Excretion of L-xylulose is the hallmark of pentosuria, the fourth of Garrod’s inborn errors of metabolism, yet the molecular basis for L-xylulose formation remains unknown. Here, by projecting coevolutionary data for 511,114 orthogroups across 1,929 eukaryotic genomes onto metabolic maps, we screen for unmapped genes in human metabolism. Among these, we show that the DUF1907 domain of C11orf54 catalyzes formation of L-xylulose by establishing a zinc-coordinated Michaelis complex with β-keto-L-gulonate (BKG). The identification of BKG decarboxylase completes the pentose pathway, in which pentose sugars are produced by decarboxylation of nonphosphorylated hexose precursors. The pathway was present in the unicellular ancestor of animals and is conserved in all deuterostomes, in contrast to the alternative L-ascorbate (vitamin C) biosynthesis pathway. An increased flux toward pentoses may have represented an evolutionary tradeoff, favoring energy metabolism and redox cofactor balance at the expense of ascorbate biosynthesis in organisms, such as humans and other Haplorhini primates, where dietary vitamin C intake prevents scurvy.

Over the past decade, long non-coding RNAs (lncRNAs) have been recognized as key players in gene regulation, influencing genome organization and expression. The locus-specific binding of these non-coding RNAs (ncRNAs) to DNA involves either a non-covalent interaction with DNA-bound proteins or a direct sequence-specific interaction through the formation of RNA:DNA triplexes. In an effort to develop a novel strategy for characterizing a triple-helix formation, we employed atomic force microscopy (AFM) to visualize and study a regulatory RNA:DNA triplex formed between the Khps1 lncRNA and the enhancer of the proto-oncogene SPHK1. The analysis demonstrates the successful formation of RNA:DNA triplexes under various conditions of pH and temperature, indicating the effectiveness of the AFM strategy. Despite challenges in discriminating between the triple-helix and R-loop configurations, this approach opens new perspectives for investigating the role of lncRNAs in gene regulation at the single-molecule level.

Metabolic networks and enzyme-molecule connections are still being elucidated. Here, through systematic analysis of gene loss and gain across the eukaryotic tree, mapped onto metabolic networks, we build a coevolutionary framework of human metabolism. Using this information, we identify unmapped genes in metabolic pathways, leading to the discovery of C11orf54 as the long-missing decarboxylase of the glucuronate/pentose pathway. These findings provide insights into an alternative route for sugar conversion in humans and other metazoans and its connection to L-ascorbate (vitamin C) biosynthesis. More broadly, our approach offers a framework for mapping missing enzymes across species.

Phosphonates are molecules containing a direct carbon‐phosphorus bond. In nature, these compounds are produced by a variety of organisms, and many environmental microbes are able to degrade specific phosphonates and feed on them. This work focuses on 2‐hydroxyethylphosphonate (HEP)—a natural compound that is found frequently in the environment, but whose microbial catabolism has remained poorly characterized. Starting from genomic analyses, we report here that specific pathways for HEP degradation in bacteria do exist and rely on the oxidation of HEP into the activated compound phosphonoacetaldehyde (PAA), which can be further processed by known hydrolases. The key conversion of HEP to PAA can be carried out by two unrelated groups of dehydrogenases: one comprises homologs of the biosynthetic enzyme PhpC (PAA reductase), whereas the other consists of newly described enzymes that we termed PbfG. Despite sharing the same substrates and using Zn ²⁺ as the metal cofactor, PhpC‐type and PbfG‐type dehydrogenases exhibit markedly different structural and catalytic features, outlining a clear example of convergent evolution. However, PbfG enzymes are catalytically more efficient and apparently more specialized for HEP degradation. Overall, our results reveal the ample distribution in bacteria of specific routes for HEP catabolism. Furthermore, although the degradation pathways for HEP and of 2‐aminoethylphosphonate (AEP; the most common natural phosphonate) share some enzymes, the corresponding gene clusters are often distinct, suggesting a selective advantage in keeping the two catabolic processes separate.