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2.
Appl Clin Inform ; 14(5): 923-931, 2023 10.
Artículo en Inglés | MEDLINE | ID: mdl-37726022

RESUMEN

OBJECTIVE: Medication discrepancies between clinical systems may pose a patient safety hazard. In this paper, we identify challenges and quantify medication discrepancies across transitions of care. METHODS: We used structured clinical data and free-text hospital discharge summaries to compare active medications' lists at four time points: preadmission (outpatient), at-admission (inpatient), at-discharge (inpatient), and postdischarge (outpatient). Medication lists were normalized to RxNorm. RxNorm identifiers were further processed using the RxNav API to identify the ingredient. The specific drugs and ingredients from inpatient and outpatient medication lists were compared. RESULTS: Using RxNorm drugs, the median percentage intersection when comparing active medication lists within the same electronic health record system ranged between 94.1 and 100% indicating substantial overlap. Similarly, when using RxNorm ingredients the median percentage intersection was 94.1 to 100%. In contrast, the median percentage intersection when comparing active medication lists across EHR systems was significantly lower (RxNorm drugs: 6.1-7.1%; RxNorm ingredients: 29.4-35.0%) indicating that the active medication lists were significantly less similar (p < 0.05).Medication lists in the same EHR system are more similar to each other (fewer discrepancies) than medication lists in different EHR systems when comparing specific RxNorm drug and the more general RxNorm ingredients at transitions of care. Transitions of care that require interoperability between two EHR systems are associated with more discrepancies than transitions where medication changes are expected (e.g., at-admission vs. at-discharge). Challenges included lack of access to structured, standardized medication data across systems, and difficulty distinguishing medications from orderable supplies such as lancets and diabetic test strips. CONCLUSION: Despite the challenges to medication normalization, there are opportunities to identify and assist with medication reconciliation across transitions of care between institutions.


Asunto(s)
Conciliación de Medicamentos , Alta del Paciente , Humanos , Cuidados Posteriores , Hospitalización , Vocabulario Controlado
3.
Int J Med Inform ; 143: 104261, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-32889387

RESUMEN

PURPOSE: Genomic analysis of individual patients is now affordable, and therapies targeting specific molecular aberrations are being tested in clinical trials. Genomically-informed therapy is relevant to many clinical domains, but is particularly applicable to cancer treatment. However, even specialized clinicians need help to interpret genomic data, to navigate the complicated space of clinical trials, and to keep up with the rapidly expanding biomedical literature. To quantitate the cognitive load on treating clinicians, we attempt to quantitate the rate of change in potential treatment options for patients considering genomically-relevant and genomically-selected therapy for cancer. MATERIALS AND METHODS: To this end, we analyzed patient-specific reports generated by a precision oncology decision support team (PODS) at a large academic cancer center. Two types of potential treatment options were analyzed: FDA-approved genomically-relevant and genomically-selected therapies and therapies available via clinical trials. We focused on two clinically-actionable alterations: ERBB2 (Her2/neu; amplified vs. non-amplified) and BRAF mutation (V600 vs. non-V600). To determine changes in available treatment options, we grouped patients into similar groups by disease site (ERBB2: breast, gastric and "other"; BRAF: melanoma, non-melanoma). RESULTS: A total of 2927 reports for 2366 unique patients were generated 8/2016-12/2018. Reports included 9902 gene variants and 150 disease classifications. BRAF mutation and ERBB2 amplification were annotated with therapeutic options in 270 reports (225 unique patients). The median survival time of a therapeutic option was nine months. CONCLUSION: When compared to "traditional" clinical practice guideline recommendations, treatment options for personalized cancer therapy change seven times more rapidly; partly due to change in knowledge and partly due to logistics such as clinical trial availability.


Asunto(s)
Oncología Médica , Medicina de Precisión , Genómica , Humanos , Mutación , Terapias en Investigación
4.
J Biotechnol ; 283: 11-21, 2018 Oct 10.
Artículo en Inglés | MEDLINE | ID: mdl-30003973

