Lateral gene transfer and the evolution of plastid-targeted proteins in the secondary plastid-containing alga Bigelowiella natans

Abstract

Chlorarachniophytes are amoeboflagellate algae that acquired photosynthesis secondarily by engulfing a green alga and retaining its plastid (chloroplast). An important consequence of secondary endosymbiosis in chlorarachniophytes is that most of the nuclear genes encoding plastid-targeted proteins have moved from the nucleus of the endosymbiont to the host nucleus. We have sequenced and analyzed 83 cDNAs encoding 78 plastid-targeted proteins from the model chlorarachniophyte Bigelowiella natans (formerly Chlorarachnion sp. CCMP621). Phylogenies inferred from the majority of these genes are consistent with a chlorophyte green algal origin. However, a significant number of genes ( approximately 21%) show signs of having been acquired by lateral gene transfer from numerous other sources: streptophyte algae, red algae (or algae with red algal endosymbionts), as well as bacteria. The chlorarachniophyte plastid proteome may therefore be regarded as a mosaic derived from various organisms in addition to the ancestral chlorophyte plastid. In contrast, the homologous genes from the chlorophyte Chlamydomonas reinhardtii do not show any indications of lateral gene transfer. This difference is likely a reflection of the mixotrophic nature of Bigelowiella (i.e., it is photosynthetic and phagotrophic), whereas Chlamydomonas is strictly autotrophic. These results underscore the importance of lateral gene transfer in contributing foreign proteins to eukaryotic cells and their organelles, and also suggest that its impact can vary from lineage to lineage.

Fig. 1.

Plastid-targeted proteins in the chlorarachniophyte alga B. natans grouped according to their inferred evolutionary origin. The left column indicates the protein, the center column describes its phylogenetic placement, and the right column indicates the phylogenetic support for its position (percentage bootstrap support out of 500 replicates) or gives the relevant figure number. Proteins with N-terminal extensions predicted to contain plastid-targeting information (see text) are highlighted by filled boxes, those with N-terminal extensions lacking obvious plastid-targeting information are indicated by half-filled boxes, and proteins encoded by 5′-truncated cDNAs are indicated by open boxes. Sequences containing insertions/deletions consistent with the placement of the B. natans protein in phylogenetic analysis are highlighted with asterisks. Proteins were designated “green algal” or of ambiguous origin according to criteria described in the text. The B. natans ClpP protease seems to be nucleomorph-encoded (NM). Phylogenies of all genes putatively derived by lateral transfer are available in Figs. 2, 3, 5, and 6.

Fig. 2.

Protein ML phylogenies showing examples of B. natans plastid-targeted proteins with the expected relationship to chlorophyte green algae. (A) Oxygen-evolving enhancer 1 (PsbO) phylogeny (-lnL = 5399.95518). (B) ATP synthase β′ subunit phylogeny (-lnL = 5134.21803). B. natans plastid-targeted sequences are shaded black and highlighted with asterisks. ML bootstrap values are provided for all nodes >50%. Additional support values (italicized) are provided for the node specifically showing the placement of the B. natans sequences and are, from top to bottom, ML, weighted neighbor-joining, and Fitch–Margoliash. Scale bars indicate the expected number of amino acid substitutions (corrected) per site.

Fig. 3.

Protein ML phylogenies showing B. natans plastid-targeted proteins derived from other algae. (A) Phosphoglycerate kinase (PGK) (-lnL = 16275.24733). (B) Delta-aminolevulinic acid dehydratase (-lnL = 8636.18318). (C) Geranylgeranyl reductase (-lnL = 4490.47915). (D) Small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) (-lnL = 4103.65322). Bootstrap values and scale bars are as in Fig. 2. PL, plastid; MT, mitochondrial.

Fig. 4.

Representative alignments showing insertions/deletions supporting the phylogenetic position of B. natans plastid-targeted protein sequences. (A) Insertion shared between delta-aminolevulinic acid dehydratase sequences of B. natans and the red alga G. gracilis. (B) Variable region of RuBisCO small subunit proteins. The B. natans sequence shares length and sequence conservation with streptophyte homologs. Numbers for both correspond to coordinates within the Arabidopsis thaliana homolog.

Fig. 5.

Protein ML phylogeny (-lnL = 8618.55993) of ribulose 5-phosphate 3-epimerase. The B. natans plastid-targeted sequence is highlighted black. Bootstrap values and scale bars are as in Fig. 2. The B. natans protein is nested within the Pseudomonadaceae, indicative of lateral transfer from a pseudomonad.