Computational Biology and Chemistry
Volume 32, Issue 6, December 2008, Pages 462-468
doi:10.1016/j.compbiolchem.2008.07.014
Discrepancy between mRNA and protein abundance: Insight from information retrieval process in computers
Degeng Wang, a,
aDivision of Cell Biology, Microbiology and Molecular Biology (CMM), Department of Biology, University of South Florida, 4202 E. Fowler Avenue – SCA110, Tampa, FL 33620, United States
Received 3 January 2008;
revised 18 June 2008;
accepted 2 July 2008.
Available online 16 July 2008.
Abstract
Discrepancy between the abundance of cognate protein and RNA molecules is frequently observed. A theoretical understanding of this discrepancy remains elusive, and it is frequently described as surprises and/or technical difficulties in the literature. Protein and RNA represent different steps of the multi-stepped cellular genetic information flow process, in which they are dynamically produced and degraded. This paper explores a comparison with a similar process in computers—multi-step information flow from storage level to the execution level. Functional similarities can be found in almost every facet of the retrieval process. Firstly, common architecture is shared, as the ribonome (RNA space) and the proteome (protein space) are functionally similar to the computer primary memory and the computer cache memory, respectively. Secondly, the retrieval process functions, in both systems, to support the operation of dynamic networks—biochemical regulatory networks in cells and, in computers, the virtual networks (of CPU instructions) that the CPU travels through while executing computer programs. Moreover, many regulatory techniques are implemented in computers at each step of the information retrieval process, with a goal of optimizing system performance. Cellular counterparts can be easily identified for these regulatory techniques. In other words, this comparative study attempted to utilize theoretical insight from computer system design principles as catalysis to sketch an integrative view of the gene expression process, that is, how it functions to ensure efficient operation of the overall cellular regulatory network. In context of this bird's-eye view, discrepancy between protein and RNA abundance became a logical observation one would expect. It was suggested that this discrepancy, when interpreted in the context of system operation, serves as a potential source of information to decipher regulatory logics underneath biochemical network operation.
Keywords: Information retrieval; Microarray analysis; Proteomic analysis; Network regulation; Computing; Omics; Systems biology
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