Genomes and evolution

Genomes and evolution

1. Prokaryotic gene and genome structure

   • Genome size is related to complexity
     • More genes corresponds to bigger genomes
     • Selection for small genomes seems to occur. This is because rapid growth and short generation times leads to a selective advantage

2. Eukaryotic gene and genome structure

   • No relationship between gene number, genome size and complexity
   • Functions of complex transcription units
     • The different proteins encoded may have slight functional differences allowing them to be specialized for particular functions, eg different regulatory protein domains could be included in different tissues
     • More specialisation and greater complexity is due to more combinations, not more genes
   • Exons
     • Exons often correspond to protein domains
       • A protein domain is a region of a protein with a specific structure or function. This region often folds independently of the rest of the protein
     • Exon shuffling
       • New genes evolve by joining together new combinations of exons
       • Occurs over evolutionary time
   • Multigene Families
     • A multigene family consists of a set of genes that arose by duplication of ancestral gene and subsequent divergence due to small changes to the nucleotide sequence
       • May contain pseudogenes that are homologous but do not produce a functional protein
       • Within a gene family, particular members may show specialized functions, eg for tissue or developmental stage specificity
     • The globin gene family
       • Haemoglobin carries oxygen in our blood and consists of four globin proteins, two copies each of α and β and the cofactor haem
         • Foetuses require haemoglobin with a higher affinity for oxygen and express the γ globin gene

3. Mechanisms of genome evolution

   • Point mutations
   • Replication strand slippage
     • Replication strand slippage can lead to misalignment of the template and newly synthesised strand and results in unequal daughter strands
       • Replication slippage also causes insertions or deletions of several nucleotides
         • Generation of simple sequence repeat
         • Trinucleotide expansion
   • Transposition (Transposons)
     • Moderately-repeated, mobile DNA sequences are interspersed throughout the genomes of prokaryotes, plants and animals
     • These sequences appear to serve no useful function: selfish DNA General
     • DNA transposons (Class 2)
       • Move via a 'Cut and Paste' mechanism
       • Short terminal inverted repeats, short flanking direct repeats at target site
       • Transposase gene (and sometimes others)
       • Transposition through DNA replicative or non replicative
     • RNA transposons (Class 1)
       • Move via a 'Copy and Paste' mechanism
       • Reverse Transcriptase
         • Reverse transcriptase produces a DNA/RNA hybrid
           • This is converted to double stranded DNA by degradation of the RNA and synthesis of a new DNA strand
       • Transposition by an RNA intermediate
       • Long terminal direct repeats, short flanking direct repeats at target site
   • Recombination
     • Repeated sequences allow misalignment and then recombination
       • Gene duplication
       • Deletion
       • Inversion

4. The human genome

   • Copy Number Variation (CNV)
     • Difference among individual organisms in the number of copies of any large DNA sequence (larger than 1000 bp)
       • Individuals vary in the number of copies of particular DNA sequences (genes, repeated sequences, any chunk of DNA)
         • Repeated DNA
           • Simple sequence repeats (highly repeated) accounts for 3% of the human genome
             • Tandem repeats spanning 20-100 kb
             • Repeat length 1-500 bp
             • Concentrated in particular regions of chromosomes, especially centromeres and telomeres
             • Most has no known function, but can be used as the basis of DNA fingerprinting as the number of SSRs varies between individuals
           • Different types of mobile DNA elements (moderately repeated) accounts for 45% of the human genome