Genome and chromosome
structure
Martin A. Lysák
CEITEC and Faculty of Science,
Masaryk University
Genome (Hans Winkler, 1920)
• Genetic material, i.e. DNA (RNA in RNA viruses)
• By genome we either mean nuclear genome (eukaryotes) or
genetic material of prokaryotes, mitochondria and chloroplasts
• Genomes contain coding DNA regions (genes) and non-coding DNA
• DNA (RNA) is associated with proteins, thus genomes are
essentially nucleoprotein structures
• Genomes differ by size and complexity
• Genomics studies genomes (their structure and evolution)
Ich schlage vor, für den haploiden Chromosomensatz,
der im Verein mit dem zugehörigen Protoplasma die
materielle Grundlage der systematischen Einheit
darstellt, den Ausdruck: das Genom zu verwenden und
Kerne, Zellen und Organismen, in denen ein
gleichartiges Genom mehr als einmal in jedem Kern
vorhanden ist, homogenomatisch zu nennen, solche
dagegen, die verschiedenartige Genome im Kern
führen, heterogenomatisch
Viruses
(not living
nucleoproteins)
Living things: five kingdomes
eukaryotesprokaryotes
Genomes
1. Viral genome
2. Prokaryotic genome
2.1 Genome of Archaea
2.2 Bacterial genome
3. Eukaryotic genome
3.1 Extra-nuclear genome
3.1.1 Mitochondrial genome
3.1.2 Plastid genome
3.1.3 Extra-chromosomal DNA
3.2 Nuclear genome
3.2.1 Nuclear architecture
3.2.2 Chromosomes
Genome size variation
Polychaos dubium
…perhaps the largest known genome –
670 billion base pairs (670 Gb)
(~200-times larger than the human
genome, 3.2 Gb; some authors suggest
treating the value with caution –
Amoeba proteus has ~34 - 43 Gb…)
Protopterus aethiopicus
C-value paradox (CA Thomas, 1971)
C-value paradox
The height of the drawings is proportional to the size of their genome (amoebae,
onions, grasshoppers, toads, humans, hens, Drosophila and Caenorhabditis).
Viruses
Viruses – physical and genome size
9.7 kb
49 kb
Pithovirus sibericum
largest virion - 1.5 m
(610 kb, dsDNA virus,
467 genes)
Pandoravirus salinus (dsDNA)
- 2.8 Mb
- 2 556 genes
- „parasites“ of amoebas
- only 6 % of genes match the known genes –
unknown part of the tree of life?
protein coding genes0.9
Science 376: 156-162 (2022)
Viruses
• single- or double-stranded
DNA or RNA (DNA and RNA
viruses)
• linear or circular
• one molecule or in segments
(RNA viruses)
• very few genes (4 to a few
hundred)
(David Baltimore, 1971)
(retroviruses)
(pararetroviruses)
Structure of the NiV nucleocapsid protein-RNA complex
Ker DS, Jenkins HT, Greive SJ, Antson AA (2021) CryoEM structure of the Nipah
virus nucleocapsid assembly. PLOS Pathogens 17(7): e1009740.
Viruses
• one linear or circular molecule
• segmented RNA virus genomes
(e.g., influenza virus: -ssRNA)
How DNA/RNA is compacted in viral
nucleocapsids
Life cycle of
influenza viruses
Viral life cycle
Endogenous viral elements (EVEs)
Viruses which integrated their genomes into genomes of their eukaryotic hosts.
