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A summary of Greg Crowther's research on methylotrophy between 2003 and 2007.
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New insights into the one-carbon metabolic network of Methylobacterium extorquens AM1
Greg Crowther
Dept. of Chemical Engineering
University of WashingtonImage: Dennis Kunkel
Microscopy, Inc.
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
The “Central Dogma” of Biology
DNA RNA Proteins
substrates products
microarrays
proteomics,enzyme
activity assays
flux rates
genomics
metabolomics
My primary interest: metabolic fluxes
DNA RNA Proteins
substrates products
flux rates
Clover leaf print showing Methylobacterium strains. Photo by Amy Springer.
Methylotrophic metabolism
• “methyl” = -CH3, “troph” = growth
• methylotrophy = growth on one-carbon compounds such as methanol (CH3OH)
- some methylotrophs can also grow on multicarbon compounds such as succinate (C4H4O4
2-)
Dissimilation
C3
Assimilation
C=OH
HC-OHH
H
H
CO2
Biomass
ATP NAD(P)H
• Carbon cycling
Methane, a greenhouse gas, is consumed by some methylotrophs.
• Bioremediation
Methylotrophs detoxify many nasty compounds (e.g., chloride-containing organics).
• Biocatalysis
Genetic engineering enables synthesis of useful chemicals (e.g., plastics) from CH3OH.
COCO22
CHCH44
Images: Marina Kalyuzhnaya; appa.asso.fr; ouraycolorado.com
Why is methylotrophy important?
Biocatalysis with methylotrophs
• Bacteria are self-replicating multistage catalysts
• Some methylotrophs make biodegradable plastics from methanol, an inexpensive/abundant/renewable feedstock
• Byproducts of metabolism are usually nontoxic
• Long-term goal: redesign methylotrophs for optimal production of useful chemicals from methanol
A B Ck1
k-1
k2
k-2
MEASURE fluxesvia label tracing
MODEL fluxesmathematically
REDIRECT fluxesvia genetic engineering
Methylotrophs are somewhat widespread in domain Bacteria…
Figure: Hugenholtz et al., J Bacteriol 180: 4765, 1998
… but M. extorquens AM1 is the best-studied species
• 100+ genes for one-carbon metabolism are characterized
• genome is sequenced
• we think we know all of the major metabolic pathways
M. extorquens AM1: a model methylotroph
• pink, rod-shaped -proteobacterium
• natural habitat: surface of leaves
demethylation of pectin produces methanol, which is released
through stomata
Meet Methylobacterium extorquens AM1
Clover leaf print showing Methylobacterium strains. Photo by Amy
Springer.
Metabolic fluxes in M. extorquens AM1
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Dissimilation (CO2 production)
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Direct assimilation pathway(Biomass production)
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Long assimilation pathway(Biomass production)
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Metabolic fluxes in M. extorquens AM1:our view as of 2005
1. The direct assimilation pathway dominates in cells growing on CH3OH.
2. HCHO is the key branch point (Biomass vs. CO2).
3. Formate dehydrogenase (FDH) may not be important?
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Metabolic fluxes in M. extorquens AM1:our view as of 2005
1. The direct assimilation pathway dominates in cells growing on CH3OH.
2. HCHO is the key branch point (Biomass vs. CO2).
3. Formate dehydrogenase (FDH) may not be important?
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Metabolic fluxes in M. extorquens AM1:our view as of 2005
1. The direct assimilation pathway dominates in cells growing on CH3OH.
2. HCHO is the key branch point (Biomass vs. CO2).
3. Formate dehydrogenase (FDH) may not be important?
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
BiomassFDH
The rest of this talk: new insights, 2006-2007
1. The direct assimilation pathway: not important!
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
BiomassFDH
2. Formate dehydrogenase:very important after all!
The direct assimilation pathway
Evidence for this pathway: deuterium assay (Marx et al., PLoS 3:e16, 2005)
GC-MS
extract, derivatize
+2 Serine (D2)+1 Serine (D)
DCOO-
CD2=H4F
CO2
CD2=H4MPT
H4MPT
CD3OD
DCDOH4F
CDH=H4F
90%+ of serine is +2 in CH3OH-grown cells, so the direct pathway appears dominant.
Potential problem with the deuterium assay
If NADPH pool gets contaminated with deuterium, flux through the long pathway will be “counted” as flux through the direct pathway.
