Genes and genomes

1
Lecture 2

• Genes and genomes
• Pathogenicity islands
• Organellar genomes

2
Gene
The physical unit of heredity. The unit of
inheritance that occupies a specific locus on a
chromosome, the existence of which can be
confirmed by the occurrence of different allelic
forms. The set of DNA sequences (exons) that
are required to produce a single polypeptide or
functional RNA. The Dictionary of Cell and
Molecular Biology http//www.mblab.gla.ac.uk/juli
an/Dict.html
3
Many ways to view a genome
genome structure GC-content repeats genome
rearrangement coding regions gene
content orthologs and paralogs synteny noncodin
g regions regulatory elements
4
DNA content and phylogeny
Base pairs per haploid genome 1-20 x 103 5-200 x
103 0.6-7 x 106 1-3 x 107 1-80 x 109 2-4 x
109 0.3-100 x 109
Species RNA virus DNA virus Bacteria Fungi Amphib
ia Mammals Flowering plants
of genes 1-20 5-300 500-5000 6000 ??? lt50,000
????
5
The human genome
6
Orthologs and paralogs
7
Orthologs and paralogs II
8
Gene families
Genes in B. subtilis
9
Gene classes
Functional category MLEP MTB virulence,
detoxification, adaptation 38 79 lipid
metabolism 79 233 information pathways
158 229 cell wall and cell
processes 329 710 stable RNAs
45 ??? insertion seqs and phages
3 149 PE/PPE 10 170 intermediary
metabolism and respiration
426 895 regulatory proteins
58 191 conserved hypotheticals 366
1041 unknown 136 280
10
Evolution of genome size
Ancestral genome approx. 4 Mb
The a-proteobacteria
11
Concept of essential genes vs. minimal genome

• Both concepts are situationally defined
• Essential genes - knock out one gene at a time
  and ask if organism survives
• Minimal genome number of genes considered
  essential for organisms to survive

Mycoplasma genitalium
12
What really are essential genes?

• Clouded by functional redundancy, which has been
  proposed to under predict essential genes
• E. coli 134 essential genes now 245
• M. genitalium only 480 genes
• 256 essential genes now 382

Csaba et al. 2006. Nature 440667 Glass et al.
2006. PNAS 103425
13
How much genetic diversity within a species?
M. tuberculosis 2 sequenced strains one bp
change/2500 bp 74 large sequence polymorphisms
(insertion/deletion). H. pylori -- At least 22
of genes are missing in any one strain. S.
agalactiae 8 sequenced strains With each new
strain -33 new genes Concept of Pan-genome
14
Definitions

• Pan-genome global gene repertoire of a
  bacterial species
• Core genome Dispensable Genome
• Core genome genes shared by all strains of the
  same species
• Dispensable genome consisting of partially
  shared and strain-specific genes, i.e. genes
  present in some but not all of the same species

15
The Open Pan Genome

• Group B strep
• Core genome -1806 genes
• Dispensable genome 906 genes
• with each genome sequenced 33 new genes
• S. pyogenes - 5 strains sequenced
• With each genome sequenced 27 new genes
• E. coli Strains 7 sequenced
• Core genome 2,865 genes
• Each new genome sequenced 441 new genes

Tettelin et al. 2005. PNAS 10213950/ Chen et al
2006 PNAS 1035977
16
The Closed Pan-Genome

• Bacillus anthracis
• Number of specific genes added to Pan-genome
  converged to 0 after the addition of a fourth
  genome
• Four genome sequences are sufficient to
  characterize species
• Mycobacterium tuberculosis
• Chlamydia trachomatis

17
Genetic diversity between species
18
Genomes, Pathogenicity Islands, and Virulence
Genomes consist (mostly) of core
sequences homogenous G-C content codon
usage. encode housekeeping genes, rRNAs,
etc. Genomic islands different G-C content
codon usage. acquired by horizontal gene
transfer. often mobile. encode accessory
functions. 17 of the E. coli K-12 genome.
19
Pathogenicity Islands
Are a subset of genome islands found in a wide
variety of bacterial pathogens 10 - 200
kb missing from related non-pathogens (e.g. E.
coli) often different G-C content codon
usage often mobile (spread easily) often
associated w/ tRNA loci encode functions
necessary for pathogenesis
20
A model pathogenicity island
Annu. Rev. Microbiol. 2000. 54641-679.
PATHOGENICITY ISLANDS AND THE EVOLUTION OF
MICROBES, Jörg Hacker, James B. Kaper
21
Some virulence factors on pathogenicity islands
Adhesins Toxins Iron uptake systems Invasins,
modulins, effectors Type III secretion
systems Type IV secretion systems
22
Adhesins mediate bacterial attachment
Organism UPEC EPEC/EHEC V. cholera
Adhesin P fimbrae intimin toxin co-regulated pilus
(TCP)
Binds uroepithelial cells intestinal
epithelia bacteria
23
PAI Toxins
Pore-forming toxins (cholera diptheria
etc.) Proteases, lipases Enterotoxins (cause
fluid accumulation, diarrhea)
24
Iron uptake systems
All living systems need some iron. Bacteria use
small iron-avid compounds called
siderophores. Systems are shared by pathogens and
non-pathogens. Iron in vivo -- 10-18 M Human
iron binding proteins Kd 10-18 M Bacterial
siderophores -- 10-23 M to 10-50 M
25
Invasins, modulins, effectors
Mediate bacterial entry into cells and/or host
activity. At least 5 in Salmonella SPI-1 --
cell invasion and apoptosis SPI-2 --
intracellular growth SPI-3/4 -- intramacrophage
survival SPI-5 -- inflammation fluid
secretion The combinations help determine the
properties of different strains.
26
Secretion systems
5 different systems. All associated with
pathogenesis. Especially type III and IV.
27
Type III Secretion Systems

