Lecture 7

Codon Usage
Course Code: MIC-403
By: Mahrukh Zakir
Email Address: [Link]@[Link]

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INTRODUCTION TO CODONS

What Are Codons?

 Codons are sequences of three nucleotides (a triplet) in messenger RNA
(mRNA) that correspond to a specific amino acid or signal during the process of
protein synthesis.
• Each codon is composed of three nitrogenous bases (adenine [A], uracil [U],
cytosine [C], and guanine [G] in RNA) and is read in a non-overlapping,
continuous manner during translation.

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TYPES OF CODONS
Start Codon (Initiation Codon):
 AUG is the most common start codon, coding for the amino acid methionine in eukaryotes and
formyl-methionine (fMet) in prokaryotes.
 Functions as a signal to the ribosome to initiate protein synthesis.
 In rare cases, alternative start codons like GUG or UUG can be used, particularly in prokaryotic
systems.
Sense Codons (61 codons):
 These codons specify one of the 20 standard amino acids used to build proteins.
Example:
UUU codes for Phenylalanine
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STOP CODONS (TERMINATION CODONS)

• UAA, UAG, and UGA do not code for any amino

acid but signal the termination of translation.
• These codons instruct the ribosome to release the
newly synthesized polypeptide chain.
• Known as nonsense codons because they do not
encode amino acids.

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HOW CODONS WORK: THE MECHANISM OF TRANSLATION

Transcription:
DNA → mRNA
Codons originate during transcription, where a DNA template is copied
into a complementary mRNA strand.
Example:
DNA sequence (template strand):
TAC GGC TTA
mRNA sequence (transcribed):
AUG CCG AAU

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TRANSLATION
Translation occurs in the ribosome, the molecular machinery responsible for protein synthesis.
Key Steps:
1. Initiation:
• The ribosome binds to the mRNA at the start codon (AUG), initiating translation.
• A tRNA carrying the anticodon UAC pairs with AUG, bringing methionine to start the
polypeptide chain.
2. Elongation:
• Codons in the mRNA are read sequentially, and tRNAs with complementary anticodons
bring the corresponding amino acids.
• Example: mRNA codon GGC pairs with tRNA anticodon CCG, delivering glycine.
3. Termination:
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• When a stop codon (UAA, UAG, UGA) is encountered, no corresponding tRNA exists.
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Figure 1

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REDUNDANCY OF THE GENETIC CODE

 Redundancy in the genetic code refers to the phenomenon

where multiple codons can code for the same amino acid.
 This feature allows for flexibility and minimizes the impact of
point mutations on protein structure and function.
Example:
The amino acid Leucine is encoded by six different codons: CUU,
CUC, CUA, CUG, UUA, and UUG.
The two amino acids that are coded for by a single codon are
methionine and tryptophan.

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DEGENERACY OF THE GENETIC CODE

• Degeneracy of the genetic code contributes to its ability to tolerate

mutations without affecting the resulting protein.
• A silent mutation occurs when a change in the nucleotide sequence
does not alter the amino acid being coded.
Example:
• Codons CUU, CUC, CUA, and CUG all encode Leucine. A mutation
from CUU (Leucine) to CUC (Leucine) results in no change to the
protein sequence.

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CODON USAGE

 Codon usage refers to the frequency at which different codons are used in a
genome.
 Codon Usage Bias is the phenomenon where certain synonymous codons
(codons that code for the same amino acid) are preferred over others in a
specific organism.
 Significance:
Affects translational speed
protein folding
accuracy.

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FACTORS INFLUENCING CODON USAGE

tRNA Abundance:
 Organisms have tRNA pools tailored to certain codons, influencing efficiency.
Translational Efficiency:
 Frequently used codons correlate with faster protein production.
 This enhances cell growth and metabolic activity in rapidly dividing organisms like bacteria.
GC Content:
 Genomic composition (e.g., GC-rich genomes prefer GC-ending codons).
 Example: Thermophilic bacteria often have GC-rich genomes, optimizing their genetic code for
thermal stability.
Mutational Pressures:
 Mutations favor certain codons based on environmental and evolutionary factors.
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 Example: Viral genomes often show codon bias to match the host’s translation machinery.
 CODON BIAS

 Codon bias occurs when some codons are used more

frequently than others for the same amino acid.
 Example:
E. coli prefers CGU for arginine, whereas humans favor
CGC.

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 MEASURING CODON USAGE BIAS

Effective Number of Codons (ENC):

Codon Adaptation Index (CAI):
Quantifies the overall codon usage bias in a gene.
Measures how closely the codon usage of a gene
matches that of highly expressed genes in the same Range:
organism.
20: Strong codon bias (only one codon is used per amino
Range: 0 to 1, where a higher score indicates a better acid).
match and thus higher potential expression.
61: No bias (all synonymous codons are used equally).
Significance: Widely used to predict gene expression
Significance: Lower ENC values indicate stronger bias, often
levels and optimize codon usage in synthetic biology.
found in highly expressed or specialized genes.

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MEASURING CODON USAGE BIAS

Relative Synonymous Codon Usage (RSCU):

Compares the observed frequency of a codon to its expected frequency if all
synonymous codons were used equally.
Formula:

Significance:
 RSCU = 1: No bias (codon used as expected).
 RSCU > 1: Codon is used more frequently than expected.
 RSCU < 1: Codon is used less frequently than expected.
CODON USAGE IN PROKARYOTES
Characteristics:
•Strong codon bias in highly expressed genes (e.g., ribosomal proteins).
•Preferences driven by selection for rapid and efficient translation.
Example:
In E. coli:
• GAA is the preferred codon for glutamate because it corresponds to the most abundant tRNA.
• This preference optimizes the translation of high-expression genes like those involved in metabolism and
stress response.

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 CODON USAGE IN EUKARYOTES

 Codon usage bias in eukaryotes is less pronounced than in

prokaryotes but remains significant, especially in highly
expressed genes.
 Eukaryotic organisms often show codon preferences that
correlate with their genomic GC content.
 GC-rich genomes tend to favor codons ending in G or C,
while AT-rich genomes show a preference for codons
ending in A or T.
Example:
• Humans tend to prefer GC-rich codons for some amino
acids, such as GGC for glycine, reflecting the overall
higher GC content in the human genome. 17
EVOLUTIONARY SIGNIFICANCE

Selective Pressures:
 Codon bias reflects adaptation to environmental pressures (e.g., thermophilic bacteria favor
GC codons for stability).
Neutral Evolution:
 Drift and mutational biases also shape codon usage.
Examples:
 Viruses evolve codon usage matching their host for replication efficiency.

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TOOLS FOR CODON USAGE ANALYSIS
Computational Tools:
 Codon Usage Database
 CAIcal (Codon Adaptation Index Calculator)
 Graphical Codon Usage Analyzer (GCUA)
 GeneOptimizer
 OPTIMIZER
 Biopython
 CodonW
 EMBOSS (European Molecular Biology Open Software Suite) cusp
Functions: Analyze patterns, calculate metrics, and optimize codon sequences.
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CAIcal (Codon Adaptation Index Calculator)

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Output

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 APPLICATIONS OF CODON USAGE IN COMPUTATIONAL
MICROBIOLOGY

 Codon usage plays a pivotal role in optimizing protein expression, understanding evolution, studying
pathogenicity, and advancing synthetic biology.
• Recombinant protein production (e.g., vaccines, enzymes).
 Computational tools help leverage codon analysis for better gene function prediction and microbial
engineering.

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