This document summarizes research on how the nematode C. elegans is affected by different bacterial diets, and the role of interspecies systems biology in understanding this. Studies found that a Comamonas bacterial diet caused different effects on C. elegans' development, fertility and lifespan compared to an E. coli diet. Further work identified vitamin B12 as a key metabolite produced at much higher levels by Comamonas that mimics the effects of this diet. Vitamin B12 was found to regulate C. elegans gene expression and accelerate development via the methionine/SAM cycle, while also mitigating toxicity from propionic acid, another metabolite affected by the bacterial diets. This research demonstrates how studying
10. Superworm: nematode C. elegans
• Hermaphrodite
• ~3 days development
• ~2 week life span
• Lineage known - 959 cells
• Transparent – GFP transgenics
• RNAi, transgenics, mutants
• Well annotated genome
• Feed individual bacterial species
• Model for diet
• Model for microbiota
11. Does bacterial diet affect
C. elegans physiology?
Life history traits
Development
Fertility
Lifespan (aging)
12. E. coli OP50
Standard Laboratory Diet
E. coli HT115
Used for RNAi feeding
Comamonas DA1877
Soil isolate
Measure developmental time, reproduction and lifespan
MacNeil et al., Cell 2013
14. Dietary changes in life-history traits
O
P50
H
T115
A B C
Totalnumberofoffspring
D
A1877
MacNeil et al Figure 1
0
50
100
150
200
250
300
O
P50H
T115D
A1877
0
10
20
30
40
50
60
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80
90
100
1
5
9
13
17
21
25
29
DA1877
OP50
HT115
0
10
20
30
40
50
60
70
80
90
100
Adult
Late L4
Mid-late L4
Mid L4
Early L4
L3
Percenttotalanimals
Percentsurvival
Days after L4
Reproduction
Comamonas: faster development, fewer offspring,
shorter lifespan
Development Lifespan
OP50 = E. coli
DA1877 = Comamonas
MacNeil et al., Cell 2013
15. Dietary changes in gene expression
Nutrigenomics
Microarray expression profiling of worms
fed different bacterial diets
16. 46 272368
Core downregulated
CUB domain
Lectin
GST
Metabolic enzyme
Transporter
Neuropeptide
Worm specific
Transcription
Other
Core upregulated
n=41 n=46
A set of core diet-response genes
MacNeil et al., Cell 2013
Are these changes transcriptional?
17. Core downregulated
CUB domain
Lectin
GST
Metabolic enzyme
Transporter
Neuropeptide
Worm specific
Transcription
Other
n=46
A proxy gene
acdh-1
Repressed >300-fold on Comamonas diet
MacNeil et al., Cell 2013
19. 5 mM
OP50HT115DA1877
A C
exp x25 exp x25
B D
DA1877 (long exp
The dietary response is transcriptional
Pacdh-1::GFP – 1.5 kb promoter
A dietary sensor in living animals
E. coli OP50
Comamonas DA1877
5 mM
OP50HT115DA1877
exp x25 exp x25
B D
DA1877 (long exp
NGM
OP50
MacNeil et al., Cell 2013
21. E. coli OP50
GFP ON
Comamonas DA1877
GFP OFF
Prediction: if Comamonas is nutrient poor,
mixing it with E. coli should alleviate this
Comamonas DA1877
+
E. coli OP50
GFP ? MacNeil et al., Cell 2013
22. The dietary and starvation responses are
distinct
DA1877
OP50*
*Exposure time 1/20
DA1877
1/200
DA1877
1/500
DA1877
1/1000
DA1877
1/10 000
DA1877
1/100 000
DA1877
OP50
1/20 exposure
1/100 DA1877
Also accelerated development and similar gene expression
changes under 1/1000 dilution
23. Small amounts of one diet can have
dramatic effects on gene expression
and physiology, even when mixed with
another diet
24. Unhealthy?+ =
Healthy?+ =
Comamonas DA1877 produces dilutable compound
to which worms respond
Two interpretations with very
different implications
26. ?
?How does C. elegans respond to
E. coli and Comamonas diets?
C. elegans genetics
Which bacterial molecules affect
gene expression and life history traits?
Bacterial genetics
Interspecies systems biology
27. C. elegans target of rapamycin (TOR)
and insulin signaling pathways
are not involved in the response
to Comamonas
MacNeil et al., Cell 2013
28. What are the gene regulatory networks
involved in the response to Comamonas?
The response to Comamonas is transcriptional
Comamonas makes a compound or signal
Transcription factors?
Signaling pathways?
