Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome
- École Normale Supérieure, CNRS, Inserm, PSL Research University, France
- Arizona State University, United States
- Université Pierre et Marie Curie, France
- University of Alberta, Canada
- CNRS, UPMC, FR2424, ABiMS, Station Biologique, France
- Sorbonne Universités, Université Pierre et Marie Curie
- Station Biologique de Roscoff, France
Figures
Figure 1 with 1 supplement
Procedure for identification of conserved plastid-targeted proteins in ochrophytes.
(Panel A) shows a schematic unrooted ochrophyte tree, with the three major ochrophyte lineages (chrysista, hypogyristea, and diatoms) denoted by different coloured labels. ‘PX’ refers to the …
Figure 1—figure supplement 1
Overview of eukaryotic diversity.
This figure, adapted from a previous review (Dorrell and Howe, 2012a), profiles the diversity of different eukaryotic nuclear lineages. Each grey ellipse corresponds to one major clade, or …
Figure 2 with 7 supplements
Verification of unusual ancestral plastid-targeted proteins.
(Panel A) lists the ten proteins selected for experimental characterisation and their most probable previous localisation prior to their establishment in the ochrophyte plastid, based on the first …
Figure 2—figure supplement 1
Exemplar ochrophyte plastid protein alignments.
This figure shows untrimmed GeneIOUS alignments for two ancestral HPPGs of unusual provenance. In each case the full length of the protein (labelled i) and N-terminal region only (ii) are shown, …
Figure 2—figure supplement 2
Tree of ochrophyte glycyl-tRNA synthetase sequences.
This tree shows the consensus unrooted Bayesian topology for a 95 taxa x 487 aa alignment of glycyl tRNA synthetase sequences. The font colour of each sequence corresponds to the taxonomic origin …
Figure 2—figure supplement 3
Tree of ochrophyte pyrophosphate dependent phosphofructo-1- kinase sequences.
This tree shows the consensus Bayesian topology inferred for a 94 taxa x 449 aa alignment of pyrophosphate-dependent PFK, with taxa and support values shown as per Figure 2—figure supplement 2. The …
Figure 2—figure supplement 4
Tree of a novel ochrophyte plastid-targeted protein.
This tree shows the consensus Bayesian topology inferred for a 16 taxa x 103 aa alignment of a plastid-targeted protein seemingly restricted to ochrophytes and one dinoflagellate lineage. Taxa are …
Figure 2—figure supplement 5
Multipartite Phaeodactylum plastid-targeted proteins.
This figure shows the localisation of GFP overexpression constructs for copies of seven proteins from the diatom Phaeodactylum tricornutum that are of non-plastid origin, but show multipartite …
Figure 2—figure supplement 6
Heterologous expression constructs of multipartite plastid-targeted proteins.
This figure shows the localisation of GFP overexpression constructs for copies of two proteins from the dinotom Glenodinium foliaceum (Panel A), and three proteins from the eustigmatophyte Nannochlor…
Figure 2—figure supplement 7
Exemplar control images for confocal microscopy.
This figure shows fluorescence patterns for wild-type Phaeodactylum tricornutum cells (i), and transformant Phaeodactylum cells expressing GFP that has not been fused to any N-terminal targeting …
Figure 3
Evolutionary origins of the ochrophyte plastid proteome.
(Panel A) displays the origins inferred by BLAST top hit, phylogenetic analysis, and combined analysis for all ancestral HPPGs. (Panel B) shows (i) a schematic diagram of stramenopile taxonomy, with …
Figure 4 with 5 supplements
Verification and origins of the green signal in ochrophyte plastids.
(Panel A) shows a schematic tree of the 11 archaeplastid sub-categories with which each green HPPG alignment was enriched prior to phylogenetic analysis. The topology of the red and green algae are …
Figure 4—figure supplement 1
Sampling richness associated with ancestral HPPGs of green algal origin.
This figure shows the number of sub-different archaeplastid orthologues for ancestral HPPGs verified by combined BLAST top hit and single-gene tree analysis to be of either green algal origin (green …
Figure 4—figure supplement 2
Heatmaps of nearest sister-groups of ancestral HPPGs of verified green origin.
