Team:Alberta/Project/Bioinformatics
From 2009.igem.org
|
Why build a minimal genome?Genomes are extremely complex. Producing a minimal genome allows for a better understanding of the function and interaction of cellular components. This better understanding can lead to optimization of synthetic processes and provides a well characterized chassis for synthetic biology. Moreover, a simplified cell can be used to study cellular processes in a controlled, characterized genetic background. Through the use of bioinformatics our team has attempted to produce a new essential gene list for a minimal genome in the ''E. coli'' bacterium. |
Why We Need Bioinformatics
''E. coli'' has over 4,500 genes. The size and complexity of this genome makes it almost impossible to manually process. An ''in silico'' approach allows for this complex data to be more easily collected, manipulated, and interpreted. Bioinformatics has aided us in accomplishing the following:
|
Literature ReviewFour essential gene lists from the literature were analyzed to construct a preliminary essential gene list
These literature lists vary greatly in size and have minimal overlap. Venn Diagram of the Number of Essential Genes Shared Between Lists in the LiteratureThe maximum number of genes in common between any two literature lists is 205, which is between Baba et al 2006 and Gerdes et al 2003. Only 48 genes were present in all four lists. |
|||||||||||||||||||||||||
Constructing the Biobytes Preliminary Essential Gene ListThe preliminary essential gene list is based on literature sources. As described in the modeling section of this wiki, the metabolic genes from this preliminary list were used as a starting point for the computer model and were greatly altered based on the model's suggestions. Non-metabolic genes in the this preliminary list were retained in the final list, described in the "Gene Selection" tab. Criteria for Gene Selection:
Genes for the following processes were included:
RNAs:The rrnC operon supplies all the rRNA’s and three of the tRNAs. This operon was selected because it includes the great number of tRNA’s. To select the other tRNA’s, all tRNA’s listed as essential in PEC were first included. One tRNA was then selected for each anticodon that differed on one of the last two bases. Differences in the first base can be accommodated by anticodon 'wobble'. At least one tRNA was included for each amino acid. The complete list of essential RNA’s can be found here . |
|||||||||||||||||||||||||
Statistics on BioBytes Preliminary Essential Gene ListTotal genes in Ecoli: 4762 Total protein coding genes in BioBytes preliminary essentials list: 332 Total number of RNA genes in BioBytes preliminary essentials list: 29 |
|||||||||||||||||||||||||
Metabolic ModelingTo verify that all genes necessary for metabolism are included in our essential gene list, a computer model was developed. This model suggested many more metabolic genes to add to our gene list. See the Gene Selection tab for the final Biobytes list of essential genes, and the Modeling section for more information on how modeling was done. |