Science1 publisherNot yet confirmed elsewhere2 min readPublished
PII proteins lock a methanogen's nitrogenase into an inactive supercomplex
Six PII complexes hold three units of a methanogen's nitrogenase inactive in the first archaeal nitrogenase structure, solved by cryo-EM. ATP and 2-oxoglutarate free the enzyme and triple its activity in vitro, a switch living cells have yet to confirm.
The Scientist · Science desk
What happened
- The PII complexes inhibit by steric blocking, occupying the space the NifH protein needs in order to associate with the NifDK core.
- The authors read the asymmetric binding of ADP and 2-oxoglutarate in the PII complexes as linking the inhibition to the cell's energy and nitrogen status.
- The structure is of a native complex taken from the methanogen Methanosarcina acetivorans itself.
- The team deposited seven cryo-EM maps across five states, including one supercomplex prepared on strictly anoxic grids.
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Why it matters
- capability With public maps of partial and full assemblies, other labs can design NifI mutations that break specific contacts and test genetically whether the lock governs fixation.
- constraint Models of methanogen nitrogen fixation cannot yet give this switch a size inside cells, because the only effect size on record is a threefold change in a test tube.
- precedent A nitrogenase controlled by assembling into a higher-order oligomer gives structural biologists a reason to look for PII-built assemblies in other nitrogen fixers, bacteria included.
The particle is large. Three NifDK heterotetramers contribute 12 protein chains and six NifI1,2 heterotrimers add 18. That makes 30 chains in all, or two PII complexes per enzyme unit [d1, d2]. The authors' name for the deposited state, (PII-DKKD-PII)3, describes the same layout: a PII complex at each end of each NifDK, repeated three times [11]. They also deposited intermediate forms, among them a NifDK unit with a single PII complex attached, labelled PII-DKKD* [11].
Working from native material [4] was the right call. A complex rebuilt from purified parts shows what proteins can do in a tube. One taken from the organism shows an assembly the cell had already made.
The functional evidence comes from a test tube. Adding 2-oxoglutarate and ATP released the NifI complexes and raised NifDK activity threefold over the enzyme before the additions [8]. The abstract reports that release only in vitro and does not give absolute rates. The authors infer the link to energy and nitrogen status from the molecules found in the PII complexes, ADP and 2-oxoglutarate [7], together with the need for ATP to trigger release [8]. That chemistry fits a sensor reading both signals at once. The thing this doesn't tell you is whether Methanosarcina opens and closes the lock as its nitrogen supply and energy state change.
Nitrogenases reduce atmospheric dinitrogen to ammonia [1]. They have been studied mostly in bacteria, while the architecture and regulation of the archaeal enzymes stayed unknown [2]. PII control of nitrogenase is an older idea. The paper's references include a 2012 review in Microbiology titled "PII signal transduction proteins: pivotal players in post-translational control of nitrogenase activity" [3]. The authors' novelty claim concerns the form the control takes, PII proteins driving the enzyme into a higher-order oligomer, and they scope it to methanogens [9]. Saying bacteria lack such an assembly goes further than the paper does.
The authors hedge their broader point. They wrote that "nitrogenase activity may be modulated through direct assembly into higher-order structures," and named evolution, regulation and biotechnological applications as directions to explore [10].
I think the structural finding is secure. The steric block is seen directly in a complex the cell built [c5, c3], and the models are public for anyone to check [11]. The claim about living cells is a well-supported hypothesis. For now it rests on bound ligands and a threefold release measured in vitro [c6, c7].
What to watch
- A Methanosarcina acetivorans strain whose NifI cannot bind NifDK, and whether its nitrogen fixation still responds to nitrogen and energy status.
- Measurements of how much cellular nitrogenase sits in the supercomplex when cells grow with and without fixed nitrogen.
- Activity of released NifDK compared directly with NifDK that never bound NifI, in absolute rates.