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1.
Nucleic Acids Res ; 52(10): 5912-5927, 2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38742632

RESUMEN

Mitochondrial single-stranded DNA-binding protein (mtSSB) is essential for mitochondrial DNA (mtDNA) replication. Recently, several mtSSB variants have been associated with autosomal dominant mitochondrial optic atrophy and retinal dystrophy. Here, we have studied at the molecular level the functional consequences of one of the most severe mtSSB variants, R107Q. We first studied the oligomeric state of this variant and observed that the mtSSBR107Q mutant forms stable tetramers in vitro. On the other hand, we showed, using complementary single-molecule approaches, that mtSSBR107Q displays a lower intramolecular ssDNA compaction ability and a higher ssDNA dissociation rate than the WT protein. Real-time competition experiments for ssDNA-binding showed a marked advantage of mtSSBWT over mtSSBR107Q. Combined, these results show that the R107Q mutation significantly impaired the ssDNA-binding and compacting ability of mtSSB, likely by weakening mtSSB ssDNA wrapping efficiency. These features are in line with our molecular modeling of ssDNA on mtSSB showing that the R107Q mutation may destabilize local interactions and results in an electronegative spot that interrupts an ssDNA-interacting-electropositive patch, thus reducing the potential mtSSB-ssDNA interaction sites.


Asunto(s)
ADN de Cadena Simple , Proteínas de Unión al ADN , Mutación , Humanos , ADN Mitocondrial/genética , ADN Mitocondrial/metabolismo , ADN de Cadena Simple/metabolismo , ADN de Cadena Simple/genética , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/química , Proteínas Mitocondriales/metabolismo , Proteínas Mitocondriales/genética , Proteínas Mitocondriales/química , Modelos Moleculares , Unión Proteica , Estructura Cuaternaria de Proteína
2.
Nucleic Acids Res ; 51(11): 5864-5882, 2023 06 23.
Artículo en Inglés | MEDLINE | ID: mdl-37207342

RESUMEN

The compaction of mitochondrial DNA (mtDNA) is regulated by architectural HMG-box proteins whose limited cross-species similarity suggests diverse underlying mechanisms. Viability of Candida albicans, a human antibiotic-resistant mucosal pathogen, is compromised by altering mtDNA regulators. Among them, there is the mtDNA maintenance factor Gcf1p, which differs in sequence and structure from its human and Saccharomyces cerevisiae counterparts, TFAM and Abf2p. Our crystallographic, biophysical, biochemical and computational analysis showed that Gcf1p forms dynamic protein/DNA multimers by a combined action of an N-terminal unstructured tail and a long helix. Furthermore, an HMG-box domain canonically binds the minor groove and dramatically bends the DNA while, unprecedentedly, a second HMG-box binds the major groove without imposing distortions. This architectural protein thus uses its multiple domains to bridge co-aligned DNA segments without altering the DNA topology, revealing a new mechanism of mtDNA condensation.


Asunto(s)
Candida albicans , ADN Mitocondrial , Proteínas de Unión al ADN , Proteínas Fúngicas , Humanos , Candida albicans/genética , Candida albicans/metabolismo , ADN Mitocondrial/metabolismo , Proteínas de Unión al ADN/metabolismo , Mitocondrias/metabolismo , Proteínas Mitocondriales/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Factores de Transcripción/metabolismo , Proteínas Fúngicas/metabolismo
3.
Artículo en Inglés | MEDLINE | ID: mdl-38754725

