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1.
Funct Integr Genomics ; 23(1): 50, 2023 Jan 27.
Artículo en Inglés | MEDLINE | ID: mdl-36707470

RESUMEN

The primary function of mitochondria is cellular respiration and energy production. Cytochrome C complex is an essential complex that transports electrons in the respiratory chain between complex III and complex IV. One of this complex's main subunits is CcmFN, which is believed to be crucial for holocytochrome assembly. In wild-type plant Hordeum vulgare subsp. spontaneum, four ccmfn cDNAs are subjected to high salt stress (500 mM salinity), 0 h (or control) (GenBank accession no. ON764850), after 2 h (GenBank accession no. ON7648515), after 12 h (GenBank accession no. ON764852), and after 24 h (GenBank accession no. ON764853) and mtDNA of ccmfn gene (GenBank accession no. ON764854). Using raw data from RNA-seq, 47 sites with nucleotide and amino acid modifications were detected. There were ten different RNA editing types, with most of them are C to U. Unusual editing types in plants have also been found, such as A to C, C to A, A to G, A to U, T to A, T to C, C to G, G to C, and T to G. High levels of editing were observed in control as well as treatments of salinity stress. Amino acid changes were found in 43 sites; nearly all showed hydrophilic to hydrophilic alterations. Only C749 showed regulation under salinity stress.


Asunto(s)
Hordeum , ARN , ARN/metabolismo , Hordeum/genética , Hordeum/metabolismo , Salinidad , Edición de ARN , Mitocondrias/genética , Mitocondrias/metabolismo , Aminoácidos/metabolismo
2.
Mol Biol Rep ; 48(8): 6057-6064, 2021 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-34374896

RESUMEN

BACKGROUND: Nad dehydrogenase complex in mtDNA has a significant role in cellular respiration. One of the largest subunits in the complex is subunit 5 (Nad5). METHODS AND RESULTS: Four cDNAs of the Hordeum vulgare subsp. spontaneum nad5 gene have been characterized and subjected to four phases of 0.5 M salinity, at 0 h (control, accession no. MT235236), after 2 h (acc. no. MT235237), after 12 h (acc. no. MT235238) and after 24 h (acc. no. MT235239). Utilizing raw data from RNA-seq, ten RNA editing sites were reported. Seven sites have common editing from C to U in positions (C1490, C1859, C1895, C1900, C1901, C1916, C1918). A rare editing event U to C was detected in two positions (U1650 and U1652) and a novel editing event U to G was for the first time in positions nad5-U231. The highest editing level was shown in 2 and 12 h after salinity exposure. After 24 h, these edits were disrupted, possibly due to the launch of the programed cell death mechanism. However, the RNA editing in positions U1650, U1652 and U231 was fixed at all exposure times. CONCLUSIONS: Although study clarified the role of salinity stress in nad5 RNA editing sites, the main achievements are first report of U to G RNA editing in plants at position U231 and first report of U to C editing in the nad5 gene at U1650 and U1652.


Asunto(s)
ADN Mitocondrial/genética , Hordeum/genética , NADH Deshidrogenasa/genética , Secuencia de Aminoácidos , Secuencia de Bases , Citosina , Guanosina , Mitocondrias/metabolismo , Proteínas Mitocondriales/genética , NADH Deshidrogenasa/metabolismo , Proteínas de Plantas/genética , Plantas/genética , ARN/genética , Edición de ARN/genética , Estrés Salino/genética , Homología de Secuencia de Aminoácido , Uracilo
3.
BMC Plant Biol ; 16(1): 216, 2016 10 06.
Artículo en Inglés | MEDLINE | ID: mdl-27716054