RESUMEN

The seven in absentia like 7 gene (At5g37890, SINAL7) from Arabidopsis thaliana encodes a RING finger protein belonging to the SINA superfamily that possesses E3 ubiquitin-ligase activity. SINAL7 has the ability to self-ubiquitinate and to mono-ubiquitinate glyceraldehyde-3-P dehydrogenase 1 (GAPC1), suggesting a role for both proteins in a hypothetical signaling pathway in Arabidopsis. In this study, the in vivo effects of SINAL7 on plant physiology were examined by over-expressing SINAL7 in transgenic Arabidopsis plants. Phenotypic and gene expression analyses suggest the involvement of SINAL7 in the regulation of several vegetative parameters, essentially those that affect the aerial parts of the plants. Over-expression of SINAL7 resulted in an increase in the concentrations of hexoses and sucrose, with a concommitant increase in plant biomass, particularly in the number of rosette leaves and stem thickness. Interestingly, using the CAB1 (chlorophyll ab binding protein 1) gene as a marker revealed a delay in the onset of senescence. Transgenic plants also displayed a remarkable level of drought resistance, indicating the complexity of the response to SINAL7 over-expression.


Asunto(s)
Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Arabidopsis/fisiología , Expresión Génica , Estrés Fisiológico , Ubiquitina-Proteína Ligasas/genética , Ubiquitina-Proteína Ligasas/metabolismo , Biomasa , Sequías , Gliceraldehído-3-Fosfato Deshidrogenasa (Fosforilante)/metabolismo , Hexosas/metabolismo , Componentes Aéreos de las Plantas/fisiología , Plantas Modificadas Genéticamente/fisiología , Transducción de Señal , Sacarosa/metabolismo , Ubiquitinación
5.
J Am Med Inform Assoc ; 23(4): 758-65, 2016 07.
Artículo en Inglés | MEDLINE | ID: mdl-27107438

RESUMEN

INTRODUCTION: Genomic profiling information is frequently available to oncologists, enabling targeted cancer therapy. Because clinically relevant information is rapidly emerging in the literature and elsewhere, there is a need for informatics technologies to support targeted therapies. To this end, we have developed a system for Automated Identification of Molecular Effects of Drugs, to help biomedical scientists curate this literature to facilitate decision support. OBJECTIVES: To create an automated system to identify assertions in the literature concerning drugs targeting genes with therapeutic implications and characterize the challenges inherent in automating this process in rapidly evolving domains. METHODS: We used subject-predicate-object triples (semantic predications) and co-occurrence relations generated by applying the SemRep Natural Language Processing system to MEDLINE abstracts and ClinicalTrials.gov descriptions. We applied customized semantic queries to find drugs targeting genes of interest. The results were manually reviewed by a team of experts. RESULTS: Compared to a manually curated set of relationships, recall, precision, and F2 were 0.39, 0.21, and 0.33, respectively, which represents a 3- to 4-fold improvement over a publically available set of predications (SemMedDB) alone. Upon review of ostensibly false positive results, 26% were considered relevant additions to the reference set, and an additional 61% were considered to be relevant for review. Adding co-occurrence data improved results for drugs in early development, but not their better-established counterparts. CONCLUSIONS: Precision medicine poses unique challenges for biomedical informatics systems that help domain experts find answers to their research questions. Further research is required to improve the performance of such systems, particularly for drugs in development.


Asunto(s)
Antineoplásicos/farmacología , Almacenamiento y Recuperación de la Información/métodos , Procesamiento de Lenguaje Natural , Neoplasias/tratamiento farmacológico , Neoplasias/genética , Medicina de Precisión , Antineoplásicos/uso terapéutico , Ensayos Clínicos como Asunto , Humanos , MEDLINE , Semántica , Unified Medical Language System
6.
Int J Biochem Cell Biol ; 70: 48-56, 2016 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-26582368

RESUMEN

The E3 ubiquitin-protein ligases are associated to various processes such as cell cycle control and diverse developmental pathways. Arabidopsis thaliana SEVEN IN ABSENTIA like 7, which has ubiquitin ligase activity, is located in the nucleus and cytosol and is expressed at several stages in almost all plant tissues suggesting an important role in plant functions. However, the mechanism underlying the regulation of this protein is unknown. Since we found that the SEVEN IN ABSENTIA like 7 gene expression is altered in plants with impaired mitochondria, and in plants deficient in the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase 1, we decided to study the possible interactions between both proteins as potential partners in plant signaling functions. We found that SEVEN IN ABSENTIA like 7 is able to interact in vitro with glyceraldehyde-3-phosphate dehydrogenase and that the Lys231 residue of the last is essential for this function. Following the interaction, a concomitant increase in the glyceraldehyde-3-phosphate dehydrogenase catalytic activity was observed. However, when SEVEN IN ABSENTIA like 7 was supplemented with E1 and E2 proteins to form a complete E1-E2-E3 modifier complex, we observed the mono-ubiquitination of glyceraldehyde-3-phosphate dehydrogenase 1 at the Lys76 residue and a dramatic decrease of its catalytic activity. Moreover, we found that localization of glyceraldehyde-3-phosphate dehydrogenase 1 in the nucleus is dependent on the expression SEVEN IN ABSENTIA like 7. These observations suggest that the association of both proteins might result in different biological consequences in plants either through affecting the glycolytic flux or via cytoplasm-nucleus relocation.


Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Regulación de la Expresión Génica de las Plantas , Gliceraldehído-3-Fosfato Deshidrogenasa (Fosforilante)/genética , Proteínas Nucleares/genética , Ubiquitina-Proteína Ligasas/genética , Transporte Activo de Núcleo Celular/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Sitios de Unión , Biocatálisis , Núcleo Celular/metabolismo , Clonación Molecular , Citosol/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Gliceraldehído-3-Fosfato Deshidrogenasa (Fosforilante)/metabolismo , Glucólisis/genética , Cinética , Mutación , Proteínas Nucleares/metabolismo , Células Vegetales/metabolismo , Unión Proteica , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Transducción de Señal , Ubiquitina-Proteína Ligasas/metabolismo , Ubiquitinación
7.
PLoS One ; 10(10): e0141443, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-26517126

RESUMEN

Frataxin plays a key role in eukaryotic cellular iron metabolism, particularly in mitochondrial heme and iron-sulfur (Fe-S) cluster biosynthesis. However, its precise role has yet to be elucidated. In this work, we studied the subcellular localization of Arabidopsis frataxin, AtFH, using confocal microscopy, and found a novel dual localization for this protein. We demonstrate that plant frataxin is targeted to both the mitochondria and the chloroplast, where it may play a role in Fe-S cluster metabolism as suggested by functional studies on nitrite reductase (NIR) and ferredoxin (Fd), two Fe-S containing chloroplast proteins, in AtFH deficient plants. Our results indicate that frataxin deficiency alters the normal functioning of chloroplasts by affecting the levels of Fe, chlorophyll, and the photosynthetic electron transport chain in this organelle.


Asunto(s)
Proteínas de Arabidopsis/fisiología , Arabidopsis/metabolismo , Cloroplastos/metabolismo , Proteínas de Unión a Hierro/fisiología , Proteínas Hierro-Azufre/metabolismo , Mitocondrias/metabolismo , Arabidopsis/genética , Arabidopsis/ultraestructura , Proteínas de Arabidopsis/análisis , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Clorofila/análisis , Cloroplastos/química , Ferredoxinas/genética , Ferredoxinas/metabolismo , Eliminación de Gen , Proteínas de Unión a Hierro/análisis , Proteínas de Unión a Hierro/genética , Microscopía Confocal , Mitocondrias/química , Proteínas Mitocondriales/fisiología , Nitrito Reductasas/genética , Nitrito Reductasas/metabolismo , Plantas Modificadas Genéticamente , Protoplastos/metabolismo , Protoplastos/ultraestructura , ARN Mensajero/genética , ARN de Planta/genética , Reacción en Cadena en Tiempo Real de la Polimerasa
8.
PLoS One ; 8(8): e73104, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-24015288

RESUMEN

Protein ubiquitination leading to degradation by the proteasome is an important mechanism in regulating key cellular functions. Protein ubiquitination is carried out by a three step process involving ubiquitin (Ub) activation by a E1 enzyme, the transfer of Ub to a protein E2, finally an ubiquitin ligase E3 catalyzes the transfer of the Ub peptide to an acceptor protein. The E3 component is responsible for the specific recognition of the target, making the unveiling of E3 components essential to understand the mechanisms regulating fundamental cell processes through the protein degradation pathways. The Arabidopsis thaliana seven in absentia-like 7 (AtSINAL7) gene encodes for a protein with characteristics from a C3HC4-type E3 ubiquitin ligase. We demonstrate here that AtSINAL7 protein is indeed an E3 protein ligase based on the self-ubiquitination in vitro assay. This activity is dependent of the presence of a Lys residue in position 124. We also found that higher AtSINAL7 transcript levels are present in tissues undergoing active cell division during floral development. An interesting observation is the circadian expression pattern of AtSINAL7 mRNA in floral buds. Furthermore, UV-B irradiation induces the expression of this transcript indicating that AtSINAL7 may be involved in a wide range of different cell processes.


