Genomic revelations of a mutualism: the pea aphid and its obligate bacterial symbiont

Abstract

The symbiosis of the pea aphid Acyrthosphion pisum with the bacterium Buchnera aphidicola APS represents the best-studied insect obligate symbiosis. Here we present a refined picture of this symbiosis by linking pre-genomic observations to new genomic data that includes the complete genomes of the eukaryotic and prokaryotic symbiotic partners. In doing so, we address four issues central to understanding the patterns and processes operating at the A. pisum/Buchnera APS interface. These four issues include: (1) lateral gene transfer, (2) host immunity, (3) symbiotic metabolism, and (4) regulation.

Fig. 1

DNA-stained confocal microscope images of aphid embryos. a Incorporation of the maternal endosymbiotic bacteria to a stage 7 embryo. The bacteria are visible as small round cells. Anterior is to top. Scale bar 14 μm. b Aggregates of large aphid bacteriocyte cells that run perpendicular to the main axis of a stage 16 embryo are clearly visible (Ba). Scale bar 50 μm. c Magnified view of aphid bacteriocyte cells showing the large polyploid bacteriocyte cell nucleus (N) and a high density of Buchnera within the cell. Scale bar 6 μm. d Cartoon of the aphid bacteriocyte. The two aphid-derived membranes are shown in green, and the Buchnera cell membrane is shown in blue (drawn to scale from Fig. 1 of Baumann et al. [5]). Scale bar 2 μm. Parthenogenetic viviparous embryos were stained with TO-PRO3 (a) or DAPI (b, c). Composite figure and cartoon courtesy of Daniel R. G. Price. Confocal microscopy images: Shuji Shigenobu (a), James Baker (b, c)

Fig. 2

Results of Mittler [34] single amino acid elimination experiment demonstrating Buchnera provisioning of essential amino acids. Nonessential amino acids (listed alphabetically) are represented by blue bars, while essential amino acids (also alphabetically listed) are shown in pink. Dark colors show data from symbiotic Myzus persicae while light colors show data from aposymbiotic M. persicae. While the data are largely qualitative, they are representative of the types of early data that established the nutritional provisioning of essential amino acids by Buchnera to their aphid hosts. Data are taken from 3day/apterous columns in Table 2 of [34]

Fig. 3

Blueprint of amino acid biosynthesis and nutritional upgrading in the A. pisum/Buchnera APS symbiosis. Essential amino acids are shown in purple, while non-essential amino acids are in green. A. pisum enzymes are shown with red arrows, while Buchnera enzymes are shown with blue arrows. Green boxes around metabolites indicate a phloem sap source and purple boxes highlight the importance of glutamine (Gln), which is a dominant amino acid in hemolymph [64] actively taken up by bacteriocytes and converted to glutamate (Glu, orange boxes). Glutamate then actively crosses the symbiosomal membrane [64, 65] where it serves as an amino donor and metabolic precursor for the synthesis of nonessential amino acids. a Asparagine (Asn), the dominant amino acid in the phloem sap diet of the pea aphid [62], aspartate (Asp), glutamate (Glu) and glutamine (Gln) are the four amino acids of central importance to the aphid/Buchnera symbiosis; at least one of these four is required as the primary source of all protein amino acids for the holosymbiont [35]. b–d Both A. pisum and Buchnera APS retain glycolysis and the pentose phosphate pathway and thus the ability to synthesize 3-phosphoglycerate, phosphoenolpyruvate, pyruvate, and eyrthrose-4-phosphate. e Aspartate (Asp) is transported across the Buchnera APS membrane where it serves as the metabolic precursor of the essential amino acids isoleucine (Ile), lysine (Lys), and threonine (Thr). Synthesis of the branched-chain essential amino acids valine (Val), leucine (Leu), and isoleucine (Ile) requires within-pathway metabolic collaboration between symbiotic partners (c, e) [11]. f In addition to the ability of Buchnera APS to synthesize glycine (Gly) from serine (b), two pathways for the biosynthesis of glycine are retained by A. pisum. g Both A. pisum and Buchnera APS retain the ability to synthesize glutamate from glutamine. Glutamate serves as the metabolic precursor of proline and arginine. Arginine (Arg), the tenth essential amino acid is synthesized by Buchnera APS where A. pisum has uniquely lost the metabolic capability to synthesize this amino acid [9, 11]. *The annotation of ACYPI000665 from KEGG (http://www.genome.jp/kegg/). h The non-essential amino acid cysteine (Cys) is synthesized by Buchnera APS from phloem sap provisioned sulfate and A. pisum synthesized serine (b). Buchnera APS has lost the capacity to synthesize the essential amino acid methionine (Met), yet strong physiological evidence exists that demonstrates that the holosymbiont possesses the capacity for methionine biosynthesis [49]. The pathway for methionine biosynthesis presented here is that of [9, 11]. The non-essential amino acid alanine (Ala) can be synthesized by both Buchnera APS and A. pisum (from Cys shown here and from pyruvate, c). i Both A. pisum and Buchnera APS retain the pentose phosphate pathway and the ability to synthesize phosphoribosyl pyrophosphate (PRPP) from ribose-5-phosphate using ribose-phosphate diphosphokinase (E.C. 2.7.6.1, A. pisum: ACYPI006288, Buchnera APS: PrsA, KEGG (http://www.genome.jp/kegg/). With the exception of the cases indicated, pathways presented were constructed using the AcypiCyc Acyrthosiphon pisum (genome paper version) and Buchnera aphidicola APS (Acyrthosiphon pisum) databases (http://acypicyc.cycadsys.org)

