Life Sciences Division

Green chemistry: getting close and personal with an enzyme synthesizing heavy-metal traps

CEA

Researchers from the Institute of Environmental Biology and Biotechnology’s joint research unit UMR6191 (CEA/CNRS/Aix-Marseille 2 University) at Cadarache working with the INRA’s Montpellier centre have just uncovered the mechanisms of action of a plant enzyme that regulates nicotianamine synthesis. Nicotianamine is able to bind heavy metals, which are widespread pollutants responsible for soil contamination and therefore a very real environmental hazard. These findings, which have been published online in the Proceedings of the National Academy of Sciences of the USA, could make it possible to optimize the development of in-plant heavy-metal biosensors and thus create a new soil remediation tool.

Nicotianamine (NA) is a tiny molecule that is ubiquitous in plants and that plays a role in regulating the concentrations of a wide range of essential metal elements, including iron, zinc and copper. It plays a key role in charging, mobilizing and distributing the ionic form of these metals in different parts of plants. NA is synthesized by the plant enzyme nicotianamine synthase (NAS), which is extremely difficult to produce and purify, making functional analysis of NAS a delicate and highly complex task.  In order to sidestep this difficulty, the iBEB-INRA team analyzed the various archaea [1] genomes sequenced to date. When looking at Methanothermobacter thermautotrophicus, they identified a gene encoding a NAS enzyme that was the mirror image of the NAs enzyme in plants, which they then managed to purify and determine the 3D structure. This archaea enzyme is able to synthesize a compound called thermo-nicotianamine that is very similar to plant-produced nicotianamine. Although the metal-binding properties of this new molecule have yet to be determined, it could still offer promising potential for biotech applications.

3D structure of the NAS from Methanothermobacter thermautotrophicus.

The thermo-nicotianamine is localized inside a cavity at the heart of the enzyme


In order to gain a deeper understanding of the mechanisms of action of NAS, the research team determined 3D structures of the enzyme at several points in the reaction to track and follow NA production step-by-step. This revealed that NA manufacture co-opts three molecules of a particular substrate: S-adenosylmethionine. Analysis of the five 3D structures obtained enabled the team to go deep into the heart of this protein and explore its functions: the active (reactive) site is embedded deep in a cavity at the enzyme core. When open, this cavity only lets one substrate molecule in at a time. The first substrate penetrates the cavity and binds to a first site at the cavity entrance.  As the second substrate molecule enters the cavity, it shifts the first substrate molecule towards a second binding site embedded deeper inside, enabling the two molecules to form a bond. The same thing happens when the third substrate molecule enters, dislodging the pair already formed to the bottom of the cavity and enabling all three molecules to finally bond. The polymerization reaction then stops, as there is no space left in the active site.

These findings open up critical insight into the thus far unknown mechanism underpinning NA synthesis in plants, and could enable the optimization of heavy-metal biosensors. The use of plants for environmental remediation is a flourishing research field, notably because it offers a safe ecological solution to the environmental threats posed by heavy metals.

[1] Archaea. Biologists divided life into three domains: eukaryotes (cells that posses a nucleus), bacteria, and archaea. Archaea are microorganisms that generally thrive in harsh environments.