Isolation and Characterization of a myo-inositol-1-phosphate Synthase Gene from Yellow Passion Fruit (Passiflora edulis f. flavicarpa) Expressed During Seed Development and Environmental Stress
TL;DR: Experimental data suggest that PeMIPS1 transcription plays an important role in the establishment of developmental programmes and during the response of plants to environmental changes, suggesting that it is important for environmental stress response.
About: This article is published in Annals of Botany.The article was published on 2007-02-01 and is currently open access. It has received 66 citations till now. The article focuses on the topics: Gene expression & Complementary DNA.
Citations
More filters
TL;DR: The current study reveals an irregular relationship between cold performance in the field and in the laboratory, and suggests that the ecological relevance of laboratory assays should be evaluated more critically in studies of thermal adaptation and hardening/acclimation.
Abstract: Summary
1. Physiological and evolutionary responses underlying thermal adaptation and acclimation are often investigated under controlled laboratory conditions. Such studies may fail to assess ecologically relevant parameters as they do not account for the complexity of the natural environment.
2. We investigated a population of Drosophila melanogaster for performance at low temperature conditions in the field using release recapture assays and in the laboratory using standard cold resistance assays. The aim of the study was to get a better understanding of the nature and underlying mechanisms of the trait measured in field recapture studies and the association between field performance and fitness measures estimated in the laboratory.
3. We performed one generation of selection on the ability to reach a resource at low temperature under field conditions. Flies that reached a resource (‘mobile’) and those that never left the release site (‘stationary’) were reared to the F1 and F2 generation in the laboratory. Subsequent field releases with these flies demonstrated a clear genetic differentiation between mobile and stationary flies in their ability to reach resources at low temperatures in the field. This indicates that mobility at low temperature is under additive genetic influence. In contrast mobile and stationary flies were generally indistinguishable when tested in standard laboratory tests of cold performance. The genetic differentiation between the two sub-populations was not linked to allelic variation in known candidate genes for cold adaptation. However, using transcriptomics we identified new candidate genes (transcripts) and pathways that differed between the mobile and stationary flies.
4. The current study reveals an irregular relationship between cold performance in the field and in the laboratory. Based on these results, we suggest that the ecological relevance of laboratory assays should be evaluated more critically in studies of thermal adaptation and hardening/acclimation.
30 citations
TL;DR: Using immunolocalization techniques, a specialized area of GmMIPS-1 expression was identified in the outer integumentary layer during early soybean seed development, and localization data provided evidence that MIPS was associated with oxalate crystal idioblasts.
Abstract: As a precursor to a large variety of compounds, myo-inositol is a central molecule required for cell metabolism and plant growth. The de novo synthesis of myo-inositol requires the activity of the enzyme D-myo-inositol-3-phosphate synthase (MIPS). MIPS cDNAs encoding one or more isoforms have been cloned from a number of species, nevertheless, little is known about the regulation of MIPS expression in developing seed. Seed-specific expression of a soybean isoform (GmMIPS-1) has been demonstrated, but tissue-specific localization during embryo development has not been reported. Using immunolocalization techniques, a specialized area of GmMIPS-1 expression was identified in the outer integumentary layer during early soybean seed development. In addition, localization data provided evidence that MIPS was associated with oxalate crystal idioblasts.
29 citations
TL;DR: expression profiling showed that TaMIPS2 is expressed during different developing seed stages upon heat stress, and the transcript levels increase in unfertilized ovaries and significant amounts are present during the recovery period providing evidence that MIPS is crucial for its role in heat stress recovery and flower development.
Abstract: Molecular dissection and a deeper analysis of the heat stress response mechanism in wheat have been poorly understood so far. This study delves into the molecular basis of action of TaMIPS, a heat stress-inducible enzyme that was identified through PCR-select subtraction technology, which is named here as TaMIPS2. MIPS (l-Myo-inositol-phosphate synthase) is important for the normal growth and development in plants. Expression profiling showed that TaMIPS2 is expressed during different developing seed stages upon heat stress. Also, the transcript levels increase in unfertilized ovaries and significant amounts are present during the recovery period providing evidence that MIPS is crucial for its role in heat stress recovery and flower development. Alternatively spliced forms from rice and Arabidopsis were also identified and their expression analysis revealed that apart from heat stress, some of the spliced variants were also inducible by drought, NaCl, Cold, ABA, BR, SA and mannitol. In silico promoter analysis revealed various cis-elements that could contribute for the differential regulation of MIPS in different plant systems. Phylogenetic analysis indicated that MIPS are highly conserved among monocots and dicots and TaMIPS2 grouped specifically with monocots. Comparative analyses was undertaken by different experimental approaches, i.e., semi-quantitative RT-PCR, quantitative RT-PCR, Genevestigator as a reference expression tool and motif analysis to predict the possible function of TaMIPS2 in regulating the different aspects of plant development under abiotic stress in wheat.
29 citations
Cites background from "Isolation and Characterization of a..."
...Phylogenetic analysis revealed little diversity among various plants MIPS, however, TaMIPS2, cloned in the present investigation grouped with monocots, while previously reported TaMIPS1 surprisingly, grouped specifically with Arabidopsis thaliana AtMIPS (Abreu and Araga 2007)....
[...]
