135 results on '"Paulinella"'
Search Results
2. The Evolutionary Origin of Primary Plastids
- Author
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Lhee, Duckhyun, Bhattacharya, Debashish, Yoon, Hwan Su, Schwartzbach, Steven D., editor, Kroth, Peter G., editor, and Oborník, Miroslav, editor
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- 2024
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3. Three-dimensional architecture and assembly mechanism of the egg-shaped shell in testate amoeba Paulinella micropora
- Author
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Mami Nomura, Keisuke Ohta, Yukinori Nishigami, Takuro Nakayama, Kei-Ichiro Nakamura, Kenjiro Tadakuma, and Josephine Galipon
- Subjects
testate amoeba ,shell formation ,FIB-SEM ,3D reconstruction ,3D printer ,Paulinella ,Biology (General) ,QH301-705.5 - Abstract
Unicellular euglyphid testate amoeba Paulinella micropora with filose pseudopodia secrete approximately 50 siliceous scales into the extracellular template-free space to construct a shell isomorphic to that of its mother cell. This shell-constructing behavior is analogous to building a house with bricks, and a complex mechanism is expected to be involved for a single-celled amoeba to achieve such a phenomenon; however, the three-dimensional (3D) structure of the shell and its assembly in P. micropora are still unknown. In this study, we aimed to clarify the positional relationship between the cytoplasmic and extracellular scales and the structure of the egg-shaped shell in P. micropora during shell construction using focused ion beam scanning electron microscopy (FIB-SEM). 3D reconstruction revealed an extensive invasion of the electron-dense cytoplasm between the long sides of the positioned and stacked scales, which was predicted to be mediated by actin filament extension. To investigate the architecture of the shell of P. micropora, each scale was individually segmented, and the position of its centroid was plotted. The scales were arranged in a left-handed, single-circular ellipse in a twisted arrangement. In addition, we 3D printed individual scales and assembled them, revealing new features of the shell assembly mechanism of P. micropora. Our results indicate that the shell of P. micropora forms an egg shape by the regular stacking of precisely designed scales, and that the cytoskeleton is involved in the construction process.
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- 2023
- Full Text
- View/download PDF
4. Algae obscura: The potential of rare species as model systems.
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Van Etten, Julia, Benites, Luiz Felipe, Stephens, Timothy G., Yoon, Hwan Su, and Bhattacharya, Debashish
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ENDANGERED species , *HORIZONTAL gene transfer , *RED algae , *ENDOSYMBIOSIS , *ALGAE - Abstract
Model organism research has provided invaluable knowledge about foundational biological principles. However, most of these studies have focused on species that are in high abundance, easy to cultivate in the lab, and represent only a small fraction of extant biodiversity. Here, we present three examples of rare algae with unusual features that we refer to as "algae obscura." The Cyanidiophyceae (Rhodophyta), Glaucophyta, and Paulinella (rhizarian) lineages have all transitioned out of obscurity to become models for fundamental evolutionary research. Insights have been gained into the prevalence and importance of eukaryotic horizontal gene transfer, early Earth microbial community dynamics, primary plastid endosymbiosis, and the origin of Archaeplastida. By reviewing the research that has come from the exploration of these organisms, we demonstrate that underappreciated algae have the potential to help us formulate, refine, and substantiate core hypotheses and that such organisms should be considered when establishing future model systems. [ABSTRACT FROM AUTHOR]
- Published
- 2023
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5. Endosymbiotic ratchet accelerates divergence after organelle origin: The Paulinella model for plastid evolution.
- Author
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Bhattacharya, Debashish, Etten, Julia Van, Benites, L. Felipe, and Stephens, Timothy G.
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RATCHETS , *LARVAL dispersal , *ENDOSYMBIOSIS , *AMOEBA ,REPRODUCTIVE isolation - Abstract
We hypothesize that as one of the most consequential events in evolution, primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet. Our proposal is supported by recent work on the photosynthetic amoeba, Paulinella, that underwent primary plastid endosymbiosis about 124 Mya. This amoeba model allows us to explore the early impacts of photosynthetic organelle (plastid) origin on the host lineage. The current data point to a central role for effective population size (Ne) in accelerating divergence post‐endosymbiosis due to limits to dispersal and reproductive isolation that reduce Ne, leading to local adaptation. We posit that isolated populations exploit different strategies and behaviors and assort themselves in non‐overlapping niches to minimize competition during the early, rapid evolutionary phase of organelle integration. The endosymbiotic ratchet provides a general framework for interpreting post‐endosymbiosis lineage evolution that is driven by disruptive selection and demographic and population shifts. Also see the video abstract here: https://youtu.be/gYXrFM6Zz6Q [ABSTRACT FROM AUTHOR]
- Published
- 2023
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- View/download PDF
6. Back to primary endosymbiosis: from plastids to artificial photosynthetic life-forms.
- Author
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Flores Tinoco, Valeria, Herrera-Estrella, Luis, and Lopez-Arredondo, Damar
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ENDOSYMBIOSIS , *PLASTIDS - Abstract
Throughout evolution, only two known primary photosynthetic endosymbiosis occurred, which originated the Archaeplastida and the Paulinella spp. Fundamental questions regarding primary endosymbiosis remain unsolved, but may now be addressed with the recent development of chimeric photosynthetic life-form. Cournoyer et al. could establish artificial photosynthetic endosymbiosis between yeast and cyanobacteria. [ABSTRACT FROM AUTHOR]
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- 2023
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7. Hypothesis: Trans‐splicing Generates Evolutionary Novelty in the Photosynthetic Amoeba Paulinella.
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Gabr, Arwa, Stephens, Timothy G., Bhattacharya, Debashish, and Wood, M.
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GENETIC variation , *AMOEBA , *GENETIC regulation , *GENETIC transformation , *RNA splicing , *GENE expression - Abstract
Plastid primary endosymbiosis has occurred twice, once in the Archaeplastida ancestor and once in the Paulinella (Rhizaria) lineage. Both events precipitated massive evolutionary changes, including the recruitment and activation of genes that are horizontally acquired (HGT) and the redeployment of existing genes and pathways in novel contexts. Here we address the latter aspect in Paulinella micropora KR01 (hereafter, KR01) that has independently evolved spliced leader (SL) trans‐splicing (SLTS) of nuclear–derived transcripts. We investigated the role of this process in gene regulation, novel gene origination, and endosymbiont integration. Our analysis shows that 20% of KR01 genes give rise to transcripts with at least one (but in some cases, multiple) sites of SL addition. This process, which often occurs at canonical cis‐splicing acceptor sites (internal introns), results in shorter transcripts that may produce 5′‐truncated proteins with novel functions. SL–truncated transcripts fall into four categories that may show: (i) altered protein localization, (ii) altered protein function, structure, or regulation, (iii) loss of valid alternative start codons, preventing translation, or (iv) multiple SL addition sites at the 5′‐terminus. The SL RNA genes required for SLTS are putatively absent in the heterotrophic sister lineage of photosynthetic Paulinella species. Moreover, a high proportion of transcripts derived from genes of endosymbiotic gene transfer (EGT) and HGT origin contain SL sequences. We hypothesize that truncation of transcripts by SL addition may facilitate the generation and expression of novel gene variants and that SLTS may have enhanced the activation and fixation of foreign genes in the host genome of the photosynthetic lineages, playing a key role in primary endosymbiont integration. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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8. Evidence for a robust photosystem II in the photosynthetic amoeba Paulinella.
