Plant Omics最新文献

{"title":"Data mining approaches highlighted transcription factors that play role in thermo-priming","authors":"F. Izadi, H. N. Zarrini, G. Kiani, N. B. Jelodar","doi":"10.21475/POJ.10.03.17.PNE468","DOIUrl":"https://doi.org/10.21475/POJ.10.03.17.PNE468","url":null,"abstract":"Abiotic stresses including heat are major threats to crop plants especially considering the global warming facts. A pre-exposure to heat stress can prime plants and enable them to encounter a severe dose of stress which is lethal to unprimed plants. In this study, in order to identifying potential key elements involved in priming responses to heat stress we analyzed a microarray series in Arabidopsis thaliana. To this end we conducted differential expression analysis, clustering, annotation and network construction by using the publicly available tools. In agreement with experimentally validated results we noticed that different genes were differentially expressed between primed and unprimed plants from which genes encoding retro-elements and proteins involved in chromatin remodeling were noteworthy. The topology analysis of constructed network highlighted the role of TFs including zinc finger and DREB in heat acclimation after priming phase. A total of 33 transcription factors were differentially expressed in primed versus unprimed plants five of which were detected to be hub and bottleneck nodes in genes network that may play a role in heat stress priming and memory additionally as potential targets to discover new insights to improve stress resistance in crop plants.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"10 1","pages":"139-145"},"PeriodicalIF":0.0,"publicationDate":"2017-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46550026","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In silico analysis and transient expression of wound-inducible promoter MPI in tomato (Lycopersicon esculentum Mill. cv. CH)","authors":"Z. Hajiahmadi, R. Shirzadian-Khorramabad, M. Kazemzad, M. M. Sohani","doi":"10.21475/POJ.10.03.17.PNE411","DOIUrl":"https://doi.org/10.21475/POJ.10.03.17.PNE411","url":null,"abstract":"Various genetic promoters are applied to generate transgenic plants. Constitutive promoters such as CaMV35S are mostly being used; however, the constitutive expression of a gene could be harmful and lead to many changes in plant metabolism, growth and development. Subsequently, using inducible promoters in plant transformation has become more useful. In this project, efficiency of the wound-inducible promoter of Maize Proteinase Inhibitor (MPI) in tomato Lycopersicon esculentum Mill. cv. CH, as a new genetic background, was investigated. Therefore, the MPI was amplified following insertion into pTZ57R/T, sequencing and subsequently ligation into binary vector pBI121. Recombinant plasmids were transferred into Agrobacterium tumefaciens AGL1 strain. The results of in silico sequence analysis of MPI specified methyl jasmonate (MeJA) and abscisic acid (ABA) as responsive motifs, which might play a role in wound signaling pathway. Therefore, tomato leaves were transformed by PBI:MPI:GUS using agroinfilteration approach following GUS expression analysis by applying histochemical GUS and qRT-PCR assays. Our results demonstrated that induction of the MPI promoter only occurred in the wounded leaves and not detected in the control leaves. GUS transcripts in the wounded leaves containing MPI promoter were 4.1 folds higher than those containing CaMV35S, and GUS histochemical assays also revealed that the MPI give higher color intensity (2.64 folds) compared to the CaMV35S. Thus, the MPI could be considered as an acceptable working and inducible promoter to generate dicot transgenic plants harboring insecticidal genes such as different types of cry genes, which just expressed when plants are being attacked by pests. Keyword: GUS reporter, MPI, Tomato, Wound inducible promoter. Abbrevation: ABA_Abscisic acid; CaMV35S_Cauliflower mosaic virus 35S; JA_Jasmonate; MeJA_Methyl jasmonate; MPI_Maize Proteinase Inhibitor; PBS_Phosphate buffered saline, Ubi_Maize ubiquitin.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"10 1","pages":"118-126"},"PeriodicalIF":0.0,"publicationDate":"2017-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49455729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Defatted coagulant seeds of Moringa oleifera and Moringa peregrena mediate alleviation of cadmium toxicity in wheat (Triticum aestivum L.) plant","authors":"R. Hassanein, A. F. Abdelkader, Heba Mohammed Faramawy","doi":"10.21475/POJ.10.03.17.PNE423","DOIUrl":"https://doi.org/10.21475/POJ.10.03.17.PNE423","url":null,"abstract":"Contaminated soil with toxic heavy metals, particularly cadmium, is an environmental originated challenge from various industrial activities such as effluents and mining and affecting crop growth. Cadmium removal