the absence of TET proteins, activation upon Kap1 depletion was blunted for some TE integrants and increased for others. CONCLUSIONS: Our results indicate that the KZFP/KAP1 complex maintains heterochromatin and DNA methylation at ICRs and TEs in naïve embryonic stem cells partly by protecting these loci from TET-mediated demethylation. Our study further unveils an unsuspected level of complexity in the transcriptional control of the endovirome by demonstrating often integrant-specific differential influences of histone-based heterochromatin modifications, DNA methylation and 5mC oxidation in regulating TEs expression.


Subject(s)
DNA-Binding Proteins/metabolism , Mouse Embryonic Stem Cells/cytology , Retroelements , Tripartite Motif-Containing Protein 28/genetics , Animals , DNA Methylation , DNA-Binding Proteins/genetics , Dioxygenases , Gene Deletion , Gene Knockout Techniques , Genomic Imprinting , Histones/metabolism , Mice , Proto-Oncogene Proteins/metabolism , Sequence Analysis, RNA , Transcriptional Activation , Tripartite Motif-Containing Protein 28/metabolism , Zinc Fingers
8.
Development ; 144(15): 2719-2729, 2017 08 01.
Article in English | MEDLINE | ID: mdl-28765213

ABSTRACT

Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs) are the largest family of transcriptional regulators in higher vertebrates. Characterized by an N-terminal KRAB domain and a C-terminal array of DNA-binding zinc fingers, they participate, together with their co-factor KAP1 (also known as TRIM28), in repression of sequences derived from transposable elements (TEs). Until recently, KRAB-ZFP/KAP1-mediated repression of TEs was thought to lead to irreversible silencing, and the evolutionary selection of KRAB-ZFPs was considered to be just the host component of an arms race against TEs. However, recent advances indicate that KRAB-ZFPs and their TE targets also partner up to establish species-specific regulatory networks. Here, we provide an overview of the KRAB-ZFP gene family, highlighting how its evolutionary history is linked to that of TEs, and how KRAB-ZFPs influence multiple aspects of development and physiology.


Subject(s)
DNA-Binding Proteins/metabolism , Repressor Proteins/metabolism , Transcription Factors/metabolism , Animals , Cell Differentiation/genetics , Cell Differentiation/physiology , DNA Transposable Elements/genetics , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/genetics , Gene Expression Regulation , Humans , Models, Biological , Repressor Proteins/chemistry , Repressor Proteins/genetics , Transcription Factors/chemistry , Transcription Factors/genetics , Zinc Fingers/genetics , Zinc Fingers/physiology
9.
PLoS One ; 12(3): e0173746, 2017.
Article in English | MEDLINE | ID: mdl-28334004

ABSTRACT

KRAB-containing poly-zinc finger proteins (KZFPs) constitute the largest family of transcription factors encoded by mammalian genomes, and growing evidence indicates that they fulfill functions critical to both embryonic development and maintenance of adult homeostasis. KZFP genes underwent broad and independent waves of expansion in many higher vertebrates lineages, yet comprehensive studies of members harbored by a given species are scarce. Here we present a thorough analysis of KZFP genes and related units in the murine genome. We first identified about twice as many elements than previously annotated as either KZFP genes or pseudogenes, notably by assigning to this family an entity formerly considered as a large group of Satellite repeats. We then could delineate an organization in clusters distributed throughout the genome, with signs of recombination, translocation, duplication and seeding of new sites by retrotransposition of KZFP genes and related genetic units (KZFP/rGUs). Moreover, we harvested evidence indicating that closely related paralogs had evolved through both drifting and shifting of sequences encoding for zinc finger arrays. Finally, we could demonstrate that the KAP1-SETDB1 repressor complex tames the expression of KZFP/rGUs within clusters, yet that the primary targets of this regulation are not the KZFP/rGUs themselves but enhancers contained in neighboring endogenous retroelements and that, underneath, KZFPs conserve highly individualized patterns of expression.