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Gabr, Arwa, Zournas, Apostolos, Stephens, Timothy G., Dismukes, G. Charles, and Bhattacharya, Debashish
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PHOTOSYSTEMS , *CHLOROPHYLL spectra , *REACTIVE oxygen species , *AMOEBA , *OXIDATION of water - Abstract
Summary: Paulinella represents the only known case of an independent primary plastid endosymbiosis, outside Archaeplastida, that occurred c. 120 (million years ago) Ma. These photoautotrophs grow very slowly in replete culture medium with a doubling time of 6–7 d at optimal low light, and are highly sensitive to photodamage under moderate light levels.We used genomic and biophysical methods to investigate the extreme slow growth rate and light sensitivity of Paulinella, which are key to photosymbiont integration.All photosystem II (PSII) genes except psb28‐2 and all cytochrome b6f complex genes except petM and petL are present in Paulinella micropora KR01 (hereafter, KR01). Biophysical measurements of the water oxidation complex, variable chlorophyll fluorescence, and photosynthesis‐irradiance curves show no obvious evidence of PSII impairment. Analysis of photoacclimation under high‐light suggests that although KR01 can perform charge separation, it lacks photoprotection mechanisms present in cyanobacteria.We hypothesize that Paulinella species are restricted to low light environments because they are deficient in mitigating the formation of reactive oxygen species formed within the photosystems under peak solar intensities. The finding that many photoprotection genes have been lost or transferred to the host‐genome during endosymbiont genome reduction, and may lack light‐regulation, is consistent with this hypothesis. [ABSTRACT FROM AUTHOR]
- Published
- 2022
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9. Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis.
- Author
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Lhee, Duckhyun, Lee, JunMo, Ettahi, Khaoula, Cho, Chung Hyun, Ha, Ji-San, Chan, Ya-Fan, Zelzion, Udi, Stephens, Timothy G, Price, Dana C, Gabr, Arwa, Nowack, Eva C M, Bhattacharya, Debashish, and Yoon, Hwan Su
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AMOEBA ,GENE expression ,CHROMATOPHORES ,ENDOSYMBIOSIS ,PROTEOMICS - Abstract
Eukaryotic photosynthetic organelles, plastids, are the powerhouses of many aquatic and terrestrial ecosystems. The canonical plastid in algae and plants originated >1 Ga and therefore offers limited insights into the initial stages of organelle evolution. To address this issue, we focus here on the photosynthetic amoeba Paulinella micropora strain KR01 (hereafter, KR01) that underwent a more recent (∼124 Ma) primary endosymbiosis, resulting in a photosynthetic organelle termed the chromatophore. Analysis of genomic and transcriptomic data resulted in a high-quality draft assembly of size 707 Mb and 32,361 predicted gene models. A total of 291 chromatophore-targeted proteins were predicted in silico, 208 of which comprise the ancestral organelle proteome in photosynthetic Paulinella species with functions, among others, in nucleotide metabolism and oxidative stress response. Gene coexpression analysis identified networks containing known high light stress response genes as well as a variety of genes of unknown function ("dark" genes). We characterized diurnally rhythmic genes in this species and found that over 49% are dark. It was recently hypothesized that large double-stranded DNA viruses may have driven gene transfer to the nucleus in Paulinella and facilitated endosymbiosis. Our analyses do not support this idea, but rather suggest that these viruses in the KR01 and closely related P. micropora MYN1 genomes resulted from a more recent invasion. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
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10. Paulinella, a model for understanding plastid primary endosymbiosis.
- Author
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Gabr, Arwa, Grossman, Arthur R., Bhattacharya, Debashish, and Palenik, B.
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NUCLEAR DNA , *NUCLEOTIDE sequence , *ENDOSYMBIOSIS , *ORGANELLES , *CYTOPLASM , *GENE expression - Abstract
The uptake and conversion of a free‐living cyanobacterium into a photosynthetic organelle by the single‐celled Archaeplastida ancestor helped transform the biosphere from low to high oxygen. There are two documented, independent cases of plastid primary endosymbiosis. The first is the well‐studied instance in Archaeplastida that occurred ca. 1.6 billion years ago, whereas the second occurred 90–140 million years ago, establishing a permanent photosynthetic compartment (the chromatophore) in amoebae in the genus Paulinella. Here, we briefly summarize knowledge about plastid origin in the Archaeplastida and then focus on Paulinella. In particular, we describe features of the Paulinella chromatophore that make it a model for examining earlier events in the evolution of photosynthetic organelles. Our review stresses recently gained insights into the evolution of chromatophore and nuclear encoded DNA sequences in Paulinella, metabolic connectivity between the endosymbiont and cytoplasm, and systems that target proteins into the chromatophore. We also describe future work with Paulinella, and the potential rewards and challenges associated with developing further this model system. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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11. From a Free-Living Cyanobacteria to an Obligate Endosymbiotic Organelle: Early Steps in Lipid Metabolism Integration in Paulinellidae.
- Author
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Maréchal, Eric
- Subjects
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GOLGI apparatus , *LIPID metabolism , *CYANOBACTERIA , *ORGANELLES , *METABOLISM , *HORIZONTAL gene transfer , *PLANT physiology - Published
- 2020
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12. Horizontal and endosymbiotic gene transfer in early plastid evolution.
- Author
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Ponce‐Toledo, Rafael I., López‐García, Purificación, and Moreira, David
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HORIZONTAL gene transfer , *ORIGIN of life , *BACTERIAL proteins , *GREEN algae , *PLASTIDS , *PLANT phylogeny , *BIOLOGICAL evolution - Abstract
Summary: Plastids evolved from a cyanobacterium that was engulfed by a heterotrophic eukaryotic host and became a stable organelle. Some of the resulting eukaryotic algae entered into a number of secondary endosymbioses with diverse eukaryotic hosts. These events had major consequences on the evolution and diversification of life on Earth. Although almost all plastid diversity derives from a single endosymbiotic event, the analysis of nuclear genomes of plastid‐bearing lineages has revealed a mosaic origin of plastid‐related genes. In addition to cyanobacterial genes, plastids recruited for their functioning eukaryotic proteins encoded by the host nucleus and also bacterial proteins of noncyanobacterial origin. Therefore, plastid proteins and plastid‐localised metabolic pathways evolved by tinkering and using gene toolkits from different sources. This mixed heritage seems especially complex in secondary algae containing green plastids, the acquisition of which appears to have been facilitated by many previous acquisitions of red algal genes (the 'red carpet hypothesis'). [ABSTRACT FROM AUTHOR]
- Published
- 2019
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13. Three-dimensional architecture and assembly mechanism of the egg-shaped shell in testate amoeba Paulinella micropora .
- Author
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Nomura M, Ohta K, Nishigami Y, Nakayama T, Nakamura KI, Tadakuma K, and Galipon J
- Abstract
Unicellular euglyphid testate amoeba Paulinella micropora with filose pseudopodia secrete approximately 50 siliceous scales into the extracellular template-free space to construct a shell isomorphic to that of its mother cell. This shell-constructing behavior is analogous to building a house with bricks, and a complex mechanism is expected to be involved for a single-celled amoeba to achieve such a phenomenon; however, the three-dimensional (3D) structure of the shell and its assembly in P. micropora are still unknown. In this study, we aimed to clarify the positional relationship between the cytoplasmic and extracellular scales and the structure of the egg-shaped shell in P. micropora during shell construction using focused ion beam scanning electron microscopy (FIB-SEM). 3D reconstruction revealed an extensive invasion of the electron-dense cytoplasm between the long sides of the positioned and stacked scales, which was predicted to be mediated by actin filament extension. To investigate the architecture of the shell of P. micropora , each scale was individually segmented, and the position of its centroid was plotted. The scales were arranged in a left-handed, single-circular ellipse in a twisted arrangement. In addition, we 3D printed individual scales and assembled them, revealing new features of the shell assembly mechanism of P . micropora . Our results indicate that the shell of P . micropora forms an egg shape by the regular stacking of precisely designed scales, and that the cytoskeleton is involved in the construction process., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Nomura, Ohta, Nishigami, Nakayama, Nakamura, Tadakuma and Galipon.)
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- 2023
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14. Red Algal Genomics: A Synopsis
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Lopez-Bautista, Juan M., Seckbach, Joseph, editor, and Chapman, David J., editor
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- 2010
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15. Genomics-Informed Insights into Endosymbiotic Organelle Evolution in Photosynthetic Eukaryotes.
- Author
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Nowack, Eva C.M. and Weber, Andreas P.M.
