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1.
Plant Signal Behav ; 6(12): 1926-31, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-22105027

RESUMO

Plants have evolved adaptations to environmental factors, including UV-B present in solar radiation. Deployment of specific adaptive phenotypes to avoid or repair UV-B damage requires physiological and developmental acclimation to variable UV-B fluence. To gain a better understanding of the events in UV-B acclimation, we have analyzed a 5min to 6h time course of transcriptome and metabolome responses in irradiated and shielded leaves and in immature maize ears to unravel the systemic physiological and developmental responses in exposed and shielded organs. Within 10 min of UV-B exposure, transcripts are changed not only in irradiated leaves, but also in shielded tissues. The number of UV-B-regulated transcripts rapidly increases with exposure length. Interestingly, after 10 min of exposure, the overlap in transcriptome changes in irradiated and shielded organs is significant; while, after 6h of UV-B, most transcripts are specific for each tissue under study. We suggest that early events in all tissues may be elicited by common signaling pathways, while at longer exposure times responses become more organ-specific. Our working hypothesis is that mobile signaling molecules are generated in irradiated organs to elicit the initial responses. We found several metabolites that rapidly change after different treatments during the timecourse; myoinositol is one candidate metabolite based on its rapid modulation in all organs. There is also support from RNA profiling: after 1h UV-B, transcripts for myoinositol-1-phosphate synthase are decreased in both irradiated and shielded leaves suggesting downregulation of biogenesis.


Assuntos
Metaboloma , Folhas de Planta/efeitos da radiação , Transdução de Sinais , Transcriptoma , Zea mays/metabolismo , Aclimatação , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Folhas de Planta/metabolismo , Luz Solar , Fatores de Tempo , Raios Ultravioleta , Zea mays/genética , Zea mays/efeitos da radiação
2.
Plant Signal Behav ; 6(8): 1146-53, 2011 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-21758019

RESUMO

UV-B radiation from normal solar fluence elicits physiological and developmental changes in plants under fluctuating environmental conditions. Most UV photobiology studies in plants utilize controlled greenhouse and growth chamber environments in which few conditions vary except the brief presence of UV-B radiation. Our purpose was to compare responses to UV-B in irradiated and shielded maize organs in field (natural solar plus 2x solar supplementation for defined periods) and greenhouse (2x solar supplementation only) conditions during a 4 hour exposure. Three parameters were assessed--transcripts, proteins, and metabolites--to determine the degree of overlap in maize responses in field and greenhouse conditions. We assessed irradiated leaves, and both shielded leaves and immature ears. After comparing transcriptome, proteome and metabolome profiles, we find there are more differences than similarities between field and greenhouse responses.


Assuntos
Metaboloma , Proteoma/análise , Transcriptoma , Raios Ultravioleta , Zea mays/efeitos da radiação , Análise de Sequência com Séries de Oligonucleotídeos , Folhas de Planta/genética , Folhas de Planta/metabolismo , Folhas de Planta/efeitos da radiação , Zea mays/genética , Zea mays/metabolismo
3.
BMC Genomics ; 12: 321, 2011 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-21679461

RESUMO

BACKGROUND: Under normal solar fluence, UV-B damages macromolecules, but it also elicits physiological acclimation and developmental changes in plants. Excess UV-B decreases crop yield. Using a treatment twice solar fluence, we focus on discovering signals produced in UV-B-irradiated maize leaves that translate to systemic changes in shielded leaves and immature ears. RESULTS: Using transcriptome and proteomic profiling, we tracked the kinetics of transcript and protein alterations in exposed and shielded organs over 6 h. In parallel, metabolic profiling identified candidate signaling molecules based on rapid increase in irradiated leaves and increased levels in shielded organs; pathways associated with the synthesis, sequestration, or degradation of some of these potential signal molecules were UV-B-responsive. Exposure of just the top leaf substantially alters the transcriptomes of both irradiated and shielded organs, with greater changes as additional leaves are irradiated. Some phenylpropanoid pathway genes are expressed only in irradiated leaves, reflected in accumulation of pathway sunscreen molecules. Most protein changes detected occur quickly: approximately 92% of the proteins in leaves and 73% in immature ears changed after 4 h UV-B were altered by a 1 h UV-B treatment. CONCLUSIONS: There were significant transcriptome, proteomic, and metabolomic changes under all conditions studied in both shielded and irradiated organs. A dramatic decrease in transcript diversity in irradiated and shielded leaves occurs between 0 h and 1 h, demonstrating the susceptibility of plants to short term UV-B spikes as during ozone depletion. Immature maize ears are highly responsive to canopy leaf exposure to UV-B.