This figure shows the specific topologies of single gene trees for HPPGs verified to be of green origin by combined BLAST and phylogenetic analysis. (Panel A) shows a reference topology of …
Figure 4—figure supplement 3
Specific origins of green HPPGs as inferred from BLAST top hit analyses.
These charts show (i) the number of BLAST top hits against each of the individual green sub-categories from HPPGs for which a green origin was identified both from BLAST top hit and single-gene tree …
Figure 4—figure supplement 4
Earliest evolutionary origins of shared plastid residues.
This figure shows the number of residues in the concatenated alignment of HPPGs of verified green origin, which have been subsequently vertically inherited in all major photosynthetic eukaryotes …
Figure 4—figure supplement 5
Origins and HECTAR based targeting tests of proteins encoded by conserved ochrophyte gene clusters.
(Panel A) shows the most probably evolutionary origin, identified using BLAST top hit analysis, for 7140 conserved gene clusters inferred to have been present in the last common ochrophyte ancestor. …
Figure 5 with 9 supplements
Functional mixing of the ancestral ochrophyte HPPGs.
(Panel A) tabulates nineteen different fundamental plastid metabolism pathways and biological processes recovered in the ancestral HPPG dataset. Detailed information concerning the origin and …
Figure 5—figure supplement 1
Reconstructed metabolism pathways and core biological processes in the ancestral ochrophyte plastid.
This figure tabulates each of the ancestral ochrophyte HPPGs corresponding to 350 central plastid metabolism and other biological processes. The ‘origin’ column shows the probable evolutionary …
Figure 5—figure supplement 2
Core plastid metabolism proteins not identified within the ancestral HPPG dataset.
https://doi.org/10.7554/eLife.23717.023
Figure 5—figure supplement 3
Tree of ochrophyte sedoheptulose- 7-bisphosphatase sequences.
This figure shows the consensus Bayesian topology inferred for a 218 taxa x 303 aa alignment of sedoheptulose-7-bisphosphatase sequences, shown as per Figure 2—figure supplement 2. Two different …
Figure 5—figure supplement 4
Tree of ochrophyte 3-dehydroquinate synthase sequences.
This figure shows the consensus Bayesian topology inferred for a 324 taxa x 387 aa alignment of 3-dehydroquinate synthase, shown as per Figure 2—figure supplement 2. Three ochrophyte plastid …
Figure 5—figure supplement 5
Tree of ochrophyte isopropylmalate dehydrogenase sequences.
This tree shows the consensus Bayesian phylogeny inferred for a 202 taxa x 592 aa alignment of isopropyl malate dehydrogenase sequences, shown as per Figure 2—figure supplement 2. Two ochrophyte …
Figure 5—figure supplement 6
Tree of ochrophyte shikimate kinase sequences.
This figure shows the consensus Bayesian topology inferred for a 127 taxa x 262 aa alignment of shikimate kinase sequences. The WAG Bayesian topology was excluded from the consensus due to …
Figure 5—figure supplement 7
KOG classes associated with different categories of HPPGs.
These pie charts profile the distribution of different KOG classes across (i) all HPPGs except for those with general function predictions only, or without any clear KOG function, (ii) the same, but …
Figure 5—figure supplement 8
Coregulation of genes incorporated into HPPGs of different origin in the model diatom Phaeodactylum tricornutum.
(Panel A) shows boxplots of the correlation coefficients between the expression profiles of genes encoding members of ancestral HPPGs of red algal origin (i), green algal origin (ii), prokaryotic …
Figure 5—figure supplement 9
Coregulation of genes incorporated into HPPGs of different origin in the model diatom Thalassiosira pseudonana.
Boxplots (Panel A) and P value statistics (Panel B) are shown as per Figure 5—figure supplement 8. Only two of the correlation value ANOVA tests (comparison of red-red and red-host correlations, and …
Figure 6 with 3 supplements
Origins of chimeric proteins in the ochrophyte plastid.