Subject(s)
Carrier Proteins/genetics , Genome/genetics , Nuclear Proteins/genetics , Repressor Proteins/genetics , Animals , Genes/genetics , Mice/genetics , Multigene Family/genetics , Phylogeny
10.
Dev Cell ; 36(6): 611-23, 2016 Mar 21.
Article in English | MEDLINE | ID: mdl-27003935

ABSTRACT

KRAB-containing zinc finger proteins (KRAB-ZFPs) are early embryonic controllers of transposable elements (TEs), which they repress with their cofactor KAP1 through histone and DNA methylation, a process thought to result in irreversible silencing. Using a target-centered functional screen, we matched murine TEs with their cognate KRAB-ZFP. We found the paralogs ZFP932 and Gm15446 to bind overlapping but distinguishable subsets of ERVK (endogenous retrovirus K), repress these elements in embryonic stem cells, and regulate secondarily the expression of neighboring genes. Most importantly, we uncovered that these KRAB-ZFPs and KAP1 control TEs in adult tissues, in cell culture and in vivo, where they partner up to modulate cellular genes. Therefore, TEs and KRAB-ZFPs establish transcriptional networks that likely regulate not only development but also many physiological events. Given the high degree of species specificity of TEs and KRAB-ZFPs, these results have important implications for understanding the biology of higher vertebrates, including humans.


Subject(s)
DNA Transposable Elements/genetics , Repressor Proteins/genetics , Repressor Proteins/metabolism , Zinc Fingers/genetics , Amino Acid Sequence , Animals , Cell Differentiation , Embryonic Stem Cells/metabolism , Endogenous Retroviruses/genetics , Endogenous Retroviruses/metabolism , Gene Expression Regulation , Humans , Mice , Mice, Knockout , Molecular Sequence Data , Nuclear Proteins/deficiency , Nuclear Proteins/genetics , Nuclear Proteins/metabolism , Repressor Proteins/deficiency , Tripartite Motif-Containing Protein 28
11.
Methods Mol Biol ; 1400: 403-17, 2016.
Article in English | MEDLINE | ID: mdl-26895067

ABSTRACT

Deposition of epigenetic marks is an important layer of the transcriptional control of retrotransposons, especially during early embryogenesis. Krüppel-associated box domain zinc finger proteins (KRAB-ZFPs) are one of the largest families of transcription factors, and collectively partake in this process by tethering to thousands of retroelement-containing genomic loci their cofactor KAP1, which acts as a scaffold for a heterochromatin-inducing machinery. However, while the sequence-specific DNA binding potential of the poly-zinc finger-containing KRAB-ZFPs is recognized, very few members of the family have been assigned specific targets. In this chapter, we describe a large-scale functional screen to identify the retroelements bound by individual murine KRAB-ZFPs. Our method is based on the automated transfection of a library of mouse KRAB-ZFP-containing vectors into 293T cells modified to express GFP from a PGK promoter harboring in its immediate vicinity a KAP1-recruiting retroelement-derived sequence. Analysis is then performed by plate reader and flow cytometry fluorescence readout. Such large-scale DNA-centered functional approach can not only help to identify the trans-acting factors responsible for silencing retrotransposons, but also serve as a model for dissecting the transcriptional networks influenced by retroelement-derived cis-acting sequences.


Subject(s)
Epigenesis, Genetic , Epigenomics/methods , Repressor Proteins/metabolism , Retroelements , Animals , Cell Line , Cloning, Molecular , Gene Expression Regulation , Gene Library , Humans , Mice , Protein Binding , Repressor Proteins/genetics , Transcription Factors/genetics , Transcription Factors/metabolism
12.
Genes Dev ; 28(13): 1397-409, 2014 Jul 01.
Article in English | MEDLINE | ID: mdl-24939876