Asunto(s)
Proteínas de Arabidopsis/metabolismo , Arabidopsis/enzimología , Regulación Enzimológica de la Expresión Génica/efectos de la radiación , Regulación de la Expresión Génica de las Plantas/efectos de la radiación , Ubiquitina-Proteína Ligasas/biosíntesis , Ubiquitinación/efectos de la radiación , Rayos Ultravioleta , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Regulación Enzimológica de la Expresión Génica/fisiología , Regulación de la Expresión Génica de las Plantas/fisiología , Ubiquitina/genética , Ubiquitina/metabolismo , Ubiquitina-Proteína Ligasas/genética , Ubiquitinación/fisiología
9.
PLoS One ; 7(12): e52644, 2012.
Artículo en Inglés | MEDLINE | ID: mdl-23285127

RESUMEN

In plant mitochondria, gene expression of translatable mRNAs is a complex process with two critical steps, RNA editing and splicing. We studied the role of RNA editing on non-coding regions of the mat-r-nad1e-nad5c transcript from wheat mitochondria. This RNA contains two trans-introns, 3'-nad1-I4 and 3'-nad5-I2, involved in different trans-splicing events, ensuring the association of nad1d-nad1e and nad5b-nad5c exons from nad1 and nad5 mRNAs respectively. The C-to-U editing changes studied here affect homologous positions on 3'-nad1-I4 and 3'-nad5-I2. It is proposed that these base changes are necessary to place an Adenosine residue in a bulging conformation characteristic of domain VI (D6) from group II introns. In this work, we investigated the role of RNA editing events on 3'-nad1-I4 and 3'-nad5-I2 in the trans-splicing process using in vivo and in organello approaches. When the branched intermediates formed during the splicing process were analyzed, the C residues from D6 intron domains from 3'-nad1-I4 and 3'-nad5-I2 were found changed to U, suggesting that RNA editing of these residues could be mandatory for splicing. This assumption was tested by expressing recombinant mat-r-nad1e transgenes introduced into mitochondria by electroporation. Mutation of the editing target residue dramatically affected trans-splicing. Interestingly, the exon joining efficiency was not recovered by compensatory mutations, suggesting that the role of RNA editing is not confined to the restoration of the secondary structure of domain D6 of the intron. Our results strongly support the hypothesis that RNA editing in trans-introns precedes maturation, and is required for the splicing reaction. In addition, this is the first report using an in organello approach to study the trans-splicing process, opening the way to future studies of this peculiar mechanism.


Asunto(s)
Intrones , Mitocondrias/genética , Edición de ARN , Trans-Empalme , Secuencia de Bases , Exones , Orden Génico , Genes de Plantas , Mitocondrias/metabolismo , Mutación , Conformación de Ácido Nucleico , ARN de Planta/química , ARN de Planta/genética , Transgenes , Triticum/genética , Triticum/metabolismo
10.
IUBMB Life ; 64(2): 120-5, 2012 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-22162179

RESUMEN

RNA editing challenges the central dogma of molecular biology by changing the genetic information at the transcript level. In plant organelles, RNAs are modified by deamination of some specific cytosine residues, but the origin of this process remains puzzling. Different from the generally accepted neutral model to explain the emergence of RNA editing in plant organelles, we propose a new hypothesis based on the nucleocytoplasmic conflict theory. We assume that mutations in organellar genomes arose first and spread into the population provided they increased the transmission of their own maternally inherited genome. RNA editing appeared subsequently as a nuclear-encoded correction mechanism to restore the transmission of the nuclear genome. In plants, a well-known consequence of the nucleocytoplasmic conflict is cytoplasmic male sterility (CMS) which is counteracted by the emergence of fertility restorer genes (Rf) belonging to the pentatricopeptide repeat (PPR) protein family. Interestingly, RNA-editing deficiency can lead to CMS, and it now clearly appears that PPR proteins are major players in RNA editing. This striking similarity between the mechanisms of fertility restoration and RNA editing can be explained if both reactions are the consequence of the same driving force, the nucleocytoplasmic conflict. Similarly, the prevalence of RNA editing in eukaryotic organellar genomes could also be a consequence of the genetic antagonism between organellar and nuclear genomes.


