Special Issue "Evolutionary and Molecular Aspects of Plastid Endosymbioses"

A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (30 September 2019).

Special Issue Editors

Prof. Dr. Miroslav Oborník
Website
Guest Editor
Biology Centre CAS, Institute of Parasitology and Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
Interests: evolution of eukaryotes; complex endosymbioses; apicomplexan parasites; diatoms; chromerids; heme biosynthesis in phototrophs
Dr. Zoltán Füssy
Website SciProfiles
Guest Editor
Biology Centre CAS, Institute of Parasitology and Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
Interests: evolution of eukaryotes; biochemistry; complex endosymbioses; euglenophytes; chromerids; bioinformatics

Special Issue Information

Dear Colleagues,

Plastids—photosynthetic organelles of eukaryotes—have been instrumental in our understanding how eukaryotes are evolving as multi-compartmented cellular entities. As postulated by Merezhkowski already in 1905, plastids ultimately arose as a result of an intracellular symbiosis (endosymbiosis) relationship of eukaryotic cells with cyanobacteria. As radical as it seemed at that time, the theory of symbiogenesis became widely accepted with the accumulation of morphological and molecular data. In fact, with the increasing number of single-celled eukaryotes that have been found to possess plastids, we are excited by how many shapes plastids take up, in terms of both morphology and biology.

Plastids that we call primary are descendants of symbionts arising from prokaryote-to-eukaryote endosymbioses with cyanobacteria. However, plastids are mildly promiscuous organelles and, through higher-order (eukaryote-to-eukaryote) endosymbiosis, they have been horizontally transferred across highly divergent eukaryotic lineages, resulting in an explosion of diversity of phototrophic eukaryotes. Through photosynthesis, plastids shifted the metabolic possibilities of their hosts, algae and plants, to a new level. The virtually infinite source of energy of light allowed them to turn inorganic molecules into biocompounds and thrive in and colonize marine, freshwater, and dry land environments of many kinds. Eukaryotic phototrophs are thus responsible for a major part of primary production on Earth.

As a result of disparate origins, plastids show high diversity in terms of biological functions and evolutionary trajectories. The genetic and metabolic integration of a phototrophic endosymbiont into a host cell results in unique evolutionary arrangements of metabolic pathways and cellular interactions. Besides photosynthesis, plastids frequently constitute a metabolic hub for carbon, nitrogen, and sulfur metabolism, as well as for the biosynthesis of cofactors and vitamins. Compound exchanges and the subtle balance of the metabolic flows between the plastid and other cell compartments is crucial for algae to succeed in competitions for resources in the long run. Surprisingly, organisms lose photosynthesis at least as frequently as they gain it. Plastid endosymbioses appear to be the most efficient evolutionary processes in nature as they cause trophic switches from heterotrophy to photoautotrophy and back again, always bringing bursts of new genetic material with high innovative potential.

With the advance of high-throughput sequencing, the diversity of life is being quickly unveiled by gathering data on a range of levels from environmental samples to single cells. Only now has it become apparent how widespread plastids are. Signs of plastid metabolism have been found in disparate inconspicuous microeukaryotes; thus, these organisms often profoundly change our view of the tree of life. Some of these long-overlooked organisms host photosynthetic plastids, some of them possess cryptic non-photosynthetic plastids; either way, they are important to a better understanding of plastid evolution, as they fill in the huge gaps between the phototrophic crown groups. Furthermore, we have to realize that plastids are not the only endosymbionts making a difference. In fact, more or less intimate relationships are formed among eukaryotes and prokaryotes in other branches of the tree of life and in environments that lack access to light. In fact, it appears that metabolic innovations similar to the acquisition of plastids are tightly linked to evolutionary success.

We compiled this Special Issue of Biomolecules to reflect the many facets of the biology of plastids. We hope this issue will provide valuable insights into the achievements and future prospects of this developing research field.