RESUMEN

BACKGROUND: The ultimate goal of this work was to detect the role of transcription factors (TFs) concordantly expressed with genes related to programmed cell death (PCD) during PCD and salt stress. This work was based on the hypothesis that TFs and their driven genes likely co-express under different stimuli. The conserved superfamily ethylene responsive factor (AP2/ERF) draw attention of the present study as it participates in the response to biotic and abiotic stimuli as well as to program cell death (PCD). RESULTS: RNA-Seq analysis was done for tobacco (N. benthamiana) leaves exposed to oxalic acid (OA) at 20 mM for 0, 2, 6, 12 and 24 h to induce PCD. Genes up-regulated after 2 h of OA treatment with known function during PCD were utilized as landmarks to select TFs with concordant expression. Knockdown mutants of these TFs were generated in tobacco via virus induced gene silencing (VIGS) in order to detect their roles during PCD. Based on the results of PCD assay, knockout (KO) T-DNA insertion mutants of Arabidopsis as well as over-expression lines of two selected TFs, namely ERF109 and TFIID5, analogs to those in tobacco, were tested under salt stress (0, 100, 150 and 200 mM NaCl). CONCLUSIONS: Results of knockdown mutant tobacco cells confirmed the influence of these two TFs during PCD. Knockout insertion mutants and over-expression lines indicated the role of ERF109 in conferring salt tolerance in Arabidopsis.


Asunto(s)
Apoptosis , Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Etilenos/metabolismo , Nicotiana/metabolismo , Proteínas de Plantas/metabolismo , Proteínas Represoras/metabolismo , Cloruro de Sodio/metabolismo , Factores de Transcripción/metabolismo , Arabidopsis/citología , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Regulación de la Expresión Génica de las Plantas , Ácido Oxálico/metabolismo , Proteínas de Plantas/genética , Proteínas Represoras/genética , Tolerancia a la Sal , Nicotiana/citología , Nicotiana/genética , Factores de Transcripción/genética
4.
Plasmid ; 72: 18-28, 2014 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-24680933

RESUMEN

Lycopene is an effective antioxidant proposed as a possible treatment for some cancers and other degenerative human conditions. This study aims at generation of a yeast strain (Saccharomyces cerevisiae) of efficient productivity of lycopene by overexpressing synthetic genes derived from crtE, crtB and crtI genes of Erwinia uredovora. These synthetic genes were constructed in accordance with the preferred codon usage in S. cerevisiae but with no changes in amino acid sequences of the gene products. S. cerevisiae cells were transformed with these synthetic crt genes, whose expression was regulated by the ADH2 promoter, which is de-repressed upon glucose depletion. The RT-PCR and Western blotting analyses indicated that the synthetic crt genes were efficiently transcribed and translated in crt-transformed S. cerevisiae cells. The highest level of lycopene in one of the transformed lines was 3.3mglycopene/g dry cell weight, which is higher than the previously reported levels of lycopene in other microorganisms transformed with the three genes. These results suggest the excellence of using the synthetic crt genes and the ADH2 promoter in generation of recombinant S. cerevisiae that produces a high level of lycopene. The level of ergosterol was reversely correlated to that of lycopene in crt-transformed S. cerevisiae cells, suggesting that two pathways for lycopene and ergosterol syntheses compete for the use of farnesyl diphosphate.


Asunto(s)
Carotenoides/biosíntesis , Farnesiltransferasa/genética , Geranilgeranil-Difosfato Geranilgeraniltransferasa/genética , Oxidorreductasas/genética , Saccharomyces cerevisiae/genética , Clonación Molecular , Ergosterol/biosíntesis , Erwinia/enzimología , Erwinia/genética , Farnesiltransferasa/biosíntesis , Expresión Génica , Genes Bacterianos , Geranilgeranil-Difosfato Geranilgeraniltransferasa/biosíntesis , Licopeno , Organismos Modificados Genéticamente/genética , Organismos Modificados Genéticamente/metabolismo , Oxidorreductasas/biosíntesis , Plásmidos , Regiones Promotoras Genéticas , Saccharomyces cerevisiae/crecimiento & desarrollo , Saccharomyces cerevisiae/metabolismo , Transformación Genética
5.
Genes (Basel) ; 13(2)2022 02 16.
Artículo en Inglés | MEDLINE | ID: mdl-35205398

RESUMEN

Congenital heart disease (CHD) encompasses a wide range of structural defects of the heart and, in many cases, the factors that predispose an individual to disease are not well understood, highlighting the remarkable complexity of CHD etiology. Evidence of familial aggregation of CHD has been demonstrated in different communities and for different cardiac lesions. Consanguinity, particularly among first cousins, is an added risk factor for these families, particularly in societies where it is considered a common cultural practice, as confirmed in previous studies conducted in Saudi Arabia and other countries. Through comprehensive genetic testing of affected families, we have been able to better understand the genetic basis of the various cardiac lesions and to delineate the molecular mechanisms involved in cardiac morphogenesis. In this review, we discuss the epidemiology and genetics of CHD in consanguineous populations focusing on Saudi Arabia as an extensive study model to address current advances and challenges in the clinical genetic diagnosis and prevention of CHD.