from the soil is a problem, therefore we introduced our approach for reinforcing cadmium tolerance in wheat plant by applying powder (1g/kg soil) of fat-free seeds 'defatted seed or seed-cake' from Moringa oleifera and Moringa peregrena trees before wheat exposure to three levels of soil contamination with cadmium in soil solution (0.5, 1.0 and 1.5 mM) for 35 days. Our data showed that accumulation of Cd in wheat was concentration-dependent and was 4-folds higher in roots than in the shoots. In shoots and roots, cadmium accumulation was 3and 2folds higher at 1.5 mM Cd, respectively. Shoot length and dry mass have reduced by 30 and 58%, respectively. In addition, the photosynthetic pigments have decreased by 50% and the protein profile was altered in leaf. Moringa defatted seeds powder had conferred protection against cadmium toxicity in wheat. Upon defatted seeds pre-treatments, Cd accumulation has diminished by 3 and 2-folds in shoots and roots, respectively and wheat growth and physiological parameters have improved spectacularly. Protein polymorphism and SDS-gel electrophoresis confirmed the appearance of eight newly expressed protein bands in response to Moringa pre-treatments in absence of Cd. Eleven new bands were also expressed under the combined effect of cadmium and Moringa together in wheat leaf and weighed: 261.38, 217.77, 177.38, 135.4, 114.0, 97.0, 74.14, 51.6, 38.2, 24.0 and 13.5 KDa. We believed that the new bands have participated with wheat tolerance. In conclusion, we suggested two strategies: first, Moringa seeds have coagulated cadmium in the soil preventing its absorption and accumulation in wheat plants. Second, wheat newly expressed protein has assisted cadmium detoxification via binding to some peptides, and/or through sequestrating cadmium in the vacuole as metallothioneins and/or polychelatins.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"10 1","pages":"127-133"},"PeriodicalIF":0.0,"publicationDate":"2017-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49002920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation, expression, and characterization of the serine protease inhibitor gene (600Hbpi) from Hevea brasiliensis leaves, RRIM600 cultivar","authors":"Dutsadee Chinnapun, Sarawoot Palipoch","doi":"10.21475/POJ.10.03.17.PNE450","DOIUrl":"https://doi.org/10.21475/POJ.10.03.17.PNE450","url":null,"abstract":"First-strand cDNA encoding a serine protease inhibitor was synthesized from RNA extracted from Hevea brasiliensis leaves, RRIM600 cultivar. A full-length cDNA of RRIM600 H. brasiliensis protease inhibitor (600Hbpi) (GenBank accession no. KJ471471) was obtained from reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The primers for 600Hbpi were created from alignments of H. brasiliensis RRIM600 latex protease inhibitor (Hb-PI) (GenBank accession no. EU295479) and H. brasiliensis protease inhibitor protein 1 (PI1) (GenBank accession no. AY221985). 600HbPI encodes a 70 amino acid protein and is a member of the potato inhibitor I (PI-I) family of serine protease inhibitors. Multiple sequence alignment of homologous PI-I family proteins revealed one motif WPEL of 600HbPI conserved across the PI-I family. The coding region for the active site of 600HbPI was predicted as Met-Glu. 600Hbpi was cloned into the pFLAG-ATS vector. Recombinant 600HbPI was expressed as 11 kDa proteins in Escherichia coli strain BL21. Protease inhibition analysis showed that recombinant 600HbPI is more effective at inhibiting subtilisin A than chymotrypsin but did not inhibit trypsin protease. These results indicate that the recombinant 600HbPI encoded a functional protease inhibitor that specifically targets the chymotrypsin and subtilisin classes of serine proteases.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"10 1","pages":"134-138"},"PeriodicalIF":0.0,"publicationDate":"2017-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"68658563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in detection of stress tolerance in plants through metabolomics approaches","authors":"N. Khan, Shahid Ali, M. Shahid, Ardashir Kharabian-Masouleh","doi":"10.21475/POJ.10.03.17.PNE600","DOIUrl":"https://doi.org/10.21475/POJ.10.03.17.PNE600","url":null,"abstract":"Heat and drought stresses are presently the principal risk on world's food quantity, limiting yield. Both of these two stresses affect plants metabolism, physiological and morphological processes, which ultimately reduces the productivity. The plant cell develops different stress induced self-defence mechanisms to reduce the effect of stresses. These defence mechanisms are developed by modifying gene expression pattern, which results in qualitative and quantitative deviations in proteins synthesis, leading to the modulation of certain metabolic and defensive pathways. New metabolic profiling technologies offer a great opportunity for biologist to