- Abstract
The conversion of free-living cyanobacteria to photosynthetic organelles of eukaryotic cells through endosymbiosis transformed the biosphere and eventually provided the basis for life on land. Despite the presumable advantage conferred by the acquisition of photoautotrophy through endosymbiosis, only two independent cases of primary endosymbiosis have been documented: one that gave rise to the Archaeplastida, and the other to photosynthetic species of the thecate, filose amoeba Paulinella. Here, we review recent genomics-informed insights into the primary endosymbiotic origins of cyanobacteria-derived organelles. Furthermore, we discuss the preconditions for the evolution of nitrogen-fixing organelles. Recent genomic data on previously undersampled cyanobacterial and protist taxa provide new clues to the origins of the host cell and endosymbiont, and proteomic approaches allow insights into the rearrangement of the endosymbiont proteome during organellogenesis. We conclude that in addition to endosymbiotic gene transfers, horizontal gene acquisitions from a broad variety of prokaryotic taxa were crucial to organelle evolution. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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16. Why is primary endosymbiosis so rare?
- Author
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Arthur R. Grossman, Debashish Bhattacharya, Victoria Calatrava, Arwa Gabr, and Timothy G. Stephens
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0106 biological sciences ,0301 basic medicine ,Symbiogenesis ,Endosymbiosis ,biology ,Physiology ,fungi ,Eukaryota ,food and beverages ,Plant Science ,biology.organism_classification ,Biological Evolution ,01 natural sciences ,Article ,03 medical and health sciences ,030104 developmental biology ,Evolutionary biology ,Organelle ,Plastids ,Paulinella ,Plastid ,Amoeba ,Symbiosis ,Phylogeny ,010606 plant biology & botany - Abstract
Endosymbiosis is a relationship between two organisms wherein one cell resides inside the other. This affiliation, when stable and beneficial for the ‘host’ cell, can result in massive genetic innovation with the foremost examples being the evolution of eukaryotic organelles, the mitochondria and plastids. Despite its critical evolutionary role, there is limited knowledge about how endosymbiosis is initially established and how host–endosymbiont biology is integrated. Here, we explore this issue, using as our model the rhizarian amoeba Paulinella, which represents an independent case of primary plastid origin that occurred c. 120 million yr ago. We propose the ‘chassis and engine’ model that provides a theoretical framework for understanding primary plastid endosymbiosis, potentially explaining why it is so rare.
- Published
- 2021
17. Chapter Two - Let There Be Light: A Contemporary Primer on Primary Plastid Endosymbiosis.
- Author
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Smith, David R.
- Subjects
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BOTANICAL periodicals , *ENDOSYMBIOSIS , *PLASTIDS , *PROKARYOTES - Abstract
Endosymbiosis, more than any other process, perhaps, is the leading narrative upon which the history of eukaryotic evolution has been written. Primary endosymbiosis, which is the uptake of a prokaryote by another living cell, has arguably been the driving force for the origins and diversification of complex life on Earth. The genetic integration of, first, a nonphotosynthetic alphaproteobacterium and, later, a photosynthetic cyanobacterium into a eukaryotic cellular framework have shaped and altered the planet's biodiversity and biogeochemistry in countless ways, from the land, to the water, to the atmosphere. If you are alive today and reading these words, it is in no small part because of endosymbiosis. Like all eukaryotes, we are the product of an ancient endosymbiotic love affair, and for plants and algae the endosymbiotic romance was a complicated triangle. Here, I recount my own passions for the topic of endosymbiosis, highlighting past and present breakthroughs as well as some of the controversies and unanswered questions that have plagued the field. I focus on the evolution of primary plastids, their genomes, and the supergroup to which they are found (the Archaeplastida), including members that have lost photosynthetic capabilities but still retain a colourless plastid. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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18. Cymbomonas tetramitiformis - a peculiar prasinophyte with a taste for bacteria sheds light on plastid evolution.
- Author
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Gagat, Przemysław and Mackiewicz, Paweł
- Abstract
Cymbomonas tetramitiformis is a peculiar green alga that unites in one cell the abilities of photosynthesis and phagocytosis, which makes it a very useful model for the study of the evolution of plastid endosymbiosis. We have pondered over this issue and propose an evolutionary scenario of trophic strategies in eukaryotes, including primary and secondary plastid endosymbioses. C. tetramitiformis is a prototroph, just like the common ancestor of Archaeplastida was, and can synthesize most small organic molecules contrary to other eukaryotic phagotrophs, e.g. some metazoans, amoebozoans, and ciliates, which have not evolved tight endosymbiotic relationships. In order to establish a permanent photosynthetic endosymbiont they do not have to become prototrophs, but have to acquire the genes necessary for plastid retention via horizontal (including endosymbiotic) gene transfer. Such processes occurred successfully in the ancestors of eukaryotes with permanent secondary plastids and thus led to their great diversification. The preservation of phagocytosis in Cymbomonas (and some other prasinophytes as well) seems to result from nutrient deficiency in their oligotrophic habitats. This forces them to supplement their diet with phagocytized prey, in contrasts to the thecate amoeba Paulinella chromatophora, which also successfully transformed cyanobacteria into permanent organelles. Although Paulinella endosymbionts were acquired very recently in comparison to primary plastids, Paulinella has lost the ability to phagocytose, most probably due to the fact that it inhabits nutrient-rich environments, which renders the phagotrophy nonessential. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
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19. Review of: 'A bipartite chromatophore transit peptide and N-terminal processing of protein in the Paulinella chromatophore'
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Luis Delaye
- Subjects
biology ,Terminal (electronics) ,Chemistry ,Transit Peptide ,Bipartite graph ,Paulinella ,biology.organism_classification ,Chromatophore ,Cell biology - Published
- 2021
20. A bipartite chromatophore targeting peptide and N-terminal processing of proteins in the Paulinella chromatophore
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Pitter F. Huesgen, Eva C. M. Nowack, Andreas Perrar, Linda Oberleitner, and Luis Macorano
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Signal peptide ,symbols.namesake ,biology ,Transit Peptide ,Organelle ,Proteome ,symbols ,Paulinella ,Golgi apparatus ,Plastid ,biology.organism_classification ,Chromatophore ,Cell biology - Abstract
The cercozoan amoeba Paulinella chromatophora contains photosynthetic organelles - termed chromatophores - that evolved from a cyanobacterium ∼100 million years ago, independently from plastids in plants and algae. Despite its more recent origin, at least one third of the chromatophore proteome consists of nucleus-encoded proteins that are imported by an unknown mechanism across the chromatophore double envelope membranes. Chromatophore-targeted proteins fall into two classes. Proteins exceeding 250 amino acids carry a conserved N-terminal sequence extension, termed the ‘chromatophore transit peptide’ (crTP), that is presumably involved in guiding these proteins into the chromatophore. Short imported proteins do not carry discernable targeting signals. To explore whether the import of protein is accompanied by their N-terminal processing, here we used a mass spectrometry-based approach to determine protein N-termini in Paulinella chromatophora and identified N-termini of 208 chromatophore-localized proteins. Our study revealed extensive N-terminal modifications by acetylation and proteolytic processing in both, the nucleus and chromatophore-encoded fraction of the chromatophore proteome. Mature N-termini of 37 crTP-carrying proteins were identified, of which 30 were cleaved in a common processing region. Our results imply that the crTP mediates trafficking through the Golgi, is bipartite and surprisingly only the N-terminal third (‘part 1’) becomes cleaved upon import, whereas the rest (‘part 2’) remains at the mature proteins. In contrast, short imported proteins remain largely unprocessed. Finally, this work sheds light on N-terminal processing of proteins encoded in an evolutionary-early-stage photosynthetic organelle and suggests host-derived post-translationally acting factors involved in dynamic regulation of the chromatophore-encoded chromatophore proteome.One sentence summaryProteins targeted to the evolutionary-early-stage photosynthetic organelle of Paulinella carry a bipartite N-terminal targeting sequence that is only partially removed upon protein import.