Asunto(s)
Cloroplastos/genética , Mitocondrias/genética , Plantas/genética , Edición de ARN , Evolución Biológica , Núcleo Celular/genética , Cloroplastos/metabolismo , Citoplasma/genética , Humanos , Mitocondrias/metabolismo , Infertilidad Vegetal , Proteínas de Plantas/metabolismo , Plantas/metabolismo , ARN de Planta/metabolismo , Reproducción
11.
Plant Signal Behav ; 6(12): 1904-7, 2011 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-22101346

RESUMEN

The transcriptomic response of A9:u-ATP9 and apetala3:u-ATP9 lines carrying a mitochondrial dysfunction in flower tissues has been characterized. Both lines showed an alteration in the transcription of several genes involved in carbon and nitrogen metabolism, stress responses, transcription factors and DNA binding proteins. Interestingly, several transcripts of photosynthetic-related genes were also affected in their expression such as the mRNAs encoding for chlorophyllase, chlorophyll binding proteins and a PSII. Moreover, chlorophyll levels were reduced and the Mg-dechelatase activity was increased, indicating an alteration in chlorophyll metabolism. Our results suggest that the mitochondrial dysfunction may also affect chloroplastic functions, and that our model could be useful to uncover retrograde signaling mechanisms operating between the three different plant genomes.


Asunto(s)
Arabidopsis/fisiología , Cloroplastos/fisiología , Mitocondrias/fisiología , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Clorofila/análisis , Cloroplastos/metabolismo , Flores/metabolismo , Flores/fisiología , Regulación de la Expresión Génica de las Plantas , Magnesio/metabolismo , Mitocondrias/metabolismo , ATPasas de Translocación de Protón Mitocondriales/genética , Plantas Modificadas Genéticamente/metabolismo , Plantas Modificadas Genéticamente/fisiología , Transcriptoma
12.
Curr Genet ; 57(5): 317-25, 2011 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-21701904

RESUMEN

In the leptosporangiate fern Osmunda regalis, cox1 gene is disrupted by a 1071-nucleotide-long group I intron that is homologous to the Marchantia polymorpha cox1 intron 4 (cox1i395g1). This intron, which shares 89% sequence identity with its bryophyte counterpart, lost the capacity to encode for a maturase due to insertion/deletion mutations. The cox1 coding region is interrupted by a stop codon in both exons. The cox1 transcript undergoes 58 C-to-U and 13 U-to-C conversions, including the suppression of two stop codons that result in the recovery of a functional cox1 ORF. Interestingly, 4 C-to-U conversions found in mRNA precursors showed that the O. regalis cox1i395g1 intron is efficiently edited. These modifications improved the sequence identity with the Marchantia cox1i395 intron. In particular, the RNA editing events affect regions involved in secondary and tertiary structures of the intron, restoring three base pairing in the structural P5a and P9 helices, and correcting a highly conserved U in the P7 helix that contributes to the catalytic core. Moreover, cox1 intron orthologous from three different fern species were found to be edited by both C-to-U and U-to-C conversions in P7 and P9. Thus, RNA editing helps to correct the conserved domains of group I introns in "true ferns", suggesting a possible link between editing and splicing. We present here the first experimental evidence of RNA editing concerning a group I intron in plant organelles.


Asunto(s)
Helechos/genética , Intrones , Mitocondrias/genética , Edición de ARN , Secuencia de Bases , Secuencia Conservada , Ciclooxigenasa 1/genética , Citidina/genética , Dryopteris/genética , Datos de Secuencia Molecular , Conformación de Ácido Nucleico , Polypodium/genética , Pliegue del ARN , Uridina/genética
13.
PLoS One ; 6(6): e20867, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-21695137

RESUMEN

The mitochondrial transcriptome from land plants undergoes hundreds of specific C-to-U changes by RNA editing. These events are important since most of them occur in the coding region of mRNAs. One challenging question is to understand the mechanism of recognition of a selected C residue (editing sites) on the transcript. It has been reported that a short region surrounding the target C forms the cis-recognition elements, but individual residues on it do not play similar roles for the different editing sites. Here, we studied the role of the -1 and +1 nucleotide in wheat cox2 editing site recognition using an in organello approach. We found that four different recognition patterns can be distinguished: (a) +1 dependency, (b) -1 dependency, (c) +1/-1 dependency, and (d) no dependency on nearest neighbor residues. A striking observation was that whereas a 23 nt cis region is necessary for editing, some mutants affect the editing efficiency of unmodified distant sites. As a rule, mutations or pre-edited variants of the transcript have an impact on the complete set of editing targets. When some Cs were changed into Us, the remaining editing sites presented a higher efficiency of C-to-U conversion than in wild type mRNA. Our data suggest that the complex response observed for cox2 mRNA may be a consequence of the fate of the transcript during mitochondrial gene expression.


