In-silico analysis of eukaryotic translation initiation factors (eIFs) in response to environmental stresses in rice (Oryza sativa)

Saïdi, A.; Hajibarat, Zohreh

doi:10.2478/s11756-020-00467-1

Cited by 11 publications

(6 citation statements)

References 52 publications

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“…In Arabidopsis and maize, UV-B light increases RPL10 expression by about 300%, and the study of its mutants revealed that this ribosomal protein is responsible for translation during UV-B exposure (Ferreyra et al, 2010). Moreover, elongation factors of the EF-1A family have been proven to be inducible by salt stress and ABA applications in rice (Zi-Yin and Shou-Yi, 1999), and the eukaryotic initiation factor EiF4A2 can be down-regulated by dehydration in rice (Saidi and Hajibarat, 2020). This suggests that translation-related clusters can convey information about stress-specific peptide biosynthesis, in this case during UV-B exposure.…”

Section: Peptide Metabolismmentioning

confidence: 99%

Proteomic Analysis Reveals the Molecular Pathways Responsible for Solar UV-B Acclimation in High-altitude Malbec Berries

Arias,

Murcia,

Berli

et al. 2023

Preprint

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Grapevine cultivation at high altitudes provides a viable option for producing premium quality wines in the context of climate change. This is primarily attributed to cooler temperatures, wider thermal amplitudes, and increased UV-B radiation. Although high UV-B levels can cause oxidative-stress, grape berries acclimate by generating UV-blocking anthocyanins and antioxidant compounds accumulated in the berry skins, thereby enhancing the organoleptic qualities and aging capacity of wine. This UV-B exclusion study examines how Malbec berries respond to solar UV-B at a high-altitude vineyard in Mendoza, Argentina (1350 m a.s.l.). The results showed that high solar UV-B acts both as a photomorphogenic signal and a stressor. The proteomic changes of berries exposed to +UV-B conditions indicate a decrease of photosynthesis and oxidative phosphorylation, coupled with an increase of glycolysis and tricarboxylic acid cycle as compensatory respiration pathways. Furthermore, numerous chaperones and proteins associated with the antioxidant system exhibited increased abundance to maintain cellular homeostasis. Lastly, veraison-stage berries exposed to +UV-B displayed an activation of the UVR8 signaling cascade and the phenylpropanoid pathway, resulting in higher concentration of phenolic compounds and more oxidation-resistant types of anthocyanins. This is the first report of field-grown grape berry proteomic modulation in response to solar UV-B, and it may have significant implications for the cultivation of high-quality winegrapes in both current and future climate scenarios.

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Section: Peptide Metabolismmentioning

confidence: 99%

Proteomic Analysis Reveals the Molecular Pathways Responsible for Solar UV-B Acclimation in High-altitude Malbec Berries

Arias,

Murcia,

Berli

et al. 2023

Preprint

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“…Previous studies have shown that CAMTAs were responsive to diverse stresses and stimuli in Arabidopsis, tomato, and soybean [11][12][13][14][15][16][17][18][19][20][21]. Enrichment of cis-elements involved in stresses/stimuli response in CAMTA promoters suggest that they are likely to respond differently to various stresses and stimuli signals, like other CAMTAs in different species.…”

Section: Prediction Of Tfbs In the Camta Genesmentioning

confidence: 99%

“…CAMTAs from tomato were identi ed to be differentially expressed genes (DEGs) during fruit development and ripening stages, indicating that calcium signaling is involved in the regulation of fruit development and ripening through calcium/calmodulin/CAMTA interactions [12]. Recently, 15 CAMTA genes were identi ed in soybean, and expression pro le revealed that they were responsive to various stresses and hormone signals [13]. Based on a study, TaCAMTA4 may function as a negative regulator in response to Puccinia triticina, since the gene silencing-based knockdown of TaCAMTA4 resulted in the enhanced resistance to P. triticina race 165 [14].…”

Section: Introductionmentioning

confidence: 99%

Evolutionary and Expression Analysis of CAMTA Gene Family in Three Species (Arabidopsis, Maize and Tomato), and Gene Expression in Response to Developmental Stages

