A genomic reappraisal of symbiotic function in the aphid/Buchnera symbiosis: reduced transporter sets and variable membrane organisations

Abstract

Buchnera aphidicola is an obligate symbiotic bacterium that sustains the physiology of aphids by complementing their exclusive phloem sap diet. In this study, we reappraised the transport function of different Buchnera strains, from the aphids Acyrthosiphon pisum, Schizaphis graminum, Baizongia pistaciae and Cinara cedri, using the re-annotation of their transmembrane proteins coupled with an exploration of their metabolic networks. Although metabolic analyses revealed high interdependencies between the host and the bacteria, we demonstrate here that transport in Buchnera is assured by low transporter diversity, when compared to free-living bacteria, being mostly based on a few general transporters, some of which probably have lost their substrate specificity. Moreover, in the four strains studied, an astonishing lack of inner-membrane importers was observed. In Buchnera, the transport function has been shaped by the distinct selective constraints occurring in the Aphididae lineages. Buchnera from A. pisum and S. graminum have a three-membraned system and similar sets of transporters corresponding to most compound classes. Transmission electronic microscopic observations and confocal microscopic analysis of intracellular pH fields revealed that Buchnera does not show any of the typical structures and properties observed in integrated organelles. Buchnera from B. pistaciae seem to possess a unique double membrane system and has, accordingly, lost all of its outer-membrane integral proteins. Lastly, Buchnera from C. cedri revealed an extremely poor repertoire of transporters, with almost no ATP-driven active transport left, despite the clear persistence of the ancestral three-membraned system.

Figure 1. Comparative genomics of bacterial transporter genes.

A: Plot of the percent of transporter genes versus genome size; B: distribution of the percent of transporter genes for 184 bacteria from the transportDB database (B). Red: intracellular obligate bacteria; Green: parasitic/pathogenic bacteria; Black: free-living bacteria.

Figure 2. Schematics of transport capabilities in BAp.

Input (blue) and output (red) compounds, predicted with the metabolic network analysis, are presented on the figure with their corresponding putative transporter families (dotted rectangles). Transporters are coloured according to their class: primary active transporters (green), secondary transporter (blue), group translocators (yellow), channels (pink), unknown (grey). Conserved transporters in the four Buchnera strains/species are outlined with red boxes. Small encircled question mark indicates that the corresponding transporter is an hypothetical candidate showing low sequence identity with the well annotated homologous reference in TCDB and/or for which the transported substrate was not known with a high accuracy for the orthologous reference sequence in TCDB (see table 1).

Figure 3. Structural analysis of bacterial (Buchnera) and symbiosomal membranes in the pea aphid.

A: low magnification view of a bacteriocyte cell showing Buchnera cells, numerous mitochondria and the vesicular system within host-cell cytoplasm; B: enlarged view of Buchnera and mitochondria, showing the three membranes of the Buchnera symbiosome; C: higher magnification view of membrane organization, with the inner/outer double membrane of a mitochondrion (with matrix and cristae), and the triple membrane surrounding Buchnera; D: another view of Buchnera and adjacent mitochondrion multiple membranes; E: highest magnification view of membrane organization, showing the m1/m2/m3 triple membranes delineating Buchnera. All intermembrane distances (see Results) were measured at the scales indicated with Olympus Analysis® software; F: lower magnification view of older maternal bacteriocytes. In all figures, the following abbreviations are used: bcy: Buchnera cytoplasm, acy: aphid bacteriocyte cytoplasm, mt: mitochondria, mtmx: mitochondrial matrix, mtim: mitochondrial inner membrane, mtom: mitochondrial outer membrane, m1: Buchnera inner membrane, m2: Buchnera outer membrane, m3: symbiosomal membrane surrounding the Buchnera cells, Nu: nucleus, ssm: symbiosome (symbiosomal vesicle), iss: intrasymbiosomal space (extracellular to Buchnera), isvs: intrasymbiosomal vesicle, icvs: intracytoplasmic vesicle.

Figure 4. Comparative analysis of symbiosomal membranes in aphid bacteriocytes from Acyrthosiphon pisum (A, B), Cinara cedri (C, D) and Baizongia pistaciae (E, F).

The canonical three membranes, shown in Figure1, are visible in A. pisum and C. cedri (B, D arrows) and should be compared with the mitochondrial two-membraned envelope (B, arrowheads). In Baizongia pistaciae, no three-layer system was identified. From this, and the transporter set data, homology can be proposed with the m1/m3 (inner membrane/symbiosomal membrane) of the other aphid species (arrows in F); abbreviations are as in Figure 1.

Figure 5. Confocal microscopic analysis of pH fields inside A.\ pisum maternal bacteriocytes.

Analysis of pH gradients within live bacteriocytes incubated with the SNARF®-AM ester pH sensitive fluorescent probe (see Methods). The main objective was to detect any pH differences between Buchnera cytoplasm (bcy, green) and aphid cytoplasm (acy) surrounding the Buchnera symbiosomes or nuclear (Nu, red) fields. A: image of the 585nm emission window (SNARF® maximum emission at acidic pH) showing the outline of packed Buchnera symbiosomes filling the cytoplasm of the bacteriocyte. The brighter object is the bacteriocyte nucleus; B: image of the 640nm emission window (SNARF® maximum emission at alkaline pH); C: ratiometric analysis of the same image at 585/640 ratio, showing uniform density, hence the absence of gradients between the acy and bcy areas; D: emission spectra of SNARF® probe controlled, in situ, in the bcy (red) and Nu (green) fields shown in A (left inlet) and the control emission spectra of the SNARF® probe (right inlet).