RESUMEN

OBJECTIVE: The International Commission on Radiological Protection has highlighted the large number of medical specialties that use fluoroscopy outside diagnostic imaging departments without radiation protection programmes for patients and staff. Vascular surgery is one of these specialties. Thoracic endovascular aortic repair (TEVAR) is a complicated procedure requiring radiation protection guidance and optimisation. The recent EU Basic Safety Standards Directive requires the use and periodic updating of diagnostic reference levels (DRLs) for interventional procedures. The aim of this study was to determine doses for patients undergoing TEVAR with mobile Xray systems and hybrid rooms (fixed Xray systems) to obtain national DRLs and to suggest optimisation actions. METHODS: This was a retrospective cross sectional study. The Spanish Chapter of Endovascular Surgery conducted a national survey in 11 autonomous communities representing around 77.6% of the Spanish population (47.33 million inhabitants). A total of 266 TEVAR procedures from 17 Spanish centres were analysed, of which 53.0% were performed in hybrid operating rooms. National DRLs were obtained and defined as the third quartile of the median values from the different participating centres. RESULTS: The proposed national DRLs are: for kerma area product (KAP), 113.81 Gy·cm2 for mobile Xray systems and 282.59 Gy·cm2 for hybrid rooms; and for cumulative air kerma (CAK) at the patient entry reference point, 228.38 mGy for mobile systems and 910.64 mGy for hybrid rooms. CONCLUSION: Based on the requirement to know radiation doses for standard endovascular procedures, this study of TEVARs demonstrated that there is an increased factor of 2.48 in DRLs for KAP when the procedure is performed in a hybrid room compared with mobile C-arm systems, and an increased factor of 3.98 in DRLs for CAK when the procedure is performed with hybrid equipment. These results will help to optimise strategies to reduce radiation doses during TEVAR procedures.

4.
Nucleic Acids Res ; 50(21): 12558-12577, 2022 11 28.
Artículo en Inglés | MEDLINE | ID: mdl-36464236

RESUMEN

The PglZ family of proteins belongs to the alkaline phosphatase superfamily, which consists of metallohydrolases with limited sequence identity but similar metal-coordination architectures in otherwise divergent active sites. Proteins with a well-defined PglZ domain are ubiquitous among prokaryotes as essential components of BREX phage defence systems and two-component systems (TCSs). Whereas other members of the alkaline phosphatase superfamily are well characterized, the activity, structure and biological function of PglZ family proteins remain unclear. We therefore investigated the structure and function of PorX, an orphan response regulator of the Porphyromonas gingivalis TCS containing a putative PglZ effector domain. The crystal structure of PorX revealed a canonical receiver domain, a helical bundle, and an unprecedented PglZ domain, similar to the general organization of the phylogenetically related BREX-PglZ proteins. The PglZ domain of PorX features an active site cleft suitable for large substrates. An extensive search for substrates revealed that PorX is a phosphodiesterase that acts on cyclic and linear oligonucleotides, including signalling molecules such as cyclic oligoadenylates. These results, combined with mutagenesis, biophysical and enzymatic analysis, suggest that PorX coordinates oligonucleotide signalling pathways and indirectly regulates gene expression to control the secretion of virulence factors.


Asunto(s)
Proteínas Bacterianas , Factores de Virulencia , Factores de Virulencia/genética , Proteínas Bacterianas/metabolismo , Oligonucleótidos , Fosfatasa Alcalina , Expresión Génica
5.
Proc Natl Acad Sci U S A ; 118(40)2021 10 05.
Artículo en Inglés | MEDLINE | ID: mdl-34593635

RESUMEN

Porphyromonas gingivalis is a keystone pathogen of the human dysbiotic oral microbiome that causes severe periodontitis. It employs a type-IX secretion system (T9SS) to shuttle proteins across the outer membrane (OM) for virulence. Uniquely, T9SS cargoes carry a C-terminal domain (CTD) as a secretion signal, which is cleaved and replaced with anionic lipopolysaccharide by transpeptidation for extracellular anchorage to the OM. Both reactions are carried out by PorU, the only known dual-function, C-terminal signal peptidase and sortase. PorU is itself secreted by the T9SS, but its CTD is not removed; instead, intact PorU combines with PorQ, PorV, and PorZ in the OM-inserted "attachment complex." Herein, we revealed that PorU transits between active monomers and latent dimers and solved the crystal structure of the ∼260-kDa dimer. PorU has an elongated shape ∼130 Å in length and consists of seven domains. The first three form an intertwined N-terminal cluster likely engaged in substrate binding. They are followed by a gingipain-type catalytic domain (CD), two immunoglobulin-like domains (IGL), and the CTD. In the first IGL, a long "latency ß-hairpin" protrudes ∼30 Å from the surface to form an intermolecular ß-barrel with ß-strands from the symmetric CD, which is in a latent conformation. Homology modeling of the competent CD followed by in vivo validation through a cohort of mutant strains revealed that PorU is transported and functions as a monomer through a C690/H657 catalytic dyad. Thus, dimerization is an intermolecular mechanism for PorU regulation to prevent untimely activity until joining the attachment complex.