• +ssRNA-RT (retroviruses) or dsDNA-RT (pararetroviruses)
• usually small DNA fragments (few genes) but also (rarely) entire viral genome, can be
inherited (fixed)
• some can remain active (rarely)
• paleovirology: EVEs („viral fossils“) but parental viruses have become extinct
• example - algae (chlorophytes): large dsDNA viruses can integrate in the host genome
(https://doi.org/10.1038/s41586-020-2924-2)
• between 78 and 1 782 genes from the virus to the algal genome, some algae have the
whole genome of a giant virus in their DNA (up to 10% of all genes)
• some genes of the EVEs duplicated, some have introns = long-term „co-evolution“ with
the host genome (two-way interaction between the viral and host genome)
Bacteria, Archaea and Eukarya (Eukaryotes):
three domains of life
Prokaryotes
Genomes of Archaea and Bacteria
• single-cell organisms
• small compact genomes
• (usually) circular DNA/chromosome (nucleoid) and plasmids
• do not have a nucleus and membrane-bound organelles
• reproduce by fission (after the chromosome is replicated)
Carsonella ruddii – smallest genome of endosymbiotic bacteria (160 kb, 182 genes)
Mycoplasma genitalium – smallest genome of free living bacteria (580 kb, 470 genes)
Sorangium cellulosum – the largest known bacterial genome (13 Mb, 9 400 genes)
Escherichia coli
4.6  106 bp = 1.5 mm
(a 1000-fold compression)
1.5 m
the archaea Methanosphaera stadtmanae
• Methanogens (methane-producing strains)
• Halophiles
• Thermophiles
• Alkalophiles
• Acidophiles
Genomes of Archaea (formerly Archaebacteria)
Archaea and methane
• usually a single circular chromosome, plasmids can be found
• Euryarchaea: multiple copies of their genomes (oligoploidy) – up to 55 copies in
Methanococcus maripaludis
• smallest genome: 491 kb (Nanoarchaeum equitans)
• largest genome: 5.8 Mb (Methanosarcina acetivorans), only 537 protein-encoding
genes
• some genes common with bacteria and eukaryotes, some unique (mostly
unknown function)
• DNA polymerase similar to eukaryotic DNA polymerases, transcription more
similar to eukaryotes (one type of RNA polymerase similar to RNA polymerase II
in eukaryotes), translation similar to both bacteria and eukaryotes
• reproduction is asexual (fission, fragmentation, budding) after the chromosome
is replicated
Genomes of Archaea
Multi-scale architecture of archaeal chromosomes
• Sulfolobus: single circular chromosome
(2.2 – 3 Mb)
• two-domain compartmentalization that
influences gene expression (domain-like
organization somewhat similar to
eukaryotes)
• coalescin (SMC-family protein*) marks the
domain with low transcription levels (B
compartment)
*SMC- Structure Maitenance of Chromosomes (protein complexes), mainly in eukaryotes (e.g., condensin, cohesin)
compartments
Archaea vs Bacteria
Cell wall is made up of
pseudopeptidoglycans:
N-acetylglucosamine
(NAG) and Nacetyltalosaminuronic
acid
(NAT)
Cell wall is made up of
peptidoglycans consisting of
N-acetylglucosamine (NAG)
and N-acetylmuramic acid
(NAM).
Introns are present in
the chromosomes of
archaea.
Introns are absent in the
chromosomes of bacteria.
Archaea are non-
pathogenic.
Do not use glycolysis
or Kreb’s cycle for
glucose oxidation but
follow metabolic
pathways similar to
these.
Bacteria might be
pathogenic or non-
pathogenic.
Glycolysis and Kreb’s
cycle are important
metabolic pathways
in bacteria for
glucose oxidation.
Bacterial genomes
Bacterial chromosome
Escherichia coli - traditional view: single circular chromosome (dsDNA)
! Some bacteria have multiple chromosomes (e.g. 3.1-Mb and 0.9-Mb circular chromosomes
in Rhodobacter sphaeroides).
