On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes

Ancestry of RNA/RNA interaction regions within segmented ribosomes

The ribosome is the universally conserved ribozyme that translates DNA coded instructions into proteins with the assistance of other RNA molecules, including transfer and messenger RNAs. Of particular interest is the segmentation phenomena, which is found in trypanosomatids and other protists. In these organisms, the large subunit ribosomal RNA is assembled from multiple smaller RNAs. This phenomenon posits several challenges to the folding and stabilization of such ribosomes to retain functionality and efficiency. In earlier studies, RNA/protein interactions were suggested to fully compensate for the fragmentation. Recently, several conserved RNA/RNA interaction regions were described in the cryo-EM structures of segmented ribosomes from trypanosomatids. These regions also seemed to aid in the folding and stabilization of such ribosomes, even before the ribosomal proteins start their association. In the present study, the existence of conserved RNA/RNA interaction regions shared between trypanosomatid and Euglena gracilis segmented ribosomes was confirmed, despite differences in segmentation patterns. Analysis of the crystallographic structures of unsegmented ribosomes from other Eukaryotes, Bacteria, and Archaea allowed us to estimate the relative age of highly conserved RNA/RNA interaction regions. These results strongly suggest that common interaction regions likely date far back into the ribosomes of the last common ancestor. Results also revealed that single hydrogen bonds are overwhelmingly facilitated by the 2'OH, a distinctive RNA feature. This supports the notion that RNA predates DNA and places some constraints on alternative nucleic acids proposals.

A Retro-Aldol Reaction Prompted the Evolvability of a Phosphotransferase System for the Utilization of a Rare Sugar

The evolution of the bacterial phosphotransferase system (PTS) linked to glycolysis is dependent on the availability of naturally occurring sugars. Although bacteria exhibit sugar specificities based on carbon catabolite repression, the acquisition and evolvability of the cellular sugar preference under conditions that are suboptimal for growth (e.g., environments rich in a rare sugar) are poorly understood. Here, we generated Escherichia coli mutants via a retro-aldol reaction to obtain progeny that can utilize the rare sugar d-tagatose. We detected a minimal set of adaptive mutations in the d-fructose-specific PTS to render E. coli capable of d-tagatose utilization. These E. coli mutant strains lost the tight regulation of both the d-fructose and N-acetyl-galactosamine PTS following deletions in the binding site of the catabolite repressor/activator protein (Cra) upstream from the fruBKA operon and in the agaR gene, encoding the N-acetylgalactosamine (GalNAc) repressor, respectively. Acquired d-tagatose catabolic pathways then underwent fine-tuned adaptation via an additional mutation in 1-phosphofructose kinase to adjust metabolic fluxes. We determined the evolutionary trajectory at the molecular level, providing insights into the mechanism by which enteric bacteria evolved a substrate preference for the rare sugar d-tagatose. Furthermore, the engineered E. coli mutant strain could serve as an in vivo high-throughput screening platform for engineering non-phosphosugar isomerases to produce rare sugars. IMPORTANCE Microorganisms generate energy through glycolysis, which might have preceded a rapid burst of evolution, including the evolution of cellular respiration in the primordial biosphere. However, little is known about the evolvability of cellular sugar preferences. Here, we generated Escherichia coli mutants via a retro-aldol reaction to obtain progeny that can utilize the rare sugar d-tagatose. Consequently, we identified mutational hot spots and determined the evolutionary trajectory at the molecular level. This provided insights into the mechanism by which enteric bacteria evolved substrate preferences for various sugars, accounting for the widespread occurrence of these taxa. Furthermore, the adaptive laboratory evolution-induced cellular chassis could serve as an in vivo high-throughput screening platform for engineering tailor-made non-phosphorylated sugar isomerases to produce low-calorigenic rare sugars showing antidiabetic, antihyperglycemic, and antitumor activities.