Prof. Dr. Miroslav Oborník
Dr. Zoltán Füssy
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • chloroplasts
  • endosymbiosis
  • horizontal gene transfer
  • photosynthesis
  • essential plastid pathways
  • plastid metabolism
  • plastid dependence
  • protein translocation
  • transporters
  • non-photosynthetic algae
  • cryptic plastids
  • next-generation sequencing
  • single-cell sequencing
  • alveolates
  • apicomplexans
  • chromerids
  • diatoms
  • euglenophytes
  • Paulinella

Published Papers (7 papers)

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Research

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Open AccessArticle
Organellar DNA Polymerases in Complex Plastid-Bearing Algae
Biomolecules 2019, 9(4), 140; https://doi.org/10.3390/biom9040140 - 07 Apr 2019
Cited by 2
Abstract
DNA replication in plastids and mitochondria is generally regulated by nucleus-encoded proteins. In plants and red algae, a nucleus-encoded enzyme called POP (plant and protist organellar DNA polymerase) is involved in DNA replication in both organelles by virtue of its dual localization. POPs [...] Read more.
DNA replication in plastids and mitochondria is generally regulated by nucleus-encoded proteins. In plants and red algae, a nucleus-encoded enzyme called POP (plant and protist organellar DNA polymerase) is involved in DNA replication in both organelles by virtue of its dual localization. POPs are family A DNA polymerases, which include bacterial DNA polymerase I (PolI). POP homologs have been found in a wide range of eukaryotes, including plants, algae, and non-photosynthetic protists. However, the phylogeny and subcellular localizations of POPs remain unclear in many algae, especially in secondary and tertiary plastid-bearing groups. In this study, we report that chlorarachniophytes possess two evolutionarily distinct POPs, and fluorescent protein-tagging experiments demonstrate that they are targeted to the secondary plastids and mitochondria, respectively. The timing of DNA replication is different between the two organelles in the chlorarachniophyte Bigelowiella natans, and this seems to be correlated to the transcription of respective POP genes. Dinoflagellates also carry two distinct POP genes, possibly for their plastids and mitochondria, whereas haptophytes and ochrophytes have only one. Therefore, unlike plants, some algal groups are likely to have evolved multiple DNA polymerases for various organelles. This study provides a new insight into the evolution of organellar DNA replication in complex plastid-bearing organisms. Full article
(This article belongs to the Special Issue Evolutionary and Molecular Aspects of Plastid Endosymbioses)
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Review