Asunto(s)
Cardiopatías Congénitas , Consanguinidad , Pruebas Genéticas , Variación Genética , Cardiopatías Congénitas/epidemiología , Cardiopatías Congénitas/genética , Humanos , Arabia Saudita/epidemiología
6.
Front Pediatr ; 10: 895298, 2022.
Artículo en Inglés | MEDLINE | ID: mdl-35783297

RESUMEN

Background: Autoimmune diseases (AIDs) share a common molecular etiology and often present overlapping clinical presentations. Thus, this study aims to explore the complex molecular basis of AID by whole exome sequencing and computational biology analysis. Methods: Molecular screening of the consanguineous AID family and the computational biology characterization of the potential variants were performed. The potential variants were searched against the exome data of 100 healthy individuals and 30 celiac disease patients. Result: A complex inheritance pattern of PAK2 (V43A), TAP2 (F468Y), and PLCL1 (V473I) genetic variants was observed in the three probands of the AID family. The PAK2 variant (V43A) is a novel one, but TAP2 (F468Y) and PLCL1 (V473I) variants are extremely rare in local Arab (SGHP and GME) and global (gnomAD) databases. All these variants were localized in functional domains, except for the PAK2 variant (V43A) and were predicted to alter the structural (secondary structure elements, folding, active site confirmation, stability, and solvent accessibility) and functional (gene expression) features. Therefore, it is reasonable to postulate that the dysregulation of PAK2, TAP2, and PLCL1 genes is likely to elicit autoimmune reactions by altering antigen processing and presentation, T cell receptor signaling, and immunodeficiency pathways. Conclusion: Our findings highlight the importance of exploring the alternate inheritance patterns in families presenting complex autoimmune diseases, where classical genetic models often fail to explain their molecular basis. These findings may have potential implications for developing personalized therapies for complex disease patients.

7.
Eur Arch Otorhinolaryngol ; 268(10): 1437-42, 2011 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-21331786

RESUMEN

Post-lingual deaf adults can develop some vocal abnormalities similar to those developed in pre-lingual deaf individuals. The aim of this work was to study the effect of cochlear implantation followed by post-operative rehabilitation on voice acoustics in post-lingual hearing impaired adults with different durations of hearing loss. The study included 35 post-lingual hearing impaired adults who underwent cochlear implantation. Patients were divided into two groups according to the duration of their hearing loss. Each group was further divided into two subgroups according to whether they received auditory rehabilitation or not. Using the Multi-Dimensional Voice Program (MDVP) parameters, comparisons were made between each subgroup of patients and the normal MDVP Saudi database, and between subgroups of patients. Most of the patients in the two groups reported significant improvement in their MDVP results post-implantation. Further, significantly deviant MDVP parameters were reported in the group of patients with longer duration of hearing loss. Patients who received rehabilitation significantly improved more than those who did not. In conclusion, it appears that cochlear implantation improves the auditory control of voice production in post-lingual deaf adults. Also, it is obvious that cochlear implantation at an early stage of hearing loss gives better results on voice control, especially if augmented with auditory rehabilitation.


Asunto(s)
Implantación Coclear , Pérdida Auditiva Sensorineural/rehabilitación , Audición/fisiología , Cuidados Posoperatorios/métodos , Recuperación de la Función/fisiología , Acústica del Lenguaje , Calidad de la Voz/fisiología , Adulto , Femenino , Estudios de Seguimiento , Pérdida Auditiva Sensorineural/fisiopatología , Pérdida Auditiva Sensorineural/cirugía , Humanos , Masculino , Estudios Retrospectivos , Factores de Tiempo , Resultado del Tratamiento
8.
J Microsc Ultrastruct ; 7(2): 78-83, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-31293889