- Published
- 2021
21. Paulinella longichromatophora sp. nov., a New Marine Photosynthetic Testate Amoeba Containing a Chromatophore.
- Author
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Kim, Sunju and Park, Myung Gil
- Subjects
FRESHWATER ecology ,PHOTOSYNTHESIS ,CHROMATOPHORES ,AMOEBA ,PLASTIDS - Abstract
The freshwater testate filose amoeba Paulinella chromatophora is the sole species in the genus to have plastids, usually termed “chromatophores”, of a Synechococcus / Prochlorococcus -like cyanobacterial origin. Here, we report a new marine phototrophic species, Paulinella longichromatophora sp. nov., using light and electron microscopy and molecular data. This new species contains two blue-green U-shaped chromatophores reaching up to 40 μm in total length. Further, the new Paulinella species is characterized by having five oral scales surrounding the pseudostomal aperture. All trees generated using three nuclear rDNA datasets (18S rDNA, 28S rDNA, and the concatenated 18S + 28S rDNA) demonstrated that three photosynthetic Paulinella species (two freshwater species, P . chromatophora and Paulinella strain FK01, and one marine species, P. longichromatophora ) congruently formed a monophyletic group with strong support (≥90% of ML and ≥0.90 of PP), but their relationship to each other within the clade remained unresolved in all trees. P. longichromatophora , nevertheless, clustered consistently together with Paulinella strain FK01 with very low support, but the clade received strong support in plastid phylogenies. Phylogenetic analyses inferred from plastid-encoded 16S rDNA and a concatenated dataset of plastid 16S + 23S rDNA demonstrated that chromatophores of all photosynthetic Paulinella species were monophyletic. The monophyletic group fell within a cyanobacteria clade having a close relationship to an α-cyanobacterial clade containing Prochlorococcus and Synechococcus species with very robust support (100% of ML and 1.0 of PP). Additionally, phylogenetic analyses of nuclear 18S rDNA and plastid 16S rDNA suggested divergent evolution within the photosynthetic Paulinella population after a single acquisition of the chromatophore. After the single acquisition of the chromatophore, ancestral photosynthetic Paulinella appears to have diverged into at least two distinct clades, one containing the marine P . longichromatophora and freshwater Paulinella strain FK01, the other P. chromatophora CCAC 0185. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
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22. Evolutionary dynamics of the chromatophore genome in three photosynthetic Paulinella species
- Author
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Sunju Kim, Debashish Bhattacharya, Hwan Su Yoon, Myung Gil Park, Ji-San Ha, and Duckhyun Lhee
- Subjects
0301 basic medicine ,Symbiogenesis ,lcsh:Medicine ,Genome ,Article ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Chromatophores ,Plastid ,Paulinella ,Amoeba ,Symbiosis ,lcsh:Science ,Gene ,Multidisciplinary ,biology ,Endosymbiosis ,Archaeplastida ,lcsh:R ,food and beverages ,biology.organism_classification ,030104 developmental biology ,Evolutionary biology ,lcsh:Q ,Genome, Protozoan ,030217 neurology & neurosurgery ,Orthologous Gene - Abstract
The thecate amoeba Paulinella is a valuable model for understanding plastid organellogenesis because this lineage has independently gained plastids (termed chromatophores) of alpha-cyanobacterial provenance. Plastid primary endosymbiosis in Paulinella occurred relatively recently (90–140 million years ago, Mya), whereas the origin of the canonical Archaeplastida plastid occurred >1,500 Mya. Therefore, these two events provide independent perspectives on plastid formation on vastly different timescales. Here we generated the complete chromatophore genome sequence from P. longichromatophora (979,356 bp, GC-content = 38.8%, 915 predicted genes) and P. micropora NZ27 (977,190 bp, GC-content = 39.9%, 911 predicted genes) and compared these data to that from existing chromatophore genomes. Our analysis suggests that when a basal split occurred among photosynthetic Paulinella species ca. 60 Mya, only 35% of the ancestral orthologous gene families from the cyanobacterial endosymbiont remained in chromatophore DNA. Following major gene losses during the early stages of endosymbiosis, this process slowed down significantly, resulting in a conserved gene content across extant taxa. Chromatophore genes faced relaxed selection when compared to homologs in free-living alpha-cyanobacteria, likely reflecting the homogeneous intracellular environment of the Paulinella host. Comparison of nucleotide substitution and insertion/deletion events among different P. micropora strains demonstrates that increases in AT-content and genome reduction are ongoing and dynamic processes in chromatophore evolution.
- Published
- 2019
23. Independent evolution of the thioredoxin system in photosynthetic Paulinella species
- Author
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Duckhyun Lhee, Debashish Bhattacharya, and Hwan Su Yoon
- Subjects
0301 basic medicine ,Symbiogenesis ,Lineage (evolution) ,Photosynthesis ,General Biochemistry, Genetics and Molecular Biology ,Article ,Evolution, Molecular ,03 medical and health sciences ,0302 clinical medicine ,Thioredoxins ,Algae ,Chromatophores ,Plastids ,Paulinella ,Plastid ,Amoeba ,Symbiosis ,Phylogeny ,biology ,Archaeplastida ,biology.organism_classification ,030104 developmental biology ,Rhizaria ,Evolutionary biology ,Thioredoxin ,General Agricultural and Biological Sciences ,030217 neurology & neurosurgery - Abstract
Redox regulation in phytoplankton is critical to monitor and stabilize metabolic pathways under changing environmental conditions(1). In plastids, the thioredoxin (TRX) system is linked to photosynthetic electron transport and fine tuning of metabolic pathways to fluctuating light levels. Expansion of the number of redox signal transmitters and their protein targets, as seen in plants, is believed to increase cell robustness(2). In this study, we searched for genes related to redox regulation in the genome of the photosynthetic amoeba Paulinella micropora KR01 (hereafter, KR01). The genus Paulinella includes testate filose amoebae, in which a single clade acquired a photosynthetic organelle, the chromatophore, from an alpha cyanobacterial donor(3). This independent primary endosymbiosis occurred relatively recently (~ 124 Ma), when compared to Archaeplastida (> 1 Ga), making photosynthetic Paulinella a valuable model for studying the earlier stages of primary endosymbiosis(4). Our comparative analysis demonstrates that this lineage has evolved a thioredoxin system similar to other algae, relying however on genes with diverse phylogenetic origins (i.e., the endosymbiont, host, bacteria, red algae). One TRX of eukaryotic provenance is targeted to the chromatophore, implicating host-endosymbiont coordination of redox regulation. A chromatophore targeted glucose-6-phosphate dehydrogenase of red algal origin suggests that Paulinella exploited the existing redox regulation system in Archaeplastida to foster integration. Our study elucidates the independent evolution of the thioredoxin system in photosynthetic Paulinella, whose parts derive from the existing genetic toolkit in diverse organisms.
