Life Sciences Division

The origins of life: French researchers review ancestral enzymes for Nature

CEA

Since 1995, researchers at the Protein Crystallogenesis and Crystallography Laboratory (Institute of Structural Biology, CEA/CNRS/UJF Grenoble) have been focused on a class of proteins that are able to metabolize various gases. They are called metalloenzymes. Could deeper insight into metalloenzymes provide deeper insight into the origins of life on Earth? Is there room for developing biotech applications by mimicking metalloenzyme functions? These are questions being addressed by researchers the world over. Juan C. Fontecilla-Camps and his team have helped make strides forward by providing insight into structure-function relationships in many of these enzymes. This has gained them a solid international reputation cemented in the fact that they have authored 3 of the top 11 most-cited papers in the field. This extensive expertise has now been acknowledged by leading science journal Nature, which has invited the team to author a review on the state-of-the-art for its Insight column. Published online on August 12, this review describes several enzymes that have the ability to metabolize gases including hydrogen (H2), carbon monoxide (CO), carbon dioxide (CO2), nitrogen (N2) and methane (CH4), going on to discuss the implications of these results before attempting to define the link tying these proteins to abiogenesis. The nature.com website also features a podcast tie-in.

Short-form summary

The most popular hypothesis for explaining the origins of life on Earth, termed autotrophic [1], posits that primordial metabolism evolved on mineral surfaces comprising iron and sulphur under reductive conditions [2]. The assertion is that reactions deploying iron sulphides generated hydrogen, which then combined with the carbon dioxide present in the atmosphere to form organic molecules. As the Earth was developing, somewhere around 4.6 to 3.5 billion years ago, the atmosphere probably contained a high content of gases like H2, CO and CO2, whereas the oceans, which contained pockets of very hot water, were relatively abundant in metal ions such as Fe2+ and Ni2+.
Since photosynthetic organisms did not appear until 2.2 billion years ago, the Earth’s biotope had to prosper in the absence of oxygen, and independently of solar energy. Current thought is that the first organisms used H2 as energy source and CO2 as carbon source.

Similar environments can be found today in a number of thermal springs in the deepest-bedded ocean seafloors, such as ‘black smoker’ sea vents [3], or the digestive tract of certain animals. There are organisms today that are capable of surviving these conditions, largely through the energy gleaned from metalloenzymes. Looking at these enzymes, what do we know about their structure, complexity and mechanism of action? Combining spectroscopy, X-ray crystallography, and chemical and computer modelling has made it possible to characterize certain aspects of the nature and function of these enzymes. Working from a handful of extensively-studied examples, the paper outlines and discusses the key points in current state-of-the-art knowledge, and looks ahead at perspectives for i) furthering insight into the origins of life on Earth and ii) designing potential biotech applications.

The review is drafted on a six-section backbone providing different standpoints for discussion on current knowledge on the structure and synthesis of these enzymes:

• Active sites: The active site of an enzyme is the site hosting the reaction that the enzyme catalyzes[4]. The active sites of the metalloenzymes are now known and fairly well characterized. This spot-review section compares and contrasts their structural features.
• Catalysis: Working from experimental data and theoretical models and combined real data with hypotheses, this section focuses in on the potential mechanisms of catalysis underpinning each of the seven metalloproteins outlined in the review.
• Structure and tunnels: This section compiles the data available on enzyme structure. Analysis reveals that these metalloenzymes present varying degrees of structural complexity, ranging from monomeric structures that are formed of only a single base unit or peptide chain through to complex multimeric structures built of several different monomers. The structure of these enzymes features tunnels enabling gases into and/or out of the active site. This section overviews current knowledge on the mechanisms and rates of in-tunnel gas diffusion and how they are regulated by changes in protein structure.
• Active-sites biosynthesis: The condition-sets governing the in-protein synthesis and assembly of active sites also appear to differ between different enzymes. Identifying the various process steps underpinning active site biosynthesis would not only provide deeper insight into the history of evolution but also open up development perspectives for biotech applications.
• Synthesis of small molecule analogs[5]: This section details research designed to synthesize compounds replicating the properties of the active sites of these metalloenzymes, in order to unlock possibilities for developing potential biotechnology applications. To illustrate the potential, hydrogenases engineered to use nickel or iron instead of the rare and expensive platinum would be of major interest for improving industrial hydrogen production system to meet increasing societally-driven demand.

• Perspectives for the future: Now that the majority of metalloenzyme active sites have been characterized, the next challenges will be to characterize the structure of the reaction intermediates as a step towards refining our models of the mechanism of action of enzymes, and to learn how active-site biosynthesis occurs. Each step forward takes us closer to understanding the origins of life on Earth.

3D structures of the enzymes explored in depth in the review

Notes:

1. An autotroph is an organism that has the ability to produce organic matter from inorganic matter, in contrast to a heterotroph which has to absorb pre-synthesized organic matter.

2. Chemical conditions that promote electron gain.

3. Black smoker: a type of undersea geyser found along ocean ridges, and through which water surges up from below the Earth’s crust and into the ocean water. These waters appear black as they contain black-coloured iron and manganese salts.

4. Catalysis is the action of a substance that increases the rate of a chemical reaction.

5. Analog: molecule possessing the same structural and functional properties as the molecule-of-interest.