Mycobacterium tuberculosis
Evolution of Functional Diversity
Douglas Young
A new horizon for preventive vaccines against tuberculosis
Madrid 7th May 2014
Field trial of BCG in badgers
Gloucestershire 2005-2009
844 badgers caught and sampled
disease detection by serology
262 captured more than once
were test negative on initial capture
22 incident cases
74% reduction
in seropositive disease
group
no of
badgers
incident
cases
% of total
cases
CI
control
82
14
17.1
(10.8-25.9)
vaccinated
179
8
4.5
(2.4-8.2)
F probability
unvaccinated cubs from vaccinated setts
had a reduced ESAT6/CFP10 IFNg response
0.001
79% reduction
in IFNg conversion
vaccination interrupts onward transmission
Chambers et al. 2011. Proc Biol Sci B. 278:1913-20
Carter et al. 2012. PLoS One 7:e49833
Bovine TB in Ethiopia
A. bovine TB in rural cattle
30000 carcasses screened in abattoirs
1500 lesioned animals, 170 ZN+ cultures
low prevalence 0.5 – 5%
58 M. bovis isolates
8 M. tuberculosis isolates (12%)
B. bovine TB in urban intensive farms
high prevalence > 50%
post-mortem: 67 cultures from 31 animals
67 M. bovis isolates
0 M. tuberculosis isolates
M. tuberculosis can cause disease in
individual animals, but it doesn’t establish
an efficient transmission cycle
Berg et al. 2009. PLoS One 4:e5068
Firdessa et al. 2012. PLoS One 7:e52851
THE CONCEPT
I want to have a vaccine that interrupts transmission:
can I target some layer of species-specific biology
that is required for an effective transmission cycle?
THE MODEL
the ideal vaccine candidate
biology involved in
effective transmission
biology involved in
making a lesion
THE STRATEGY
I don’t have an experimental model for transmission,
so I’m going to try and infer biology by looking at evolution of human isolates
Global phylogeny of M. tuberculosis
Lineage 7
Lineage 4
Lineage 1
Lineage 3
Lineage 5
Lineage 2
Lineage 6
Comas et al. 2013. Nat Genet 45:1176
animal strains
Do toxin-antitoxin modules regulate “persistence”?
transcription higher in Lineage 1
transcription higher in Lineage 2
Rose et al. 2013. Genome Biol Evol 5:1849-62
in vitro transcription profiling reveals strain variation in transcript abundance
but there’s very little evidence of genomic diversity of TA modules
Number of TA modules
0
10
20
30
40
50
60
70
80
M. tuberculosis
M. canettii 60008
M. canettii 70010
Mycobacterium sp. JDM601
M. gastri
M. kansasii
M. xenopi
M. yongonense
M. paratuberculosis
M. smegmatis mc2 155
M. avium
M. marinum
M. abscessus
M. ulcerans
M. phlei
M. hassiacum
Mycobacterium sp. MCS
M. gilvum
M. smegmatis JS623
M. chubuense
blue: chromosome
red: plasmid
TAs and phylogeny
high TA mycobacteria (>10 modules) in red
100
88
M. paratuberculosis
deletion of lon protease
M. yongonense
65
rpoC sequence, GTR+G+I,
Maximum Likelihood
phylogeny, 100 bootstrap
M avium
M. kansasii
76
100
M. gastri
M. ulcerans
79
100
M. marinum
ddn
nitroreductase
ddn
nitroreductase
lactate
dehydrogenase
lon protease
lactate
dehydrogenase
M. canettii 70010
90
100
99
100
ddn
nitroreductase
M. tuberculosis
M. canettii 60008
M. xenopi
Mycobacterium sp. JDM601
62
M. phlei
96
M. hassiacum
M. smegmatis JS623
57
M. chubuense
100
100
M. gilvum
Mycobacterium sp. MCS
100
M. smegmatis MC2 155
M. abscessus
0.02
plasmids
lactate
dehydrogenase
What else is carried on mycobacterial plasmids?
toxin-antitoxin modules
metal ion detox and efflux
cytochrome P450s
adenylate cyclases
diguanylate cyclases
Type VII secretion loci
mce loci
...
organism
adenylate cyclase
domains
M. tuberculosis
16
M. marinum
31
M. ulcerans
15
M. smegmatis mc2 155
7
M. smegmatis JS623
48
ESX locus on pMK12478
MKAN_
chromosome 00155
56%
MKAN_
plasmid 29475
57%
00160
00195
53%
91%
29470
29465
29460
PE
PPE
52%
Mtb Rv1783 Rv1784
eccB5
eccC5
00200
00205
00210
00215
00220
00225
95%
45%
50%
55%
34%
72%
29455
29450
29445
29435
29430
29425
29420
pseudo
94%
45%
48%
57%
31%
72%
Rv1792 Rv1793 Rv1794
Rv1795 Rv1796 Rv1797 Rv1798
esxM
eccD5
esxN
Rv1785 Rv1786 Rv1787 Rv1788 Rv1789 Rv1790 Rv1791
cyp143
PPE25
PE18
29440
PPE26
PPE27
PE19
99% identical sequence in M. yongonense plasmid pMyong1
100% identical sequence in M. parascrofulaceum (plasmid?)
mycP5
eccE5
eccA5
MCE locus on pMYCCH01
transposase
M. chubuense plasmid pMYCCH01
5787
5786
5785
5784
5783
5782
5781
5780
5779
5778
5777
5776
80%
78%
60%
66%
63%
61%
64%
71%
52%
50%
50%
49%
yrbE1A
yrbE1B
mce1A
mce1B
mce1C
mce1D
lprK
mce1F
M. tuberculosis Mce1
Rv0175 Rv0176 Rv0177 Rv0178
5775
mce1R fadD5
5788
transposase
no more horizontal
gene transfer!
M. kansasii
niche isolation?
M. gastri
M. ulcerans
M. marinum
M. canettii 70010
M. tuberculosis
M. canettii 60008
M. xenopi
cobF deletion
Deletion of cobF (vitamin B12) in M. tuberculosis
cobF
M. canettii
deletion in M. tuberculosis
M. tuberculosis
other methyltransferases may
(partially?) compensate
Gopinath et al. 2013. Future Microbiol 8:1405
The Great M. tuberculosis Schism
pyruvate kinase SNP
alanine dehydrogenase frameshift
PhoR SNP
cobL (+MK) deletion (RD9)
more relaxed approach
to host restriction?
increasing
species adaptation?
M. tuberculosis may have evolved
to rely on vitamin B12 provided by the host?
niche adaptation
• bioavailability of B12 in primates versus ruminants?
• effect of diet – vegetarian versus meat-eating?
• gut microbiome?
The optional metabolome of vitamin B12
AMINO ACID
BIOSYTHESIS
MetH
homocysteine
methylmalonate
(MutAB)
MetE
propionyl CoA
methylcitrate
(PrpCD)
methionine
DNA REPLICATION
succinate
deoxyribonucleotide
NrdEF
NrdZ
ribonucleotide
B12-independent
B12-dependent
ENERGY
Lineage 5
Lineage 6
Lineage 4
22 independent
SNPs and frameshifts
predicted to impair
function of MetH
Lineage 2
Lineage 3
reduced reliance on
B12-dependent
pathways?
Lineage 7
Lineage 1
post-Neolithic?
human lung
niche
adaptation
mycobacteria
freely exchanging
flexible functionality
immunological
vomiting
niche
isolation
no turning back
(no horizontal transfer)
industrial remediation
transmission
cycle