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Malate Synthase (MS) activity have been shown to increase co-ordinately (along with other enzymes from the glyoxylate and TCA cycle) with patterns of lipid breakdown (see Figure ) during germination in different plant species, and has been used as a marker for glyoxysomal activity [, ]. We found three different glyoxysomal MS isoform genes [Clone ID: Gm-r1070-7761, Gm-r1070-8044, Gm-r1088-2873] with similar expression profiles that start with up regulation during the initial phases of germination, down regulation right after the cotyledonary functional transition and during the photosynthetic phase (see Table ).
A soybean 70-mer oligo array containing 19,200 features was used to study the modulation of the global transcript profile of soybean cotyledons at 6 different time points relative to the imbibed seed. Our time study covered the cotyledon functional transition from nutrient storage to photosynthesis during seedling development. One of the major advantages of using an oligo array of this nature is that it allows to clearly discriminate the expression levels in terms of transcript abundance of different gene family members, enzymatic isoforms and protein subunits. This is due to the fact that each 70-mer oligo has been carefully designed to represent the high sequence variability found at the most possible 3'end region of cDNA clones of the soybean EST collection. The results of our study define which specific gene family member, enzymatic isoform or protein subunit is likely to be a co-participant of this particular biological process providing an important tool, not only for gene discovery but also to postulate possible mechanisms of expression regulation and control.
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More interestingly, we found more than 60 specific soybean genes (see Additional file : Complete collection of 3,594 genes with statistically significant data) with unknown function and no homology with any other plant species genes in the data base that have a similar expression profile to the genes previously described in the glyoxylate pathway. Furthermore the glyoxylate cycle has been also associated with chlorophyll breakdown, opening the possibility of further unknown elements associated with this pathway in plants [, ]. We believe that these soybean unknown genes represent a valuable source to discover and characterize new genes that most likely play an important biological role during the processes of cell division, lipid mobilization through the glyoxylate cycle and chloroplast assembly during seedling development and the functional transition. These genes also have the potential to be key elements in the regulatory and control mechanisms associated with these metabolic processes.
After LOWESS normalization, filtering by expression level and a Welch ANOVA analysis we found that the transcript abundance profile of 3,594 genes in the soybean cotyledons was significantly modulated when compared to the transcript profile observed within the imbibed seed at least in one of the time point measurements taken during seedling development (see Additional file : Complete collection of 3,594 genes with statistically significant data). In Arabidopsis the transcriptome of the imbibed seed is composed of mRNAs stored during seed development as well as the neosynthesized transcripts during water absortion . In our study, the transcript profiles from stages 2–7 were compared to the already imbibed seed (48 hrs after initiation of imbibition). Classification by gene ontologies and cluster analysis by k-means of over and under expressed genes provided a broader view of gene expression and modulation in the soybean cotyledons during this process and more specifically during the cotyledonary functional transition from nutrient storage to photosynthesis. The already identified and characterized genes reported in the literature, validate and support our data while the unidentified genes represent excellent candidates for discovering new elements of significant importance involved in soybean seedling development. Because organisms have adopted a strategy of expressing batteries of genes under common regulatory mechanisms, the individual transcripts in the clusters presented are most likely regulated and controlled in a coordinate manner. All the results obtained have been deposited in the NCBI Gene Expression Omnibus (GEO) database as accession number GSE6534.
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Although each particular set obtained by cluster analysis represents a different group of genes with similar expression profiles, we can observe that sets 1, 2, 5, 8 and 11 contain genes whose expression profile displays up regulation during the first 3 to 4 stages, and variable levels of expression during the last 2 stages defined. The products of over-expressed genes during these initial stages may play a fundamental role in achieving the required functions of the cotyledon during the onset of seedling growth and specifically during the functional transition. Genes whose products participate in protein biosynthesis are especially abundant in this group (120 genes) (see Table , Additional file : Complete collection of 3,594 genes with statistically significant data) along with several transcription factors, regulators, elongation factors as well as ribosomal and aminoacid-metabolism genes. The data obtained clearly indicates high protein metabolism activity during the first stages of seedling development through the functional transition, and low activity during the later stages when the main function of these tissues is photosynthesis. Also a high number of genes were found within the subcategory of electron transport and protein and nuclei acid metabolism.
After normalization and statistical analysis we determined that 3,594 genes presented a statistically significant altered expression in relation to the imbibed seed in at least one of the time points defined for the study. Detailed analysis of this data identified individual, specific elements of the glyoxylate pathway that play a fundamental role during the functional transition of the cotyledon from nutrient storage to photosynthesis. The dynamics between glyoxysomes and peroxisomes is evident during these series of events. We also identified several other genes whose products could participate co-ordinately throughout the functional transition and the associated mechanisms of control and regulation and we described multiple unknown genetic elements that by association have the potential to make a major contribution to this biological process.
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Organelle Structure and Function
*Chlorophyll B; The chlorophyll that occurs only in plants & green algae. It functions as a light harvesting chlorophyll pigment that pass on the light excitation to chlorophyll a. It absorbs well at wavelength of 450-500 nm & 600-650 nm
Since many photosynthetic organisms live where light in higher spectrums of PAS such as 600nm & higher penetrate less if at all (in particular algae, zooxanthellae, & cynaobacteria), many have adapted to ways to still harvest this light energy.
These organisms use Phycobilisomes which are light harvesting antennae of photosystem II (Chlorophyll synthesis in the Photosynthic Action Spectrum-PAS).
Structure and Function of the Cell - BiologyGuide
The soybean (Glycine max) cotyledon is a specialized tissue whose main function is to serve as a nutrient reserve that supplies the needs of the young plant throughout seedling development. During this process the cotyledons experience a functional transition to a mainly photosynthetic tissue. To identify at the genetic level the specific active elements that participate in the natural transition of the cotyledon from storage to photosynthetic activity, we studied the transcript abundance profile at different time points using a new soybean oligonucleotide chip containing 19,200 probes (70-mer long).
plant | Definition, Evolution, Ecology ..
Several other enzymes related with the glyoxylate cycle are FDH, OCD and GXC. We found one specific element for each of these enzymes in our collection of genes with statistically significant data: Clone ID: Gm-r1021-2716 for FDH; Clone ID: Gm-r1089-8230 for OCD and Clone ID: Gm-c1062-4128 for GXC. The gene for FDH shows low levels of expression relative to the imbibed seed during the first stages of seedling development, high levels of expression at the onset of the functional transition and during the photosynthetic phase (green tissues). The expression profile of the gene for OCD on the other hand shows down regulation throughout the entire study indicating that this particular branch of the cycle may not be required in the soybean cotyledon during the functional transition in the process of seedling development. Finally we found that the expression profile of the GXC gene our study is up regulated in all stages with a reduction of expression during the green phase (stages 6 and 7).
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