A team of researchers led by scientists from Rutgers University, New Jersey, USA, have brought us a little closer to understanding how the first self-replicating organisms arose on earth. And it didn't need magic supernatural deities to make it happen.
The Rutgers-led team have discovered the structures of proteins that may be responsible for the origins of life in the primordial soup of ancient Earth. They have published their findings, open access, in Science Advances
.
Writing in Rutgers Today, John Cramer explains:
We saw that the metal-binding cores of existing proteins are indeed similar even though the proteins themselves may not be. We also saw that these metal-binding cores are often made up of repeated substructures, kind of like LEGO blocks. Curiously, these blocks were also found in other regions of the proteins, not just metal-binding cores, and in many other proteins that were not considered in our study. Our observation suggests that rearrangements of these little building blocks may have had a single or a small number of common ancestors and given rise to the whole range of proteins and their functions that are currently available -- that is, to life as we know it.
Professor Yana Bromberg, Lead author
Department of Biochemistry and Microbiology
Rutgers University-New Brunswick, New Jersey, USA
The researchers explored how primitive life may have originated on our planet from simple, non-living materials. They asked what properties define life as we know it and concluded that anything alive would have needed to collect and use energy, from sources such as the Sun or hydrothermal vents.
In molecular terms, this would mean that the ability to shuffle electrons was paramount to life. Since the best elements for electron transfer are metals (think standard electrical wires) and most biological activities are carried out by proteins, the researchers decided to explore the combination of the two — that is, proteins that bind metals.
We have very little information about how life arose on this planet, and our work contributes a previously unavailable explanation. This explanation could also potentially contribute to our search for life on other planets and planetary bodies. Our finding of the specific structural building blocks is also possibly relevant for synthetic biology efforts, where scientists aim to construct specifically active proteins anew.
Professor Yana Bromberg.
They compared all existing protein structures that bind metals to establish any common features, based on the premise that these shared features were present in ancestral proteins and were diversified and passed down to create the range of proteins we see today.
Evolution of protein structures entails understanding how new folds arose from previously existing ones, so the researchers designed a computational method that found the vast majority of currently existing metal-binding proteins are somewhat similar regardless of the type of metal they bind to, the organism they come from or the functionality assigned to the protein as a whole.
Structures of central spheres are composed of likely ancient motifs.
(A) Structure of iron-binding Corynebacterium ammoniagenes R2 protein with highlighted motifs. Thick ribbon representations highlight residues within the peptide sphere, and colored segments indicate motifs. Here, pieces of motifs may be outside the sphere, e.g., thin red and green strands while the purple one is completely outside the sphere.
(B) Structural alignments of motifs across all clusters. Clusters 2 and 5 had aligned to the largest number of PDB structures and are, thus, likely the oldest
(A) Structure of iron-binding Corynebacterium ammoniagenes R2 protein with highlighted motifs. Thick ribbon representations highlight residues within the peptide sphere, and colored segments indicate motifs. Here, pieces of motifs may be outside the sphere, e.g., thin red and green strands while the purple one is completely outside the sphere.
(B) Structural alignments of motifs across all clusters. Clusters 2 and 5 had aligned to the largest number of PDB structures and are, thus, likely the oldest
AbstractIn summary, the authors have shown how the earliest biologically active molecules could have been relatively simple peptides (short chains of amino acids) bound to metals. These could have arisen from inorganic origins on the primordial earth, so bridging the gap between inorganic and organic molecules. Fully functional proteins could then have assembled from these simple subunits, and been refined by an evolutionary process.
Biological redox reactions drive planetary biogeochemical cycles. Using a novel, structure-guided sequence analysis of proteins, we explored the patterns of evolution of enzymes responsible for these reactions. Our analysis reveals that the folds that bind transition metal–containing ligands have similar structural geometry and amino acid sequences across the full diversity of proteins. Similarity across folds reflects the availability of key transition metals over geological time and strongly suggests that transition metal–ligand binding had a small number of common peptide origins. We observe that structures central to our similarity network come primarily from oxidoreductases, suggesting that ancestral peptides may have also facilitated electron transfer reactions. Last, our results reveal that the earliest biologically functional peptides were likely available before the assembly of fully functional protein domains over 3.8 billion years ago.