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Open AccessReview
Nucleotide Transport and Metabolism in Diatoms
Biomolecules 2019, 9(12), 761; https://doi.org/10.3390/biom9120761 - 21 Nov 2019
Abstract
Plastids, organelles that evolved from cyanobacteria via endosymbiosis in eukaryotes, provide carbohydrates for the formation of biomass and for mitochondrial energy production to the cell. They generate their own energy in the form of the nucleotide adenosine triphosphate (ATP). However, plastids of non-photosynthetic [...] Read more.
Plastids, organelles that evolved from cyanobacteria via endosymbiosis in eukaryotes, provide carbohydrates for the formation of biomass and for mitochondrial energy production to the cell. They generate their own energy in the form of the nucleotide adenosine triphosphate (ATP). However, plastids of non-photosynthetic tissues, or during the dark, depend on external supply of ATP. A dedicated antiporter that exchanges ATP against adenosine diphosphate (ADP) plus inorganic phosphate (Pi) takes over this function in most photosynthetic eukaryotes. Additional forms of such nucleotide transporters (NTTs), with deviating activities, are found in intracellular bacteria, and, surprisingly, also in diatoms, a group of algae that acquired their plastids from other eukaryotes via one (or even several) additional endosymbioses compared to algae with primary plastids and higher plants. In this review, we summarize what is known about the nucleotide synthesis and transport pathways in diatom cells, and discuss the evolutionary implications of the presence of the additional NTTs in diatoms, as well as their applications in biotechnology. Full article
(This article belongs to the Special Issue Evolutionary and Molecular Aspects of Plastid Endosymbioses)
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Open AccessReview
What Happened to the Phycobilisome?
Biomolecules 2019, 9(11), 748; https://doi.org/10.3390/biom9110748 - 19 Nov 2019
Cited by 1
Abstract
The phycobilisome (PBS) is the major light-harvesting complex of photosynthesis in cyanobacteria, red algae, and glaucophyte algae. In spite of the fact that it is very well structured to absorb light and transfer it efficiently to photosynthetic reaction centers, it has been completely [...] Read more.
The phycobilisome (PBS) is the major light-harvesting complex of photosynthesis in cyanobacteria, red algae, and glaucophyte algae. In spite of the fact that it is very well structured to absorb light and transfer it efficiently to photosynthetic reaction centers, it has been completely lost in the green algae and plants. It is difficult to see how selection alone could account for such a major loss. An alternative scenario takes into account the role of chance, enabled by (contingent on) the evolution of an alternative antenna system early in the diversification of the three lineages from the first photosynthetic eukaryote. Full article
(This article belongs to the Special Issue Evolutionary and Molecular Aspects of Plastid Endosymbioses)
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Open AccessReview
There Is Treasure Everywhere: Reductive Plastid Evolution in Apicomplexa in Light of Their Close Relatives
Biomolecules 2019, 9(8), 378; https://doi.org/10.3390/biom9080378 - 19 Aug 2019
Cited by 5
Abstract
The phylum Apicomplexa (Alveolates) comprises a group of host-associated protists, predominately intracellular parasites, including devastating parasites like Plasmodium falciparum, the causative agent of malaria. One of the more fascinating characteristics of Apicomplexa is their highly reduced (and occasionally lost) remnant plastid, termed [...] Read more.
The phylum Apicomplexa (Alveolates) comprises a group of host-associated protists, predominately intracellular parasites, including devastating parasites like Plasmodium falciparum, the causative agent of malaria. One of the more fascinating characteristics of Apicomplexa is their highly reduced (and occasionally lost) remnant plastid, termed the apicoplast. Four core metabolic pathways are retained in the apicoplast: heme synthesis, iron–sulfur cluster synthesis, isoprenoid synthesis, and fatty acid synthesis. It has been suggested that one or more of these pathways are essential for plastid and plastid genome retention. The past decade has witnessed the discovery of several apicomplexan relatives, and next-generation sequencing efforts are revealing that they retain variable plastid metabolic capacities. These data are providing clues about the core genes and pathways of reduced plastids, while at the same time further confounding our view on the evolutionary history of the apicoplast. Here, we examine the evolutionary history of the apicoplast, explore plastid metabolism in Apicomplexa and their close relatives, and propose that the differences among reduced plastids result from a game of endosymbiotic roulette. Continued exploration of the Apicomplexa and their relatives is sure to provide new insights into the evolution of the apicoplast and apicomplexans as a whole. Full article
(This article belongs to the Special Issue Evolutionary and Molecular Aspects of Plastid Endosymbioses)
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Open AccessReview
Metabolic Innovations Underpinning the Origin and Diversification of the Diatom Chloroplast
Biomolecules 2019, 9(8), 322; https://doi.org/10.3390/biom9080322 - 30 Jul 2019
Cited by 4
Abstract
