Elucidation of host and symbiont contributions to peptidoglycan metabolism based on comparative genomics of eight aphid subfamilies and their Buchnera

Pea aphids (Acyrthosiphon pisum) are insects containing genes of bacterial origin with putative functions in peptidoglycan (PGN) metabolism. Of these, rlpA1-5, amiD, and ldcA are highly expressed in bacteriocytes, specialized aphid cells that harbor the obligate bacterial symbiont Buchnera aphidicola, required for amino acid supplementation of the host's nutrient-poor diet. Despite genome reduction associated with endosymbiosis, pea aphid Buchnera retains genes for the synthesis of PGN while Buchnera of many other aphid species partially or completely lack these genes. To explore the evolution of aphid horizontally-transferred genes (HTGs) and to elucidate how host and symbiont genes contribute to PGN production, we sequenced genomes from four deeply branching lineages, such that paired aphid and Buchnera genomes are now available for 17 species representing eight subfamilies. We identified all host and symbiont genes putatively involved in PGN metabolism. Phylogenetic analyses indicate that each HTG family was present in the aphid shared ancestor, but that each underwent a unique pattern of gene loss or duplication in descendant lineages. While four aphid rlpA gene subfamilies show no relation to symbiont PGN gene repertoire, the loss of aphid amiD and ldcA HTGs coincides with the loss of symbiont PGN metabolism genes. In particular, the coincident loss of host amiD and symbiont murCEF in tribe Aphidini, in contrast to tribe Macrosiphini, suggests either 1) functional linkage between these host and symbiont genes, or 2) Aphidini has lost functional PGN synthesis and other retained PGN pathway genes are non-functional. To test these hypotheses experimentally, we used cell-wall labeling methods involving a d-alanine probe and found that both Macrosiphini and Aphidini retain Buchnera PGN synthesis. Our results imply that compensatory adaptations can preserve PGN synthesis despite the loss of some genes considered essential for this pathway, highlighting the importance of the cell wall in these symbioses. Author summaryThroughout evolution, animals have sometimes gained novel abilities by acquiring bacterial genes through horizontal gene transfer. For some insects harboring bacterial symbionts, horizontally-transferred genes may enable hosts to regulate symbiosis by influencing symbiont cell wall metabolism. While mealybug horizontally-transferred genes work collectively to synthesize the symbiont cell wall, the role of aphid horizontally-transferred genes in symbiont cell wall metabolism is unclear. We examined whether different aphid horizontally-transferred genes co-occur with symbiont genes underlying cell wall metabolism across different aphid lineages, indicative of linked function. We included 17 aphid species representing eight distantly related lineages, four of which we sequenced for this study. We found that two of the three horizontally-acquired gene families are present only when symbionts possess cell wall pathway genes, while the third shows no correlation. These results reveal that despite their putative involvement in symbiont cell wall synthesis, aphid horizontally-acquired genes operate independently from one another and likely have lineage-specific functions. Furthermore, we observed that symbiont cell wall synthesis is maintained in one aphid lineage despite loss of genes considered essential for producing the cell wall, implying that other adaptations preserve the cell wall in aphid species with incomplete cell wall synthesis pathways.

Automated summary

Pea aphids contain genes of bacterial origin with putative functions in peptidoglycan metabolism. Some of these genes are highly expressed in specialized aphid cells that harbor the obligate bacterial symbiont Buchnera aphidicola, required for amino acid supplementation. While pea aphid retains genes for the synthesis of peptidoglycan, other aphid species lack these genes. Through genome sequencing and phylogenetic analyses, this study explores the evolution of horizontally-transferred genes in aphids and their contribution to peptidoglycan production. The results suggest a functional linkage between certain host and symbiont genes, and highlight the importance of compensatory adaptations in preserving peptidoglycan synthesis.