! Linear chromosomes in some bacteria (1970,
1989 by PFGE: Borrelia burgdorferi, size c. 1 Mb)
Problematic ends of linear chromosomes:
• palindromic hairpin loops (hairpin telomeres)
• invertron telomeres – inverted terminal repeats and
covalently attached capping (terminal) proteins
Bacteria Chromosome organization
Agrobacterium tumefaciens One linear and one circular
Bacillus subtilis Single and circular
Bacillus subtilis Single and linear
Borrelia burgdorferi Single and linear
Escherichia coli Single and circular
Paracoccus denitrificans Three circular
Pseudomonas aeruginosa Single and circular
Rhodobacter sphaeroides Two circular
Streptomyces griseus Linear
Vibrio cholerae Two circular
Vibrio fluvialis Two circular
Escherichia coli
4.6  106 bp = 1.5 mm
(a 1000-fold compression)
1.5 m
• one linear chromosome (906 kb)
• 12 linear plasmids (6 to 72 kb)
• 2 circular plasmids (each 30 kb)
Genome of Borrelia miyamotoi (example)12linearplasmids
Borrelia miyamotoi is a bacteria is
in the relapsing fever group
of Borrelia. Although it’s not closely
related to the Lyme disease
bacteria, it can cause a Lyme-likeillness.
Symptoms include fever,
headaches, muscle aches and chills,
rash uncommon. Diagnosis is by
PCR testing that is now available at
several labs. Treatment is
doxycycline. B. miyamotoi was
identified in 1995 in ticks from
Japan.
3D structuring of bacterial circular chromosome
DNA supercoiling
chromosomal
interaction
domains (CIDs)
long and highly
expressed gene clusters
10-kb domains
Hi-C analysis (heatmap)
Bacterial genomes – trends in content and size
• 160 kb to 13 Mb
• most of the genome (85-90%) is nonrepetitive
DNA (coding DNA), while noncoding
regions only take a small part
• bacteria have relatively small amounts of
junk (non-coding) DNA → a high correlation
between the number of genes and the
genome size in bacteria
• the lifestyles of bacteria play an integral role
in their respective genome sizes. Free-living
bacteria have the largest genomes out of the
three types of bacteria; however, they have
fewer pseudogenes than bacteria that have
recently acquired pathogenicity. Parasitic and
endosymbiotic bacteria can rely on host
environments to provide gene products.
Ochman and Davalos, Science 2006
Free-living species— selection effective in removing deleterious sequences →
large genomes containing relatively few pseudogenes (red) or mobile genetic
elements (yellow).
In recently derived pathogens, the availability of host-supplied nutrients combined
with decreases in effective population sizes allows for the accumulation of
pseudogenes and of transposable elements.
In long-term host-dependent species, the ongoing mutational bias toward
deletions has removed all superfluous sequences, resulting in a highly reduced
genome containing few, if any, pseudogenes or transposable elements.
LGT, lateral gene transfer.
What is the role of plasmid DNA?
- usually small (1- 200 kb), usually circular
DNAs; independent replication
Plasmid mobility
What is the role of plasmid DNA?
Plasmids generally contain genes that confer some sort
of advantage for survival and reproduction:
• Genes providing protection from toxic substances (including
antibiotic resistence). Plasmids carrying antibiotic resistance
genes are key contributors to the uncontrollable spread of
bacterial pathogens, particularly in hospitals
• Genes enabling the metabolism of additional sources of
energy
• Genes for toxins to kill microbial competitors, enhance
pathogenicity
• Genes involved in gene transfer by conjugation
• New evidence that suggests that plasmids might accelerate
bacterial evolution, mainly by promoting the evolution of
plasmid-encoded genes, but also by enhancing the
adaptation of their host chromosome
Plasmids and major
transitions in the evolution
of bacteria
Rhodobacteraceae (marine
bacteria) - plasmids responsible
for the ability to undergo
anoxygenic photosynthesis
the aphid endosymbiont Buchnera
aphidicola – plasmids responsible
for synthesizing essential amino
acids and vitamins required for the
bacterium–aphid symbiotic
relationship (advantage for aphid)
Eukaryotes
Prokaryotes vs Eukaryotes
• Simple, small (0.1 – 5 m)
• Do not have membrane-bound structures (nucleus,
mitochondria)
• Nucleoid: DNA
• Cell wall: protection from the outside environment. Most
bacteria have a rigid cell wall made from carbohydrates and
peptidoglycans.