Of all the eukaryotic algal groups, diatoms make the most substantial contributions to photosynthesis in the contemporary ocean. Understanding the biological innovations that have occurred in the diatom chloroplast may provide us with explanations to the ecological success of this lineage and clues [...] Read more.
Of all the eukaryotic algal groups, diatoms make the most substantial contributions to photosynthesis in the contemporary ocean. Understanding the biological innovations that have occurred in the diatom chloroplast may provide us with explanations to the ecological success of this lineage and clues as to how best to exploit the biology of these organisms for biotechnology. In this paper, we use multi-species transcriptome datasets to compare chloroplast metabolism pathways in diatoms to other algal lineages. We identify possible diatom-specific innovations in chloroplast metabolism, including the completion of tocopherol synthesis via a chloroplast-targeted tocopherol cyclase, a complete chloroplast ornithine cycle, and chloroplast-targeted proteins involved in iron acquisition and CO2 concentration not shared between diatoms and their closest relatives in the stramenopiles. We additionally present a detailed investigation of the chloroplast metabolism of the oil-producing diatom Fistulifera solaris, which is of industrial interest for biofuel production. These include modified amino acid and pyruvate hub metabolism that might enhance acetyl-coA production for chloroplast lipid biosynthesis and the presence of a chloroplast-localised squalene synthesis pathway unknown in other diatoms. Our data provides valuable insights into the biological adaptations underpinning an ecologically critical lineage, and how chloroplast metabolism can change even at a species level in extant algae. Full article
(This article belongs to the Special Issue Evolutionary and Molecular Aspects of Plastid Endosymbioses)
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Open AccessReview
Small Genomes and Big Data: Adaptation of Plastid Genomics to the High-Throughput Era
Biomolecules 2019, 9(8), 299; https://doi.org/10.3390/biom9080299 - 24 Jul 2019
Abstract
Plastid genome sequences are becoming more readily available with the increase in high-throughput sequencing, and whole-organelle genetic data is available for algae and plants from across the diversity of photosynthetic eukaryotes. This has provided incredible opportunities for studying species which may not be [...] Read more.
Plastid genome sequences are becoming more readily available with the increase in high-throughput sequencing, and whole-organelle genetic data is available for algae and plants from across the diversity of photosynthetic eukaryotes. This has provided incredible opportunities for studying species which may not be amenable to in vivo study or genetic manipulation or may not yet have been cultured. Research into plastid genomes has pushed the limits of what can be deduced from genomic information, and in particular genomic information obtained from public databases. In this Review, we discuss how research into plastid genomes has benefitted enormously from the explosion of publicly available genome sequence. We describe two case studies in how using publicly available gene data has supported previously held hypotheses about plastid traits from lineage-restricted experiments across algal and plant diversity. We propose how this approach could be used across disciplines for inferring functional and biological characteristics from genomic approaches, including integration of new computational and bioinformatic approaches such as machine learning. We argue that the techniques developed to gain the maximum possible insight from plastid genomes can be applied across the eukaryotic tree of life. Full article
(This article belongs to the Special Issue Evolutionary and Molecular Aspects of Plastid Endosymbioses)
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Open AccessReview
Endosymbiotic Evolution of Algae, Secondary Heterotrophy and Parasitism
Biomolecules 2019, 9(7), 266; https://doi.org/10.3390/biom9070266 - 08 Jul 2019
Cited by 6
Abstract
Photosynthesis is a biochemical process essential for life, serving as the ultimate source of chemical energy for phototrophic and heterotrophic life forms. Since the machinery of the photosynthetic electron transport chain is quite complex and is unlikely to have evolved multiple independent times, [...] Read more.
Photosynthesis is a biochemical process essential for life, serving as the ultimate source of chemical energy for phototrophic and heterotrophic life forms. Since the machinery of the photosynthetic electron transport chain is quite complex and is unlikely to have evolved multiple independent times, it is believed that this machinery has been transferred to diverse eukaryotic organisms by endosymbiotic events involving a eukaryotic host and a phototrophic endosymbiont. Thus, photoautotrophy, as a benefit, is transmitted through the evolution of plastids. However, many eukaryotes became secondarily heterotrophic, reverting to hetero-osmotrophy, phagotrophy, or parasitism. Here, I briefly review the constructive evolution of plastid endosymbioses and the consequential switch to reductive evolution involving losses of photosynthesis and plastids and the evolution of parasitism from a photosynthetic ancestor. Full article
(This article belongs to the Special Issue Evolutionary and Molecular Aspects of Plastid Endosymbioses)
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