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Cold stress in plants have been described by many plant science and biology reviews as the major environmental factor limiting the geographical seasons and distribution of plants in modern agricultural practice (reference). Cold stress adversely effects plant growth, development and seed production by inducing a direct inhibition of plant metabolic reaction and the indirect inhibition of water uptake by inducing cellular dehydration in plants (Chinnusamy et al., 2007). Over the years, plant biologists have sought to understand the mechanism by which cold tolerance can be induced in important economical crops; for example, cotton, rice, soybean, tomato, and maize (Chinnusamy et al., 2007). The success came when changes in gene expression was discovered in plants acclimation to cold stress. This was the catalyst that lunched the exploration in the cold tolerance molecular mechanism (references).
Additional insight to gain valuable understanding of the gene function and expression studies involved with cold acclimation is being sought after from the plant Arabidopsis thaliana, an important model genetic organism for genomic studies (reference). Successful sequencing of the Arabidopsis entire genome has provided a better understanding of the mechanism involved in plant development and adaptation to biotic and abiotic factors such as, pest, weed, draught, high salinity, high or low temperatures (Mahajan and Tuteja, 2005). The practical advantage of the Arabidopsis small genomic size structured within five chromosomes, and the availability of powerful research tools, for example, the polymerase chain reaction (PCR) technology, and microarray technology have made the Arabidopsis thaliana the preferred candidate for this study and possibly understand how freezing tolerance can be acquired in plants (Mahajan and Tuteja, 2005).
In Arabidopsis, many of the cold response genes have been isolated and identified, the ICE cold stress signaling cascade was established. The inducer of CBF expression 1 (ICE1) signaling cascade includes: a MYC-type basic helix-loop-helix transcription factor called Inducer of CBF expression 1 (ICE1); C-repeat binding factors (CBF1 - CBF3) and their regulons including the dehydration response elements (DRE), the COR genes, and a group of transcriptional activators (RAP2.1, ZAT10, RAP2.6) (Shinozaki et al., 2003).
The advent of microarray technology has enabled analysis of many of the transcription factors within the ICE1 cascade from mutant, wild-type, and transgenic Arabidopsis plants (Vogel et al., 2005). With each new data being generated from new microarray experiments, plant biologists are faced with the challenge of understanding the connections that exists between different stress regulons in the cold-responsive pathways in plant (Benedict et al., 2006).
This essay describes a meta-analysis study of transcriptomics data generated using microarray for the ICE1-mediated signaling cascade in Arabidopsis by Benedict et al. (2006).
The ICE signaling model as a linear cascade
Reports from studies have shown that a number of different transcription factors are involved with the regulation of low temperature stress response. Benedict et al. assembled a model representation for the low temperature transcriptional responses in Arabidopsis as a linear cascade based on previous studies. The cascade starts with the phosphorylation of ICE1 protein when exposed to cold treatment. This in turn induces the activation of the CBF3 transcriptional activator by binding to the MYC recognition elements in the CBF3 promoter (figure 1). The CBF3, and its other low temperature reactive paralogs, in turn induces the transcription of a group of genes (component of the CBF regulon) containing the transcriptional activators RAP2.6, RAP2.1, ZAT12, and the DRE. Placed outside the ICE1-signaling cascade is the ZAT12, which represses the CBFs 1, 2 and 3 and their downstream transcription factors, as well as its own regulon. Likewise is the HOS9, considered to be an independent repressor of the ICE1 transcription (figure 1) (Benedict et al. 2006).
Adopted from: (Benedict et al., 2006)
Figure 1. A schematic diagram assembled by Benedict et al. describing the low temperature signal transduction in Arabidopsis as a linear cascade based on previous reviews. Representations: ovals- transcription factors; â€œREGâ€Â boxes- transcription factor regulons. Coloured boxes- cis-elements coupled to the upstream transcription factors contained by the promoter space (solid black line) followed by the transcription factor coding sequence or REG box ( - ICEr1; - ICEr2; - DRE; and - EP2). Connections represented by dashed arrows are unknown mechanism but with experimental confirmations. Gene activation is represented with triangular arrowheads while gene repression is represented with flattened arrowheads. Following are the list of genes with related Arabidopsis Genome Initiative number modeled in the schematic representation: ICE1- AT3G26744; CBF1- AT4G25490; CBF2- AT4G25470; CBF3- AT4G25480; RAP2.1- AT1G46768; RAP2.6- AT1G43160; ZAT10- AT1G27730; ZAT12- AT5G59820; AND HOS9- AT2G01500 (Benedict et al., 2006).