...Phylogenetic analyses Phylogenetic analysis revealed little diversity among various plants MIPS, however, TaMIPS2, cloned in the present investigation grouped with monocots, while previously reported TaMIPS1 surprisingly, grouped specifically with Arabidopsis thaliana AtMIPS (Abreu and Araga 2007)....
[...]
...Previous literature also suggests that the expression of Passiflora edulis MIPS gene is organ-specific and its transcription increases after 16 h of heat stress at 37 C (Abreu and Araga 2007)....
[...]
TL;DR: The identifications of these differentially accumulated proteins indicates the presence of a specific different metabolic network in YL and suggests that YL possess slower chloroplast development, weaker photosynthesis, and a less abundant energy supply than GL.
Abstract: Yellow-green leaf mutants are common in higher plants, and these non-lethal chlorophyll-deficient mutants are ideal materials for research on photosynthesis and plant development A novel xantha mutant of Ginkgo biloba displaying yellow-colour leaves (YL) and green-colour leaves (GL) was identified in this study The chlorophyll content of YL was remarkably lower than that in GL The chloroplast ultrastructure revealed that YL had less dense thylakoid lamellae, a looser structure and fewer starch grains than GL Analysis of the photosynthetic characteristics revealed that YL had decreased photosynthetic activity with significantly high nonphotochemical quenching To explain these phenomena, we analysed the proteomic differences in leaves and chloroplasts between YL and GL of ginkgo using two-dimensional gel electrophoresis (2-DE) coupled with MALDI-TOF/TOF MS In total, 89 differential proteins were successfully identified, 82 of which were assigned functions in nine metabolic pathways and cellular processes Among them, proteins involved in photosynthesis, carbon fixation in photosynthetic organisms, carbohydrate/energy metabolism, amino acid metabolism, and protein metabolism were greatly enriched, indicating a good correlation between differentially accumulated proteins and physiological changes in leaves The identifications of these differentially accumulated proteins indicates the presence of a specific different metabolic network in YL and suggests that YL possess slower chloroplast development, weaker photosynthesis, and a less abundant energy supply than GL These studies provide insights into the mechanism of molecular regulation of leaf colour variation in YL mutants
26 citations
Cites background from "Isolation and Characterization of a..."
...MIPS has been found to play a key role in the biosynthesis of inositol and inositol phosphate and to be important in plant development and environmental stress tolerance [59]....
[...]
TL;DR: The identification of some novel genes – such as SnRK1-type protein kinase; 17 kDa, class I, small heat shock protein; and RNase S-like protein precursor genes – may offer a new avenue for better understanding the salt stress response in plants.
Abstract: In the present study, we have used an annealing-control-primer (ACP)-based differentially display RTPCR method to identify salt-stress-induced differentially expressed genes (DEGs) in barley leaves. Using 120 ACPs, a total of 11 up-regulated genes were identified and sequenced. Temporal expression patterns of some up-regulated DEGs in response to salt stress were further analyzed by Northern blot analysis. The possible roles of these identified genes are discussed within the context of their putative role in response to salt stress. Thus, the identification of some novel genes – such as SnRK1-type protein kinase; 17 kDa, class I, small heat shock protein; and RNase S-like protein precursor genes – may offer a new avenue for better understanding the salt stress response in plants, knowledge which might be helpful for developing future strategies.
23 citations
Cites background from "Isolation and Characterization of a..."
...…of D-glucose 6-phosphate to 1-myoinositol-1-phosphate, the first and rate-limiting step in the biosynthesis of all inositol-containing compounds (Abreu and Aragao, 2007); its derivatives are commonly studied with respect to cell signaling and membrane biogenesis, but they also participate in…...
[...]
References
More filters
TL;DR: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved and modifications are incorporated into a new program, CLUSTAL W, which is freely available.
Abstract: The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
63,427 citations
"Isolation and Characterization of a..." refers methods in this paper
...The alignment was performed using CLUSTAL W (Thompson et al., 1994)....
[...]
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
57,055 citations
"Isolation and Characterization of a..." refers methods in this paper
...Phylogenetic trees were then constructed using the neighbour-joining algorithm (Saitou and Nei, 1987)....
[...]
TL;DR: Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Abstract: Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or “transition” type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or “transversion” type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = — (1/2) ln {(1 — 2P — Q) }. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = — (1/2) ln (1 — 2P — Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
26,016 citations
"Isolation and Characterization of a..." refers methods in this paper
...Thus, to consider this unequal probability of the substitution types, the Kimura 2-parameter (Kimura, 1980) was used to compute distances between each pair of sequences....
[...]
TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Abstract: With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
12,124 citations
"Isolation and Characterization of a..." refers methods in this paper
...Phylogenetic analyses were carried out using the MEGA (Molecular Evolutionary Genetic Analysis) version 3.1 software program (Kumar et al., 2004)....
[...]
TL;DR: A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed and it is estimated that 10% of all plant proteins are mitochondrial and 14% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10%.
4,268 citations
"Isolation and Characterization of a..." refers background in this paper
...The TargetP 1.1 (Emanuelsson et al., 2000) and ChloroP (Emanuelsson et al., 1999) program algorithms predicted no signal, chloroplast transit or mitochondrial targeting peptides in the N-terminal region of the PeMIPS1....
[...]