Asunto(s)
Proteínas Bacterianas/genética , Sistemas de Secreción Bacterianos/genética , Proteínas de la Membrana/genética , Porphyromonas gingivalis/genética , Serina Endopeptidasas/genética , Catálisis , Dominios Proteicos/genética , Transporte de Proteínas/genética , Virulencia/genética
6.
J Stroke Cerebrovasc Dis ; 32(11): 107334, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37677897

RESUMEN

INTRODUCTION: Stroke mortality has declined in recent decades, but there appears to be a slowdown in the decline in recent years. We analyze the trends in stroke mortality in La Rioja (Spain) for the period 1999-2022. METHODS: We evaluated stroke mortality using statistical data from the mortality registry of La Rioja (Spain). We adjusted the rates by age and sex and analyzed both overall strokes and subtypes: hemorrhagic and ischemic. To analyze the trend in mortality rates we constructed joinpoint regression models, with associated annual percentage change (APC) RESULTS: Age-standardized stroke mortality declined between 1999 and 2022: females from 98.0 to 29.2 per 100 000; males, from 131.6 to 44.8 per 100 000. We found a decrease in overall stroke mortality in all age groups, except those under 65 years old. Ischemic stroke mortality showed declines in the first decade (APC: 7.3%, CI95%: 4.1-19.1%) and increases in the second decade (APC: 1.6%, CI95%: -1.6-11.7%) among men. In women, the rates declined between 2018 and 2022(APC: -6.6%, CI95%: -5.1-30.6%) after an increase between 2015 and 2017 (APC: 23.5%, CI95%: -20.2-38.3%). For hemorrhagic stroke, we found a consistent rate of decline throughout the entire time period in men (APC: 2.4%, CI95%: 0.9 a 4.0%). In women, rates increased during the period 1999-2009(APC: 1.9%, CI95%: -2.1-22.8%) and decreased 2010-2022 (APC: 6.5%, CI95%: 4.0-25.6%). CONCLUSIONS: Stroke mortality rates have decreased, more so for haemorrhagic than ischaemic strokes.

7.
Plant Physiol ; 185(1): 67-76, 2021 02 25.
Artículo en Inglés | MEDLINE | ID: mdl-33631804

RESUMEN

When germinating in the light, Arabidopsis (Arabidopsis thaliana) seedlings undergo photomorphogenic development, characterized by short hypocotyls, greening, and expanded cotyledons. Stressed chloroplasts emit retrograde signals to the nucleus that induce developmental responses and repress photomorphogenesis. The nuclear targets of these retrograde signals are not yet fully known. Here, we show that lincomycin-treated seedlings (which lack developed chloroplasts) show strong phenotypic similarities to seedlings treated with ethylene (ET) precursor 1-aminocyclopropane-1-carboxylic acid, as both signals inhibit cotyledon separation in the light. We show that the lincomycin-induced phenotype partly requires a functioning ET signaling pathway, but could not detect increased ET emissions in response to the lincomycin treatment. The two treatments show overlap in upregulated gene transcripts, downstream of transcription factors ETHYLENE INSENSITIVE3 and EIN3-LIKE1. The induction of the ET signaling pathway is triggered by an unknown retrograde signal acting independently of GENOMES UNCOUPLED1. Our data show how two apparently different stress responses converge to optimize photomorphogenesis.