• Cell membrane (plasma membrane)
• Capsule: Some bacteria have a layer of carbohydrates that
surrounds the cell wall called the capsule. The capsule
helps the bacterium attach to surfaces.
• Fimbriae: thin, hair-like structures that help with cellular
attachment.
• Pili: rod-shaped structures involved in multiple roles,
including attachment and DNA transfer.
• Flagella: thin, tail-like structures that assist in movement
• Transcription and translation are coupled (translation begins
during mRNA synthesis)
• Complex, cell bigger (10 – 100 m)
• Multicellular, some single-cell eukaryotes
• Nucleus and other organelles enclosed by a plasma
membrane
• Nucleolus: production of ribosomal RNA molecules
• Plasma membrane: a phospholipid bilayer that
surrounds the entire cell and encompasses the
organelles within.
• Cytoskeleton or cell wall: provides structure, allows for
cell movement, and plays a role in cell division.
• Mitochondria: responsible for energy production.
• Endoplasmic reticulum: an organelle dedicated to
protein maturation and transportation.
• Vesicles and vacuoles: membrane-bound sacs involved
in transportation and storage.
• Transcription in the nucleus (mRNA), translation in
cytoplasm
• the circular/linear DNA is packaged →
nucleoid (50 or more loops/domains bound to
a central protein scaffold, attached to the
cell membrane) = DNA is negatively
supercoiled, that is, it is twisted upon itself
• several DNA-binding proteins (the most
common HU, HLP-1 and H-NS; these are
histone-like proteins)
• chromosomes contain both DNA and proteins
(mostly histones, but also non-histone proteins)
• each chromosome is a single linear doublestranded
DNA molecule
• the extensive packaging of DNA in chromosomes
results from three levels of folding (nucleosomes,
„30-nm fibres“ and radial loops)
• the length of the packaged DNA molecule varies.
In humans, the shortest DNA molecule in a
chromosome is about 1.6 cm and the longest is
about 8.4 cm
Prokaryotes vs Eukaryotes (more differences)
Origin of eukaryotic genomes (eukaryogenesis)
• prokaryotic cells occurred c. 1 billion years after the Earth was formed – i.e.
about 3.5 billion years ago
• eukaryotic cells emerged about 2.5 billion years ago
• Lynn Margulis (in the 1960s): endosymbiotic theory of the origin of an
eukaryotic cell
• eukaryotic nuclear genes appear to originated from the Archaea,
mitochondria appear to be of the bacterial origin
Paramecium bursaria
with Zoochlorella
algae
Origin of Eukaryotes within the Archaea
• Eocyte hypothesis (James A. Lake and others, 1984): eukaryotes emerged within
Crenarchaeota (formerly eocytes), a phylum of the Archaea; based on the shapes of
ribosomes in the Crenarchaeota and eukaryotes being more similar than ribosomes of
eukaryotes and bacteria (or other Archaea)
• later studies suggested that eukaryotes might have originated within Thaumarchaeota
(today Crenarcheaota and Thaumarchaeota belong to the superphylum TACK)
Last universal common ancestor
• Asgard - another superphylum of the
Archea was not known in the 1980s
• it appears that eukaryotes originated
within Heimdallarchaeota
• in cladistic view, eukaryotes are
Archaea, similarly as birds are
dinosaurs
Prometheoarchaeum syntrophicum
Imachi H, Nobu MK, Nakahara N, et al. Isolation of an archaeon at the prokaryote-eukaryote interface. Nature. 2020;577(7791): 519-525.