RESUMEN

PURPOSE: The aim of this study was to investigate the correlation between the use of anabolic-androgenic steroids (AASs) among the population of Jeddah, Saudi Arabia, and their knowledge and attitudes. METHODS: This was a community-based, cross-sectional observational study. This study was conducted using a questionnaire that was distributed among the population during the period from February 3, 2018, to February 25, 2018. This questionnaire comprised 31 questions, designed to evaluate the knowledge and attitudes toward using AASs. RESULTS: A total of 300 participants were enrolled in the study. The mean age of the population was 30.66 ± 9.2 years. Fourteen participants admitted using AASs, with a percentage of 4.7%, among whom 85.7% were male (P = 0.0005). Seventy-eight percent of AAS users believed that AASs do not cause tolerance when taken for a longtime (P = 0.023). However, the majority of both AAS users and nonusers did not agree on taking AASs for a longtime. Our results showed a strong correlation between not taking AASs and not consuming energy drinks (P = 0.0023). Half of our respondents exhibited poor knowledge regarding the side effects of AASs. The level of knowledge did not correlate with the use of AAS, gender, exercising, or consuming energy drinks. CONCLUSION: The results showed poor knowledge regarding using AASs among the population of Jeddah. Thus, we recommend having a national awareness program in order to prevent the possible side effects of misusing AASs.

9.
Viruses ; 11(8)2019 08 05.
Artículo en Inglés | MEDLINE | ID: mdl-31387326

RESUMEN

: Dromedary camels are the natural reservoirs of the Middle East respiratory syndrome coronavirus (MERS-CoV). Camels are mostly bred in East African countries then exported into Africa and Middle East for consumption. To understand the distribution of MERS-CoV among camels in North Africa and the Middle East, we conducted surveillance in Egypt, Senegal, Tunisia, Uganda, Jordan, Saudi Arabia, and Iraq. We also performed longitudinal studies of three camel herds in Egypt and Jordan to elucidate MERS-CoV infection and transmission. Between 2016 and 2018, a total of 4027 nasal swabs and 3267 serum samples were collected from all countries. Real- time PCR revealed that MERS-CoV RNA was detected in nasal swab samples from Egypt, Senegal, Tunisia, and Saudi Arabia. Microneutralization assay showed that antibodies were detected in all countries. Positive PCR samples were partially sequenced, and a phylogenetic tree was built. The tree suggested that all sequences are of clade C and sequences from camels in Egypt formed a separate group from previously published sequences. Longitudinal studies showed high seroprevalence in adult camels. These results indicate the widespread distribution of the virus in camels. A systematic active surveillance and longitudinal studies for MERS-CoV are needed to understand the epidemiology of the disease and dynamics of viral infection.


Asunto(s)
Camelus/virología , Infecciones por Coronavirus/veterinaria , Infecciones por Coronavirus/virología , Coronavirus del Síndrome Respiratorio de Oriente Medio/clasificación , África/epidemiología , Animales , Anticuerpos Antivirales/sangre , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/transmisión , Reservorios de Enfermedades/virología , Estudios Longitudinales , Medio Oriente/epidemiología , Coronavirus del Síndrome Respiratorio de Oriente Medio/genética , Coronavirus del Síndrome Respiratorio de Oriente Medio/inmunología , Filogenia , Vigilancia de la Población , Estudios Seroepidemiológicos
10.
Saudi Med J ; 29(4): 610-3, 2008 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-18382810

RESUMEN

Nonorganic dysphonia may present a challenging diagnosis, and management. Here, we present a severe form of nonorganic dysphonia, which we termed as arytenoidal dysphonia. It was a severe form of muscle tension dysphonia, which was described earlier in literature although with different nomenclature. The outcome of the accent method of voice therapy was also presented. We concluded that accent method of voice therapy is proven to be an effective treatment modality of arytenoidal dystonia.