- Published
- 2021
24. Correction to: The Photosynthetic Adventure of Paulinella Spp
- Author
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Katarzyna Sidorczuk, Paweł Mackiewicz, Filip Pietluch, and Przemysław Gagat
- Subjects
biology ,Botany ,Paulinella ,biology.organism_classification ,Adventure ,Photosynthesis - Published
- 2021
25. The Puzzle of Metabolite Exchange and Identification of Putative Octotrico Peptide Repeat Expression Regulators in the Nascent Photosynthetic Organelles of Paulinella chromatophora
- Author
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Linda Oberleitner, Gereon Poschmann, Luis Macorano, Stephan Schott-Verdugo, Holger Gohlke, Kai Stühler, and Eva C. M. Nowack
- Subjects
0106 biological sciences ,Microbiology (medical) ,Membrane permeability ,proteome ,lcsh:QR1-502 ,Mitochondrion ,Biology ,cyanobacteria ,01 natural sciences ,Microbiology ,lcsh:Microbiology ,03 medical and health sciences ,cercozoa ,ddc:570 ,evolution ,Organelle ,Gene expression ,Paulinella ,Plastid ,Original Research ,030304 developmental biology ,0303 health sciences ,organellogenesis ,biology.organism_classification ,Chromatophore ,Cell biology ,Transmembrane domain ,Rhizaria ,metabolite transport ,Proteome ,envelope membranes ,010606 plant biology & botany - Abstract
The cercozoan amoeba Paulinella chromatophora contains photosynthetic organelles - termed chromatophores - that evolved from a cyanobacterium, independently from plastids in plants and algae. Despite the more recent origin of the chromatophore, it shows tight integration into the host cell. It imports hundreds of nucleus-encoded proteins, and diverse metabolites are exchanged across the two chromatophore envelope membranes. However, the limited set of chromatophore-encoded transporters appears insufficient for supporting metabolic connectivity or protein import. Furthermore, chromatophore-localized biosynthetic pathways as well as multiprotein complexes include proteins of dual genetic origin, suggesting coordination of gene expression levels between chromatophore and nucleus. These findings imply that similar to the situation in mitochondria and plastids, nuclear factors evolved that control metabolite exchange and gene expression in the chromatophore. Here we show by mass spectrometric analyses of enriched insoluble protein fractions that, unexpectedly, nucleus-encoded transporters are not inserted into the chromatophore inner envelope membrane. Thus, despite the apparent maintenance of its barrier function, canonical metabolite transporters are missing in this membrane. Instead we identified several expanded groups of short chromatophore-targeted orphan proteins. Members of one of these groups are characterized by a single transmembrane helix, and others contain amphipathic helices. We hypothesize that these proteins are involved in modulating membrane permeability. Furthermore, we identified an expanded family of chromatophore-targeted helical repeat proteins. These proteins show similar domain architectures as known organelle-targeted octotrico peptide repeat expression regulators in algae and plants suggesting their convergent evolution as nuclear regulators of gene expression levels in the chromatophore.ImportanceThe endosymbiotic acquisition of mitochondria and plastids >1 billion years ago was central for the evolution of eukaryotic life. However, owing to their ancient origin, these organelles provide only limited insights into the initial stages of organellogenesis. The chromatophore in Paulinella evolved ~100 million years ago and thus, offers the possibility to gain valuable insights into early stages and common rules in organelle evolution. Critical to organellogenesis appears to be the establishment of nuclear control over metabolite exchange and gene expression in the endosymbiont. Here we show that the mechanism generating metabolic connectivity of the chromatophore fundamentally differs from the one for mitochondria and plastids, but likely rather resembles the poorly understood mechanism in various bacterial endosymbionts in plants and insects. Furthermore, we describe a novel class of chromatophore-targeted helical repeat proteins which evolved convergently to plastid-targeted expression regulators and are likely involved in gene expression control in the chromatophore.
- Published
- 2020
26. Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis
- Author
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Timothy G. Stephens, Dana C. Price, Hwan Su Yoon, Ji San Ha, Eva C. M. Nowack, Udi Zelzion, Arwa Gabr, Khaoula Ettahi, Ya Fan Chan, JunMo Lee, Duckhyun Lhee, Chung Hyun Cho, and Debashish Bhattacharya
- Subjects
0106 biological sciences ,Symbiogenesis ,food.ingredient ,Genome, Plastid ,Biology ,AcademicSubjects/SCI01180 ,01 natural sciences ,Genome ,Amoeba (genus) ,03 medical and health sciences ,food ,Organelle ,Genetics ,Chromatophores ,Paulinella ,Plastid ,Amoeba ,Symbiosis ,Molecular Biology ,Gene ,Ecology, Evolution, Behavior and Systematics ,Discoveries ,030304 developmental biology ,primary endosymbiosis ,0303 health sciences ,chromatophore ,Endosymbiosis ,AcademicSubjects/SCI01130 ,photosynthetic amoeba ,biology.organism_classification ,Evolutionary biology ,Transcriptome ,gene coexpression analysis ,Genome, Protozoan ,010606 plant biology & botany - Abstract
Eukaryotic photosynthetic organelles, plastids, are the powerhouses of many aquatic and terrestrial ecosystems. The canonical plastid in algae and plants originated >1 Ga and therefore offers limited insights into the initial stages of organelle evolution. To address this issue, we focus here on the photosynthetic amoeba Paulinella micropora strain KR01 (hereafter, KR01) that underwent a more recent (∼124 Ma) primary endosymbiosis, resulting in a photosynthetic organelle termed the chromatophore. Analysis of genomic and transcriptomic data resulted in a high-quality draft assembly of size 707 Mb and 32,361 predicted gene models. A total of 291 chromatophore-targeted proteins were predicted in silico, 208 of which comprise the ancestral organelle proteome in photosynthetic Paulinella species with functions, among others, in nucleotide metabolism and oxidative stress response. Gene coexpression analysis identified networks containing known high light stress response genes as well as a variety of genes of unknown function (“dark” genes). We characterized diurnally rhythmic genes in this species and found that over 49% are dark. It was recently hypothesized that large double-stranded DNA viruses may have driven gene transfer to the nucleus in Paulinella and facilitated endosymbiosis. Our analyses do not support this idea, but rather suggest that these viruses in the KR01 and closely related P. micropora MYN1 genomes resulted from a more recent invasion.
- Published
- 2020
27. PAULINELLA, A MODEL FOR UNDERSTANDING PLASTID PRIMARY ENDOSYMBIOSIS
- Author
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Arwa Gabr, Arthur R. Grossman, and Debashish Bhattacharya
- Subjects
0106 biological sciences ,Symbiogenesis ,Archaeplastida ,010604 marine biology & hydrobiology ,Model system ,Plant Science ,Aquatic Science ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Biological Evolution ,Article ,Rhizaria ,High oxygen ,Evolutionary biology ,Phylogenetics ,Organelle ,Chromatophores ,Plastids ,Plastid ,Paulinella ,Amoeba ,Symbiosis ,Phylogeny - Abstract
The uptake and conversion of a free-living cyanobacterium into a photosynthetic organelle by the single-celled Archaeplastida ancestor helped transform the biosphere from low to high oxygen. There are two documented, independent cases of plastid primary endosymbiosis. The first is the well-studied instance in Archaeplastida that occurred ca. 1.6 billion years ago, whereas the second occurred 90-140 million years ago, establishing a permanent photosynthetic compartment (the chromatophore) in amoebae in the genus Paulinella. Here, we briefly summarize knowledge about plastid origin in the Archaeplastida and then focus on Paulinella. In particular, we describe features of the Paulinella chromatophore that make it a model for examining earlier events in the evolution of photosynthetic organelles. Our review stresses recently gained insights into the evolution of chromatophore and nuclear encoded DNA sequences in Paulinella, metabolic connectivity between the endosymbiont and cytoplasm, and systems that target proteins into the chromatophore. We also describe future work with Paulinella, and the potential rewards and challenges associated with developing further this model system.
- Published
- 2020
28. The Photosynthetic Adventure of Paulinella Spp
- Author
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Paweł Mackiewicz, Przemysław Gagat, Filip Pietluch, and Katarzyna Sidorczuk
- Subjects
Cyanobacteria ,0303 health sciences ,biology ,Endosymbiosis ,Archaeplastida ,Rhizaria ,biology.organism_classification ,03 medical and health sciences ,Botany ,Green algae ,Paulinella ,Plastid ,Cercozoa ,030304 developmental biology - Abstract
Paulinella photosynthetic species are unicellular, silica shell-forming amoebas classified into the supergroup Rhizaria. They crawl at the bottom of freshwater and brackish environments with the help of filose pseudopodia. These protists have drawn the attention of the scientific community because of two photosynthetic bodies, called chromatophores, that fill up their cells permitting fully photoautotrophic existence. Paulinella chromatophores, similarly to primary plastids of the Archaeplastida supergroup (including glaucophytes, red algae as well as green algae and land plants), evolved from free-living cyanobacteria in the process of endosymbiosis. Interestingly, these both cyanobacterial acquisitions occurred independently, thereby undermining the paradigm of the rarity of endosymbiotic events. Chromatophores were derived from α-cyanobacteria relatively recently 60-140 million years ago, whereas primary plastids originated from β-cyanobacteria more than 1.5 billion years ago. Since their acquisition, chromatophore genomes have undergone substantial reduction but not to the extent of primary plastid genomes. Consequently, they have also developed mechanisms for transport of metabolites and nuclear-encoded proteins along with appropriate targeting signals. Therefore, chromatophores of Paulinella photosynthetic species, similarly to primary plastids, are true cellular organelles. They not only show that endosymbiotic events might not be so rare but also make a perfect model for studying the process of organellogenesis. In this chapter, we summarize the current knowledge and retrace the fascinating adventure of Paulinella species on their way to become photoautotrophic organisms.