Asunto(s)
Arabidopsis/crecimiento & desarrollo , Arabidopsis/genética , Arabidopsis/metabolismo , Etilenos/metabolismo , Desarrollo de la Planta/efectos de los fármacos , Reguladores del Crecimiento de las Plantas/metabolismo , Transducción de Señal/genética , Factores de Transcripción/genética , Regulación de la Expresión Génica de las Plantas/efectos de los fármacos , Genes de Plantas , Variación Genética , Genotipo , Luz , Transducción de Señal/efectos de los fármacos
8.
J Med Syst ; 46(12): 104, 2022 Dec 06.
Artículo en Inglés | MEDLINE | ID: mdl-36471095

RESUMEN

OBJECTIVE: The objective of this paper is to review and analyze the current state of telemedicine and ehealth in the field of vascular surgery. METHODS: This paper collects the relevant information obtained after reviewing the articles related to telemedicine in vascular surgery, published from 2012 to 2022 contained in scientific databases. In addition, the results obtained are statistically studied based on various factors, such as the year of publication or the search engine. In this way, we obtain a complete vision of the current state of telemedicine in the field of vascular surgery. RESULTS: After performing this search and applying selection criteria, 29 articles were obtained for subsequent study and discussion, of which 20 were published in the second half of the decade, representing 70% of the results. In the analysis carried out according to the search criteria used, it can be seen that using the word telemedicine we obtained 69% of the articles while with the criteria mHealth and eHealth we only obtained 22% and 9% of the results, respectively. It can be seen that the filter with the most potential content articles was "vascular surgery AND telemedicine". In the analysis performed according to the search engine, it was observed that the Google Scholar database contains 93% of the articles found in the massive search and the relevant articles contained therein represent 52% of the total. CONCLUSION: An upward trend has been observed in recent years, with a clear increase in the number of publications and much lower figures in the first years. One aspect to highlight is that 47.8% of the articles analyzed focus only on postoperative treatment, which may be due to the help provided by telemedicine in detecting surgical site infections by sending images and videos, this being one of the most common postoperative complications. The analyzed works show the importance of telemedicine in vascular surgery and identify possible future lines of research. In the analysis carried out on the origin of the selected relevant papers, an important interest of the US in this topic is demonstrated since more than 50% of the research contains authors from this country, it is also observed that there is no research from Spain, so this research would be an initial step to determine the weaknesses of telemedicine in this field of medicine and a good opportunity to open a research gap in this branch.


Asunto(s)
Telemedicina , Humanos , Biometría , Bases de Datos Factuales , España , Telemedicina/métodos , Procedimientos Quirúrgicos Vasculares
9.
Nucleic Acids Res ; 47(7): 3680-3698, 2019 04 23.
Artículo en Inglés | MEDLINE | ID: mdl-30715486

RESUMEN

Newly synthesized mitochondrial RNA is concentrated in structures juxtaposed to nucleoids, called RNA granules, that have been implicated in mitochondrial RNA processing and ribosome biogenesis. Here we show that two classical mtDNA replication factors, the mtDNA helicase Twinkle and single-stranded DNA-binding protein mtSSB, contribute to RNA metabolism in mitochondria and to RNA granule biology. Twinkle colocalizes with both mitochondrial RNA granules and nucleoids, and it can serve as bait to greatly enrich established RNA granule proteins, such as G-rich sequence factor 1, GRSF1. Likewise, mtSSB also is not restricted to the nucleoids, and repression of either mtSSB or Twinkle alters mtRNA metabolism. Short-term Twinkle depletion greatly diminishes RNA granules but does not inhibit RNA synthesis or processing. Either mtSSB or GRSF1 depletion results in RNA processing defects, accumulation of mtRNA breakdown products as well as increased levels of dsRNA and RNA:DNA hybrids. In particular, the processing and degradation defects become more pronounced with both proteins depleted. These findings suggest that Twinkle is essential for RNA organization in granules, and that mtSSB is involved in the recently proposed GRSF1-mtRNA degradosome pathway, a route suggested to be particularly aimed at degradation of G-quadruplex prone long non-coding mtRNAs.