GC-MS
extract, derivatize
+2 Serine (D2)+2 Serine (D2)
DCOO-
CD2=H4F
CO2
CD2=H4MPT
H4MPT
CD3OD
DCDOH4F
CD2=H4F NADPD
0
5
10
15
20
25
30
35
40
45
0 5 10 15 20 25 30
Incubation time (s)
+2/
+1
rati
o
If NADPH pool gets contaminated with deuterium, the +2/+1 ratio should increase as incubation time increases (and more deuterium enters the pool).
Conclusion: contamination does occur and might be a problem.
Testing for NADPH contamination
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Other reasons to question the direct pathway
1. If we knock out an enzyme in the long pathway, the cells can’t grow on CH3OH.
Why can’t they just use the direct pathway? HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
X
Other reasons to question the direct pathway
2. We can’t find an enzyme that catalyzes HCHO + H4F.
• Vorholt et al. (J Bacteriol 2000): cell extracts don’t enhance reaction rate
• My data (J Bacteriol 2005): fae2 and fae3, the genes most likely to encode the enzyme (if it exists), can be knocked out without slowing growth on CH3OH
0
0.1
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0 10 20 30
Time (hours)
Cel
l den
sity
(O
D60
0)
wild-type(N=5)
fae2/3(N=5)
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Other reasons to question the direct pathway
3. The nonenzymatic rate constant for HCHO + H4F is much lower than the deuterium and 14C assay data would suggest.
Measure 14C-CO2
Add 14C-CH3OH
Measure 14C-Biomass HCOO-
CH2=H4F
Serine Cycle
CH2=H4MPT
H4MPTHCHOH4F
Estimates of direct pathway flux
Direct pathway flux estimated from 14C-biomass and deuterium assays= (total flux) * (direct flux / total flux) = 0.3 mM/s
14C assay deuterium assay
Is the rate constant for HCHO + H4F high enough to achieve this flux?
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
0
0.02
0.04
0.06
0.08
0.1
0.12
6 6.5 6.7 7
pH
v6, 1
/(m
M*s
)
rate = V6*[H4F]*[HCHO]
• V6 < 0.08 mM-1s-1
• [H4F] < 0.15 mM (Vorholt et al. 1998)
• [HCHO] < 1 mM
rate = (0.08 mM-1s-1)*(0.1 mM)*(0.5 mM) = 0.004 mM/s << 0.3 mM/s
Conclusion: the deuterium assay may greatly overestimate the biomass flux coming from the direct pathway.
Estimates of direct pathway flux
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Testing the direct pathway by studying a long-pathway mutant
Conclusion:
Flux through the direct pathway is insignificant.
If the direct pathway is “real”:
• deuterium assay should detect +2 serine
• 14C assay should detect biomass flux
… NO!
… NO!
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
X
Can the long pathway handle the entire CH3OH flux?
Enzyme activities from literature (converted to mM/s):
1. MDH 1.52. Fae 53. MtdA/MtdB 10-284. Mch 115. Fhc 0.2-1.1
Preliminary conclusion:Enzyme activities appear sufficient for handling all CH3OH.
1
2
3
4
5
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
This is a question for kinetic modeling (in progress).
Maximum total CH3OH intake = 1.4 mM/s
Conclusion on the direct pathway
Flux through the direct assimilation pathway is insignificant.
Key supporting evidence:
• mutations in long pathway prevent growth on CH3OH
• no detectable enzyme activity
• rate constant for HCHO + H4F is very small
• no +2 serine in long-pathway mutant (deuterium assay)
• no biomass flux in long-pathway mutant (14C assay)
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Formate dehydrogenase (FDH)
Background:
Chistoserdova et al. (J Bacteriol 186: 22, 2004) studied three FDH genes, each of which was shown to be functional in vivo.HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
BiomassFDH1-3
Formate dehydrogenase (FDH)
Weird findings for the triple mutant:
• It still grows on CH3OH!
• CO2 production seems unimpaired!
Possible interpretations:
• There is at least one more FDH.
• CO2 is produced “downstream” of the one-carbon network.
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
BiomassFDH1-3X
A fourth formate dehydrogenase!
A gene with sequence homology to other FDHs is upregulated in the triple mutant (E. Skovran’s microarray analysis).
This gene was knocked out along with the other three.
The quadruple mutant cannot grow on CH3OH (L. Chistoserdova), suggesting that there are 4 (and only 4) FDHs.
What do the flux data show?