(Panel A) tabulates eight ancestral HPPGs containing domains of cyanobacterial and non-cyanobacterial origin, as previously identified (Méheust et al., 2016) that were inherited by the ochrophyte …
Figure 6—figure supplement 1
Alignments of an ochrophyte-specific riboflavin biosynthesis fusion protein.
(Panel A) shows alignments of the full length (i) and cyclohydrolase domain only (ii) of a plastid-targeted GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase protein conserved …
Figure 6—figure supplement 2
Origins of ochrophyte plastid 3,4-dihydroxy-2-butanone 4- phosphate synthase.
This figure shows the consensus Bayesian topology inferred for a 22 taxa x 206 aa alignment of 3,4-dihydroxy-2-butanone 4-phosphate synthase domains from different lineages, inferred using Jones and …
Figure 6—figure supplement 3
An ochrophyte-specific Tic20 fusion protein.
This figure shows alignments of the full length (i) and conserved region only (ii) of plastid Tic20 sequences, displayed as per Figure —figure supplement 1.
Figure 7 with 2 supplements
Ancient and bidirectional connections between the ochrophyte plastid and mitochondria.
(Panel A) shows Mitotracker-Orange stained P. tricornutum lines expressing GFP fusion constructs for the N-terminal regions of histidyl- and prolyl-tRNA synthetase sequences from P. tricornutum and …
Figure 7—figure supplement 1
Experimental verification of additional ochrophyte dual-targeted proteins.
(Panel A) shows Mitotracker-orange stained Phaeodactylum tricornutum lines expressing four additional dual-targeted proteins (glycyl-, leucyl-, and methionyl-tRNA synthetases, and a predicted …
Figure 7—figure supplement 2
Comparison of different in silico targeting prediction programmes for the identification of dual-targeted ochrophyte proteins.
(Panel A) shows Mitofates scores for ochrophyte proteins verified experimentally to be dual-targeted in this and a previous study (Gile et al., 2015). (Panel B) shows Mitofates scores for all …
Figure 8 with 6 supplements
Footprints of an ancient endosymbiosis in the haptophyte plastid proteome.
(Panel A) indicates the number of ancestral ochrophyte HPPGs that included sequences from other algal lineages in single-gene tree analyses, and whether those algal lineages branched within or …
Figure 8—figure supplement 1
Origin of proteins of ochrophyte origin in different CASH lineages.
This figure profiles the evolutionary origins of proteins inferred by single-gene phylogenetic analysis to have been transferred from the ochrophytes into other lineages that have acquired plastids …
Figure 8—figure supplement 2
Heatmaps of nearest sister-groups to haptophytes in ancestral ochrophyte HPPG trees.
This figure shows the specific ochrophyte lineages implicated in the origin of haptophyte plastid-targeted proteins, as inferred from the nearest ochrophyte sister-groups to haptophytes in trees of …
Figure 8—figure supplement 3
Internal evolutionary affinities of haptophyte plastid-targeted proteins incorporated into ancestral ochrophyte HPPGs.
This figure profiles the evolutionary origins of haptophyte plastid-targeted proteins incorporated into ancestral ochrophyte HPPGs by BLAST top hit analysis. Separate values are provided for query …
Figure 8—figure supplement 4
Evidence for gene transfer from pelagophytes and dictyochophytes into haptophytes.
(Panel A) shows the next deepest sister groups identified for haptophyte proteins of hypogyristean origin in single-gene trees. The pie chart (i) compares the number of single-gene trees in which …
Figure 8—figure supplement 5
Earliest possible origin points of uniquely conserved sites in haptophyte plastid-targeted proteins.
This figure shows the total number of residues that are uniquely shared between a 37 proteins that have clearly been transferred between the ochrophytes and haptophytes, and are of subsequently …
Figure 8—figure supplement 6
Evolutionary origin of ancestral haptophyte genes.
This figure shows the most likely evolutionary origin assigned by BLAST top hit analysis to the 12728 conserved gene families inferred to have been present in the last common haptophyte ancestor.
Figure 9 with 3 supplements
Non-ochrophyte origins of the haptophyte plastid genome.