Asunto(s)
Complejo IV de Transporte de Electrones/genética , Mitocondrias/genética , Mutación Puntual/genética , Edición de ARN/genética , Triticum/citología , Triticum/genética , Secuencia de Bases , Mitocondrias/enzimología , ARN Mensajero/genética , ARN Mensajero/metabolismo , Triticum/enzimología
14.
Mol Plant ; 4(1): 127-43, 2011 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-20978083

RESUMEN

We characterized the transcriptomic response of transgenic plants carrying a mitochondrial dysfunction induced by the expression of the unedited form of the ATP synthase subunit 9. The u-ATP9 transgene driven by A9 and APETALA3 promoters induce mitochondrial dysfunction revealed by a decrease in both oxygen uptake and adenine nucleotides (ATP, ADP) levels without changes in the ATP/ADP ratio. Furthermore, we measured an increase in ROS accumulation and a decrease in glutathione and ascorbate levels with a concomitant oxidative stress response. The transcriptome analysis of young Arabidopsis flowers, validated by qRT-PCR and enzymatic or functional tests, showed dramatic changes in u-ATP9 plants. Both lines display a modification in the expression of various genes involved in carbon, lipid, and cell wall metabolism, suggesting that an important metabolic readjustment occurs in plants with a mitochondrial dysfunction. Interestingly, transcript levels involved in mitochondrial respiration, protein synthesis, and degradation are affected. Moreover, the levels of several mRNAs encoding for transcription factors and DNA binding proteins were also changed. Some of them are involved in stress and hormone responses, suggesting that several signaling pathways overlap. Indeed, the transcriptome data revealed that the mitochondrial dysfunction dramatically alters the expression of genes involved in signaling pathways, including those related to ethylene, absicic acid, and auxin signal transduction. Our data suggest that the mitochondrial dysfunction model used in this report may be useful to uncover the retrograde signaling mechanism between the nucleus and mitochondria in plant cells.


Asunto(s)
Arabidopsis/metabolismo , Carbono/metabolismo , Flores/metabolismo , Regulación de la Expresión Génica de las Plantas , Mitocondrias/metabolismo , Arabidopsis/genética , Arabidopsis/crecimiento & desarrollo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Flores/genética , Flores/crecimiento & desarrollo , Mitocondrias/genética , Transducción de Señal
15.
FEBS J ; 278(3): 470-81, 2011 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-21166997

RESUMEN

Frataxin, a conserved mitochondrial protein implicated in cellular iron homeostasis, has been involved as the iron chaperone that delivers iron for the Fe-S cluster and heme biosynthesis. However, its role in iron metabolism remains unclear, especially in photosynthetic organisms. In previous work, we found that frataxin deficiency in Arabidopsis results in decreased activity of the mitochondrial Fe-S proteins aconitase and succinate dehydrogenase, despite the increased expression of the respective genes, indicating an important role for Arabidopsis thaliana frataxin homolog (AtFH). In this work, we explore the hypothesis that AtFH can participate in heme formation in plants. For this purpose, we used two Arabidopsis lines, atfh-1 and as-AtFH, with deficiency in the expression of AtFH. Both lines present alteration in several transcripts from the heme biosynthetic route with a decrease in total heme content and a deficiency in catalase activity that was rescued with the addition of exogenous hemin. Our data substantiate the hypothesis that AtFH, apart from its role in protecting bioavailable iron within mitochondria and the biogenesis of Fe-S groups, also plays a role in the biosynthesis of heme groups in plants.


Asunto(s)
Proteínas de Arabidopsis/fisiología , Arabidopsis/metabolismo , Hemo/biosíntesis , Proteínas Mitocondriales/fisiología , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Hierro/metabolismo , Proteínas Mitocondriales/genética , Proteínas Mitocondriales/metabolismo , Fenotipo , Plantas Modificadas Genéticamente/metabolismo , ARN Mensajero/metabolismo
16.
Nucleic Acids Res ; 38(20): 7112-21, 2010 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-20615898

RESUMEN

Most plant mitochondria messenger RNAs (mRNAs) undergo editing through C-to-U conversions located mainly in exon sequences. However, some RNA editing events are found in non-coding regions at critical positions in the predicted secondary and tertiary structures of introns, suggesting that RNA editing could be important for splicing. Here, we studied the relationships between editing and splicing of the mRNA encoding the ribosomal protein S10 (rps10), which has a group II intron and five editing sites. Two of them, C2 and C3, predicted to stabilize the folded structure of the intron necessary for splicing, were studied by using rps10 mutants introduced into isolated potato mitochondria by electroporation. While mutations of C2 involved in EBS2/IBS2 interactions did not affect splicing, probably by the presence of an alternative EBS2' region in domain I of the intron, the edition of site C3 turned out to be critical for rps10 mRNA splicing; only the edited (U) form of the transcript was processed. Interestingly, RNA editing was strongly reduced in transcripts from two different intronless genes, rps10 from potato and cox2 from wheat, suggesting that efficient RNA processing may require a close interaction of factors engaged in different maturation processes. This is the first report linking editing and splicing in conditions close to the in vivo situation.