Assuntos
Perfilação da Expressão Gênica , Metaboloma , Transdução de Sinais , Raios Ultravioleta , Zea mays/efeitos da radiação , Folhas de Planta/genética , Folhas de Planta/metabolismo , Folhas de Planta/efeitos da radiação , Proteoma/metabolismo , Fatores de Tempo , Zea mays/genética , Zea mays/metabolismo
4.
Front Plant Sci ; 2: 33, 2011.
Artigo em Inglês | MEDLINE | ID: mdl-22666224

RESUMO

Because of their sessile lifestyle, plants have evolved adaptations to environmental factors, including UV-B present in solar radiation. To gain a better understanding of the initial events in UV-B acclimation, we have analyzed a 10 min to 1 h time course of transcriptome responses in irradiated and shielded leaves, and immature maize ears to unravel the systemic physiological and developmental responses in exposed and shielded organs. After 10 min of UV-B exposure, 262 transcripts are changed by at least two-fold in irradiated leaves, and this number doubles after 1 h. Indicative of the rapid modulation of transcription, 130 transcripts are only changed after 10 min. This is true not only in irradiated leaves, but also in shielded tissues. After 10 min of exposure, the overlap in transcriptome changes in irradiated and shielded organs is significant; however, after 30 min of UV-B, there are only two transcripts showing similar UV-B regulation between the three organs; 35 are similarly regulated in both IL and SL. Therefore, at longer irradiation times, there is more specificity of responses, and these are organ-specific. We suggest that early signaling in different tissues may be elicited by common signaling pathways, while at longer exposure times responses become more specific. To identify metabolites as possible signaling molecules, we looked for compounds that increased within 5-90 min in both irradiated and shielded leaves, to explain the kinetics of profound transcript changes within 1 h. We found that myoinositol is one such candidate metabolite; and we also demonstrate that if 0.1 mM myoinositol is applied to leaves of greenhouse maize, some metabolites that are changed by UV-B are also changed similarly by the chemical treatment. Therefore, this metabolite can partially mimic UV irradiation.

5.
Plant Biotechnol J ; 6(8): 782-98, 2008 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-18643947

RESUMO

SUMMARY: Maize seedling transcriptome responses to six abiotic perturbations (heat, cold, darkness, desiccation, salt, ultraviolet-B) were analysed. Approximately 7800 transcripts were expressed in one or more treatments compared with light-grown seedlings plus juvenile leaves from field-grown plants. Approximately 5200 transcripts were expressed in one or more treatments and absent in light-grown seedlings. Approximately 2000 transcripts were unique to one treatment. Salt and heat elicited the largest number of transcript changes; however, salt resulted in mostly a decreased abundance of transcripts, whereas heat shock resulted in mostly an increased abundance of transcripts. A total of 384 transcripts were common to all stress treatments and not expressed in light-grown seedlings; 146 transcripts were present in light-grown seedlings and absent from all stress treatments. A complex pattern of overlapping transcripts between treatments was found, and a significant pattern of congruence in the direction of transcript change between pairs of treatments was uncovered. From the analysis, it appears that the scope of gene expression changes is determined by the challenge, indicating specificity in perception and response. Nonetheless, transcripts regulated by multiple responses are generally affected in the same manner, indicating common or converging regulatory networks. The data are available for additional analysis through a searchable database.


Assuntos
Meio Ambiente , Perfilação da Expressão Gênica , Genes de Plantas , Zea mays/genética , Biologia Computacional , Etiquetas de Sequências Expressas , Regulação da Expressão Gênica de Plantas , Genoma de Planta/genética , Temperatura Alta , Análise de Sequência com Séries de Oligonucleotídeos , RNA de Plantas/genética , Cloreto de Sódio/farmacologia , Zea mays/efeitos dos fármacos
6.
Plant J ; 50(4): 637-48, 2007 May.
Artigo em Inglês | MEDLINE | ID: mdl-17419846

RESUMO

Oligonucleotide arrays were used to profile gene expression in dissected maize anthers at four stages: after-anther initiation, at the rapid mitotic proliferation stage, pre-meiosis, and meiotic prophase I. Nearly 9200 sense and antisense transcripts were detected, with the most diverse transcriptome present at the pre-meiotic stage. Three male-sterile mutants lacking a range of normal cell types resulting from a temporal progression of anther failure were compared with fertile siblings at equivalent stages by transcription profiles. The msca1 mutant has the earliest visible phenotype, develops none of the normal anther cell types and exhibits the largest deviation from fertile siblings. The mac1 mutant has an excess of archesporial derivative cells and lacks a tapetum and middle layer, resulting in moderate transcriptional deviations. The ms23 mutant lacks a differentiated tapetum and shows the fewest differences from fertile anthers. By combining the data sets from the comparisons between individual sterile and fertile anthers, candidate genes predicted to play important roles during maize anther development were assigned to stages and to likely cell types. Comparative analyses with a data set of anther-specific genes from rice highlight remarkable quantitative similarities in gene expression between these two grasses.