(Panels A and B), respectively, show gene-rich and taxon-rich phylogenies of plastid-encoded proteins from red algae and plastids of red algal origin with the glaucophyte Cyanophora paradoxa as …
Figure 9—figure supplement 1
Alternative topology tests of plastid genome trees.
Tests were performed with the RAxML + JTT trees inferred for the gene-rich (panel A) and taxon-rich (panel B) plastid-encoded protein alignments. In each case, a schematic diagram of the tree …
Figure 9—figure supplement 2
Fast site removal and clade deduction analysis of plastid genome trees.
(Panel A) shows the support values obtained for Bayesian + Jones trees inferred from modified versions of the taxon-rich plastid multigene alignment from which the 13 fastest evolving site …
Figure 9—figure supplement 3
Single-gene tree topologies associated with individual plastid-encoded genes.
These heatmaps show the first sister-groups identified to haptophytes, and members of the pelagophyte/dictyochophyte clade, in single-gene trees of component genes included in concatenated trees of …
Figure 10 with 2 supplements
Schematic diagram of events giving rise to the ancestral ochrophyte plastid proteome.
Each cell diagram depicts a different stage in the ochrophyte plastid endosymbiosis; each protein depicted represents one or more proteins inferred in this study to have been nucleus-encoded and …
Figure 10—figure supplement 1
Complex origins of different ancestral ochrophyte HPPGs.
(Panel A) shows the evolutionary positions of lineages with histories of secondary endosymbiosis in trees of ancestral ochrophyte HPPGs verified by combined BLAST top hit and single-gene tree …
Figure 10—figure supplement 2
Different scenarios for the origins of haptophyte plastids.
This schematic tree diagram shows different possibilities for the origins of the haptophyte plastid as predicted from the data within this study. No inference is made here regarding the ultimate …
Tables
Table 1
Glossary Box. A schematic figure of eukaryotic taxonomy, showing the evolutionary origins of nuclear and plastid lineages, adapted from previous reviews (Dorrell and Howe, 2012a), is shown in Figure …
| Complex plastids | Plastids acquired through the endosymbiosis of a eukaryotic alga. These include secondary plastids of ultimate red algal origin (such as those found in ochrophytes, haptophytes and cryptomonads), secondary plastids derived from green algae (such as those found in euglenids or chlorarachniophytes), or tertiary plastids such as those found in dinotoms and certain other dinoflagellates (resulting from the endosymbioses of eukaryotic algae that themselves contain plastids of complex origin). |
| CASH lineages | The four major lineages of algae with plastids of secondary or higher red origin, that is to say Cryptomonads, Alveolates (dinoflagellates, and apicomplexans), Stramenopiles, and Haptophytes. |
| Stramenopiles | A diverse and ecologically major component of the eukaryotic tree, containing both photosynthetic members (the ochrophytes), which possess complex plastids of red algal origin, and aplastidic and non-photosynthetic members (e.g. oomycetes, labyrinthulomycetes, and the human pathogen Blastocystis), which form the earliest-diverging branches. It is debated when within stramenopile evolution the extant ochrophyte plastid was acquired. |
| Ochrophytes | Photosynthetic and plastid-bearing members of the stramenopiles, including many ecologically important lineages (diatoms, kelps, pelagophytes) and potential model lineages for biofuels research (Nannochloropsis). Ochrophytes possess plastids of ultimate red origin, and form the most significant component of eukaryotic marine phytoplankton (Dorrell and Smith, 2011; de Vargas et al., 2015). |
| Haptophytes | Single-celled, photosynthetic eukaryotes, possessing complex plastids of ultimate red origin. Some haptophytes (the coccolithophorids) are renowned for their ability to form large blooms (visible from space), and to form intricate calcareous shells (Dorrell and Smith, 2011; Bown, 1998), which if deposited on the ocean floor go on to form a major component of limestone and other sedimentary rocks. |
| HPPG | ‘Homologous plastid protein group’. Proteins identified in this study to possess plastid-targeting sequences that are homologous to one another, as defined by BLAST-based HPPG assembly and single gene phylogenetic analysis. |