Fig. 3

Blueprint of amino acid biosynthesis and nutritional upgrading in the A. pisum/Buchnera APS symbiosis. Essential amino acids are shown in purple, while non-essential amino acids are in green. A. pisum enzymes are shown with red arrows, while Buchnera enzymes are shown with blue arrows. Green boxes around metabolites indicate a phloem sap source and purple boxes highlight the importance of glutamine (Gln), which is a dominant amino acid in hemolymph [64] actively taken up by bacteriocytes and converted to glutamate (Glu, orange boxes). Glutamate then actively crosses the symbiosomal membrane [64, 65] where it serves as an amino donor and metabolic precursor for the synthesis of nonessential amino acids. a Asparagine (Asn), the dominant amino acid in the phloem sap diet of the pea aphid [62], aspartate (Asp), glutamate (Glu) and glutamine (Gln) are the four amino acids of central importance to the aphid/Buchnera symbiosis; at least one of these four is required as the primary source of all protein amino acids for the holosymbiont [35]. b–d Both A. pisum and Buchnera APS retain glycolysis and the pentose phosphate pathway and thus the ability to synthesize 3-phosphoglycerate, phosphoenolpyruvate, pyruvate, and eyrthrose-4-phosphate. e Aspartate (Asp) is transported across the Buchnera APS membrane where it serves as the metabolic precursor of the essential amino acids isoleucine (Ile), lysine (Lys), and threonine (Thr). Synthesis of the branched-chain essential amino acids valine (Val), leucine (Leu), and isoleucine (Ile) requires within-pathway metabolic collaboration between symbiotic partners (c, e) [11]. f In addition to the ability of Buchnera APS to synthesize glycine (Gly) from serine (b), two pathways for the biosynthesis of glycine are retained by A. pisum. g Both A. pisum and Buchnera APS retain the ability to synthesize glutamate from glutamine. Glutamate serves as the metabolic precursor of proline and arginine. Arginine (Arg), the tenth essential amino acid is synthesized by Buchnera APS where A. pisum has uniquely lost the metabolic capability to synthesize this amino acid [9, 11]. *The annotation of ACYPI000665 from KEGG (http://www.genome.jp/kegg/). h The non-essential amino acid cysteine (Cys) is synthesized by Buchnera APS from phloem sap provisioned sulfate and A. pisum synthesized serine (b). Buchnera APS has lost the capacity to synthesize the essential amino acid methionine (Met), yet strong physiological evidence exists that demonstrates that the holosymbiont possesses the capacity for methionine biosynthesis [49]. The pathway for methionine biosynthesis presented here is that of [9, 11]. The non-essential amino acid alanine (Ala) can be synthesized by both Buchnera APS and A. pisum (from Cys shown here and from pyruvate, c). i Both A. pisum and Buchnera APS retain the pentose phosphate pathway and the ability to synthesize phosphoribosyl pyrophosphate (PRPP) from ribose-5-phosphate using ribose-phosphate diphosphokinase (E.C. 2.7.6.1, A. pisum: ACYPI006288, Buchnera APS: PrsA, KEGG (http://www.genome.jp/kegg/). With the exception of the cases indicated, pathways presented were constructed using the AcypiCyc Acyrthosiphon pisum (genome paper version) and Buchnera aphidicola APS (Acyrthosiphon pisum) databases (http://acypicyc.cycadsys.org)