Trends in reconstruction of three nucleus-encoded, plastid-localized pathways for the heme, chlorophyll a and isopentenyl diphosphate biosynthesises in two separate dinoflagellate lineages bearing non-canonical plastids
A peer-reviewed article of this Preprint also exists.
Author and article information
Abstract
Background: The ancestral dinoflagellate most likely established a peridinin-containing plastid, which have been inherited to the extant photosynthetic descendants. However, kareniacean dinoflagellates and Lepidodinium species were known to bear “non-canonical” plastids lacking peridinin, which were established through haptophyte and a green algal endosymbioses, respectively. For plastid function and maintenance, the aforementioned dinoflagellates were known to use nucleus-encoded proteins vertically inherited from the ancestral dinoflagellates (vertically inherited- or VI-type), and those acquired from non-dinoflagellate organisms (including the endosymbiont). These observations indicated that the proteomes of the non-canonical plastids derived from a haptophyte and a green alga were modified by “exogenous” genes acquired from non-dinoflagellate organisms. However, there was no systematic evaluation addressing how “exogenous” genes reshaped individual metabolic pathways localized in a non-canonical plastid.
Results: In this study, we surveyed transcriptomic data from two kareniacean species (Karenia brevis and Karlodinium veneficum) and Lepidodinium chlorophorum, and identified proteins involved in three plastid metabolic pathways synthesizing chlorophyll a (Chl a), heme and isoprene. The origins of the individual proteins of our interest were investigated, and assessed how the three pathways were modified before and after the algal endosymbioses, which gave rise to the current non-canonical plastids. We observed a clear difference in the contribution of VI-type proteins across the three pathways. In both Karenia/Karlodinium and Lepidodinium, we observed a substantial contribution of VI-type proteins to the isoprene and heme biosynthesises. In sharp contrast, VI-type protein was barely detected in the Chl a biosynthesis in the three dinoflagellates.
Discussion: Pioneering works hypothesized that the ancestral kareniacean species had lost the photosynthetic activity prior to haptophyte endosymbiosis. The absence of VI-type proteins in the Chl a biosynthetic pathway in Karenia or Karlodinium is in good agreement with the putative non-photosynthetic nature proposed for their ancestor. The dominance of proteins with haptophyte origin in the Karenia/Karlodinium pathway suggests that their ancestor rebuilt the particular pathway by genes acquired from the endosymbiont. Likewise, we here propose that the ancestral Lepidodinium likely experienced a non-photosynthetic period and discarded the entire Chl a biosynthetic pathway prior to the green algal endosymbiosis. Nevertheless, Lepidodinium rebuilt the pathway by genes transferred from phylogenetically diverse organisms, rather than the green algal endosymbiont. We explore the reasons why green algal genes were barely utilized to reconstruct the Lepidodinium pathway.
Cite this as
2017. Trends in reconstruction of three nucleus-encoded, plastid-localized pathways for the heme, chlorophyll a and isopentenyl diphosphate biosynthesises in two separate dinoflagellate lineages bearing non-canonical plastids. PeerJ Preprints 5:e3488v1 https://doi.org/10.7287/peerj.preprints.3488v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This is a submission to PeerJ for review.
Sections
Supplemental Information
Fig S1. ML phylogenies of 8 proteins involved in C5 pathway for the heme biosynthesis (with full sequence names)
We provide the maximum-likelihood bootstrap values (MLBPs), which are equal or greater than 50%. Color-coding for subtrees/branches are same as described in Fig. 2. Page 1, glutamyl-tRNA reductase (GTR). Page 2, glutamate-1-semialdehyde 2,1-aminomutase (GSAT). Page 3, delta-aminolevulinic acid dehydratase (ALAD). Page 4, porphobilinogen deaminase (PBGD). Page 5, Uroporphyrinogen III synthase (UROS). Page 6, uroporphyrinogen decarboxylase (UROD). Page 7, coproporphyrinogen oxidase (CPOX). Page 8, protoporphyrinogen IX oxidase (PPOX). Page 9, ferrochelatase (FeCH).
Fig S2. ML phylogenies of 7 proteins involved in the Chl a biosynthetic pathway (with full sequence names)
The details of this figure are same as those of Fig. S1. Page 1, ChlD, one of the two nucleus-encoded subunits of Mg-chelatase (MgCH). Page 2, ChlH, the other nucleus-encoded subunit of MgCH. Page 3, S-adenosylmethionine:Mg-protoporphyrin O-methyltransferase (MgPMT). Page 4, divinyl chlorophyllide a 8-vinyl-reductase using ferredoxin for electron donor (F-DVR). Page 5, divinyl chlorophyllide a 8-vinyl-reductase using NADPH for electron donor (N-DVR). Page 6, light-dependent protochlorophyllide reductase (POR). Page 7, chlorophyll synthase (CS).
Fig S3. ML phylogenies of 7 proteins involved in the non-mevalonate pathway for IPP biosynthesis (with full sequence name)
The details of this figure are same as those of Fig. S1. Page 1, 1-deoxy-D-xylulose-5-phosphate (DXP) synthase (DXS). Page 2, DXP reductoisomerase (IspC/DXR). Page 3, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD). Page 4, 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE). Page 5, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (IspF). Page 6, 1-hydroxy-2-methyl-2-butenyl 4-diphosphate (HMB-PP) synthase (IspG). Page 7, HMB-PP reductase (IspH).
Summary of the Karenia, Karlodinium and Lepidodinium transcripts encoding proteins involved in the heme biosynthesis
Summary of the Karenia, Karlodinium and Lepidodinium transcripts encoding proteins involved in the Chl a biosynthesis
Summary of the Karenia, Karlodinium and Lepidodinium transcripts encoding proteins involved in the IPP biosynthesis
Summary of the alignments analyzed in this study
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Eriko Matsuo conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper, conducted phylogenetic analyses.
Yuji Inagaki conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
The RNA-seq data obtained from a dioflagellate Lepidodoinium chlorophorum was deposited in GenBank database (SRA no. NNNN).
Data Deposition
The following information was supplied regarding data availability:
The research in this article generated no data except the DNA sequence data deposited in GenBank
Funding
E. M. was supported by a research fellowship from the Japanese Society for Promotion of Sciences (JSPS) for Young Scientists (no. 15J00821). This work was supported in part by grants from the JSPS awarded to Y. I. (23117006 and 16H04826). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