- Published
- 2020
29. Paulinella chromatophora – niezwykła fotosyntetyczna przygoda ameby i sinicy
- Author
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Paweł Mackiewicz, Katarzyna Sidorczuk, and Przemysław Gagat
- Subjects
Amoeba (genus) ,food.ingredient ,food ,biology ,Endosymbiosis ,Algae ,Evolutionary biology ,Organelle ,Gene transfer ,Paulinella chromatophora ,Paulinella ,Plastid ,biology.organism_classification - Abstract
Pochłonięcie sinicy przez cudzożywne eukarionty i przekształcenie jej w plastyd na drodze endosymbiozy około 1.5 miliarda lat temu było jednym z najważniejszychwydarzeń w ewolucji życia na naszej planecie. Plastydy umożliwiły eukariontom odżywianie z wykorzystaniem światła słonecznego dając początek niezliczonej liczbie nowych gatunków roślin i glonów zaangażowanych w istotne relacje troficzne w skali całego globu. Ze względu na złożoność procesu przekształcenia endosymbionta bakteryjnego w organellum komórkowe, zjawisko endosymbiozy sinicy do niedawna uważane było za niepowtarzalne i wyjątkowe. Poglądy te podważyło odkrycie ameby Paulinella chromatophora zawierającej dwa fotosyntetyczne ciałka (chromatofory) właśnie pochodzenia sinicowego. Paulinella stanowi zatem drugi przykład endosymbiozy między sinicą a eukariontem, która miała miejsce stosunkowo niedawno, około 90-140 milionów lat temu. Niniejsza praca opisuje przemiany, jakim uległy sinicowe endosymbionty P. chromatophora, aby stać się organellami komórkowymi, w szczególności endosymbiontyczny transfer genów i ewolucję systemu importu białek do chromatoforów.
- Published
- 2018
30. Characterization and Biosynthesis of Lipids in Paulinella micropora MYN1: Evidence for Efficient Integration of Chromatophores into Cellular Lipid Metabolism
- Author
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Toru Yoshitomi, Naoki Sato, and Natsumi Mori-Moriyama
- Subjects
Fatty Acid Synthases ,Magnetic Resonance Spectroscopy ,Physiology ,Plant Science ,Cyanobacteria ,Organelle ,Chromatophores ,Paulinella ,chemistry.chemical_classification ,biology ,Endosymbiosis ,Fatty Acids ,Lipid metabolism ,Cell Biology ,General Medicine ,biology.organism_classification ,Lipid Metabolism ,Chromatophore ,Lipids ,Biosynthetic Pathways ,Chloroplast ,chemistry ,Biochemistry ,Isotope Labeling ,lipids (amino acids, peptides, and proteins) ,Polyunsaturated fatty acid - Abstract
The chromatophores found in the cells of photosynthetic Paulinella species, once believed to be endosymbiotic cyanobacteria, are photosynthetic organelles that are distinct from chloroplasts. The chromatophore genome is similar to the genomes of α-cyanobacteria and encodes about 1,000 genes. Therefore, the chromatophore is an intriguing model of organelle formation. In this study, we analyzed the lipids of Paulinella micropora MYN1 to verify that this organism is a composite of cyanobacterial descendants and a heterotrophic protist. We detected glycolipids and phospholipids, as well as a betaine lipid diacylglyceryl-3-O-carboxyhydroxymethylcholine, previously detected in many marine algae. Cholesterol was the only sterol component detected, suggesting that the host cell is similar to animal cells. The glycolipids, presumably present in the chromatophores, contained mainly C16 fatty acids, whereas other classes of lipids, presumably present in the other compartments, were abundant in C20 and C22 polyunsaturated fatty acids. This suggests that chromatophores are metabolically distinct from the rest of the cell. Metabolic studies using isotopically labeled substrates showed that different fatty acids are synthesized in the chromatophore and the cytosol, which is consistent with the presence of both type I and type II fatty acid synthases, supposedly present in the cytosol and the chromatophore, respectively. Nevertheless, rapid labeling of the fatty acids in triacylglycerol and phosphatidylcholine by photosynthetically fixed carbon suggested that the chromatophores efficiently provide metabolites to the host. The metabolic and ultrastructural evidence suggests that chromatophores are tightly integrated into the whole cellular metabolism.
- Published
- 2019
31. Genomics-Informed Insights into Endosymbiotic Organelle Evolution in Photosynthetic Eukaryotes
- Author
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Eva C. M. Nowack and Andreas P.M. Weber
- Subjects
0106 biological sciences ,0301 basic medicine ,Symbiogenesis ,Physiology ,Genomics ,Plant Science ,medicine.disease_cause ,01 natural sciences ,03 medical and health sciences ,Organelle ,medicine ,Photosynthesis ,Paulinella ,Plastid ,Symbiosis ,Molecular Biology ,Organelles ,biology ,Endosymbiosis ,Archaeplastida ,Eukaryota ,Protist ,Cell Biology ,biology.organism_classification ,Biological Evolution ,030104 developmental biology ,Evolutionary biology ,010606 plant biology & botany - Abstract
The conversion of free-living cyanobacteria to photosynthetic organelles of eukaryotic cells through endosymbiosis transformed the biosphere and eventually provided the basis for life on land. Despite the presumable advantage conferred by the acquisition of photoautotrophy through endosymbiosis, only two independent cases of primary endosymbiosis have been documented: one that gave rise to the Archaeplastida, and the other to photosynthetic species of the thecate, filose amoeba Paulinella. Here, we review recent genomics-informed insights into the primary endosymbiotic origins of cyanobacteria-derived organelles. Furthermore, we discuss the preconditions for the evolution of nitrogen-fixing organelles. Recent genomic data on previously undersampled cyanobacterial and protist taxa provide new clues to the origins of the host cell and endosymbiont, and proteomic approaches allow insights into the rearrangement of the endosymbiont proteome during organellogenesis. We conclude that in addition to endosymbiotic gene transfers, horizontal gene acquisitions from a broad variety of prokaryotic taxa were crucial to organelle evolution.
- Published
- 2018
32. Identification of a Marine Cyanophage in a Protist Single-cell Metagenome Assembly.
- Author
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Bhattacharya, Debashish, Price, Dana C., Bicep, Cedric, Bapteste, Eric, Sarwade, Mihir, Rajah, Veeran D., and Yoon, Hwan Su
- Subjects
- *
MARINE algae , *METAGENOMICS , *MICROBIAL diversity , *SPECIES diversity , *BACTERIAL transformation , *PHYLOGENY - Abstract
Analysis of microbial biodiversity is hampered by a lack of reference genomes from most bacteria, viruses, and algae. This necessitates either the cultivation of a restricted number of species for standard sequencing projects or the analysis of highly complex environmental DNA metagenome data. Single-cell genomics ( SCG) offers a solution to this problem by constraining the studied DNA sample to an individual cell and its associated symbionts, prey, and pathogens. We used SCG to study marine heterotrophic amoebae related to Paulinella ovalis (A. Wulff) P.W. Johnson, P.E. Hargraves & J.M. Sieburth (Rhizaria). The genus Paulinella is best known for its photosynthetic members such as P. chromatophora Lauterborn that is the only case of plastid primary endosymbiosis known outside of algae and plants. Here, we studied the phagotrophic sister taxa of P. chromatophora that are related to P. ovalis and found one SCG assembly to contain α-cyanobacterial DNA. These cyanobacterial contigs are presumably derived from prey. We also uncovered an associated cyanophage lineage (provisionally named phage PoL_ MC2). Phylogenomic analysis of the fragmented genome assembly suggested a minimum genome size of 200 Kbp for phage PoL_ MC2 that encodes 179 proteins and is most closely related to Synechococcus phage S- SM2. For this phage, gene network analysis demonstrates a highly modular genome structure typical of other cyanophages. Our work demonstrates that SCG is a powerful approach for discovering algal and protist biodiversity and for elucidating biotic interactions in natural samples. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