Potential living link between Archaea and eukaryotes
• Prometheoarchaeum syntrophicum - an archeon of the Asgard
superphylum
• from the ocean floor (2 533 m water depth, Japan)
• support for the hypothesis of eukaryogenesis via endosymbiosis:
the host archaeon engulfed the metabolic partner/bacteria (future
mitochondrion) using extracellular structures and simultaneously formed
a primitive chromosome-surrounding structure similar to the nuclear
membrane:
Origin of Eukaryotes – viral eukaryogenesis
(Philip Bell, 2001, 2020)
• A hypothesis that the eukaryotic nucleus could originated from a virus infecting an archaeal
ancestor (donor of cytoplasm)
• This virus(es) could be similar to large, complex DNA viruses (such as Mimivirus) that are
capable of protein biosynthesis
• The virus-derived nucleus probably acquired some genes from the archaeal host genome
and bacterial genome(s)
• A similar proces, when a bacteriophage hijacks bacterial cell‘s machinery and forms a
nucleus-like structure, was observed by Chaikeeratisak et al. (2017, Science):
https://www.youtube.com/watch?v=0xM5BhQ2kc8&feature=emb_title
(and chloroplast)
Extra-nuclear genomes and extra-chromosomal DNA in eukaryotes
(outside the chromosomes and typically also outside the nucleus)
Mitochondrial genome (mtDNA)
• human mtDNA includes 16,569 base pairs and encodes 13 proteins, 2 rRNAs, 22
tRNAs
• animals: usually circular DNA molecule, but also linear genome
• plants and fungi (circular, rarely linear), 3 types of mt genome:
- a circular genome that has introns (19 to 1 000 kb)
- a circular genome (20 – 1 000 kb) that also has a plasmid-like structure (1 kb)
(plasmids sometimes integrated in the circular chromosome)
- a mt genome consisting of linear DNA molecules
• Silene conica: enormous mtDNA genome – 11.3 Mb
• mitochondrion of the cucumber (Cucumis sativus): 3 circular chromosomes (1
556, 84 and 45 kb)
• female inheritance (rerely male inheritance)
Kingdom Introns Size Shape Description
Animal No 11–28 kb Circular Single molecule
Fungi,
Plant,
Protista
Yes
19–1000
kb
Circular Single molecule
Fungi,
Plant,
Protista
No
20–1000
kb
Circular
Large molecule and small plasmid
like structures
Protista No 1–200 kb Circular Heterogeneous group of molecules
Fungi,
Plant,
Protista
No 1–200 kb Linear Homogeneous group of molecules
Protista No 1–200 kb Linear Heterogeneous group of molecules
The remains of King Richard III were identified by
comparing his mtDNA with that of two matrilineal
descendants of his sister.
Chloroplast genome (plastome)
• each chloroplast contains ~100 copies of DNA in young
leaves, declining to 15 - 20 copies in older leaves. These
usually cluster into nucleoids containing several identical
chloroplast DNA rings; many nucleoids in each chloroplast
• usually circular DNA molecule, but frequently also in a linear
shape; 120 – 170 kp long
• quadripartite structure: small (SSC) and large single copy
(LSC) section, 2 inverted repeats (IRs)
• IRs contain 3 rRNA genes, 2 tRNA genes; loss of one IR
multiple times
• land plants (129 genes in average, min. 64, max. 313),
parasitic plants (no photosynthesis): reduced no. of genes
(63 genes) vs. gene no. increase (Pelargonium): 180 genes
(243 kb)
• land plants: coding 4 ribosomal RNAs, 30–31 tRNAs, 21
ribosomal proteins, and 4 RNA polymerase subunits; genes
important for photosynthesis
Arabidopsis thaliana
154-kb plastome genome
SSC short single copy section
LSC long single copy section
IR inverted repeats
Chloroplast genome (plastome)
• prokaryotic origin (cyanobacterium), endosymbiosis; chloroplast
ribosomes are similar to bacterial ribosomes
• less genes than prokaryotic ancestors: transfer of thousands of
genes to the nucleus (e.g., c. 18% of Arabidopsis nuclear DNA
(4500 protein-coding genes) originated in chloroplast)
• ~95% of chloroplast proteins are encoded by nuclear genome
• positive correlation between nuclear genome size and length of
transferred cp DNA fragments (the largest in rice, 131 kb, almost
entire cp genome), integrated mainly to pericentromeric regions
in rice (many removed during evolution)
• chloroplast genome evolves about 10-times slower than the
nuclear genome
• mostly uniparental maternal inheritance, less common
uniparental paternal and biparental inheritance; gymnosperms
inherit plastids from male parent (pollen); interspecies hybrids:
plastid inheritance can be mixed; 20% of angiosperms (e.g.