ABSTRACT

Mobile elements are important evolutionary forces that challenge genomic integrity. Long interspersed element-1 (L1, also known as LINE-1) is the only autonomous transposon still active in the human genome. It displays an unusual pattern of evolution, with, at any given time, a single active L1 lineage amplifying to thousands of copies before getting replaced by a new lineage, likely under pressure of host restriction factors, which act notably by silencing L1 expression during early embryogenesis. Here, we demonstrate that in human embryonic stem (hES) cells, KAP1 (KRAB [Krüppel-associated box domain]-associated protein 1), the master cofactor of KRAB-containing zinc finger proteins (KRAB-ZFPs) previously implicated in the restriction of endogenous retroviruses, represses a discrete subset of L1 lineages predicted to have entered the ancestral genome between 26.8 million and 7.6 million years ago. In mice, we documented a similar chronologically conditioned pattern, albeit with a much contracted time scale. We could further identify an L1-binding KRAB-ZFP, suggesting that this rapidly evolving protein family is more globally responsible for L1 recognition. KAP1 knockdown in hES cells induced the expression of KAP1-bound L1 elements, but their younger, human-specific counterparts (L1Hs) were unaffected. Instead, they were stimulated by depleting DNA methyltransferases, consistent with recent evidence demonstrating that the PIWI-piRNA (PIWI-interacting RNA) pathway regulates L1Hs in hES cells. Altogether, these data indicate that the early embryonic control of L1 is an evolutionarily dynamic process and support a model in which newly emerged lineages are first suppressed by DNA methylation-inducing small RNA-based mechanisms before KAP1-recruiting protein repressors are selected.


Subject(s)
Gene Expression Regulation , Long Interspersed Nucleotide Elements/genetics , Animals , DNA (Cytosine-5-)-Methyltransferases/metabolism , DNA Methylation , Embryonic Stem Cells , Evolution, Molecular , Humans , Mice , Repressor Proteins/genetics , Tripartite Motif-Containing Protein 28
13.
Genome Res ; 24(8): 1251-9, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24879558

ABSTRACT

Endogenous retroelements (EREs) account for about half of the mouse or human genome, and their potential as insertional mutagens and transcriptional perturbators is suppressed by early embryonic epigenetic silencing. Here, we asked how ERE control is maintained during the generation of induced pluripotent stem cells (iPSCs), as this procedure involves profound epigenetic remodeling. We found that all EREs tested were markedly up-regulated during the reprogramming of either mouse embryonic fibroblasts, human CD34(+) cells, or human primary hepatocytes. At the iPSC stage, EREs of some classes were repressed, whereas others remained highly expressed, yielding a pattern somewhat reminiscent of that recorded in embryonic stem cells. However, variability persisted between individual iPSC clones in the control of specific ERE integrants. Both during reprogramming and in iPS cells, the up-regulation of specific EREs significantly impacted on the transcription of nearby cellular genes. While transcription triggered by specific ERE integrants at highly precise developmental stages may be an essential step toward obtaining pluripotent cells, the broad and unspecific unleashing of the repetitive genome observed here may contribute to the inefficiency of the reprogramming process and to the phenotypic heterogeneity of iPSCs.


Subject(s)
Endogenous Retroviruses/genetics , Induced Pluripotent Stem Cells/physiology , Transcriptome , Animals , Cells, Cultured , Cellular Reprogramming , Gene Silencing , Humans , Mice , Up-Regulation
14.
Biochim Biophys Acta ; 1834(1): 191-6, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23102706

ABSTRACT

S-nitrosylation is associated with signal transduction and microbicidal activity of nitric oxide (NO). We have recently described the S-nitrosylation of Mycobacterium tuberculosis protein tyrosine phosphatase A, PtpA, an enzyme that plays an important role in mycobacteria survival inside macrophages. This post-translational modification decreases the activity of the enzyme upon modification of a single Cys residue, C53. The aim of the present work was the investigation of the effect of S-nitrosylation in PtpA kinetic parameters, thermal stability and structure. It was observed that the K(M) of nitrosylated PtpA was similar to its unmodified form, but the V(max) was significantly reduced. In contrast, treatment of PtpA C53A with GSNO, did not alter either K(M) or V(max). These results confirmed that PtpA S-nitrosylation occurs specifically in the non-catalytic C53 and that this modification does not affect substrate affinity. Using circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy techniques it was shown that PtpA S-nitrosylation decreased protein thermal stability and promoted a local effect in the surroundings of the C53 residue, which interfered in both protein stability and function.


