Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration

Zachary F. Hallberg, Chi Ho Chan, Todd A. Wright, Philip J. Kranzusch, Kevin W. Doxzen, James J. Park, Daniel R Bond, Ming C. Hammond

Research output: Contribution to journalArticle

Abstract

A newfound signaling pathway employs a GGDEF enzyme with unique activity compared to the majority of homologs associated with bacterial cyclic di-GMP signaling. This system provides a rare opportunity to study how signaling proteins natively gain distinct function. Using genetic knockouts, riboswitch reporters, and RNA-Seq, we show that GacA, the Hypr GGDEF in Geobacter sulfurreducens, specifically regulates cyclic GMP-AMP (3',3'-cGAMP) levels in vivo to stimulate gene expression associated with metal reduction separate from electricity production. To reconcile these in vivo findings with prior in vitro results that showed GacA was promiscuous, we developed a full kinetic model combining experimental data and mathematical modeling to reveal mechanisms that contribute to in vivo specificity. A 1.4 Å-resolution crystal structure of the Geobacter Hypr GGDEF domain was determined to understand the molecular basis for those mechanisms, including key cross-dimer interactions. Together these results demonstrate that specific signaling can result from a promiscuous enzyme.

Original languageEnglish (US)
JournaleLife
Volume8
DOIs
StatePublished - Apr 9 2019

Fingerprint

Geobacter
Respiration
Riboswitch
Metals
Electricity
Enzymes
Theoretical Models
RNA
Gene Expression
Gene expression
Dimers
Proteins
Crystal structure
Kinetics
cyclic guanosine monophosphate-adenosine monophosphate

Keywords

  • E. coli
  • Geobacter sulfurreducens
  • Hypr GGDEF
  • biochemistry
  • cGAMP signaling
  • chemical biology
  • cyclic di-GMP
  • cyclic dinucleotide
  • infectious disease
  • microbiology
  • riboswitch

Cite this

Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration. / Hallberg, Zachary F.; Chan, Chi Ho; Wright, Todd A.; Kranzusch, Philip J.; Doxzen, Kevin W.; Park, James J.; Bond, Daniel R; Hammond, Ming C.

In: eLife, Vol. 8, 09.04.2019.

Research output: Contribution to journalArticle

Hallberg, Zachary F. ; Chan, Chi Ho ; Wright, Todd A. ; Kranzusch, Philip J. ; Doxzen, Kevin W. ; Park, James J. ; Bond, Daniel R ; Hammond, Ming C. / Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration. In: eLife. 2019 ; Vol. 8.
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