Alfalfa, Medicago sativa) have biparental inheritance
• glyphosate – synthetic herbicide patented by Monsanto in 1974
• known as Roundup
• Roundup Ready crops (GMOs)
• glyphosate: inhibition of a critical gene involved in amino acid synthesis, 5ENOLPYRUVYLSHIKIMATE-3-PHOSPHATE
SYNTHASE (EPSPS)
• emergence of glyphosate-resistant weed species (48), such as Amaranthus palmeri
• principle of the resistence: increase of EPSPS copy number due to the origin of a selfreplicating
eccDNA replicon (contains other genes, transposable elements)
• 399 435 bp in length, 59 genes
• the replicon contains elements controling its self-replication
• probably inherited through chromosome tethering (association with dividing chromosomes)
• the replicon can be used for crop improvement (engineering of synthetic replicons)
Extrachromosomal circular DNA (eccDNA)
• yeast, plants, animals
• size from a few hundred base pairs to hundreds of kilobases
• orgin from chromosomes
• can be „re-inserted“ into chromosomes
Eukaryotes: nuclear genome size variation (64 000-fold)
Encephalitozoon intestinalis
2.3 Mb (0.0023 Gb)
Paris japonica
149 Gb
A/B compartment-associated regions are on the multi-Mb scale and correlate with either open and expressionactive
chromatin (A compartments) or closed and expression-inactive chromatin (B compartments)
Eukaryotic nuclear genome – nuclear architecture
Interphase chromosomes – chromosome territories
The distribution of chromosomes and genes is nonrandom with some chromosomes
preferentially occupying internal positions and others occupying peripheral positions.
Chromosome territories
Hi-C maps: high-throughput Chromosome Conformation Capture
TAD
Interphase territories consist of loops.
Usually a loop = topologically associated domain (TAD)
= lamina-
associated
domains
(LADs)
= mainly CTCF („insulator“) protein
Promoter (P) of a gene can be pulled
together with an enhancer (E) if they
are not separated by a CTCF
boundary
Cohesins and condensins
(SMC proteins – Structural Maintenance of Chromosomes proteins)
Eukaryotic chromosome
Eukaryotic chromosome
• genomes are variable in size, gene number and proportion of non-coding DNA
• genome size is generally not correlated with organismal complexity (C-value paradox)
• viral genomes cannot replicate without a host, composed of either RNA or DNA
• prokaryotes are typically haploid, usually having a single circular chromosome (nucleoid); eukaryotes
are diploid, DNA is organized into multiple linear chromosomes found in the nucleus
• protein-based supercoiling and packaging of DNA to fit inside a cell; eukaryotes and archaea use
histone proteins, bacteria use different proteins with similar function
• prokaryotic and eukaryotic genomes both contain non-coding DNA (introns, repetitive DNA tandemly
repeated or dispersed = transposable elements)
• prokaryotes: extrachromosomal DNA is maintained as plasmids
• eukaryotes: extrachromosomal DNA within organelles of prokaryotic origin (mitochondria and
chloroplasts) - origin by endosymbiosis; plus eccDNA
• eukaryotic chromosomes: essential structures – centromere and telomeres
Genome structure: brief summary