Asunto(s)
Trastornos de la Voz/terapia , Entrenamiento de la Voz , Adolescente , Femenino , Humanos , Tono Muscular , Trastornos de la Voz/fisiopatología
11.
Sci Rep ; 8(1): 6403, 2018 04 23.
Artículo en Inglés | MEDLINE | ID: mdl-29686365

RESUMEN

Transcriptomic analysis was conducted in leaves of Arabidopsis T-DNA insertion ERF109-knocked out (KO) mutant or plants overexpressing (OE) the gene to detect its role in driving expression of programmed cell death- (PCD-) or growth-related genes under high salt (200 mM NaCl) stress. The analysis yielded ~22-24 million reads, of which 90% mapped to the Arabidopsis reference nuclear genome. Hierarchical cluster analysis of gene expression and principal component analysis (PCA) successfully separated transcriptomes of the two stress time points. Analysis indicated the occurrence of 65 clusters of gene expression with transcripts of four clusters differed at the genotype (e.g., WT (wild type), KO ERF109 or OE ERF109 ) level. Regulated transcripts involved DIAP1-like gene encoding a death-associated inhibitor of reactive oxygen species (ROS). Other ERF109-regulated transcripts belong to gene families encoding ROS scavenging enzymes and a large number of genes participating in three consecutive pathways, e.g., phenylalanine, tyrosine and tryptophan biosynthesis, tryptophan metabolism and plant hormone signal transduction. We investigated the possibility that ERF109 acts as a "master switch" mediator of a cascade of consecutive events across these three pathways initially by driving expression of ASA1 and YUC2 genes and possibly driving GST, IGPS and LAX2 genes. Action of downstream auxin-regulator, auxin-responsive as well as auxin carrier genes promotes plant cell growth under adverse conditions.


Asunto(s)
Arabidopsis/genética , Arabidopsis/fisiología , Genes de Plantas , Estrés Salino , Arabidopsis/crecimiento & desarrollo , Análisis por Conglomerados , Mutación con Ganancia de Función , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Mutación con Pérdida de Función , Reguladores del Crecimiento de las Plantas/metabolismo , Regiones Promotoras Genéticas , ARN Mensajero/genética , Especies Reactivas de Oxígeno/metabolismo , Análisis de Secuencia de ARN , Transducción de Señal , Triptófano/biosíntesis , Triptófano/metabolismo
12.
C R Biol ; 340(1): 1-6, 2017 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-27890577

RESUMEN

RNA-Seq of the Catharanthus roseus SRA database was done in order to detect putative universal stress proteins (USPs) and their possible controlling factors. Previous analysis indicated the existence and characterization of uspA-like genes. In silico analysis of RNA-Seq database in several plant tissues revealed the possible functions and regulations of some uspA-like transcripts whose transcription factors (TFs) that might drive their expression were detected. BLAST indicated the existence of TF superfamilies erf (ethylene-responsive TF), bHLH (basic helix-loop-helix) and WRKY that might regulate several uspA-like genes. This data was proven via semi-quantitative RT-PCR in four plant tissues. Several of these transcription factor superfamilies are known for their action in the plant defense against biotic and abiotic stresses.


Asunto(s)
Catharanthus/genética , Genes de Plantas/genética , Factores de Transcripción/genética , Simulación por Computador , Bases de Datos Genéticas , Regulación de la Expresión Génica de las Plantas , ARN de Planta/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Estrés Fisiológico/genética , Regulación hacia Arriba/genética
13.
Plant Methods ; 13: 41, 2017.
Artículo en Inglés | MEDLINE | ID: mdl-28539970

RESUMEN

BACKGROUND: The main aim of this study was to improve fungal resistance in bread wheat via transgenesis. Transgenic wheat plants harboring barley chitinase (chi26) gene, driven by maize ubi promoter, were obtained using biolistic bombardment, whereas the herbicide resistance gene, bar, driven by the CaMV 35S promoter was used as a selectable marker. RESULTS: Molecular analysis confirmed the integration, copy number, and the level of expression of the chi26 gene in four independent transgenic events. Chitinase enzyme activity was detected using a standard enzymatic assay. The expression levels of chi26 gene in the different transgenic lines, compared to their respective controls, were determined using qRT-PCR. The transgene was silenced in some transgenic families across generations. Gene silencing in the present study seemed to be random and irreversible. The homozygous transgenic plants of T4, T5, T6, T8, and T9 generations were tested in the field for five growing seasons to evaluate their resistance against rusts and powdery mildew. The results indicated high chitinase activity at T0 and high transgene expression levels in few transgenic families. This resulted in high resistance against wheat rusts and powdery mildew under field conditions. It was indicated by proximate and chemical analyses that one of the transgenic families and the non-transgenic line were substantially equivalent. CONCLUSION: Transgenic wheat with barley chi26 was found to be resistant even after five generations under artificial fungal infection conditions. One transgenic line was proved to be substantially equivalent as compared to the non-transgenic control.