Adopted from: (Benedict et al. 2006)
ICE1 transcriptomic profiling
Previous studies have identified gene regulons sharing a common transcription factors in the ICE1 cascade relative to the subsets of genes that were either expressed in response to cold temperatures or contrarily expressed in transcription factor mutant/overexpressor Arabidopsis plants. Better still, the regulons sharing a common transcription factor should contain in their promoters, the cis-element of that particular transcription factor (its cis-regulon) (Chinnusamy et al., 2006; Yang et al., 2005). Studying the activities of the cis-regulon related with a transcription factor should therefore give an impartial result of its interconnected regulons downstream the cascade and is expected to be more confirmative amongst different researchers and various experimental results (Benedict et al., 2006).
Microarray technology (using oligonucleotides or cDNA) supporting near full Arabidopsis genome transcriptomic studies to identify transcription factors within the ICE1 cascade induced by cold stress has brought about a large collection of experimental data generated from mutant, wild-type, and transgenic Arabidopsis plants describing the different transcriptomes under low temperature growth conditions (Benedict et al., 2006; Shinozaki et al., 2003). This vast information provides an avenue to investigate examined overlaps in regulon characteristics, for example, promoter elements, that may be occurring at rates extensively higher or lower than random possibility. Therefore, using statistical analysis, it is possible to identify the relationship between transcription factors identified by the means of reverse genetics (and characteristics determined with microarray analysis) and the cis-elements occurring at rates higher or lower than random chance in the promoters of the transcription factors regulon members (Benedict et al., 2006). Benedict et al. was able to carry out a cis-regulon analysis to verify many of the connections in the proposed model of the ICE1 cascade. More importantly, is to verify whether the ICE1 model is a linear cascade of transcriptional activations and/or repressions eventually mediating COR gene expression.
The ICE1 linear cascade lacks consensus
Microarray analysis in combination with forward and reverse genetic studies has largely contributed to the elucidation of the ICE1 induced cold temperature transcriptional cascade (reference). The ICE1 cold temperature induction pathway can be described as a linear cascade based on previous reviews, involving numerous transcription factors to which their connections (if any) in the cascade to other downstream target genes are unknown (figure 1). Therefore, identifying and categorizing target genes for many of these transcription factors lacking well-defined cis-elements are complicated (Benedict et al., 2006). Benedict et al. concluded that the proposed ICE1 cold temperature signaling cascade lacks consensus. The authors pointed out that there is lack of correlation between the ICE region 1 (ICEr1) consensus (figure1), and low tempareture gene induction (Benedict et al., 2006).
Figure 2. A schematic diagram assembled by Benedict et al. describing the low temperature signal transduction in Arabidopsis as a linear cascade based on previous reviews. Representations: ovals- transcription factors; â€œREGâ€Â boxes- transcription factor regulons. Coloured boxes- cis-elements coupled to the upstream transcription factors contained by the promoter space (solid black line) followed by the transcription factor coding sequence or REG box ( - ICEr1; - ICEr2; - DRE; and - EP2)
Adopted from: (Benedict et al., 2006)
On the other hand, their ICEr3 and ICEr4 consensus identified bioinformatically (figure 2) presented in gene regulons and coordinately induced with observed transcript accumulation in ICE1 and partially preceding induction of genes containing DRE. In addition, Benedict et al. claimed that their statistical analysis was able to link HOS9, ZAT12 represented in previous ICE1 cascade (figure 1) as ICE1 independent transcription repressors, CBF2, and, NACO72 to the low temperature induced ICE1 signaling pathway (Benedict et al., 2006).
The significance of the study
Benedict et al. was able to generate an ICE cold temperature signaling model (figure 2) based on meta-analysis of publicly accessible trascriptomic data generated using microarray studies. Their model presents the missing links in the previously unknown ICE regulatory connections with ZAT12, HOS9, PHYA, and NAC072 which could also be subjected to future experimental verifications. Their findings in the ice1 mutants affected genes of the ICEr3 cis-element being enhanced in their promoters as well as being linked to a cis-regulon