Asunto(s)
ADN Helicasas/genética , ADN Mitocondrial/genética , Proteínas de Unión al ADN/genética , Proteínas Mitocondriales/genética , Proteínas de Unión a Poli(A)/genética , Replicación del ADN/genética , Humanos , Mitocondrias/genética , Mitocondrias/metabolismo , Procesamiento Postranscripcional del ARN/genética , ARN Mitocondrial/química , ARN Mitocondrial/genética
10.
Nucleic Acids Res ; 47(12): 6519-6537, 2019 07 09.
Artículo en Inglés | MEDLINE | ID: mdl-31114891

RESUMEN

Human mitochondrial DNA (h-mtDNA) codes for 13 subunits of the oxidative phosphorylation pathway, the essential route that produces ATP. H-mtDNA transcription and replication depends on the transcription factor TFAM, which also maintains and compacts this genome. It is well-established that TFAM activates the mtDNA promoters LSP and HSP1 at the mtDNA control region where DNA regulatory elements cluster. Previous studies identified still uncharacterized, additional binding sites at the control region downstream from and slightly similar to LSP, namely sequences X and Y (Site-X and Site-Y) (Fisher et al., Cell 50, pp 247-258, 1987). Here, we explore TFAM binding at these two sites and compare them to LSP by multiple experimental and in silico methods. Our results show that TFAM binding is strongly modulated by the sequence-dependent properties of Site-X, Site-Y and LSP. The high binding versatility of Site-Y or the considerable stiffness of Site-X tune TFAM interactions. In addition, we show that increase in TFAM/DNA complex concentration induces multimerization, which at a very high concentration triggers disruption of preformed complexes. Therefore, our results suggest that mtDNA sequences induce non-uniform TFAM binding and, consequently, direct an uneven distribution of TFAM aggregation sites during the essential process of mtDNA compaction.


Asunto(s)
ADN Mitocondrial/química , ADN Mitocondrial/metabolismo , Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/metabolismo , Proteínas Mitocondriales/química , Proteínas Mitocondriales/metabolismo , Factores de Transcripción/química , Factores de Transcripción/metabolismo , Secuencia de Bases , Humanos , Poli A , Regiones Promotoras Genéticas , Unión Proteica , Multimerización de Proteína , Termodinámica
11.
J Transl Med ; 18(1): 356, 2020 09 18.
Artículo en Inglés | MEDLINE | ID: mdl-32948200

RESUMEN

BACKGROUND: Mesenchymal stromal cells are a safe and promising option to treat knee osteoarthritis as previously demonstrated in different clinical trials. However, their efficacy, optimal dose and addition of adjuvants must be determined. Here, we evaluated the clinical effects of a dose of 100 × 106 bone marrow mesenchymal stromal cells (BM-MSCs) in combination with Platelet Rich Plasma (PRGF®) as adjuvant in a randomized clinical trial. METHODS: A phase II, multicenter, randomized clinical trial with active control was conducted. Sixty patients diagnosed with knee OA were randomly assigned to 3 weekly doses of PRGF® or intraarticular administration of 100 × 106 cultured autologous BM-MSCs plus PRGF®. Patients were followed up for 12 months, and pain and function were assessed using VAS and WOMAC and by measuring the knee range of motion range. X-ray and magnetic resonance imaging analyses were performed to analyze joint damage. RESULTS: No adverse effects were reported after BM-MSC administration or during follow-up. According to VAS, the mean value (SD) for PRGF® and BM-MSC with PRGF® went from 5 (1.8) to 4.5 (2.2) (p = 0.389) and from 5.3 (1.9) to 3.5 (2.5) (p = 0.01), respectively at 12 months. In WOMAC, the mean (SD) baseline and 12-month overall WOMAC scores in patients treated with PRGF® was 31.9 (16.2) and 22.3 (15.8) respectively (p = 0.002) while that for patients treated with BM-MSC plus PRGF® was 33.4 (18.7) and 23.0 (16.6) (p = 0.053). Although statistical significances between groups have been not detected, only patients being treated with BM-MSC plus PRGF® could be considered as a OA treatment responders following OARSI criteria. X-ray and MRI (WORMS protocol) revealed no changes in knee joint space width or joint damage. CONCLUSIONS: Treatment with BM-MSC associated with PRGF® was shown to be a viable therapeutic option for osteoarthritis of the knee, with clinical improvement at the end of follow-up. Further phase III clinical trials would be necessary to confirm the efficacy. Trial registration Clinical Trials.gov identifier NCT02365142. Nº EudraCT: 2011-006036-23.


