Genomes

Genomes

Complete set of genetic material defining a species

Heritable unit

DNA, not protein, is the fundamental heritable unit

B-DNA

Right-handed, dsDNA, favored in cellular life

A-DNA

Form found in bacteria/viruses, stable in harsh environments

Z-DNA

Transient form with regulatory role

Transient DNA

Includes Holliday intermediates, cruciform, hairpins

DNA backbone

Poly(ADP-deoxyribose), polyanionic

Base stacking

Planar heterocyclic bases stacked perpendicular to backbone

Orientation

DNA strands are antiparallel

Grooves

Molecules interact at major and minor grooves

RNA genomes

Exist only in viruses, not cellular life

Influenza genome

Segmented RNA genome example

Chromosomes

Eukaryotes linear, prokaryotes circular

Ploidy

Eukaryotes haploid or polyploid, prokaryotes mostly haploid

EVEs

Endogenous viral elements integrated into chromosomes

E. coli EVEs

18 prophages in chromosome

Chromosome size

Ranges 0.2 Mb (Carsonella) to 670 Gbp (Polychaos)

Non-coding DNA

90% in eukaryotes, ~15% in prokaryotes

Extrachromosomal

Includes plasmids, mitochondria, chloroplast DNA

Plasmids

Extrachromosomal ccDNA, 0.5 Kbp to >2 Mbp

F-plasmid

140 kbp plasmid in E. coli

Genome mosaic

Ex. Vibrio cholerae has two chromosomes

Genome packaging

E. coli chromosome 1.35 mm vs. cell 1.5 µm

Histones

Used in eukaryotes and some archaea to package DNA

Nucleosomes

DNA + histones, organized into chromatin

Archaeasomes

Histone variants in archaea, chromatin-like structures

Nucleoid

Prokaryotic genome region, not membrane-bound

Loop domains

Supercoiled, stabilized by NAPs

NAPs

Proteins aiding packaging, replication, regulation

Topoisomerases

Enzymes altering DNA topology for packaging

Topo I (prok)

Relaxes supercoiling

Topo II (prok)

Introduces supercoiling

Topo I (euk)

Relaxes and introduces supercoiling

Topo II (euk)

Relaxes supercoiling

Gyrase

Prototypic class II topoisomerase in E. coli

GyrA

Binds, cuts, and re-ligates DNA

GyrB

ATPase energizing GyrA

Quinolones

Antibiotics targeting GyrA, block replication

Ciprofloxacin

Example quinolone antibiotic

Genome def.

Term introduced by Hans Winkler, ca. 1920

Transforming principle

Discovered by Griffith, Avery et al.

Supercoiling

DNA packaging state altered by topoisomerases

Class I topos

Single-strand breaks, relax supercoils

Class II topos

Double-strand breaks, manage supercoils

Omega protein

Topo I in E. coli, discovered 1971

NAP examples

IHF, Fis, HU, H-NS proteins

Chromatin

Nucleosomes further organized in nucleus

Prokaryotic histones

Absent in bacteria, present in archaea

Plasmid example

2μ plasmid in yeast

Genome variation

Size, structure vary among microbes

Carsonella

Smallest known chromosome ~0.2 Mb

Polychaos

Largest known chromosome ~670 Gbp

Eukaryotic nucleus

DNA packaged inside nuclear membrane

Prokaryotic nucleus

Absent, DNA in nucleoid