14.
J Am Acad Audiol ; 27(5): 380-387, 2016 05.
Artículo en Inglés | MEDLINE | ID: mdl-27179257

RESUMEN

PURPOSE: The aim of this work is to examine the efficacy of using computer-based training program (Rannan) as an intervention approach to enhance sound detection and discrimination in Arabic-speaking children with cochlear implants (CIs). RESEARCH DESIGN: A prospective study comparing performance between two groups of children. Participants were divided into two equal groups that were matched in age and programming strategies. Group I received the traditional clinic-based therapy and group II received the same traditional therapy approach in addition to a computer-based program. STUDY SAMPLE: A total of 26 children with CIs in the age range of 3-6.5 yr were recruited from King Abdulaziz University Hospital. DATA COLLECTION AND ANALYSIS: Listening Progress Profile and Infant-Toddler Meaningful Integration Scale were used preoperatively, and to compare performance between the two groups at 1-, 3-, 6-, and 12-mo after device-fitting. Data were subjected to mixed analysis of variance. RESULTS: Both assessment tools (Listening Progress Profile and Infant-Toddler Meaningful Integration Scale) revealed that group II scored higher than group I. CONCLUSION: The study demonstrated that using computer-based training in addition to the traditional rehabilitation therapy can serve as a facilitative tool to enhance the benefit achieved from CI.


Asunto(s)
Percepción Auditiva , Implantes Cocleares , Pérdida Auditiva/rehabilitación , Percepción del Habla , Niño , Preescolar , Femenino , Humanos , Lenguaje , Masculino , Estudios Prospectivos , Programas Informáticos
15.
Electron. j. biotechnol ; Electron. j. biotechnol;50: 68-76, Mar. 2021. ilus, tab, graf
Artículo en Inglés | LILACS | ID: biblio-1292417

RESUMEN

BACKGROUND: Jasmonic acid (JA) is a signal transducer molecule that plays an important role in plant development and stress response; it can also efficiently stimulate secondary metabolism in plant cells. RESULTS: RNA-Seq technology was applied to identify differentially expressed genes and study the time course of gene expression in Rhazya stricta in response to JA. Of more than 288 million total reads, approximately 27% were mapped to genes in the reference genome. Genes involved during the secondary metabolite pathways were up- or downregulated when treated with JA in R. stricta. Functional annotation and pathway analysis of all up- and downregulated genes identified many biological processes and molecular functions. Jasmonic acid biosynthetic, cell wall organization, and chlorophyll metabolic processes were upregulated at days 2, 6, and 12, respectively. Similarly, the molecular functions of calcium-transporting ATPase activity, ADP binding, and protein kinase activity were also upregulated at days 2, 6, and 12, respectively. Time-dependent transcriptional gene expression analysis showed that JA can induce signaling in the phenylpropanoid and aromatic acid pathways. These pathways are responsible for the production of secondary metabolites, which are essential for the development and environmental defense mechanism of R. stricta during stress conditions. CONCLUSIONS: Our results suggested that genes involved in flavonoid biosynthesis and aromatic acid synthesis pathways were upregulated during JA stress. However, monoterpenoid indole alkaloid (MIA) was unaffected by JA treatment. Hence, we can postulate that JA plays an important role in R. stricta during plant development and environmental stress conditions.


Asunto(s)
Ciclopentanos/metabolismo , Apocynaceae/genética , Oxilipinas/metabolismo , Reguladores del Crecimiento de las Plantas/metabolismo , Estrés Fisiológico , Flavonoides/biosíntesis , Secuencia de Bases , Expresión Génica , Ambiente , Transcriptoma
16.
C R Biol ; 338(10): 643-9, 2015 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-26318047

RESUMEN

Nucleotide sequences of the C. roseus SRA database were assembled and translated in order to detect putative universal stress proteins (USPs). Based on the known conserved USPA domain, 24 Pfam putative USPA proteins in C. roseus were detected and arranged in six architectures. The USPA-like domain was detected in all architectures, while the protein kinase-like (or PK-like), (tyr)PK-like and/or U-box domains are shown downstream it. Three other domains were also shown to coexist with the USPA domain in C. roseus putative USPA sequences. These domains are tetratricopeptide repeat (or TPR), apolipophorin III (or apoLp-III) and Hsp90 co-chaperone Cdc37. Subsequent analysis divided USPA-like domains based on the ability to bind ATP. The multiple sequence alignment indicated the occurrence of eight C. roseus residues of known features of the bacterial 1MJH secondary structure. The data of the phylogenetic tree indicated several distinct groups of USPA-like domains confirming the presence of high level of sequence conservation between the plant and bacterial USPA-like sequences.