Asunto(s)
Trasplante de Células Madre Mesenquimatosas , Células Madre Mesenquimatosas , Osteoartritis de la Rodilla , Plasma Rico en Plaquetas , Humanos , Inyecciones Intraarticulares , Osteoartritis de la Rodilla/terapia , Resultado del Tratamiento
12.
Eur J Vasc Endovasc Surg ; 60(6): 837-842, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-32912764

RESUMEN

OBJECTIVE: The International Commission on Radiological Protection (ICRP) has highlighted the large number of medical specialties using fluoroscopy outside imaging departments without programmes of radiation protection (RP) for patients and staff. Vascular surgery is one of these specialties and endovascular aneurysm repair (EVAR) is one of the most challenging procedures requiring RP guidance and optimisation actions. The recent European Directive on Basic Safety Standards requires the use and regular update of diagnostic reference levels (DRL) for interventional procedures. The objective of the study was to know the doses of patients undergoing EVAR with mobile Xray systems and with hybrid rooms (fixed Xray systems), to obtain national DRLs and suggest optimisation actions. METHODS: The Spanish Chapter of Endovascular Surgery launched a national survey that involved hospitals for 10 autonomous communities representing the 77% of the Spanish population (46.7 million inhabitants). Patient dose values from mobile Xray systems were available from nine hospitals (sample of 165 EVAR procedures) and data from hybrid rooms, from seven hospitals, with dosimetric data from 123 procedures. The initial national DRLs have been obtained, as the third quartile of the median values from the different centres involved in the survey. RESULTS: The proposed national DRLs are 278 Gy cm2 for hybrid rooms and 87 Gy cm2 for mobile Xray systems, and for cumulative air kerma (cumulative AK) at the patient entrance reference point, 1403 mGy for hybrid rooms, and 292 mGy for mobile systems. CONCLUSION: An audit of patient doses for EVAR procedures to identify optimised imaging protocol strategies is needed. It is also appropriate to evaluate the diagnostic information required for EVAR procedures. The increase by a factor of 3.2 (for kerma area product) and 4.8 (for cumulative AK) in the DRLs needs to be justified when the procedures are performed in the hybrid rooms rather than with mobile Xray systems.


Asunto(s)
Aneurisma/diagnóstico por imagen , Procedimientos Endovasculares , Fluoroscopía/normas , Exposición a la Radiación/normas , Estándares de Referencia , Anciano , Anciano de 80 o más Años , Aneurisma/cirugía , Fluoroscopía/instrumentación , Humanos , Persona de Mediana Edad , Seguridad del Paciente , Sistemas de Atención de Punto/normas , Exposición a la Radiación/prevención & control , Radiometría , España
13.
J Environ Manage ; 276: 111293, 2020 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-33007713

RESUMEN

Sustainable land management practices can be suitable vehicles to simultaneously address the causes and consequences of land degradation, desertification, and climate change in land managed systems. Here, we assess the potential of a variety of sustainable land management practices that, beyond addressing specific and local issues, assist in tackling Mediterranean Basin-wide land-use challenges. With this work, we aim to highlight those options that simultaneously promote local and regional Basin-wide adaptation. To do that, we developed a novel multi-objective assessment that evaluates the effectiveness of 104 practices adopted within the Mediterranean Basin and documented in the World Overview of Conservation Approaches and Technologies global database. Results indicate that agroforestry and green covers in perennial woody crops can promote multiple ecosystem services while addressing climate change adaptation. We further argue that these two practices together with reforestation, assist in regulating the hydrological cycle of the Basin and in maintaining its multifunctional landscape. Lastly, we reflect on potential biophysical and socio-economic barriers and opportunities associated with the implementation of the three practices. Our approach provides a Basin-wide integrated view that facilitates the coordination of sustainable management strategies across the Mediterranean region.