Asunto(s)
Regulación de la Expresión Génica de las Plantas , Intrones , Edición de ARN , Empalme del ARN , ARN/metabolismo , Mitocondrias/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , ARN/química , Precursores del ARN/química , Precursores del ARN/metabolismo , ARN Mensajero/química , ARN Mensajero/metabolismo , ARN Mitocondrial , Proteínas Ribosómicas/genética , Proteínas Ribosómicas/metabolismo , Solanum tuberosum/genética
17.
Plant Physiol ; 150(1): 84-95, 2009 May.
Artículo en Inglés | MEDLINE | ID: mdl-19261733

RESUMEN

Mitochondrial complex II (succinate dehydrogenase) is part of the tricarboxylic acid cycle and the respiratory chain. Three nuclear genes encode its essential iron-sulfur subunit in Arabidopsis (Arabidopsis thaliana). One of them, SUCCINATE DEHYDROGENASE2-3 (SDH2-3), is specifically expressed in the embryo during seed maturation, suggesting that SDH2-3 may have a role as the complex II iron-sulfur subunit during embryo maturation and/or germination. Here, we present data demonstrating that three abscisic acid-responsive elements and one RY-like enhancer element, present in the SDH2-3 promoter, are involved in embryo-specific SDH2-3 transcriptional regulation. Furthermore, we show that ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEAFY COTYLEDON2, three key B3 domain transcription factors involved in gene expression during seed maturation, control SDH2-3 expression. Whereas ABI3 and FUS3 interact with the RY element in the SDH2-3 promoter, the abscisic acid-responsive elements are shown to be a target for bZIP53, a member of the basic leucine zipper (bZIP) family of transcription factors. We show that group S1 bZIP53 protein binds the promoter as a heterodimer with group C bZIP10 or bZIP25. To the best of our knowledge, the SDH2-3 promoter is the first embryo-specific promoter characterized for a mitochondrial respiratory complex protein. Characterization of succinate dehydrogenase activity in embryos from two homozygous sdh2-3 mutant lines permits us to conclude that SDH2-3 is the major iron-sulfur subunit of mature embryo complex II. Finally, the absence of SDH2-3 in mutant seeds slows down their germination, pointing to a role of SDH2-3-containing complex II at an early step of germination.


Asunto(s)
Proteínas de Arabidopsis/genética , Arabidopsis/genética , Regulación de la Expresión Génica de las Plantas , Proteínas Hierro-Azufre/genética , Semillas/genética , Succinato Deshidrogenasa/genética , Factores de Transcripción/fisiología , Arabidopsis/embriología , Arabidopsis/metabolismo , Proteínas de Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Proteínas de Arabidopsis/fisiología , Secuencia de Bases , Sitios de Unión , Germinación/genética , Proteínas Hierro-Azufre/química , Proteínas Hierro-Azufre/metabolismo , Datos de Secuencia Molecular , Regiones Promotoras Genéticas , Estructura Terciaria de Proteína , Subunidades de Proteína/química , Subunidades de Proteína/genética , Subunidades de Proteína/metabolismo , Semillas/crecimiento & desarrollo , Semillas/metabolismo , Succinato Deshidrogenasa/química , Succinato Deshidrogenasa/metabolismo , Factores de Transcripción/química
18.
Curr Genet ; 55(1): 69-79, 2009 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-19112563

RESUMEN

We studied the genomic structure and RNA editing of mitochondrial cox1, cox2, cob and atp9 from the horsetail Equisetum arvense, a representative of an old fern lineage. Editing of cox1, cob and atp9 mRNAs occur only by C-to-U transitions. No changes were found in cox2 transcripts constituting one of the rare examples of unedited mitochondrial mRNA in land plants. From three intervening sequences in cox1, cox1i395 and cox1i624 are group IB introns homologous to the Marchantia polymorpha cox1 introns, and cox1i747 is a group IIA intron different to other introns found in plant mtDNA. The group II intron cox2i373 is very similar to other introns found in cox2 from vascular plants. While cob and atp9 have no introns and display the gene structure found in seed plants, various nucleotide substitutions abolish the only potential ORF, a LAGLIDADG endonuclease present in cox1i395. Thus, E. arvense mitochondria conserve two group I introns from non-vascular plants, probably inherited from a common ancestor with liverworts. Analogous to seed plants, E. arvense has no potential mitochondrial splicing factors encoded in these introns. This is the first report concerning the presence of vertically inherited group I introns in vascular plant mitochondria.