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
0
2
4
6
8
10
12
14
16
wild-type triplemutant
quadruplemutantC
O2
flu
x, n
mo
l/(m
in*m
L*O
D)
My 14C-CO2 flux data
CO2 production is similar in the
wild-type and triple mutant, but is virtually eliminated in the quadruple mutant.
→ Consistent with the hypothesis that there are 4 and only 4 FDHs.
→ Contradicts the hypothesis that there is significant CO2 production “downstream” of the one-carbon network.
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
HCOO- consumption data (J. Vorholt)
Capacity to consume HCOO- (as measured by 13C NMR spectroscopy), in nmol/(mg*min)
Wild-type AM1 18.5
Quadruple FDH mutant 4.7
Why does the quadruple mutant still consume some HCOO-, since CO2 production is almost 0?
Does this HCOO- go into biomass via the long pathway?
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Biomass flux is not impaired in either the triple or quadruple mutant.
0
0.2
0.4
0.6
0.8
1
1.2
wild-type triplemutant
quadruplemutant
Bio
mas
s fl
ux,
n
mo
l/(m
in*m
L*O
D)
My 14C-Biomass flux data
→ HCOO- consumed by the quadruple mutant goes into biomass via the long pathway.
(This happens in the wild-type and triple mutant as well.)
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Conclusions on formate dehydrogenase
We have now identified all of the major FDHs (4 of them).
CH3OH can enter the serine cycle via the long pathway, but cannot easily be converted to CO2 at that point. Thus cells lacking FDH1-4 cannot grow on CH3OH alone.
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
BiomassFDH1-4
Metabolic fluxes in M. extorquens AM1:our view as of 2007
1. The enzyme-mediated long pathway is the cell’s only significant route for assimilating CH3OH.
2. Therefore HCOO-, not HCHO, is the key branch point.
3. Formate dehydrogenase (FDH) is important after all!
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Metabolic fluxes in M. extorquens AM1:our view as of 2007
1. The enzyme-mediated long pathway is the cell’s only significant route for assimilating CH3OH.
2. Therefore HCOO-, not HCHO, is the key branch point.
3. Formate dehydrogenase (FDH) is important after all!
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Metabolic fluxes in M. extorquens AM1:our view as of 2007
1. The enzyme-mediated long pathway is the cell’s only significant route for assimilating CH3OH.
2. Therefore HCOO-, not HCHO, is the key branch point.
3. Formate dehydrogenase (FDH) is important after all!
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
BiomassFDH1-4
Ongoing and future work
C1 metabolic network
• Since HCOO- is the key branch point, study the regulation of FDHs and FtfL.
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
BiomassFDH1-4
FtfL
Ongoing and future work
HCOO-
CH2=H4F
Serine Cycle
CO2
CH2=H4MPT
H4MPT
CH3OH
HCHOH4F
Biomass
Interaction of C1 and multicarbon networks
• Two versions of the glyoxylate regeneration cycle have been proposed (Korotkova et al. 2002; Albers et al. 2006). Which occurs in AM1?
• How (in terms of enzyme regulation/activity, metabolite levels, and fluxes) do cells transition from succinate (C4H4O4
2-) use to CH3OH use?
Undergrads can do this stuff!
Accessible techniques
• enzyme and metabolite assays
• cloning, transformation, PCR
• growth assays
• mathematical modeling
Preliminary success
• Dan Yates
• Jason Lum
Summary of metabolism research
A B Ck1
k-1
k2
k-2
MEASURE fluxesvia label tracing
MODEL fluxesmathematically
REDIRECT fluxesvia genetic engineering
Long-term goal:
Redesign methylotrophs for optimal production of useful chemicals from methanol.
Lidstrom lab members:
Mila Chistoserdova, Ph.D.
Marina Kalyuzhnaya, Ph.D.
Mary Lidstrom, Ph.D.
Jonathan Miller, M.S.
Betsy Skovran, Ph.D.
Tim Strovas, Ph.D.
Acknowledgments
Former lab members:Kelly FitzGerald, Ph.D. (UW Tech Transfer)Xiaofeng Guo, Ph.D. (Brigham & Women’s)Chris Marx, Ph.D. (Harvard)Steve Van Dien, Ph.D. (Genomatica)Julia Vorholt, Ph.D. (ETH Zurich)
Additional collaborator:George Kosály, Ph.D. (UW Mech Eng)
Funding: Kirschstein NRSA (NIH)
Acknowledgments
The End
Image: hancockpub.lib.in.us