Asunto(s)
Conservación de los Recursos Naturales , Ecosistema , Agricultura , Cambio Climático , Humanos , Región Mediterránea
14.
Nucleic Acids Res ; 45(2): 951-967, 2017 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-27899643

RESUMEN

The mitochondrial genome (mtDNA) is assembled into nucleo-protein structures termed nucleoids and maintained differently compared to nuclear DNA, the involved molecular basis remaining poorly understood. In yeast (Saccharomyces cerevisiae), mtDNA is a ∼80 kbp linear molecule and Abf2p, a double HMG-box protein, packages and maintains it. The protein binds DNA in a non-sequence-specific manner, but displays a distinct 'phased-binding' at specific DNA sequences containing poly-adenine tracts (A-tracts). We present here two crystal structures of Abf2p in complex with mtDNA-derived fragments bearing A-tracts. Each HMG-box of Abf2p induces a 90° bend in the contacted DNA, causing an overall U-turn. Together with previous data, this suggests that U-turn formation is the universal mechanism underlying mtDNA compaction induced by HMG-box proteins. Combining this structural information with mutational, biophysical and computational analyses, we reveal a unique DNA binding mechanism for Abf2p where a characteristic N-terminal flag and helix are crucial for mtDNA maintenance. Additionally, we provide the molecular basis for A-tract mediated exclusion of Abf2p binding. Due to high prevalence of A-tracts in yeast mtDNA, this has critical relevance for nucleoid architecture. Therefore, an unprecedented A-tract mediated protein positioning mechanism regulates DNA packaging proteins in the mitochondria, and in combination with DNA-bending and U-turn formation, governs mtDNA compaction.


Asunto(s)
ADN Mitocondrial/química , ADN Mitocondrial/metabolismo , Proteínas de Unión al ADN/metabolismo , Genoma Mitocondrial , Conformación de Ácido Nucleico , Secuencia de Bases , Proteínas de Unión al ADN/química , Conformación Molecular , Simulación del Acoplamiento Molecular , Simulación de Dinámica Molecular , Poli A , Unión Proteica , Dominios y Motivos de Interacción de Proteínas , Origen de Réplica , Termodinámica
16.
Biophys J ; 114(10): 2386-2396, 2018 05 22.
Artículo en Inglés | MEDLINE | ID: mdl-29248151

RESUMEN

Human mitochondrial transcription factor A (TFAM) distorts DNA into a U-turn, as shown by crystallographic studies. The relevance of this U-turn is associated with transcription initiation at the mitochondrial light strand promoter (LSP). However, it has not been yet discerned whether a tight U-turn or an alternative conformation, such as a V-shape, is formed in solution. Here, single-molecule FRET experiments on freely diffusing TFAM/LSP complexes containing different DNA lengths show that a DNA U-turn is induced by progressive and cooperative binding of the two TFAM HMG-box domains and the linker between them. SAXS studies further show compaction of the protein upon complex formation. Finally, molecular dynamics simulations reveal that TFAM/LSP complexes are dynamic entities, and the HMG boxes induce the U-turn against the tendency of the DNA to adopt a straighter conformation. This tension is resolved by reversible unfolding of the linker, which is a singular mechanism that allows a flexible protein to stabilize a tight bending of DNA.


Asunto(s)
Proteínas de Unión al ADN/química , Proteínas de Unión al ADN/metabolismo , ADN/química , ADN/metabolismo , Fenómenos Mecánicos , Proteínas Mitocondriales/química , Proteínas Mitocondriales/metabolismo , Factores de Transcripción/química , Factores de Transcripción/metabolismo , Fenómenos Biomecánicos , Difusión , Humanos , Simulación de Dinámica Molecular , Conformación de Ácido Nucleico , Dominios Proteicos , Soluciones
17.
Nucleic Acids Res ; 43(7): e43, 2015 Apr 20.
Artículo en Inglés | MEDLINE | ID: mdl-25552413

RESUMEN

DNA structure and topology pervasively influence aspects of DNA metabolism including replication, transcription and segregation. However, the effects of DNA topology on DNA-protein interactions have not been systematically explored due to limitations of standard affinity assays. We developed a method to measure protein binding affinity dependence on the topology (topological linking number) of supercoiled DNA. A defined range of DNA topoisomers at equilibrium with a DNA binding protein is separated into free and protein-bound DNA populations using standard nitrocellulose filter binding techniques. Electrophoretic separation and quantification of bound and free topoisomers combined with a simple normalization procedure provide the relative affinity of the protein for the DNA as a function of linking number. Employing this assay we measured topology-dependent DNA binding of a helicase, a type IB topoisomerase, a type IIA topoisomerase, a non-specific mitochondrial DNA binding protein and a type II restriction endonuclease. Most of the proteins preferentially bind negatively supercoiled DNA but the details of the topology-dependent affinity differ among proteins in ways that expose differences in their interactions with DNA. The topology-dependent binding assay provides a robust and easily implemented method to probe topological influences on DNA-protein interactions for a wide range of DNA binding proteins.