Asunto(s)
Catharanthus/metabolismo , Proteínas de Choque Térmico/genética , Proteínas de Plantas/genética , Adenosina Trifosfato/metabolismo , Secuencia de Aminoácidos , Proteínas de Arabidopsis/química , Proteínas Bacterianas/química , Secuencia de Bases , Catharanthus/genética , Secuencia Conservada , Bases de Datos Genéticas , Proteínas de Choque Térmico/química , Datos de Secuencia Molecular , Filogenia , Proteínas de Plantas/química , Estructura Terciaria de Proteína , Alineación de Secuencia , Homología de Secuencia , Especificidad de la Especie
17.
C R Biol ; 338(5): 285-97, 2015 May.
Artículo en Inglés | MEDLINE | ID: mdl-25882349

RESUMEN

Wild salt-tolerant barley (Hordeum spontaneum) is the ancestor of cultivated barley (Hordeum vulgare or H. vulgare). Although the cultivated barley genome is well studied, little is known about genome structure and function of its wild ancestor. In the present study, RNA-Seq analysis was performed on young leaves of wild barley treated with salt (500mM NaCl) at four different time intervals. Transcriptome sequencing yielded 103 to 115 million reads for all replicates of each treatment, corresponding to over 10 billion nucleotides per sample. Of the total reads, between 74.8 and 80.3% could be mapped and 77.4 to 81.7% of the transcripts were found in the H. vulgare unigene database (unigene-mapped). The unmapped wild barley reads for all treatments and replicates were assembled de novo and the resulting contigs were used as a new reference genome. This resulted in 94.3 to 95.3% of the unmapped reads mapping to the new reference. The number of differentially expressed transcripts was 9277, 3861 of which were unigene-mapped. The annotated unigene- and de novo-mapped transcripts (5100) were utilized to generate expression clusters across time of salt stress treatment. Two-dimensional hierarchical clustering classified differential expression profiles into nine expression clusters, four of which were selected for further analysis. Differentially expressed transcripts were assigned to the main functional categories. The most important groups were "response to external stimulus" and "electron-carrier activity". Highly expressed transcripts are involved in several biological processes, including electron transport and exchanger mechanisms, flavonoid biosynthesis, reactive oxygen species (ROS) scavenging, ethylene production, signaling network and protein refolding. The comparisons demonstrated that mRNA-Seq is an efficient method for the analysis of differentially expressed genes and biological processes under salt stress.


Asunto(s)
Secuencia de Bases , Hordeum/efectos de los fármacos , Hordeum/genética , Hojas de la Planta/fisiología , ARN de Planta/genética , Cloruro de Sodio/farmacología , Transcriptoma/genética , Mapeo Cromosómico , Transporte de Electrón/genética , Flavonoides/biosíntesis , Regulación de la Expresión Génica de las Plantas , Genoma de Planta , Familia de Multigenes/efectos de los fármacos , Reacción en Cadena de la Polimerasa , Especies Reactivas de Oxígeno/metabolismo , Salinidad , Análisis de Secuencia de ARN , Estrés Fisiológico/genética
18.
C R Biol ; 337(2): 86-94, 2014 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-24581802

