Methylobacterium extorquens:Metabolic superstar

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Meet Methylobacterium extorquens

• methylotroph: grows on one-carbon compounds

e.g., methanol (CH3OH)

• also grows on multicarbon compounds

e.g., succinate (C4H4O42-)

• natural habitat: leaf surfaces

• pink!

Why is M. extorquens a “metabolic superstar”?

• Talented

- ability to use C1 fuel is unusual

• Versatile

- can switch between C1, C2, C3, and C4 fuels

• Full of potential

- may become a model system for understanding metabolic transitions in other organisms

- may become genetically engineered to convert methanol into valuable materials (e.g., plastics)

The M. extorquens genome is sequenced.What more do we need to know?

Genome = all the genes

“Central dogma” of biology:

DNA RNA Proteins

substrates products

The genes indicate a cell’s metabolic potential…(Which reactions can occur?)

…Genes alone tell us littleabout metabolic transitions

DNA RNA Proteins

substrates products

…Genes alone tell us littleabout metabolic transitions

DNA RNA Proteins

newsubstrates

newproducts

The big question

How does M. extorquens sense changes in fuel availability and respond appropriately?

An inappropriate response might lead to a buildup of formaldehyde, which is toxic.

methanol(CH3OH)

formaldehyde(HCHO)

Multiple measurements forunderstanding metabolic transitions

DNA RNA Proteins

substrates products

microarrays

proteomics,enzyme

activity assays

flux rates

genomics

metabolomics

My focus: flux ratesthrough biochemical pathways

HCOOH

CH2=H4FSerine

CO2

CH2=H4MPT

H4MPT

CH3OH

HCHOCH3OH

HCHOH4F

Biomass

OUTSIDE OF CELL

INSIDE OF CELL

14C assay measuresbiomass and CO2 production

HCOOH

CH2=H4FSerine

CO2

CH2=H4MPT

H4MPT

CH3OH

HCHOCH3OH

HCHOH4F

Biomass

(radioactive)Add

C.J. Marx et al., PLoS Biol 3(2): e16, 2005

OUTSIDE OF CELL

INSIDE OF CELL

Deuterium assay measures “short” and “long” routes of biomass production

DCOOH CO2

CD2=H4MPT

H4MPT

CD3OD

DCDOCD3OD

DCDOH4F

Add

CD2=H4FCDH=H4F

Serine (D2)

Serine (D)

Biomass

C.J. Marx et al., PLoS Biol 3(2): e16, 2005

OUTSIDE OF CELL

INSIDE OF CELL

Conclusion(adapted from A.L. Webber & T. Rice [1971])

I don’t know how they do it –Switching fuels like a hybrid.And when they change, They really change.If the levels of succinateStart to fall,They’ll shift to methanol…

Yes, now we have their genome,But I don’t see what it tells us.It’s the genes; it’s just the genes.And the genes don’t changeWhen the fuels do,So how do the cells respond?We need more clues!

Measure pathway flux;Measure RNA;Check metabolites;Do enzyme assays!Hey, M. extorquens, soon we’ll knowWhat you’re all about…

Don’t you think it’s rather daunting?All this work, all this data.No other group would take this on.So we’ll be first to get resultsAnd get our grant renewedWhen it’s reviewed.They’ll think we’re shrewd…Or else we’re screwed.

I’d like to thank the Academy…

Current Lidstrom lab members/collaboratorsGundula Bosch, Ph.D.Mila Chistoserdova, Ph.D.Xiaofeng GuoMarina Kalyuzhnaya, Ph.D.George Kosaly, Ph.D.Mary Lidstrom, Ph.D.Jonathan MillerBetsy Skovran, Ph.D.Tim StrovasDan Yates

Former lab membersKelly FitzGerald, Ph.D.Chris Marx, Ph.D.Yoko Okubo, Ph.D. Steve Van Dien, Ph.D. Julia Vorholt, Ph.D.

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The End