Purine catabolism by enterobacteria

Purines are abundant among organic nitrogen sources and have high nitrogen content. Accordingly, microorganisms have evolved different pathways to catabolize purines and their metabolic products such as allantoin. Enterobacteria from the genera Escherichia, Klebsiella and Salmonella have three such pathways. First, the HPX pathway, found in the genus Klebsiella and very close relatives, catabolizes purines during aerobic growth, extracting all four nitrogen atoms in the process. This pathway includes several known or predicted enzymes not previously observed in other purine catabolic pathways. Second, the ALL pathway, found in strains from all three species, catabolizes allantoin during anaerobic growth in a branched pathway that also includes glyoxylate assimilation. This allantoin fermentation pathway originally was characterized in a gram-positive bacterium, and therefore is widespread. Third, the XDH pathway, found in strains from Escherichia and Klebsiella spp., at present is ill-defined but likely includes enzymes to catabolize purines during anaerobic growth. Critically, this pathway may include an enzyme system for anaerobic urate catabolism, a phenomenon not previously described. Documenting such a pathway would overturn the long-held assumption that urate catabolism requires oxygen. Overall, this broad capability for purine catabolism during either aerobic or anaerobic growth suggests that purines and their metabolites contribute to enterobacterial fitness in a variety of environments.

Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges

Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits. We argue that LGT poses insurmountable challenges for detailed and rich in details reconstructions and propose, instead, a middle-ground position with the reconstruction of a slim LCA based on traits under strong pressures of Negative Natural Selection, and for the need of consilience with evidence from organismal biology and geochemistry. We defend a cautionary perspective that goes beyond the statistical analysis of gene similarities and assumes the broader consequences of evolving empirical data and epistemic pluralism in the reconstruction of early life.

Protometabolic Reduction of NAD+ with α-Keto Acids

Deciphering the origins of the chemistry that supports life has frequently centered on determining prebiotically plausible paths that produce the molecules found in biology. What has been less investigated is how the energy released from the breakdown of foodstuff is coupled to the persistence of the protocell. To gain better insight into how such coupled chemistry could have emerged prebiotically, we probed the reactivity of the ribodinucleotide NAD⁺ with small organic molecules that were previously identified as potential constituents of protometabolism. We find that NAD⁺ is readily reduced nonenzymatically by α-keto acids, such as pyruvate and oxaloacetate, during oxidative decarboxylation. In the presence of FAD and a terminal electron acceptor, the consumption of α-keto acids by NAD⁺ initiates a plausible prebiotic electron transport chain. The observed reactivity suggests that components of the RNA world were capable of initiating the chemistry needed to capture the energy released from catabolism to drive anabolism.

An appeal to magic? The discovery of a non-enzymatic metabolism and its role in the origins of life

Until recently, prebiotic precursors to metabolic pathways were not known. In parallel, chemistry achieved the synthesis of amino acids and nucleotides only in reaction sequences that do not resemble metabolic pathways, and by using condition step changes, incompatible with enzyme evolution. As a consequence, it was frequently assumed that the topological organisation of the metabolic pathway has formed in a Darwinian process. The situation changed with the discovery of a non-enzymatic glycolysis and pentose phosphate pathway. The suite of metabolism-like reactions is promoted by a metal cation, (Fe(II)), abundant in Archean sediment, and requires no condition step changes. Knowledge about metabolism-like reaction topologies has accumulated since, and supports non-enzymatic origins of gluconeogenesis, the S-adenosylmethionine pathway, the Krebs cycle, as well as CO2 fixation. It now feels that it is only a question of time until essential parts of metabolism can be replicated non-enzymatically. Here, I review the 'accidents' that led to the discovery of the non-enzymatic glycolysis, and on the example of a chemical network based on hydrogen cyanide, I provide reasoning why metabolism-like non-enzymatic reaction topologies may have been missed for a long time. Finally, I discuss that, on the basis of non-enzymatic metabolism-like networks, one can elaborate stepwise scenarios for the origin of metabolic pathways, a situation that increasingly renders the origins of metabolism a tangible problem.