Asunto(s)
ADN/metabolismo , ADN/química , Proteínas de Unión al ADN/metabolismo , Conformación de Ácido Nucleico , Unión Proteica
18.
Nucleic Acids Res ; 43(8): 4284-95, 2015 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-25824949

RESUMEN

The mitochondrial replicative helicase Twinkle is involved in strand separation at the replication fork of mitochondrial DNA (mtDNA). Twinkle malfunction is associated with rare diseases that include late onset mitochondrial myopathies, neuromuscular disorders and fatal infantile mtDNA depletion syndrome. We examined its 3D structure by electron microscopy (EM) and small angle X-ray scattering (SAXS) and built the corresponding atomic models, which gave insight into the first molecular architecture of a full-length SF4 helicase that includes an N-terminal zinc-binding domain (ZBD), an intermediate RNA polymerase domain (RPD) and a RecA-like hexamerization C-terminal domain (CTD). The EM model of Twinkle reveals a hexameric two-layered ring comprising the ZBDs and RPDs in one layer and the CTDs in another. In the hexamer, contacts in trans with adjacent subunits occur between ZBDs and RPDs, and between RPDs and CTDs. The ZBDs show important structural heterogeneity. In solution, the scattering data are compatible with a mixture of extended hexa- and heptameric models in variable conformations. Overall, our structural data show a complex network of dynamic interactions that reconciles with the structural flexibility required for helicase activity.


Asunto(s)
ADN Helicasas/química , ADN Helicasas/ultraestructura , Proteínas Mitocondriales/química , Proteínas Mitocondriales/ultraestructura , ADN Helicasas/metabolismo , Humanos , Proteínas Mitocondriales/metabolismo , Modelos Moleculares , Multimerización de Proteína , Estructura Terciaria de Proteína , Dispersión del Ángulo Pequeño , Homología Estructural de Proteína , Difracción de Rayos X
19.
J Basic Microbiol ; 57(12): 1037-1044, 2017 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-28940512

RESUMEN

Environmental mixed pollution by both organic and inorganic compounds are detected worldwide. Phytoremediation techniques have been proposed as ecofriendly methods for cleaning up polluted sites. Several studies have demonstrated enhanced dissipation of contaminants at the root-soil interface through an increase in microbial activity caused by the release of plant root exudates (REs). The aim of this study was to evaluate the effectiveness for Cr(VI) and lindane removal by Streptomyces M7 cultured in a co-contaminated system in presence of maize REs. Our results showed when REs were added to the contaminated minimal medium (MM) as the only carbon source, microbial removal of Cr(VI) and lindane increased significantly in comparison to contaminant removal obtained in MM with glucose 1 g L-1 . The maximum removal of 91% of lindane and 49.5% of Cr(VI) were obtained in the co-contaminated system. Moreover, Streptomyces M7 showed plant growth promoting traits which could improve plant performance in contaminated soils. The results presented in this study provide evidence that maize REs improved growth of Streptomyces M7 when REs were used as a carbon source in comparison to glucose. Consequently, lindane and Cr(VI) removal was considerably enhanced making evident the phytoremediation potential of the actinobacteria-plant partnership.


Asunto(s)
Carcinógenos Ambientales/metabolismo , Cromo/metabolismo , Hexaclorociclohexano/metabolismo , Insecticidas/metabolismo , Exudados de Plantas/metabolismo , Streptomyces/metabolismo , Zea mays/metabolismo , Carbono/metabolismo , Medios de Cultivo/química , Exudados de Plantas/aislamiento & purificación , Raíces de Plantas/metabolismo , Streptomyces/crecimiento & desarrollo
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