RESUMEN

The wild plant species Calotropis procera (C. procera) has many potential applications and beneficial uses in medicine, industry and ornamental field. It also represents an excellent source of genes for drought and salt tolerance. Genes encoding proteins that contain the conserved universal stress protein (USP) domain are known to provide organisms like bacteria, archaea, fungi, protozoa and plants with the ability to respond to a plethora of environmental stresses. However, information on the possible occurrence of Usp in C. procera is not available. In this study, we uncovered and characterized a one-class A Usp-like (UspA-like, NCBI accession No. KC954274) gene in this medicinal plant from the de novo assembled genome contigs of the high-throughput sequencing dataset. A number of GenBank accessions for Usp sequences were blasted with the recovered de novo assembled contigs. Homology modelling of the deduced amino acids (NCBI accession No. AGT02387) was further carried out using Swiss-Model, accessible via the EXPASY. Superimposition of C. procera USPA-like full sequence model on Thermus thermophilus USP UniProt protein (PDB accession No. Q5SJV7) was constructed using RasMol and Deep-View programs. The functional domains of the novel USPA-like amino acids sequence were identified from the NCBI conserved domain database (CDD) that provide insights into sequence structure/function relationships, as well as domain models imported from a number of external source databases (Pfam, SMART, COG, PRK, TIGRFAM).


Asunto(s)
Calotropis/genética , Genes de Plantas/genética , Genoma de Planta/genética , Secuenciación de Nucleótidos de Alto Rendimiento , Algoritmos , Secuencia de Aminoácidos , Bases de Datos Genéticas , Sequías , Modelos Genéticos , Modelos Moleculares , Datos de Secuencia Molecular , Filogenia , ARN de Planta/química , ARN de Planta/genética , Alineación de Secuencia
19.
C R Biol ; 337(9): 499-502, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25242688

RESUMEN

Wheat is the most important cereal in the world in terms of acreage and productivity. We sequenced and assembled the plastid genome of one Egyptian wheat cultivar using next-generation sequence data. The size of the plastid genome is 133,873 bp, which is 672 bp smaller than the published plastid genome of "Chinese Spring" cultivar, due mainly to the presence of three sequences from the rice plastid genome. The difference in size between the previously published wheat plastid genome and the sequence reported here is due to contamination of the published genome with rice plastid DNA, most of which is present in three sequences of 332, 131 and 131 bp. The corrected plastid genome of wheat has been submitted to GenBank (accession number KJ592713) and can be used in future comparisons.


Asunto(s)
Genoma de Planta/genética , Genoma de Plastidios/genética , Triticum/genética , ADN de Plantas/genética , Bases de Datos de Ácidos Nucleicos , Datos de Secuencia Molecular , Mapeo Nucleótido , Oryza/genética
20.
Funct Plant Biol ; 41(1): 87-95, 2013 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-32480969

RESUMEN

Loss-of-function and gain-of-function approaches were utilised to detect the physiological importance of glycerol biosynthesis during salt stress and the role of glycerol in conferring salt tolerance in Arabidopsis. The salt stress experiment involved wild type (WT) and transgenic Arabidopsis overexpressing the yeast GPD1 gene (analogue of Arabidopsis GLY1 gene). The experiment also involved the Arabidopsis T-DNA insertion mutants gly1 (for suppression of glycerol 3-phosphate dehydrogenase or G3PDH), gli1 (for suppression of glycerol kinase or GK), and act1 (for suppression of G3P acyltransferase or GPAT). We evaluated salt tolerance levels, in conjunction with glycerol and glycerol 3-phosphate (G3P) levels and activities of six enzymes (G3PDH, ADH (alcohol dehydrogenase), ALDH (aldehyde dehydrogenase), GK, G3PP (G3P phosphatase) and GLYDH (glycerol dehydrogenase)) involved in the glycerol pathway. The GPD1 gene was used to overexpress G3PDH, a cytosolic NAD+-dependent key enzyme of cellular glycerol biosynthesis essential for growth of cells under abiotic stresses. T2 GPD1-transgenic plants and those of the two mutants gli1 and act1 showed enhanced salt tolerance during different growth stages as compared with the WT and gly1 mutant plants. These results indicate that the participation of glycerol, rather than G3P, in salt tolerance in Arabidopsis. The results also indicate that the gradual increase in glycerol levels in T2 GPD1-transgenic, and gli1 and act1 mutant plants as NaCl level increases whereas they dropped at 200mM NaCl. However, the activities of the G3PDH, GK, G3PP and GLYDH at 150 and 200mM NaCl were not significantly different. We hypothesise that mechanism(s) of glycerol retention/efflux in the cell are affected at 200mM NaCl in Arabidopsis.

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