2022

JGEBR

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The calmodulin-binding transcriptional activator (CAMTA) family has been known to be one of the fast responsive stress proteins. In this study, 17 CAMTA genes were selected in Arabidopsis, tomato and maize. The chromosomal distributions, gene structures, duplication patterns, phylogenetic tree, and developmental stage of the 17 CAMTAgenes in the three species were analyzed to further investigate their functions. According to the synteny analysis, CAMTA genes of maize and tomatorevealed higher similarity with each other as compared with Arabidopsis. A higher than 90 percent identity was observed between maize CAMTA genes (ZmCAMTA2 and ZmCAMTA3) and tomato CAMTA genes (SlCAMTA4, SlCAMTA4.1). To detect expression levels in different plant tissues, mRNA analysis of CAMTA genes were performed using publicly available expression data in the genvestigator. The aim of study was to identify and characterize CAMTA genes in three species, for the first time, via insilico genome-wide analysis approach. AtCAMTA1 and AtCAMTA2 and SlCAMTA2 and ZmCAMTA1 and ZmCAMTA2 genes were up-regulated during all developmental stages. The conserved motifs and gene structure in most proteins in each group were similar, validating the CAMTA phylogenetic classification. This study could be considered as a useful source for future CAMTA comparative studies in different plant species.

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“…Recent studies in different plant species have shown that the lack of eIF4A (DEAD-box) gene leads to decreased root formation, delayed flowering, and abnormal ovule formation suggesting that eIF4A plays an essential role in growth and development of plants (Peng et al, 2008;Maršálová et al, 2016). The Arabidopsis genome encodes eIF4A, required for the coordination between cell cycle progression and cell size (Bush et al, 2015;Saidi & Hajibarat, 2020).…”

Section: Analysis Of Rpl and Rps In Response To Bacterial Stressesmentioning

confidence: 99%

Identification of responsive genes and analysis of genes with bacterial-inducible cis-regulatory elements in the promoter regions in Oryza sativa L.

Saïdi

Hajibarat

2020

AAS

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Bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most critical diseases in rice. In order to study rice responsive genes to bacterial stress, microarray data were retrieved from GEO dataset. To identify the responsive genes to biotic stress (bacteria) bioinformatic tools were employed and the data presented in the forms of heatmap, gene ontology, gene network, and cis-element prediction were used. Almost all responsive genes were down-regulated at around 3 h time point and up-regulated 24 h time point in response to bacterial stress in rice varieties (Oryza sativa subs. japonica ‘IR64’, ‘IRBB5’, ‘IRBB7’ and ‘Y73’). Gene ontology showed that genes are involved in different biological processes including translation and cellular protein metabolic processes. Network analysis showed that genes expressed in response to pathogen infection (Xoo) included protein translation, eukaryotic initiation factors (eIFs), ribosomal proteins, protein ubiquitin, and MAPK genes. The genes expressed in response to bacterial stress can enable plant balance between synthesis and degradation of proteins which in turn allows plants for further growth and development. TATA-box and CAAT box had the highest number of cis elements involved in bacterial stress. These genes can provide novel insights into regulatory mechanisms in biotic stress responses in rice. Identification of bacterial stress response/tolerance genes of rice can assist the molecular breeding of new rice varieties tolerant to bacterial stress.

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In-silico analysis of eukaryotic translation initiation factors (eIFs) in response to environmental stresses in rice (Oryza sativa)

Cited by 11 publications

References 52 publications

Proteomic Analysis Reveals the Molecular Pathways Responsible for Solar UV-B Acclimation in High-altitude Malbec Berries

Proteomic Analysis Reveals the Molecular Pathways Responsible for Solar UV-B Acclimation in High-altitude Malbec Berries

Evolutionary and Expression Analysis of CAMTA Gene Family in Three Species (Arabidopsis, Maize and Tomato), and Gene Expression in Response to Developmental Stages

Identification of responsive genes and analysis of genes with bacterial-inducible cis-regulatory elements in the promoter regions in Oryza sativa L.

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