2 - Genome Diversity and Organisation of DNA

• The genome is the sequence of nucleotides in DNA that comprises the genetic makeup of the organism
• The genome size is always presented as the total amount of DNA contained within one copy of a single genome
• Viral genomes are extremely diverse and generally much smaller than cellular organisms
• Viral genomes can be DNA or RNA, single-stranded or double-stranded, circular or linear, and genes may overlap
• Bacteriophage lamda has a genome size of ~48.5 kbp and has double-stranded linear DNA that can circularise when infecting E.coli to allow replication
• The first genome to ever be sequenced was of Bacteriophage phiX174 as it has single-standed DNA and ~5,200 nt
• SARS-CoV-2 virus has a genome size of ~30,000 nt, has single-stranded RNA and is linear
• In rotaviruses, the genome is distributed between 11 linear molecules
• In rotaviruses, the genome is distributed between 11 linear molecules
• Bacteria generally have smaller genomes than eukaryotes
• Gene density is lower in eukaryotes than prokaryotes
• Genome size does not consistently correlate with organism complexity - the "C-value" or "genome" paradox
• Similar organisms can show a large range in genome size
• Genomes often have transposable elements that can lead to increases in genome size
• In mammals, genome size is usually a small number of Gbp
• Transposable elements are sections of DNA that can copy themselves and move around the genome
• The genome consists of genes and intergenic regions that don't contain "typical" gene units - "junk DNA"
• The function of "junk" DNA is often to code for RNA that is not translated
• A gene is a region that controls a discrete hereditary characteristic, often with a specific product such as a protein
• Much of junk DNA is made of transposable elements
• DNA sequence in genomes is classified by abundance
• "Unique" DNA sequences have one to a few copies per genome
• "Moderately repetitive" DNA sequences have a few to 10^5 copies per genome
• "Highly repetitive" DNA sequences have 10^5 to 10^7 copies per genome
• Prokaryotes have mostly unique sequence DNA
• Eukaryotes have a mix of unique and repetitive DNA
• The human genome is approximately 50% unique sequence and 50% repeat sequence
• DNA is packaged into linear (eukaryotes) or circular (prokaryotes) units called chromosomes
• Only 2% of the human genome codes for proteins
• E.coli is a good bacterial model organism because:

  • Bacterial genomes are usually a single, circular, dsDNA chromosome
  • The E.coli genome is 1.5 mm long
  • Chromosomal DNA is localised to the nucleoid
  • Replicates quickly
  • Easy to culture
• Plasmids are small, extrachromosomal circular DNA modules that may confer advantages to host bacteria
• Borrelia burgdorferi is an outlier to general bacterial genome structure and causes Lyme disease and has one large dsDNA linear chromosome and contains essential extrachromosomal linear and circular DNA
• Bacterial DNA must be organised and compacted to fit into a cell much shorter than the length of a DNA molecule
• DNA compaction in bacterial nucleoid is less well-understood than eukaryotic chromosome structure
• First stage of DNA packing involves the binding of small, positively charged proteins along the DNA to counteract the negative charges on the DNA backbone
• Bacterial Nucleoid Associated Proteins (NAPS) such as Integration Host Factor (IHF) bend DNA to facilitate packaging and supercoiling
• Examples of NAPS:

  • Integration Host Factor (IHF)
  • Factor for Inversion Stimulation (FIS)
  • Structural Maintenance of Chromosomes (SMC)
  • HU (histone-like protein)
  • HNS (histone-like nucleoid structuring protein)
• Bacterial DNA is arranged into ~400 independent negatively supercoiled looped domains of ~10 kbp each
• Supercoils are generated by topoisomerases
• Eukaryotic genomes are distributed across multiple, linear chromosomes with varied DNA content