33. Ancient Gene Paralogy May Mislead Inference of Plastid Phylogeny.
- Author
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Qiu, Huan, Yang, Eun Chan, Bhattacharya, Debashish, and Yoon, Hwan Su
- Abstract
Because of its ancient origin more than 1 billion years ago, the highly reduced plastid genomes of Plantae (e.g., plant chloroplasts) provide limited insights into the initial stages of endosymbiont genome reduction. The photosynthetic amoeba Paulinella provides a more useful model to study this process because its alpha-cyanobacterium–derived plastid originated ∼60 Ma and the genome still contains ∼1,000 genes. Here, we compared and contrasted features associated with genome reduction due to primary endosymbiosis in Paulinella plastids and in marine, free-living strains of the picocyanobacterium, Prochlorococcus. Both types of genomes show gene inactivation, concerted evolution, and contraction of gene families that impact highly conserved single-copy phylogenetic markers in the plastid such as psbA, psbC, and psbD. Our data suggest that these photosystem II genes may provide misleading phylogenetic signal because each of the constituent Plantae lineages has likely undergone a different, independent series of events that led to their reduction to a single copy. This issue is most problematic for resolving basal Plantae relationships when differential plastid gene loss was presumably ongoing, as we observe in Paulinella species. Our work uncovers a key, previously unappreciated aspect of organelle genome reduction and demonstrates “work-in-progress” models such as Paulinella to be critical to gain a fuller understanding of algal and plant genome evolution. [ABSTRACT FROM PUBLISHER]
- Published
- 2012
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34. Differential Gene Retention in Plastids of Common Recent Origin.
- Author
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Reyes-Prieto, Adrian, Yoon, Hwan Su, Moustafa, Ahmed, Yang, Eun Chan, Andersen, Robert A., Boo, Sung Min, Nakayama, Takuro, Ishida, Ken-ichiro, and Bhattacharya, Debashish
- Abstract
The cyanobacterium-derived plastids of algae and plants have supported the diversification of much of extant eukaryotic life. Inferences about early events in plastid evolution must rely on reconstructing events that occurred over a billion years ago. In contrast, the photosynthetic amoeba Paulinella chromatophora provides an exceptional model to study organelle evolution in a prokaryote–eukaryote (primary) endosymbiosis that occurred approximately 60 mya. Here we sequenced the plastid genome (0.977 Mb) from the recently described Paulinella FK01 and compared the sequence with the existing data from the sister taxon Paulinella M0880/a. Alignment of the two plastid genomes shows significant conservation of gene order and only a handful of minor gene rearrangements. Analysis of gene content reveals 66 differential gene losses that appear to be outright gene deletions rather than endosymbiotic gene transfers to the host nuclear genome. Phylogenomic analysis validates the plastid ancestor as a member of the Synechococcus–Prochlorococcus group, and the cyanobacterial provenance of all plastid genes suggests that these organelles were not targets of interphylum gene transfers after endosymbiosis. Inspection of 681 DNA alignments of protein-encoding genes shows that the vast majority have dN/dS ratios <<1, providing evidence for purifying selection. Our study demonstrates that plastid genomes in sister taxa are strongly constrained by selection but follow distinct trajectories during the earlier phases of organelle evolution. [ABSTRACT FROM PUBLISHER]
- Published
- 2010
- Full Text
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35. Expression of hcp in freshwater Synechococcus spp., a gene encoding a hyperconserved protein in picocyanobacteria.
- Author
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Kutovaya, Olga A., Michael, R., Mckay, L., and Bullerjahn, George S.
- Subjects
CYANOBACTERIA ,MARINE organisms ,AMINO acids ,MARINE plankton ,BACTERIAL genetics - Abstract
The article presents a study which examines the relation of Hyperconserved protein (HCP) in the freshwater picocyanobacterial clade member Synechococcus spp. The study was conducted on LS 0504, KD3a, and ARC-11 strains of Synechococcus spp. that are collected from Laurentian Great Lakes in North America. It reveals that the four Synechococcus spp. strains that were tested was 100% HCP conserved. It adds that a polypeptide of 95 amino acids has been indicated by marine picocyanobacterial genomes.
- Published
- 2010
- Full Text
- View/download PDF
36. Six new marine species of the genus Paulinella (Rhizopoda: Filosea, or Rhizaria: Cercozoa).
- Author
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Nicholls, Kenneth H.
- Abstract
Six new marine species of the testate amoebid genus Paulinella are described using light and electron microscopic observations of material from Canada's Pacific Ocean coastal waters. In order of test (shell) size, from smallest to largest, the following new species are proposed: P. carsoni sp. nov., P. agassizi sp. nov., P. suzukii sp. nov., P. lauterborni sp. nov., P. multipora sp. nov. and P. gigantica sp. nov. Included in this survey are new observations on P. indentata Hannah, Rogerson & Anderson, from Canadian Pacific Ocean locations, but previously known only from Scottish coastal waters, and the common brackish/freshwater species P. chromatophora, from Ontario (Canada). These new discoveries more than double the number of previously known species of Paulinella, a genus significant for its role as a secondary producer in marine benthic ecosystems and for the possible role of its type species (P. chromatophora) as a model system for the endosymbiosis hypothesis of the evolution of chloroplast-bearing organisms. [ABSTRACT FROM PUBLISHER]
- Published
- 2009
- Full Text
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37. Diversity of the Photosynthetic Paulinella Species, with the Description of Paulinella micropora sp. nov. and the Chromatophore Genome Sequence for strain KR01
- Author
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Giuseppe C. Zuccarello, Jong Im Kim, Takuro Nakayama, Eun Chan Yang, Robert A. Andersen, Hwan Su Yoon, and Duckhyun Lhee
- Subjects
0301 basic medicine ,Whole genome sequencing ,Genetics ,biology ,Phylogenetic tree ,Endosymbiosis ,Biodiversity ,biology.organism_classification ,Microbiology ,Genome ,03 medical and health sciences ,030104 developmental biology ,Species Specificity ,Phylogenetics ,Microscopy, Electron, Scanning ,Chromatophores ,Paulinella ,Cercozoa ,Genome, Protozoan ,Phylogeny ,GC-content - Abstract
The thecate filose amoeba Paulinella chromatophora is a good model organism for understanding plastid organellogenesis because its chromatophore was newly derived from an alpha-cyanobacterium. Paulinella chromatophora was the only known photosynthetic Paulinella species until recent studies that suggested a species level of diversity. Here, we described a new photosynthetic species P. micropora sp. nov. based on morphological and molecular evidence from a newly established strain KR01. The chromatophore genome of P. micropora KR01 was fully determined; the genome was 976,991bp in length, the GC content was 39.9%, and 908 genes were annotated. A pairwise comparison of chromatophore genome sequences between strains KR01 and FK01, representing two different natural populations of P. micropora, showed a 99.85% similarity. Differences between the two strains included single nucleotide polymorphisms (SNPs) in CDSs, which resulted in 357 synonymous and 280 nonsynonymous changes, along with 245 SNPs in non-coding regions. Indels (37) and microinversions (14) were also detected. Species diversity for photosynthetic Paulinella was surveyed using samples collected from around the world. We compared our new species to two photosynthetic species, P. chromatophora and P. longichromatophora. Phylogenetic analyses using four gene markers revealed three distinct lineages of photosynthetic Paulinella species including P. micropora sp. nov.
