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Alternative splicing studies of the reactive oxygen species gene network in Populus reveal two isoforms of high-isoelectric-point superoxide dismutase.

Identifieur interne : 003711 ( Main/Exploration ); précédent : 003710; suivant : 003712

Alternative splicing studies of the reactive oxygen species gene network in Populus reveal two isoforms of high-isoelectric-point superoxide dismutase.

Auteurs : Vaibhav Srivastava [Suède] ; Manoj Kumar Srivastava ; Kamel Chibani ; Robert Nilsson ; Nicolas Rouhier ; Michael Melzer ; Gunnar Wingsle

Source :

RBID : pubmed:19176719

Descripteurs français

English descriptors

Abstract

Recent evidence has shown that alternative splicing (AS) is widely involved in the regulation of gene expression, substantially extending the diversity of numerous proteins. In this study, a subset of expressed sequence tags representing members of the reactive oxygen species gene network was selected from the PopulusDB database to investigate AS mechanisms in Populus. Examples of all known types of AS were detected, but intron retention was the most common. Interestingly, the closest Arabidopsis (Arabidopsis thaliana) homologs of half of the AS genes identified in Populus are not reportedly alternatively spliced. Two genes encoding the protein of most interest in our study (high-isoelectric-point superoxide dismutase [hipI-SOD]) have been found in black cottonwood (Populus trichocarpa), designated PthipI-SODC1 and PthipI-SODC2. Analysis of the expressed sequence tag libraries has indicated the presence of two transcripts of PthipI-SODC1 (hipI-SODC1b and hipI-SODC1s). Alignment of these sequences with the PthipI-SODC1 gene showed that hipI-SODC1b was 69 bp longer than hipI-SODC1s due to an AS event involving the use of an alternative donor splice site in the sixth intron. Transcript analysis showed that the splice variant hipI-SODC1b was differentially expressed, being clearly expressed in cambial and xylem, but not phloem, regions. In addition, immunolocalization and mass spectrometric data confirmed the presence of hipI-SOD proteins in vascular tissue. The functionalities of the spliced gene products were assessed by expressing recombinant hipI-SOD proteins and in vitro SOD activity assays.

DOI: 10.1104/pp.108.133371
PubMed: 19176719
PubMed Central: PMC2663752


Affiliations:


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Le document en format XML

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<term>Amino Acid Sequence (MeSH)</term>
<term>Chromatography, Gel (MeSH)</term>
<term>Escherichia coli (metabolism)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Gene Regulatory Networks (MeSH)</term>
<term>Genes, Plant (MeSH)</term>
<term>Introns (genetics)</term>
<term>Isoelectric Point (MeSH)</term>
<term>Molecular Sequence Data (MeSH)</term>
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<term>Plant Stems (enzymology)</term>
<term>Plant Stems (ultrastructure)</term>
<term>Populus (cytology)</term>
<term>Populus (enzymology)</term>
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<term>Protein Isoforms (chemistry)</term>
<term>Protein Isoforms (genetics)</term>
<term>Protein Isoforms (metabolism)</term>
<term>Protein Structure, Secondary (MeSH)</term>
<term>Protein Transport (MeSH)</term>
<term>RNA Splice Sites (genetics)</term>
<term>Reactive Oxygen Species (metabolism)</term>
<term>Reverse Transcriptase Polymerase Chain Reaction (MeSH)</term>
<term>Sequence Analysis, Protein (MeSH)</term>
<term>Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization (MeSH)</term>
<term>Superoxide Dismutase (chemistry)</term>
<term>Superoxide Dismutase (genetics)</term>
<term>Superoxide Dismutase (metabolism)</term>
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<term>Analyse de séquence de protéine (MeSH)</term>
<term>Chromatographie sur gel (MeSH)</term>
<term>Données de séquences moléculaires (MeSH)</term>
<term>Escherichia coli (métabolisme)</term>
<term>Espèces réactives de l'oxygène (métabolisme)</term>
<term>Gènes de plante (MeSH)</term>
<term>Introns (génétique)</term>
<term>Isoformes de protéines (composition chimique)</term>
<term>Isoformes de protéines (génétique)</term>
<term>Isoformes de protéines (métabolisme)</term>
<term>Point isoélectrique (MeSH)</term>
<term>Populus (cytologie)</term>
<term>Populus (enzymologie)</term>
<term>Populus (génétique)</term>
<term>Populus (ultrastructure)</term>
<term>RT-PCR (MeSH)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Réseaux de régulation génique (MeSH)</term>
<term>Sites d'épissage d'ARN (génétique)</term>
<term>Spectrométrie de masse MALDI (MeSH)</term>
<term>Structure secondaire des protéines (MeSH)</term>
<term>Superoxide dismutase (composition chimique)</term>
<term>Superoxide dismutase (génétique)</term>
<term>Superoxide dismutase (métabolisme)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Tiges de plante (cytologie)</term>
<term>Tiges de plante (enzymologie)</term>
<term>Tiges de plante (ultrastructure)</term>
<term>Transport des protéines (MeSH)</term>
<term>Épissage alternatif (génétique)</term>
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<term>Protein Isoforms</term>
<term>Superoxide Dismutase</term>
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<term>Isoformes de protéines</term>
<term>Superoxide dismutase</term>
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<term>Populus</term>
<term>Tiges de plante</term>
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<term>Populus</term>
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<term>Tiges de plante</term>
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<term>Alternative Splicing</term>
<term>Introns</term>
<term>Populus</term>
<term>Protein Isoforms</term>
<term>RNA Splice Sites</term>
<term>Superoxide Dismutase</term>
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<term>Introns</term>
<term>Isoformes de protéines</term>
<term>Populus</term>
<term>Sites d'épissage d'ARN</term>
<term>Superoxide dismutase</term>
<term>Épissage alternatif</term>
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<term>Escherichia coli</term>
<term>Protein Isoforms</term>
<term>Reactive Oxygen Species</term>
<term>Superoxide Dismutase</term>
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<term>Escherichia coli</term>
<term>Espèces réactives de l'oxygène</term>
<term>Isoformes de protéines</term>
<term>Superoxide dismutase</term>
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<term>Populus</term>
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<term>Amino Acid Sequence</term>
<term>Chromatography, Gel</term>
<term>Gene Expression Regulation, Plant</term>
<term>Gene Regulatory Networks</term>
<term>Genes, Plant</term>
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<term>Reverse Transcriptase Polymerase Chain Reaction</term>
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<term>Point isoélectrique</term>
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<term>Réseaux de régulation génique</term>
<term>Spectrométrie de masse MALDI</term>
<term>Structure secondaire des protéines</term>
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<div type="abstract" xml:lang="en">Recent evidence has shown that alternative splicing (AS) is widely involved in the regulation of gene expression, substantially extending the diversity of numerous proteins. In this study, a subset of expressed sequence tags representing members of the reactive oxygen species gene network was selected from the PopulusDB database to investigate AS mechanisms in Populus. Examples of all known types of AS were detected, but intron retention was the most common. Interestingly, the closest Arabidopsis (Arabidopsis thaliana) homologs of half of the AS genes identified in Populus are not reportedly alternatively spliced. Two genes encoding the protein of most interest in our study (high-isoelectric-point superoxide dismutase [hipI-SOD]) have been found in black cottonwood (Populus trichocarpa), designated PthipI-SODC1 and PthipI-SODC2. Analysis of the expressed sequence tag libraries has indicated the presence of two transcripts of PthipI-SODC1 (hipI-SODC1b and hipI-SODC1s). Alignment of these sequences with the PthipI-SODC1 gene showed that hipI-SODC1b was 69 bp longer than hipI-SODC1s due to an AS event involving the use of an alternative donor splice site in the sixth intron. Transcript analysis showed that the splice variant hipI-SODC1b was differentially expressed, being clearly expressed in cambial and xylem, but not phloem, regions. In addition, immunolocalization and mass spectrometric data confirmed the presence of hipI-SOD proteins in vascular tissue. The functionalities of the spliced gene products were assessed by expressing recombinant hipI-SOD proteins and in vitro SOD activity assays.</div>
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