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BIO403 Unit 2.3 Assessments

Codon Preference

Green fluorescent protein (GFP) absorbs blue light and emits green light. GFP is cloned from jellyfish, and it has been genetically engineered into a variety of living organisms. The codons in the jellyfish gene are not always read efficiently in the genetically modified organism. Modifying the cloned jellyfish DNA sequence is tedious, but necessary if the codon preference of the jellyfish and the codon preference of the target organism are different. Please see Fuhrmann, et al. (2002)1 for an example.

In this assessment, you will investigate the leucine and proline codon usage in the jellyfish GFP open reading frame and the general codon usage in E. coli2. After comparing the codon usages, you will predict if the GFP cDNA sequence should be modified or not before GFP has 18 leucine and 11 proline in its amino acid sequence. Each of these amino acids is coded by several codons. I used the jellyfish cDNA sequence3 and BioTools4 to construct the following table.

codon
number of amino acid in GFP
codon
number of amino acid in GFP
Leu
UUG
0
Pro
CCG
0
Leu
UUA
4
Pro
CCA
7
Leu
CUG
1
Pro
CCU
2
Leu
CUA
2
Pro
CCC
2
Leu
CUU
11
Leu
CUC
0

Please compare the codons that are used to code for leucine and proline to the codon preference table of Escherichia coli. Use this information to select the best answer.

  1. There are 4 codons that are used for leucine and 3 codons that are used for proline in GFP. All of these codons are recognized in E.coli, therefore it is not necessary to modify the GFP cDNA.
  2. Change CUU codons in the GFP cDNA to CUG. Also, change CCA and CCC codons to CCG.
  3. Change CUU and CUA codons in the GFP cDNA to CUG. Also, change CCA and CCC codons to CCG.
  4. Change CUU and CUA codons in the GFP cDNA to CUG. Also, change CCA codons to CCG.
  5. Change all leucine codons in GFP cDNA to CUG, and change all proline codons to CCG.

1Reading: Wiley Online Library: Markus Fuhrmann, et al.’s “A Synthetic Gene Coding for the Green Fluorescent Protein (GFP) Is a Versatile Reporter in Chlamydomonas reinhardtii

Link: Wiley Online Library: Markus Fuhrmann, et al.’s “A Synthetic Gene Coding for the Green Fluorescent Protein (GFP) Is a Versatile Reporter in Chlamydomonas reinhardtii” (HTML or PDF)

Instructions: This publication exemplifies that codon preference differences can hinder gene expression. Please review this publication as you are instructed in BIO403 subunit 2.3. In order to express GFP in the unicellular alga Chlamydomonas reinhardtii, the cloned jellyfish DNA sequence had to be modified based on codon preferences.

Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

2Reading: San Diego State University's version of S. Maloy, et al's Genetic Analysis of Pathogenic Bacteria: Microbial Genetics: "Codon Usage in E.coli"

Link: San Diego State University's version of S. Maloy, et al's Genetic Analysis of Pathogenic Bacteria: Microbial Genetics: "Codon Usage in E. coli"

Instruction: Please note that codons are used at different frequency. Identify the most and the least abundant proline and leucine codons.

Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

3Reading: National Center for Biotechnology Information: GenBank: Inouye and Tsuji's "Aequorea victoria Green-fluorescent Protein (GFP) mRNA, Complete Cds"

Link: National Center for Biotechnology Information: GenBank: Inouye and Tsuji's "Aequorea victoria Green-fluorescent Protein (GFP) mRNA, Complete Cds"

Instructions: The accession number of the GFP cDNA is L29345. Please note that the start of open reading frame in this cDNA is 26 and the end is 742. This cDNA region was submitted to BioTools.

Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

4Reading: eBioInfogen: BioTools' "Codon Usage"

Link: eBioInfogen: BioTools' "Codon Usage"

Instructions: Please note that this program allows codon usage calculation in a selected DNA sequence. It is important to analyze only the open reading frame of the protein, because noncoding regions do not contribute to codon usage.

Terms of Use: Please respect the copyright and terms of use displayed on the webpage above.

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