understand defence mechanism of plants under stress conditions. Metabolomics technologies presently enabled the using of different multi-variate analyses, generated from various hyphenated and chromatographic discovery systems, such as gas or liquid chromatography together with mass spectrometry, or nuclear magnetic resonance (NMR) based methods. Investigation and mining of metabolomics data can be done through a blend of different statistical methods, such as independent component analysis and analysis of variance. Metabolomics in combination with gene expression, protein interaction and other different regulatory pathways can be useful to diverse organisms with trivial alterations. In recent time, this technology has been used to investigate drought tolerance in plant crops to find particular stress related patterns in metabolic expression. These studies identified the vital roles of primary and secondary metabolites associated with abiotic stress tolerance.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"10 1","pages":"153-163"},"PeriodicalIF":0.0,"publicationDate":"2017-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46002549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Isolation of high quality RNA from soil-grown Ilex paraguariensis roots suitable for next-generation sequencing and gene expression analyses","authors":"E. H. Avico, R. Acevedo, P. Calzadilla, O. Ruiz, P. Sansberro","doi":"10.21475/POJ.10.04.17.PNE745","DOIUrl":"https://doi.org/10.21475/POJ.10.04.17.PNE745","url":null,"abstract":"Fil: Avico, Edgardo Hernan. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Nordeste. Instituto de Botanica del Nordeste. Universidad Nacional del Nordeste. Facultad de Ciencias Agrarias. Instituto de Botanica del Nordeste; Argentina","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"10 1","pages":"205-209"},"PeriodicalIF":0.0,"publicationDate":"2017-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41435961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A simple protein extraction method for proteomic analysis of mahogany (Swietenia macrophylla) embryos","authors":"N. Alias, W. Kamaruddin, N. M. Amin, N. Muhammad, N. Noor","doi":"10.21475/POJ.10.04.17.PNE323","DOIUrl":"https://doi.org/10.21475/POJ.10.04.17.PNE323","url":null,"abstract":"In any proteomic studies, protein extraction and sample preparation are the most crucial steps for obtaining optimal results. This is to ensure extracted proteins are not only high in yield but also clean from contaminants that could affect downstream proteomic applications such as two dimensional gel electrophoresis (2-DE) and mass spectrometry. Tissues from plants and trees such as Swietenia macrophylla are often rich in non-protein contaminating substances, which could interfere in the proteomic applications. S. macrophylla or also known as the mahogany is one of the most valuable tree species in the world. Studies on proteins for this tree as well as its seeds are very limited. We have extracted proteins from S. macrophylla seeds (specifically embryo tissues) using three different methods, each having different lysis buffer recipes. Furthermore, another set of samples were precipitated using trichloroacetic acid/acetone prior to the three extraction methods to further purify the protein samples. The results from 2-DE analysis showed approximately 240 protein spots were detected from the successful protocol using a lysis buffer of 9 M urea, 4% CHAPS, 0.5% triton X-100 and 100 mM DTT without TCA/acetone precipitation. This study highlights the aspects of sample preparation for S. macrophylla embryos, focusing on the total protein extraction and resolution in SDS-PAGE as well as 2-DE. Furthermore, this is the very first report of the proteome 2DE profile from S. macrophylla embryo.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"10 1","pages":"176-182"},"PeriodicalIF":0.0,"publicationDate":"2017-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43248206","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrative meta-analysis of protein interaction data identified multiple GID/MRCTLH protein complexes in plants","authors":"M. Miquel, C. Vicient","doi":"10.21475/POJ.10.04.17.PNE212","DOIUrl":"https://doi.org/10.21475/POJ.10.04.17.PNE212","url":null,"abstract":"GID/MRCTLH is a protein complex involved in the regulation of several cellular processes through the polyubiquitination and proteosome degradation. It has been described in yeast and mammals. Genes coding for homologous proteins are also present in plant genomes but have been little studied. BLAST analyses revealed that genes coding for members of the GID/MRCTLH complex are found in multiple copies in plants, compared to mammals and yeast. The potential structure of the Arabidopsis GID/MRCTLH complex was estimated based on the Arabidopsis protein interaction database Interactome 2.0. According to these data, Arabidopsis may contain two GID/MRCTLH complexes instead of the one described in yeast and mammals. The structure of the two Arabidopsis complexes seem to be similar to the yeast GID complex, and seem to interact with several other proteins out of the complex. These data suggest that, similarly to yeast and mammals, the plant GID/MRCTLH complexes are involved in the regulation of several cellular processes through proteosome protein degradation.