• Injectisome permits bacteria docked at the cell
  membrane to deliver effector proteins across the
  membrane
• Various families of injectisomes (e.g. SP2-2,
  SPI-2, YSC)
• Found in a wide variety of pathogens
• Chlamydia trachomatis, Yersinia pestis,
  Pseudomonas aeruginosa, Bordatella pertussis,
  Salmonella enterica, Vibrio parahemolyticus,
  Yersinia enterocolitica,

28
Type III Secretion

• Over 100 different effector proteins
• Roles of effector proteins
• Invasion of cells
• Inhibition of phagocytosis
• Down regulation of pro inflammatory responses
• Induction of apoptosis
• Prevention of autophagy
• Modulation of intracellular trafficking

29
Targets of effector proteins

• Small GTP binding proteins
• Mitogen-activated protein kinases
• I?B
• phosphoinositides

30
Type IV

• Delivery of bacterial effector proteins
• Mediate horizontal gene transfer
• Contribute to genome plasticity
• Evolution of infectious pathogens
• Dissemination of antibiotic resistance and other
  virulent factors
• Discovered a T4SS responsible for formation of
  conjugative pilus and conjugative transfer of a
  genomic island (Juhas et al. 2006. J. Bacteriol)

31
Stages in evolution
of PAI
Gal-Mor and Finlay. 2006. Cell. Microbiol. 31707
32
Organelle Genomes
Probably arose through endosymbiosis of
bacteria Mitochondria -- respiration. Chloropla
st -- photosynthesis in plants/algae. Plastid --
??? in the Apicomplexa. -- Protozoan
parasites responsible for malaria, toxoplasmosis,
etc.
33
Mitochondrial DNAs

• Mitochondria contain multiple mtDNA molecules.
• Genes in mtDNA encode rRNAs, tRNAs, and proteins
  of the mt respiratory chain.
• apcytochrome B (CYb) and cytochrome c
  oxidase I (COI)
• The size and coding capacity of mtDNA varies
  considerably in different organisms.
• The products of mitochondrial genes are not
  exported.
• Mutations in mtDNA cause several genetic diseases
  in humans.
• Mitochondrial inhereitance is distinct from
  nuclear.

34
Human mtDNA
16,569 bp
35
Mitochondrial diseases in humans
36
Mitochondrial diseases in humans
Respiratory disorders Parkinsons
disease Alzheimers disease Bipolar disorder
37
Parasite mtDNAs can be very varied
Trypanosomes Plasmodium
38
Trypanosome mtDNAs - the kinetoplast
Maxicircles 20 - 40 kb. 50 copies per
cell. carry normal mt genes, but
mutated. Minicircles 0.6 - 2.5 kb. 5000 -
10,000 copies per cell. carry no obvious genes
(gRNAs) Minicircles and maxicircles are
catenated together...
39
kDNA
40
Many trypanosme mtRNAs are edited
Mistakes in maxicircle RNAs are fixed
post-transcriptionally. The information is found
on minicircle guide RNAs (gRNAs). Our definition
of a gene must be altered to accommodate this
process. More on this from Jean Feagin.
41
MtDNA of the Apicomplexans
Only 6 kb in Plasmodium falciparum (smallest
known). Linear molecules. Highly conserved
sequence. Coding regions abut one
another. Studied by Jean Feagin (SBRI)...
42
The MtDNA of P. falciparum
Presumed rRNA
LSU
SSU
500 nt
43
The Plastid of the Apicomplexa
A unique organelle with its own genome. Homology
with chloroplast DNAs, but no photosynthetic
genes. 35 kb circle in Plasmodium
falciparum. Function is unknown.