Subject(s)
Bacterial Proteins/chemistry , Mutation, Missense , Mycobacterium tuberculosis/enzymology , Protein Tyrosine Phosphatases/chemistry , Amino Acid Substitution , Animals , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Circular Dichroism , Enzyme Stability/genetics , Humans , Macrophages/enzymology , Macrophages/metabolism , Mycobacterium tuberculosis/genetics , Nitric Oxide/genetics , Nitric Oxide/metabolism , Nuclear Magnetic Resonance, Biomolecular , Protein Structure, Tertiary , Protein Tyrosine Phosphatases/genetics , Protein Tyrosine Phosphatases/metabolism
15.
J Med Chem ; 55(1): 390-402, 2012 Jan 12.
Article in English | MEDLINE | ID: mdl-22136336

ABSTRACT

Tuberculosis (TB) is a major infectious disease caused by Mycobacterium tuberculosis (Mtb). According to the World Health Organization (WHO), about 1.8 million people die from TB and 10 million new cases are recorded each year. Recently, a new series of naphthylchalcones has been identified as inhibitors of Mtb protein tyrosine phosphatases (PTPs). In this work, 100 chalcones were designed, synthesized, and investigated for their inhibitory properties against MtbPtps. Structure-activity relationships (SAR) were developed, leading to the discovery of new potent inhibitors with IC(50) values in the low-micromolar range. Kinetic studies revealed competitive inhibition and high selectivity toward the Mtb enzymes. Molecular modeling investigations were carried out with the aim of revealing the most relevant structural requirements underlying the binding affinity and selectivity of this series of inhibitors as potential anti-TB drugs.


Subject(s)
Antitubercular Agents/chemical synthesis , Bacterial Proteins/antagonists & inhibitors , Chalcones/chemical synthesis , Models, Molecular , Mycobacterium tuberculosis/enzymology , Protein Tyrosine Phosphatases/antagonists & inhibitors , Amino Acid Sequence , Antitubercular Agents/chemistry , Bacterial Proteins/chemistry , Benzene Derivatives/chemical synthesis , Benzene Derivatives/chemistry , Chalcones/chemistry , Humans , Kinetics , Molecular Sequence Data , Naphthalenes/chemical synthesis , Naphthalenes/chemistry , Protein Binding , Protein Tyrosine Phosphatase, Non-Receptor Type 1/antagonists & inhibitors , Protein Tyrosine Phosphatase, Non-Receptor Type 1/chemistry , Protein Tyrosine Phosphatases/chemistry , Sequence Alignment , Structure-Activity Relationship
16.
Chem Commun (Camb) ; 46(40): 7501-3, 2010 Oct 28.
Article in English | MEDLINE | ID: mdl-20830431

ABSTRACT

M. tuberculosis PtpA and PtpB, the only two phosphotyrosine phosphatases (Ptps) present in this pathogen, play an important role in mycobacteria survival inside macrophages. The aim of the present work was to investigate M. tuberculosis PtpA and PtpB susceptibility to S-nitrosylation, a reversible covalent bond between nitric oxide (NO) and specific cysteine (sulfur) residues in proteins. PtpB was not modified by NO, in contrast, PtpA Cys53 was identified by site directed mutagenesis as the target of S-nitrosylation.


Subject(s)
Cysteine/metabolism , Mycobacterium tuberculosis/enzymology , Nitric Oxide/metabolism , Protein Tyrosine Phosphatases/metabolism , Cysteine/genetics , Models, Molecular , Mutagenesis, Site-Directed , Mycobacterium tuberculosis/genetics , Protein Tyrosine Phosphatases/genetics
17.
J Virol ; 84(11): 5790-801, 2010 Jun.
Article in English | MEDLINE | ID: mdl-20219908

ABSTRACT

Retroviruses are both powerful evolutionary forces and dangerous threats to genome integrity. As such, they have imposed strong selective pressure on their hosts, notably triggering the emergence of restriction factors, such as TRIM5 alpha, that act as potent barriers to their cross-species transmission. TRIM5 alpha orthologues from different primates have distinct retroviral restriction patterns, largely dictated by the sequence of their C-terminal PRYSPRY domain, which binds the capsid protein of incoming virions. Here, by combining genetic and functional analyses of human and squirrel monkey TRIM5 alpha, we demonstrate that the coiled-coil domain of this protein, thus far essentially known for mediating oligomerization, also conditions the spectrum of antiretroviral activity. Furthermore, we identify three coiled-coil residues responsible for this effect, one of which has been under positive selection during primate evolution, notably in New World monkeys. These results indicate that the PRYSPRY and coiled-coil domains cooperate to determine the specificity of TRIM5 alpha-mediated capture of retroviral capsids, shedding new light on this complex event.