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"10 1","pages":"169-175"},"PeriodicalIF":0.0,"publicationDate":"2017-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43969108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcription Factors-microRNAs regulatory network in response to multiple stresses in Arabidopsis thaliana","authors":"F. Izadi, Roohollah Nikfekr, Jahad Soorni","doi":"10.21475/POJ.10.04.17.PNE516","DOIUrl":"https://doi.org/10.21475/POJ.10.04.17.PNE516","url":null,"abstract":"Transcription factors (TFs) by interacting with the DNA binding sites of stress responsive gene promoters, control a cascade of reactions in plant cells also on the other hand microRNAs (miRNAs) act on dozen of genes involving in response to a particular stress condition via many of biological proceses. Less than 6% of the responding transcripts showed antagonistic responses to stress combinations that require delineation of regulatory interactions underlying multiple concurrent stresses instead of a single biotic or abiotic stress. Therefore, inferring transcriptional networks including both of TFs and miRNAs as two classes of regulators likely will reveal more aspects of complex interlayers especially in a combination of stresses. Utilizing 207 microarrays, we performed data mining approaches fallowing by network construction. As a result, 17 TFs and 12 miRNAs were identified as the most potential regulators in response to a combination of biotic and abiotic stresses. Seven stress responsive TFs targeted 1697 transcripts in ARACNE based constructed network which classified in a cohort of common metabolisms under investigated treatments. The generated network was validated via comparison with a reference network and further motif enrichment. The study identified TFs like ERF/AP2 family also miRNAs including miR5658 and miR172 their crosstalk may undertake transcriptome changes in response to stresses.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"10 1","pages":"183-189"},"PeriodicalIF":0.0,"publicationDate":"2017-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47608009","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of suitable reference genes by quantitative real-time PCR for gene expression normalization in sunflower","authors":"A. Ochogavía, M. Novello, L. Picardi","doi":"10.21475/POJ.10.04.17.PNE831","DOIUrl":"https://doi.org/10.21475/POJ.10.04.17.PNE831","url":null,"abstract":"Quantitative real-time PCR (qPCR) is currently the most accurate method for detecting differential gene expression, but depends greatly on normalization with stably expressed housekeeping genes. Transcriptomics analyses and experimental validation in different plant species have shown that the reliability of these endogenous controls can be influenced by, growth conditions and organs/tissues examined. Thus, reliable validation of reference genes is required to ensure proper normalization. This paper presents a systematic comparison of ten potential reference genes in sunflower: five commonly used genes (Actin, Elongation Factor1, Plastid-encode RNA polymerase, Tubulin, and Ubiquitin, as ACT, EF1, PEP, TUB, and UBQ respectively), as well as five new candidates (Translation initiation factor, MicroRNA precursors 171 and 156, Ask-interacting protein, and Protein of unknown function, as ETIF5, MIR171, MIR156, SKIP, and UNK2 respectively). Reference gene expression stability was examined by qPCR across 20 biological samples, representing different tissues at various developmental stages. Expression of all 10 genes was variable to some extent, but that of ACT, UNK2, and EF1 was overall the most stable. A combination of ETIF5/UNK2/EF1 would be appropriate to use as a reference panel for normalizing gene expression data among vegetative tissues, whereas the combination of ACT/MIR156/UNK2 is most suitable for reproductive tissues. Reference genes selected in this study were further validated by examining relative expression of ahas1, one of three acetohydroxyacid synthase genes of sunflower. Our identification and validation of suitable normalizer genes will be of use to ensure accurate results in future transcriptomics studies in this crop.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"10 1","pages":"210-218"},"PeriodicalIF":0.0,"publicationDate":"2017-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41543748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}