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Bacterial genome structures
”Bacterial”Genome Structures4BIM - AMIG - INSA
M. Bailly-Bechet, from J. Lobry
Universite Claude Bernard Lyon I – France
http://pbil.univ-lyon1.fr/members/mbailly/AMIG.html
1 [email protected] Bacterial genome structures
Bacterial genome structures
Outline
1 Introduction
2 Chromosomes Topology & Counts
3 Genome size
4 Replichores and gene orientation
5 Chirochores
6 G+C content
7 Codon usage
2 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
Introduction
1 Introduction
2 Chromosomes Topology & Counts
3 Genome size
4 Replichores and gene orientation
5 Chirochores
6 G+C content
7 Codon usage
3 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
Phylogenetic position
The three kingdoms
Universal Tree of Life
PseudomonasEscherichia
Halobacterium
Methanobacterium
Desulfurococcus
Halococcus
Methanococcus
Thermoproteus
Thermus
AnacystisBacillus
Physarum
CrithidiaTetrahymena
ProrocentrumSaccharomycesOryza
Homo
Drosophila
Streptomyces
4 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
Phylogenetic position
The three kingdoms: eucarya, archaea and eubacteria
Universal Tree of Life
PseudomonasEscherichia
Halobacterium
Methanobacterium
Desulfurococcus
Halococcus
Methanococcus
Thermoproteus
Thermus
AnacystisBacillus
Physarum
CrithidiaTetrahymena
ProrocentrumSaccharomycesOryza
Homo
Drosophila
Streptomyces
EUCARYA
ARCHAEA
EUBACTERIA
5 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
Phylogenetic position
The three kingdoms: root 1
Universal Tree of Life
PseudomonasEscherichia
Halobacterium
Methanobacterium
Desulfurococcus
Halococcus
Methanococcus
Thermoproteus
Thermus
AnacystisBacillus
Physarum
CrithidiaTetrahymena
ProrocentrumSaccharomycesOryza
Homo
Drosophila
Streptomyces
EUCARYA
Root
PROCARYOTA
ARCHAEA
EUBACTERIA
6 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
Phylogenetic position
The three kingdoms: root 2
Universal Tree of Life
PseudomonasEscherichia
Halobacterium
Methanobacterium
Desulfurococcus
Halococcus
Methanococcus
Thermoproteus
Thermus
AnacystisBacillus
Physarum
CrithidiaTetrahymena
ProrocentrumSaccharomycesOryza
Homo
Drosophila
Streptomyces
EUCARYA
Root ARCHAEA
EUBACTERIA
7 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
Phylogenetic position
The three kingdoms: root 3
Universal Tree of Life
PseudomonasEscherichia
Halobacterium
Methanobacterium
Desulfurococcus
Halococcus
Methanococcus
Thermoproteus
Thermus
AnacystisBacillus
Physarum
CrithidiaTetrahymena
ProrocentrumSaccharomycesOryza
Homo
Drosophila
Streptomyces
EUCARYA
Root
ARCHAEA
EUBACTERIA
8 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
Phylogenetic position
The three kingdoms: no root
Universal Tree of LifeUniversal Tree of Life
PseudomonasEscherichia
Halobacterium
Methanobacterium
Desulfurococcus
Halococcus
Methanococcus
Thermoproteus
Thermus
AnacystisBacillus
Physarum
CrithidiaTetrahymena
ProrocentrumSaccharomycesOryza
Homo
Drosophila
Streptomyces
EUCARYA
ARCHAEA
EUBACTERIA
9 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
General bacterial features
Half of biomass on earth. . . but very few species
Estimate : 5.1030 bacterial cells on Earth
Cell size : ∼ 1µm3 = 10−18m3
Total volume : (17 km)3 ⇒ Half of biomass on Earth
On 1.7 106 known species (Le Guyader & Lecointre, ClassificationPhylogenetique du Vivant)
Bacteria : 5000 species
Insects : 1 000 000 species
Mammals : 4300 species
10 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
General bacterial features
First species classification
An old trend
508Eucaryota0 Bacteria
Aristotle (-384,-322)
11 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
General bacterial features
Small bacteria
Little BacteriaAntony van Leeuwenhoek (1632-1723)
12 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
General bacterial features
0.1 mm = 100 µm
Thickness ≈ 100 µm.
1 Me ≈ 1 m1 Ge ≈ 1 km
13 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
General bacterial features
Bacterial cell size is in µm
14 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
General bacterial features
1 colony ≈ 106 cells
Little Bacteria
1 colony ≈ 106 cells
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Bacterial genome structures
Introduction
General bacterial features
A giant: Thiomargarita namibiensis can measure 750µm
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Bacterial genome structures
Introduction
General bacterial features
Mycoplasma genitalium
The bar is 25 µm long. So you can put(
75025
)3= 27000
mycoplasmae in 1 big Thiomargarita.
17 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
General bacterial features
Few morphological traits
18 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
General bacterial features
Bacterial classification
Classification of Bacteria
• Was based mainly on physiology and growth conditions
E. coli
Most bacteria defy cultivation...
19 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
General bacterial features
Bacterial classification: ”Candidatus Pelagibacterubique”
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Bacterial genome structures
Introduction
General bacterial features
Bacterial classification: Candidatus
Candidatus examples:
”Candidatus Arsenophonus triatominarum”
”Candidatus Arthromitus”
”Candidatus Blochmannia”
”Candidatus Blochmannia floridanus”
”Candidatus Blochmannia herculeanus”
”Candidatus Burkholderia kirkii”
”Candidatus Glomeribacter gigasporarum”
”Candidatus Xiphinematobacter brevicolli”
21 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
Environments
Bacterial environments
Bacteria can live in very diverse environments:
ground (Streptomyces coelicolor )
on plants (Bacillus subtilis)
in water (Anabaena)
in cells (Salmonella enterica)
on the surface of cells (Escherichia coli)
22 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
Environments
Bacterial environments (II)
But also:
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Bacterial genome structures
Introduction
Environments
A big example: Grand Prismatic Spring, Yellowstone,USA
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Bacterial genome structures
Introduction
Public health
Are all bacteria microbes?
Bacteria are often known as ”microbes”, which is partly true.Pathogen organisms can be bacteria, eukaryotic cells (fungi,parasites), or viruses.Bacteria are indeed responsible for:
25 [email protected] Bacterial genome structures
Bacterial genome structures
Introduction
Public health
Are bacteria important for health?
Quizz (try first without Internet!) :
How many human cells do the human body harbour?
How many bacterial cells do the human body harbour?
What is the major DNA in your body?
What happens to organisms with no bacteria?
26 [email protected] Bacterial genome structures
