Computational genomic study of LTP pathway in the context of Raf/Ksr homologue in human and chimpanzee
Paper Details
Computational genomic study of LTP pathway in the context of Raf/Ksr homologue in human and chimpanzee
Abstract
LTP (Long Term Potentiation) pathway, which is responsible for long-term memory development is defined as the long-lasting enhancement in communication between two neurons that results from stimulating them simultaneously. One of the most important genes concerning this LTP pathway is Raf which actually encodes for KSR1 (kinase suppressor of ras-1) compartmentalizes Hippocampal Signal Transduction and sub serves synaptic plasticity and Memory formation has been explored through the use of comparative genomics in this work. For this purpose, syntenic regions for KSR1 genes in human, chimpanzee, mouse and other organisms are computationally searched to find about the conserved regions and their function through the course of evolution. A coding region was found on chromosome 16 syntenic region for KSR1 of chimpanzee. Sequence comparisons among members of the Raf family reveal the presence of three blocks of conserved sequences: conserved regions (CR) 1, 2, and 3. In this work conserved regions are found in near the C-terminal and N-terminal region was absent in both human and chimpanzee which suggests C terminal region is very important and N –terminal region is dispensable for raf-1 activity which supports the previous finding. Phylogenetic analysis showed that the KSR1 of human and chimpanzee are evolutionary distant from other organisms and human is most closely related with chimpanzee than any other organism which is also supported by previous evolutionary concept.
Vojtek AB, Der CJ. 1998. Increasing complexity of the Ras signaling pathway. J. Biol. Chem. 273, 19925– 19928.
Barbazuk W, Korf I, Kadavi C, Heyen J, Tate S, Wun E, Bedell J, McPherson J, Johnson S. 2000. The syntenic relationship of the zebrafish and human genomes. Genome Research 10, 1351–1358.
Catherin AK. 2005. Lipid binding and the scaffolding function of the Kinase Suppressor of Ras. PhD thesis, University of Pittsburgh, USA, 15-27.
Cooke SF, Bliss TV. 2006. Plasticity in the human central nervous system. Brain 129, 1659–73.
Dawson DA, Akesson M, Burke T, Pemberton JM, Slate J, Hansson B. 2007. “Gene order and recombination rate in homologous chromosome regions of the chicken and a passerine bird”. Mol. Biol. Evol. 24, 1537–52.
Sieburth S, Sundaram M, Howard RM, Han M. 1999. A PP2A regulatory subunit positively regulates Ras-mediated signaling during Caenorhabditis elegans vulval induction. Genes Dev. 13, 2562–2569.
Morrison DK. 2001. Ksr: a mapk scaffold of the ras pathway. J. Cell Sci. 114, 1609–1612.
Engström PG, Ho Sui SJ, Drivenes O, Becker TS, Lenhard B. 2007. Genomic regulatory blocks underlie extensive microsynteny conservation in insects. Genome Research 17, 1898–908.
Heger A, Ponting CP. 2007. Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes. Genome Res. 17, 1837–49.
K Kornfeld, Hom DB, Horvitz HR. 1995. The ksr-1 gene encodes a novel protein kinase involved in ras-mediated signaling in Caenorhabditis elegans. Cell 83, 903–913.
Sundaram M, Han M. 1995. The C. elegans ksr-1 gene encodes a novel Raf-related kinase involved in Ras-mediated signal transduction. Cell 83, 889–901.
Therrien M, Michaud NR, Rubin G, Morrison DK. 1996. KSR modulates signal propagation within the MAPK cascade. Genes Dev. 10, 2684–2695.
Moreno-Hagelsieb G, Treviño V, Pérez-Rueda E, Smith TF, Collado-Vides J. 2001. Transcription unit conservation in the three domains of life: a perspective from Escherichia coli. Trends in Genetics 17, 175–177.
Passarge EB, Horsthemke RA, Farber. 1999. Incorrect use of the term synteny. Nature Genetics 23, 387-93.
Postlethwait J, Woods I, Ngo-Hazelett P, Yan Y, Kelly P, Chu F, Huang H, Hill-Force A, and Talbot W. 2000. Zebrafish comparative genomics and the origins of vertebrate chromosomes. Genome Res. 10, 1890–1902
Poyatos JF, Hurst LD. 2007. The determinants of gene order conservation in yeasts. Genome Biol. 8, 233-40.
Shahani N. 2007. A Comparative study of genes related to Long-Term potentiation (LTP) and memory development. 4th year thesis, University of Dhaka, Bangladesh, 10-23.
Sara CS, Caterina MH, Michele KD, Deborah KM, Sweatt JD. 2006. Kinase Suppressor of Ras1 Compartmentalizes Hippocampal Signal Transduction and Subserves Synaptic Plasticity and Memory Formation. Neuron 50, 7 65-79.
Yu-Hua C, Kevin P, Toni HJ, Paul Dent, Thomas WS, Richard J. 1995. Functional Mapping of the N-terminal Regulatory Domain in the Human Raf-1 Protein Kinase. J Biol Chem. 270, 14100-14106.
Farzana Ahmed, Abdullah-Al-Emran (2011), Computational genomic study of LTP pathway in the context of Raf/Ksr homologue in human and chimpanzee; IJB, V1, N4, August, P36-50
https://innspub.net/computational-genomic-study-of-ltp-pathway-in-the-context-of-raf-ksr-homologue-in-human-and-chimpanzee/
Copyright © 2011
By Authors and International
Network for Natural Sciences
(INNSPUB) https://innspub.net
This article is published under the terms of the
Creative Commons Attribution License 4.0