Biology subjects

Shepherd, J. N.

Publications and source records attributed to Shepherd, J. N..

3 recordsLinked to original sources

bioRxiv2026

Lateral gene transfer introduced the microbial anaerobiosis-related gene rquA into early animals

Lateral gene transfer (LGT) enables rapid metabolic innovation in microbes, but its evolutionary importance in animals remains debated. Among metabolic traits with major ecological consequences, adaptations to low-oxygen conditions often involve modifications of mitochondrial electron transport and the quinones that mediate electron flow. Rhodoquinone-based anaerobic metabolism occurs in several eukaryotic lineages, yet the evolutionary routes by which animals acquired this capability are poorly understood. Here we show that freshwater sponges possess a rhodoquinone biosynthesis gene, rquA, previously restricted to microbial lineages, which was acquired by lateral gene transfer and functionally integrated into sponge metabolism. Heterologous expression of rquA from the model freshwater sponge Ephydatia muelleri enables rhodoquinone production in yeast, consistent with functional conservation. In E. muelleri, the rquA gene is upregulated under hypoxia and rhodoquinone is detectable across all lifestages, however, it is most abundant in early development in the pluiripotent gemmules. Using comparative genomics, we find that the presence of rquA in freshwater sponges correlates with loss of key genes of the ubiquinone biosynthesis pathway, suggesting these animals cannot synthesize ubiquinone de novo and we show that E. muelleri can convert exogenous ubiquinone to rhodoquinone. Rhodoquinone levels were significantly higher in rquA-encoding freshwater sponges compared to marine sponges that were sampled from natural environments. This study reveals that an early animal lineage acquired a microbial metabolism-related gene via lateral gene transfer during or before the transition to freshwater environments, enabling rhodoquinone utilization and potentially enhancing tolerance to oxygen fluctuations. Thereby, demonstrating how LGT shapes energy metabolism even in multicellular organisms.

evolutionary biology↗

bioRxiv2020

Alternative splicing of COQ-2 determines the choice between ubiquinone and rhodoquinone biosynthesis in helminths

Parasitic helminths use two benzoquinones as electron carriers in the electron transport chain. In aerobic environments they use ubiquinone (UQ) but in anaerobic environments inside the host, they require rhodoquinone (RQ) and greatly increase RQ levels. The switch to RQ synthesis is driven by substrate selection by the polyprenyltransferase COQ-2 but the mechanisms underlying this substrate choice are unknown. We found that helminths make two coq-2 isoforms, coq-2a and coq-2e, by alternative splicing. COQ-2a is homologous to COQ2 from other eukaryotes but the COQ-2e-specific exon is only found in species that make RQ and its inclusion changes the enzyme core. We show COQ-2e is required for RQ synthesis and for survival in cyanide in C. elegans. Crucially, we see a switch from COQ-2a to COQ-2e as parasites transition into anaerobic environments. We conclude that under anaerobic conditions helminths switch from UQ to RQ synthesis via alternative splicing of coq-2.

molecular biology↗

bioRxiv2019

The kynurenine pathway is essential for rhodoquinone biosynthesis in Caenorhabditis elegans

A key metabolic adaptation for some species that face hypoxia as part of their life-cycle involves an alternative electron transport chain in which rhodoquinone (RQ) is required for fumarate reduction and ATP production. RQ biosynthesis in bacteria and protists requires ubiquinone (Q) as a precursor. In contrast, Q is not a precursor for RQ biosynthesis in animals such as parasitic helminths, and this pathway has remained elusive. We used Caenorhabditis elegans as a model animal to elucidate several key steps in RQ biosynthesis. Through RNA interference and a series of mutants, we found that arylamine metabolites from the kynurenine pathway are essential precursors for RQ biosynthesis de novo. Deletion of kynu-1, which encodes a kynureninase that converts L-kynurenine (KYN) into anthranilic acid (AA), and 3-hydroxykynurenine (HKYN) into 3-hydroxyanthranilic acid (3HAA), completely abolishes RQ biosynthesis, but does not affect Q levels. Deletion of kmo-1, which encodes a kynurenine 3-monooxygenase that converts KYN to HKYN, drastically reduces RQ, but not Q levels. Knockdown of the Q biosynthetic genes, coq-5 and coq-6, affects both Q and RQ levels demonstrating that common enzymes are used in both biosynthetic pathways. Our study reveals that two pathways for RQ biosynthesis have independently evolved. In contrast to bacteria, where amination is the last step in RQ biosynthesis, worms begin with the arylamine precursor, AA or 3HAA. Since RQ is absent in mammalian hosts of helminths, inhibition of RQ biosynthesis may have broad implications for targeting parasitic infections which cause important neglected tropical diseases.

biochemistry↗