Subject(s)
Carrier Proteins/metabolism , Proteins/metabolism , Animals , Antiviral Restriction Factors , Base Sequence , Binding Sites , Capsid Proteins/metabolism , Carrier Proteins/chemistry , Host-Pathogen Interactions , Humans , Macaca , Protein Structure, Tertiary , Proteins/chemistry , Retroviridae , Saimiri , Species Specificity , Tripartite Motif Proteins , Ubiquitin-Protein Ligases
18.
Gene ; 448(1): 1-6, 2009 Dec 01.
Article in English | MEDLINE | ID: mdl-19699281

ABSTRACT

Kynureninase has been described in bacteria, fungi and animals as an enzyme involved in the catabolic degradation pathway of l-tryptophan. This pyridoxal 5'-phosphate (PLP)-dependent enzyme catalyzes the hydrolytic cleavage of l-kynurenine and 3-hydroxy-l-kynurenine to yield l-alanine and either anthranilic or 3-hydroxyanthranilic acid, respectively. We identified a putative kynureninase gene from a Trypanosoma cruzi project aiming at the structural and functional characterization of more than 100 proteins differentially expressed during metacyclogenesis. This gene encodes a protein similar in size and sequence to kynureninases from other sources. This open reading frame was cloned and the recombinant enzyme was overexpressed. Recombinant T. cruzi kynureninase was purified to homogeneity and its identity was confirmed by mass spectrometry. The apparent molecular mass of the native T. cruzi kynureninase was estimated by gel filtration, suggesting that the protein is a homodimer. Circular dichroism spectrum indicated a mixture of alpha-helix and beta-sheet structure, expected for an aminotransferase fold. l-kynurenine, preferentially hydrolyzed by prokaryotic inducible kynureninases, and 3-hydroxy-l-kynurenine, the preferred substrate in fungi and vertebrates, are both catabolized equally well by T. cruzi kynureninase. Further experimental assays will be performed to fully understand the importance of this enzyme for T. cruzi metabolism.


Subject(s)
Databases, Protein , Hydrolases/metabolism , Trypanosoma cruzi/enzymology , Amino Acid Sequence , Animals , Chromatography, Gel , Circular Dichroism , Humans , Hydrolases/chemistry , Hydrolases/genetics , Hydrolases/isolation & purification , Models, Molecular , Molecular Sequence Data , Protein Structure, Tertiary , Reading Frames , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Sequence Alignment , Sequence Homology, Amino Acid
19.
Biochem Biophys Res Commun ; 387(4): 712-6, 2009 Oct 02.
Article in English | MEDLINE | ID: mdl-19632197

ABSTRACT

Transthyretin-related proteins (TRPs) constitute a family of proteins structurally related to transthyretin (TTR) and are found in a large range of bacterial, fungal, plant, invertebrate, and vertebrate species. However, it was recently recognized that both prokaryotic and eukaryotic members of this family are not functionally related to transthyretins. TRPs are in fact involved in the purine catabolic pathway and function as hydroxyisourate hydrolases. An open reading frame encoding a protein similar to the Escherichia coli TRP was identified in Herbaspirillum seropedicae genome (Hs_TRP). It was cloned, overexpressed in E. coli, and purified to homogeneity. Mass spectrometry data confirmed the identity of this protein, and circular dichroism spectrum indicated a predominance of beta-sheet structure, as expected for a TRP. We have demonstrated that Hs_TRP is a 5-hydroxyisourate hydrolase and by site-directed mutagenesis the importance of three conserved catalytic residues for Hs_TRP activity was further confirmed. The production of large quantities of this recombinant protein opens up the possibility of obtaining its 3D-structure and will help further investigations into purine catabolism.


Subject(s)
Herbaspirillum/metabolism , Prealbumin/biosynthesis , Amino Acid Sequence , Circular Dichroism , Molecular Sequence Data , Mutation , Open Reading Frames , Prealbumin/chemistry , Prealbumin/genetics , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/genetics
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