Assuntos
Meiose , RNA Mensageiro/genética , Zea mays/genética , Sequência de Bases , Primers do DNA , Perfilação da Expressão Gênica , Genes de Plantas , Análise de Sequência com Séries de Oligonucleotídeos , Reação em Cadeia da Polimerase
7.
Genome Biol ; 7(3): R22, 2006.
Artigo em Inglês | MEDLINE | ID: mdl-16542496

RESUMO

BACKGROUND: There are thousands of maize lines with distinctive normal as well as mutant phenotypes. To determine the validity of comparisons among mutants in different lines, we first address the question of how similar the transcriptomes are in three standard lines at four developmental stages. RESULTS: Four tissues (leaves, 1 mm anthers, 1.5 mm anthers, pollen) from one hybrid and one inbred maize line were hybridized with the W23 inbred on Agilent oligonucleotide microarrays with 21,000 elements. Tissue-specific gene expression patterns were documented, with leaves having the most tissue-specific transcripts. Haploid pollen expresses about half as many genes as the other samples. High overlap of gene expression was found between leaves and anthers. Anther and pollen transcript expression showed high conservation among the three lines while leaves had more divergence. Antisense transcripts represented about 6 to 14 percent of total transcriptome by tissue type but were similar across lines. Gene Ontology (GO) annotations were assigned and tabulated. Enrichment in GO terms related to cell-cycle functions was found for the identified antisense transcripts. Microarray results were validated via quantitative real-time PCR and by hybridization to a second oligonucleotide microarray platform. CONCLUSION: Despite high polymorphisms and structural differences among maize inbred lines, the transcriptomes of the three lines displayed remarkable similarities, especially in both reproductive samples (anther and pollen). We also identified potential stage markers for maize anther development. A large number of antisense transcripts were detected and implicated in important biological functions given the enrichment of particular GO classes.


Assuntos
Perfilação da Expressão Gênica , RNA de Plantas/genética , Transcrição Gênica , Zea mays/genética , Etiquetas de Sequências Expressas , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Análise de Sequência com Séries de Oligonucleotídeos , Filogenia , Folhas de Planta/genética , Pólen/genética , Reação em Cadeia da Polimerase , Polimorfismo Genético , RNA Antissenso/genética , Zea mays/classificação
8.
Genome Biol ; 5(10): R82, 2004.
Artigo em Inglês | MEDLINE | ID: mdl-15461800

RESUMO

Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertions and screening of RescueMu plasmid libraries identified plants containing probable germinal insertions. Although frequently recovered parental insertions and insertion hotspots reduce the efficiency of gene discovery per plasmid, RescueMu targets a large variety of genes and produces knockout mutants.


Assuntos
Elementos de DNA Transponíveis/genética , Genoma de Planta , Mutagênese Insercional/genética , Mutagênese Insercional/métodos , Zea mays/genética , Análise Mutacional de DNA , DNA de Plantas/genética , Biblioteca Gênica , Genes de Plantas/genética , Fenótipo , Plasmídeos/genética , Zea mays/citologia
9.
Funct Integr Genomics ; 3(1-2): 25-32, 2003 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-12590340

RESUMO

The Maize Gene Discovery Project (MGDP) is a 5-year NSF-funded plant genome initiative that began in 1998. The MGDP collaboration involves researchers at six universities from diverse disciplines with the common goal of discovering new maize genes and developing tools for the phenotypic characterization of maize mutants. The project utilizes several approaches: EST sequencing, cDNA microarray production, and the discovery of gene function and genomic sequence through the use of a recombinant Mu1 transposon ( RescueMu). Current achievements of the MGDP (NSF 98-72657) include the sequencing of over 120,000 maize ESTs from diverse cDNA libraries, and over 70,000 RescueMu flanking sequences, as well as the cataloguing of mutant seed and cob phenotypes of 23,000 maize ears, 6,200 families of maize seedlings, and 4,000 families of adult maize plants carrying MuDR/Mu and RescueMu insertion alleles. A consolidation of over 24,000 unique sequences from 19 libraries has been made into the first two of the planned set of four "Unigene" microarray slides. In addition, slides for four EST libraries have been produced. These microarray slides, EST clones, library plates of immortalized RescueMu bacterial cultures, and seed are all available online (http://www.zmdb.iastate.edu). The ZmDB website posts periodic assemblies of all maize EST and genomic sequences available from GenBank. ZmDB is also a portal for sequence analysis software designed to aid in gene discovery: MuSeqBox, GeneSeqer, and SplicePredictor. In addition, ZmDB contains links to other plant and genetics websites.


Assuntos
Genes de Plantas , Genoma de Planta , Zea mays/genética , Alelos , Biologia Computacional , Elementos de DNA Transponíveis , DNA Complementar/metabolismo , Bases de Dados Genéticas , Etiquetas de Sequências Expressas , Biblioteca Gênica , Modelos Genéticos , Análise de Sequência com Séries de Oligonucleotídeos , Fenótipo
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