29. What are the gene regulatory networks
involved in the response to Comamonas?
Forward and reverse genetic screens
Activators
146
Worms cannot respond
to Comamonas diet
Repressors
35
Multiple NHRs
(worms have 271!)
30. Most repressors are metabolic
genes, not transcription factors
Watson, MacNeil et al., Cell 2013
35. ? ?
How does C. elegans respond to
E. coli and Comamonas diets?
C. elegans genetics
Which bacterial molecules affect
gene expression and life history traits?
Bacterial genetics
Interspecies systems biology
36. Screen I: E. coli deletion collection
Watson et al., Cell 2014
70 genes
7 genes
38. From mutants to metabolites
Sequence Comamonas genome – identify genes
Map E. coli and Comamonas mutant genes onto metabolic
network using KEGG
Annotate biological processes/pathways
Annotate candidate metabolites –
mutant gene leads to buildup of precursor
and lack of product
39. A bacterial metabolic network implicated
in the C. elegans dietary response
Watson et al., Cell 2014
43. Ado-Cbl and Me-Cbl are two forms
of vitamin B12
Mutation in either
C. elegans gene
interferes with the
response to Comamonas
44. Watson, MacNeil et al., Cell 2013
Vitamin B12 is in the C. elegans
dietary response network
45. Is vitamin B12 the
Comamonas dilutable
molecule?
Mass spectrometry of bacteria
46. Amy Caudy (U Toronto)
Vitamin B12 levels in Comamonas are
orders of magnitude higher than in E. coli
Watson et al., Cell 2014
47. Vitamin B12 pathway status correlates
perfectly with dietary sensor activity
48. Vitamin B12 pathway status correlates
perfectly with dietary sensor activity
49. A metabolic network connecting
the two vitamin B12 pathways
Me-Cbl
Ado-Cbl
Propionyl-CoA
Watson et al., Cell 2014
50. How does the gene regulatory network
respond to Comamonas or E. coli?
51. B12 fails to repress GFP expression in
propionyl-CoA breakdown mutants
52. Vitamin B12 is not sufficient to
drive sensor repression
Model: balance between
Vitamin B12 and propionyl-CoA
Chemical epistasis:
add both B12 and propionic acid
55. So far all experiments with sensor
Does vitamin B12 mimic broad
Changes in C. elegans gene
Expression elicited by
Comamonas diet?
qRT-PCR of 28 Comamonas-response genes
56. Vitamin B12 mimics Comamonas-induced
changes in C. elegans gene expression
Two types of B12-regulated genes
Type 1:
responsive to propionic acid
Type 2:
not responsive to propionic acid
Watson et al., Cell 2014
57. Does vitamin B12 supplementation by Comamonas
Explain its effects on C. elegans life history traits?
58. Vitamin B12 accelerates C. elegans development
B12 reduces fertility
B12 has no effect on lifespan
Watson et al., Cell 2014
59. How does B12 accelerate development?
Watson et al., Cell 2014
60. Vitamin B12 developmental acceleration
occurs via methionine/SAM cycle
Mutants in propionic acid breakdown are accelerated by B12
Mutants in methionine/SAM cycle are not accelerated by B12
Watson et al., Cell 2014
68. Conclusions
C. elegans and bacteria are a
powerful interspecies system:
Nutritional networks
Effects of microbiota (SCFAs/vitamin B12)
69. Acknowledgements
Lesley MacNeil
Emma Watson
Safak Yilmaz
Ashlyn Ritter
Jote Bulcha
Juan Fuxman Bass
Aurian Garcia Gonzales
Gabrielle Giese
Amy Holdorf
Mike Hoy
Rudi Kaushik
Akihiro Mori
Shaleen Shrestha
Alex Tamburino
Efsun Arda
(now at Stanford)
Julie Zhu (UMMS)
Adam Rosebrock
Amy Caudy (U Toronto)
NIDDK
NIGMS
Notas del editor
Surprisingly, the majority of repressors were not TFs. Instead 24 of the 33 genes encode metabolic enzymes found in four specific pathways.
One other interesting realization that we made was that most of the metabolic repressors found in our screens that could reverse the transcriptional diet response in C elegans have human orthologs associated with mendelian diseases. Here is a disease network with all the metabolic repressors from our screens connected to their human orthologs. These human orthologs are connected to their associated inborn metabolic disorders. Most of these orders are managed clinically by dietary intervention, and here on the right are dietary components that patients must avoid (red) or supplement (green), and as you can see these disorders have a lot of similarities in their dietary treatments.