Thus, life is a special, very complex form of motion of matter, but this form did not always exist, and it is not separated from inorganic nature by an impassable abyss; rather, it arose from inorganic nature as a new property in the process of evolution of the world. We must study the history of this evolution if we want to solve the problem of the origin of life. [A. I. Oparin (1)]
INTRODUCTION
How did life appear on our planet? A. Oparin’s 1924 theory of abiotic evolution of carbon-based molecules in a primordial soup (2, 3) suggests a means to the end. However, the evolutionary path beyond the formation of individual molecules remains one of the most profoundly unanswered questions in biology. Although the first self-replicating biological molecules were possibly the catalytic RNA fragments, i.e., ribozymes (4, 5), propagating ribozymes requires energy. Biologically catalyzed redox reactions, i.e., proton-coupled electron transfer, drive the energy requirements of all life on Earth (6). This observation implies that redox reactions must have been among the first (if not the first) functionalities acquired by early life. Hence, understanding the evolution of the biological nanomachinery responsible for the catalysis of redox reactions (, 8) can potentially elucidate the origin of life.
In the Archean Ocean, a small subset of transition metals were soluble and could have facilitated biological electron transfer reactions (9). Although redox RNAs may have also recruited peptide cofactors early on for stability and efficiency of electron transfer (10), their role is trivial compared with proteins. Extant redox enzymes often incorporate metals and metal-containing ligands (11). The original redox-active metal-binding peptide structures would have made an excellent starting point for diversification into a range of functionalities (12–14). That is, if redox-coupled catalysis was among the first functionalities to have evolved, could it have been the origin of elementary metal-binding motifs to the biological functional repertoire? In initial stages of life, a small number of ancient motifs were consistently reused in emergent biological functions/properties (15–19). Multiple interacting peptides may have driven higher-order diversification.
Here, we trace the evolution of metal-binding proteins. The origin(s) of biologically catalyzed redox reactions have been obscured by the marked expansion of protein folds following the Great Oxidation Event approximately 2.35 billion years ago (20, 21). Hence, a phylogeny of these proteins rooted in sequence space is nearly impossible (22). The arrangement of multiple independent peptides into catalytically active structures further complicates any sequence-based evolutionary analysis. Such an analysis would require accounting for the coevolution of nonsequential amino acid sequences that describe structural domains. We therefore chose to focus on elucidating the evolution of these peptides based on their structures.
Evolution of protein structures entails understanding how new folds arose from previously existing ones. Using network analysis, we trace distant relationships between metal-binding proteins. We observed that existing transition metal–binding folds are similar structurally and carry similar sequences within the overlapping structures. This observation suggests that they might have had a single or small number of common ancestors. Moreover, while metal-binding folds in both current redox and nonredox proteins are similar, the central structures are most often derived from redox proteins. These central structures are enriched in prebiotically available amino acids. Our analysis suggests that “simple” folds, found in extant oxidoreductases, may have been incorporated into the complete contemporary range of metal binding and molecular functionality carried out by many enzyme families. Last, we identified small structural motifs that are frequently repeated within our network-central structures. These motifs describe the appearance of central folds and are thus likely at the root of life.
Bromberg, Yana; Aptekmann, Ariel A.; Mahlich, Yannick; Cook, Linda; Senn, Stefan; Miller, Maximillian; Nanda, Vikas; Ferreiro Diego U.; Falkowski, Paul G.
Quantifying structural relationships of metal-binding sites suggests origins of biological electron transfer
Science Advances 8(2); 2022; DOI: 10.1126/sciadv.abj3984
Copyright: © 2022 The authors. Published by American Association for the Advancement of Science
Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
Science has thrown another bucket of truth into the gap creationists have constructed as somewhere to sit their ever-shrinking little god, and as always, no gods were found. The desperate hope of creationists that, unlike every other gap that science has closed over the years, this one will prove to contain a god and depend on magic, is looking ever more forlorn. No doubt, the time is coming when, like every other factual claim in the Bible that science has proven to be wrong, this one will join the ever-growing list of metaphors and allegories.
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