Evolution of an Alternative Genetic Code in the Providencia Symbiont of the Hematophagous Leech Haementeria acuecueyetzin

Abstract

Strict blood-feeding animals are confronted with a strong B-vitamin deficiency. Blood-feeding leeches from the Glossiphoniidae family, similarly to hematophagous insects, have evolved specialized organs called bacteriomes to harbor symbiotic bacteria. Leeches of the Haementeria genus have two pairs of globular bacteriomes attached to the esophagus which house intracellular “Candidatus Providencia siddallii” bacteria. Previous work analyzing a draft genome of the Providencia symbiont of the Mexican leech Haementeria officinalis showed that, in this species, the bacteria hold a reduced genome capable of synthesizing B vitamins. In this work, we aimed to expand our knowledge on the diversity and evolution of Providencia symbionts of Haementeria. For this purpose, we sequenced the symbiont genomes of three selected leech species. We found that all genomes are highly syntenic and have kept a stable genetic repertoire, mirroring ancient insect endosymbionts. Additionally, we found B-vitamin pathways to be conserved among these symbionts, pointing to a conserved symbiotic role. Lastly and most notably, we found that the symbiont of H. acuecueyetzin has evolved an alternative genetic code, affecting a portion of its proteome and showing evidence of a lineage-specific and likely intermediate stage of genetic code reassignment.

Discovery of a novel symbiotic lineage associated with a hematophagous leech from the genus Haementeria

“…The one notable exception is the absence of nudB . However, the nudB gene is not universally conserved across endosymbionts of blood-feeding organisms ( 27 , 28 , 57 ). In fact, it has been shown that many phosphatases display wide-range substrate specificities in Escherichia coli ( 65 , 66 ), suggesting that other phosphatase(s) encoded in the symbiont’s genome might be fulfilling a similar role to nudB .…”

“…These bacteriomes harbor the gammaproteobacterial symbiont ‘Candidatus Providencia siddallii‘ (hereafter Pr. siddallii ), which has been shown to hold small A+T-biased genome-preserving complete pathways for B vitamin biosynthesis ( 28 ). These characteristics, along with congruence between the phylogenetic relations among the leech hosts and symbionts, support the obligate and “ancient” nature of Pr.…”

A new guest to the blood feast: a novel symbiotic lineage associated with a haematophagous leech from the genusHaementeria

“…In addition, the novel symbiont retains redundant enzymes for some metabolic steps of the B vitamin biosynthetic pathways, unlike Pr. siddallii and other well established symbionts (Bennett and Moran, 2015; Koga and Moran, 2014; Manzano-Marín and Latorre, 2016; Manzano-Marín et al ., 2023b). These metabolic features all support a younger age for the association of Haementeria leeches with Pluralibacter compared to that with Provdencia .…”

“…The one notable exception is the absence of nudB. However, the nudB gene is not universally conserved across endosymbionts of blood-feeding organisms (Manzano-Marín et al, 2015, 2023bŘíhová et al, 2023). In fact, it has been shown that many phosphatases display a wide-range substrate specificities in Escherichia coli (Haase et al, 2013;Kuznetsova et al, 2006), suggesting other phosphatase(s) encoded in the symbiont's genome might be fulfilling a similar role to nudB.…”

“…These bacteriomes harbor the gammaproteobacterial symbiont Candidatus Providencia siddallii (hereafter Pr. siddallii ), which has been shown to hold an small A+T-biased genome preserving complete pathways for B vitamin biosynthesis (Manzano-Marín et al ., 2023b). These characteristics, along with congruence between the phylogenetic relations among the leech hosts and symbionts, support the obligate and “ancient” nature of Pr.…”