COO-III-4. Genome composition and optimal growth temperature

Overview

Teaching: 0 min
Exercises: 30 min

Questions

• How do genomes evolve under different environmental constraints?

Objectives

• Explore protein composition adaptation to high temperatures

Protein compositions

Organisms that live at high temperatures require different genome and protein composition to withstand these conditions. Here, we will analyse the inferred proteome composition of these genomes and characterise their differences.

cd ~/GenomeBioinformatics/Block1/COO-III
mkdir 09_composition
cd 09_composition
ln -s ../01_genomeData/bin.3/*faa .
ln -s ../01_genomeData/heim/prokka*/*faa .
rename GCA heim_GCA GCA*
ln -s ../01_genomeData/pangui/prokka_GCA_0*/*faa .
rename GCA pangui_GCA GCA*
ln -s ../04_genomeDensity/col_prokka/prokka_Col_02*/*faa .

Now explore two different tools to visualise amino acid frequences:

~/data_bb3bcg20/bin/scripts/aa_freq_plot.sh bin.3.faa

Exercise: Visualise changes in proteome composition

Can you see any general trends in amino acid frequency changes?

for f in Col*faa; do ~/data_bb3bcg20/bin/scripts/aa_freq_plot.sh $f; done

for f in heim*faa; do ~/data_bb3bcg20/bin/scripts/aa_freq_plot.sh $f; done

for f in pangui*faa; do ~/data_bb3bcg20/bin/scripts/aa_freq_plot.sh $f; done

mkdir aa_freqs; mv *txt aa_freqs/

It may be very difficult to visualise when confronting all amino acids at the same time, but some of the amino acid categories that are most affected by adaptations to higher temperatures are Charged amino acids (both positive and negative) and Polar amino acids. Let’s focus our analyses on these.

Exercise: How do charged and polar amino acid compositions change under different temperatures?

for f in *faa; do ~/data_bb3bcg20/bin/scripts/aa_chargedpolar_plot4.sh $f; done

mkdir Charged_polar

mv *polar Charged_polar/; mv *charged Charged_polar/; mv *ratio.txt Charged_polar

Solution

for group in bin.3 Col heim pangui; do echo $group; perl ~/data_bb3bcg20/bin/scripts/stats.pl <(cat Charged_polar/$group*_ratio.txt); echo; done

Generally, charged amino acids are more common in thermophile genomes, while polar amino acids are less used.

Key Points