Asunto(s)
Equisetum/genética , Intrones/genética , Marchantia/genética , Mitocondrias/genética , Proteínas Mitocondriales/genética , Sistemas de Lectura Abierta/fisiología , Edición de ARN/genética , Secuencia de Bases , Clonación Molecular , ADN de Plantas/química , ADN de Plantas/genética , ADN de Plantas/metabolismo , Mitocondrias/metabolismo , Proteínas Mitocondriales/metabolismo , Datos de Secuencia Molecular , Conformación de Ácido Nucleico , Reacción en Cadena de la Polimerasa , Empalme del ARN , ARN de Planta/química , ARN de Planta/genética , ARN de Planta/metabolismo , Homología de Secuencia de Ácido Nucleico
19.
Methods Enzymol ; 424: 483-500, 2007.
Artículo en Inglés | MEDLINE | ID: mdl-17662855

RESUMEN

Plant mitochondrial gene expression is a complex process involving multiple steps such as transcription, cis- and trans-splicing, RNA trimming, RNA editing, and translation. One of the main hurdles in understanding more about these processes has been the inability to incorporate engineered genes into mitochondria. We recently reported an in organello approach on the basis of the introduction of foreign DNA into isolated plant mitochondria by electroporation. This procedure allows the investigation of transcriptional and posttranscriptional processes, such as splicing and RNA editing, by use of site-directed mutagenesis. Foreign gene expression in organello is strongly dependent on the functional status of mitochondria, thus providing relevant information in conditions closer to the situation found in vivo. The study of mutants that affect RNA splicing and editing provides a novel and powerful method to explain the role of specific sequences involved in these processes. Here we describe a protocol to "transform" isolated plant mitochondria that has allowed us to investigate successfully some aspects of RNA editing.


Asunto(s)
Bioquímica/métodos , Regulación de la Expresión Génica de las Plantas , Mitocondrias/genética , Proteínas de Plantas/genética , Edición de ARN/genética , Electroporación , Técnicas Genéticas , Mitocondrias/metabolismo , Plásmidos/metabolismo , ARN/metabolismo , Procesamiento Postranscripcional del ARN , Empalme del ARN , Reacción en Cadena de la Polimerasa de Transcriptasa Inversa , Análisis de Secuencia de ADN , Solanum tuberosum/genética , Triticum/genética
20.
Protein Expr Purif ; 51(2): 157-61, 2007 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-16879981

RESUMEN

Frataxin, a nuclear-encoded mitochondrial protein, has been proposed to participate in Fe-S cluster assembly, mitochondrial energy metabolism, respiration, and iron homeostasis. However, its precise function remains elusive. Frataxin is highly conserved in living organisms with no major structural changes, in particular at the C-terminal protein domain, suggesting that it plays a key function in all organisms. Recently, a plant gene, AtFH, with significant homology to other members of the frataxin family has been described. To gain insight on the frataxin role in plants, the frataxin domain was expressed in Escherichia coli BL21-codonPlus (DE3)-RIL cells and purified using a Ni-chelating column. The purified protein, added to a mixture containing Fe(II) and H2O2, attenuates the Fenton reaction indicating that the recombinant plant frataxin is functional. The procedure described here produced high yield of 99% pure protein through only one chromatographic step, suitable for further structure-function studies.


Asunto(s)
Proteínas de Arabidopsis/biosíntesis , Proteínas de Arabidopsis/aislamiento & purificación , Proteínas de Unión a Hierro/biosíntesis , Proteínas de Unión a Hierro/aislamiento & purificación , Proteínas Mitocondriales/biosíntesis , Proteínas Mitocondriales/aislamiento & purificación , Arabidopsis/química , Proteínas de Arabidopsis/metabolismo , Clonación Molecular , Escherichia coli/metabolismo , Peróxido de Hidrógeno/química , Hierro/química , Proteínas de Unión a Hierro/metabolismo , Proteínas Mitocondriales/metabolismo , Frataxina
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