- Published
- 2017
38. Large DNA virus promoted the endosymbiotic evolution to make a photosynthetic eukaryote
- Author
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Asao Fujiyama, Takuro Nakayama, Mitsuhiro Matsuo, Atsushi Katahata, Makoto Tachikawa, Yohei Minakuchi, Atsushi Toyoda, Yuji Inagaki, Ryoma Kamikawa, Yutaka Suzuki, Soichirou Satoh, Junichi Obokata, Mami Nomura, Ken-ichiro Ishida, Hideki Noguchi, and Takayuki Hata
- Subjects
Whole genome sequencing ,biology ,Endosymbiosis ,Evolutionary biology ,Organelle ,Eukaryote ,DNA virus ,Paulinella ,biology.organism_classification ,Genome ,Gene - Abstract
Chloroplasts in photosynthetic eukaryotes originated from a cyanobacterial endosymbiosis far more than 1 billion years ago1-3. Due to this ancientness, it remains unclear how this evolutionary process proceeded. To unveil this mystery, we analysed the whole genome sequence of a photosynthetic rhizarian amoeba4, Paulinella micropora5,6, which has a chloroplast-like organelle that originated from another cyanobacterial endosymbiosis7-10 about 0.1 billion years ago11. Here we show that the predacious amoeba that engulfed cyanobacteria evolved into a photosynthetic organism very quickly in the evolutionary time scale, probably aided by the drastic genome reorganization activated by large DNA virus. In the endosymbiotic evolution of eukaryotic cells, gene transfer from the endosymbiont genome to the host nucleus is essential for the evolving host cell to control the endosymbiont-derived organelle12. In P. micropora, we found that the gene transfer from the free-living and endosymbiotic bacteria to the amoeba nucleus was rapidly activated but both simultaneously ceased within the initiation period of the endosymbiotic evolution, suggesting that the genome reorganization drastically proceeded and completed. During this period, large DNA virus appeared to have infected the amoeba, followed by the rapid amplification and diversification of virus-related genes. These findings led us to re-examine the conventional endosymbiotic evolutionary scenario that exclusively deals with the host and the symbiont, and to extend it by incorporating a third critical player, large DNA virus, which activates the drastic gene transfer and genome reorganization between them. This Paulinella version of the evolutionary hypothesis deserves further testing of its generality in evolutionary systems and could shed light on the unknown roles of large DNA viruses13 in the evolution of terrestrial life.
- Published
- 2019
39. Paulinella micropora KR01 holobiont genome assembly for studying primary plastid evolution
- Author
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Che Ok Jeon, Dana C. Price, Duckhyun Lhee, Chung Hyun Cho, Debashish Bhattacharya, Hwan Su Yoon, JunMo Lee, Arwa Gabr, Ya Fan Chan, Sang Eun Jeong, Udi Zelzion, and Ji San Ha
- Subjects
Holobiont ,Genetics ,biology ,Endosymbiosis ,Archaeplastida ,Rhizaria ,Plastid ,Paulinella ,biology.organism_classification ,Mesorhizobium amorphae ,Genome - Abstract
The widespread algal and plant (Archaeplastida) plastid originated >1 billion years ago, therefore relatively little can be learned about plastid integration during the initial stages of primary endosymbiosis by studying these highly derived species. Here we focused on a unique model for endosymbiosis research, the photosynthetic amoeba Paulinella micropora KR01 (Rhizaria) that underwent a more recent independent primary endosymbiosis about 124 Mya. A total of 149 Gbp of PacBio and 19 Gbp of Illumina data were used to generate the draft assembly that comprises 7,048 contigs with N50=143,028 bp and a total length of 707 Mbp. Genome GC-content was 44% with 76% repetitive sequences. We predicted 32,358 genes that contain 73% of the complete, conserved genes in the BUSCO database. The mean intron length was 882 bp, which is significantly greater than in other Rhizaria (86∼184 bp). Symbiotic bacteria from the culture were isolated and completed genomes were generated from three species (Mesorhizobium amorphae Pch-S, Methylibium petroeiphilum Pch-M, Polaromonas sp. Pch-P) with one draft genome (Pimelobacter simplex Pch-N). Our holobiont data establish P. micropora KR01 as a model for studying plastid integration and the role of bacterial symbionts in Paulinella biology.
- Published
- 2019
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40. Horizontal and endosymbiotic gene transfer in early plastid evolution
- Author
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Rafael I. Ponce-Toledo, David Moreira, Purificación López-García, Ecologie Systématique et Evolution (ESE), and Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0106 biological sciences ,0301 basic medicine ,Gene Transfer, Horizontal ,Physiology ,[SDV]Life Sciences [q-bio] ,Plant Science ,01 natural sciences ,Genome ,Article ,03 medical and health sciences ,Algae ,Organelle ,Plastids ,Photosynthesis ,Plastid ,Paulinella ,Symbiosis ,Gene ,ComputingMilieux_MISCELLANEOUS ,biology ,Endosymbiosis ,Archaeplastida ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,fungi ,food and beverages ,biology.organism_classification ,Biological Evolution ,030104 developmental biology ,Gene Expression Regulation ,Evolutionary biology ,010606 plant biology & botany - Abstract
Plastids evolved from a cyanobacterium that was engulfed by a heterotrophic eukaryotic host and became a stable organelle. Some of the resulting eukaryotic algae entered into a number of secondary endosymbioses with diverse eukaryotic hosts. These events had major consequences on the evolution and diversification of life on Earth. Although almost all plastid diversity derives from a single endosymbiotic event, analysis of nuclear genomes of plastid-bearing lineages has revealed a mosaic origin of plastid-related genes. In addition to cyanobacterial genes, plastids recruited for their functioning eukaryotic proteins encoded by the host nucleus and also bacterial proteins of non-cyanobacterial origin. Thus, plastid proteins and plastid-localized metabolic pathways evolved by tinkering using the gene toolkits provided by the cyanobacterial endosymbiont, its eukaryotic host, and other bacteria. This mixed heritage seems especially complex in secondary algae containing green plastids, the acquisition of which appears to have been facilitated by many previous acquisitions of red algal genes (the “red carpet hypothesis”).
- Published
- 2019
- Full Text
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41. Evolution: Protein Import in a Nascent Photosynthetic Organelle
- Author
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John M. Archibald
- Subjects
0301 basic medicine ,food.ingredient ,biology ,macromolecular substances ,biology.organism_classification ,Proteomics ,Photosynthesis ,Biological Evolution ,Chromatophore ,General Biochemistry, Genetics and Molecular Biology ,Cell biology ,Amoeba (genus) ,03 medical and health sciences ,030104 developmental biology ,food ,Organelle ,Plastids ,Paulinella ,Plastid ,Amoeba ,Cercozoa ,Symbiosis ,General Agricultural and Biological Sciences - Abstract
Summary An amoeba named Paulinella harbours ‘chromatophores', cyanobacterium-derived photosynthetic bodies that evolved independent of plastids. Proteomics has shown that hundreds of nucleus-encoded proteins are targeted to the chromatophore, revealing the host cell's contributions to its recently established organelle.
- Published
- 2017
42. How did cyanobacteria first embark on the path to becoming plastids?: lessons from protist symbioses
- Author
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Gregory S. Gavelis and Gillian H. Gile
- Subjects
0301 basic medicine ,Symbiogenesis ,Biology ,Cyanobacteria ,medicine.disease_cause ,Microbiology ,03 medical and health sciences ,Genetics ,medicine ,Humans ,Plastids ,Photosynthesis ,Plastid ,Paulinella ,Symbiosis ,Molecular Biology ,Obligate ,Phototroph ,Endosymbiosis ,Eukaryota ,Protist ,biology.organism_classification ,Biological Evolution ,030104 developmental biology ,Evolutionary biology ,Eukaryote ,Directed Molecular Evolution ,Genetic Engineering - Abstract
Symbioses between phototrophs and heterotrophs (a.k.a 'photosymbioses') are extremely common, and range from loose and temporary associations to obligate and highly specialized forms. In the history of life, the most transformative was the 'primary endosymbiosis,' wherein a cyanobacterium was engulfed by a eukaryote and became genetically integrated as a heritable photosynthetic organelle, or plastid. By allowing the rise of algae and plants, this event dramatically altered the biosphere, but its remote origin over one billion years ago has obscured the sequence of events leading to its establishment. Here, we review the genetic, physiological and developmental hurdles involved in early primary endosymbiosis. Since we cannot travel back in time to witness these evolutionary junctures, we will draw on examples of unicellular eukaryotes (protists) spanning diverse modes of photosymbiosis. We also review experimental approaches that could be used to recreate aspects of early primary endosymbiosis on a human timescale.
- Published
- 2018
43. Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer
- Author
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Junichi Obokata, Mami Nomura, Atsushi Katahata, Soichirou Satoh, Ken-ichiro Ishida, Mitsuhiro Matsuo, Motomichi Matsuzaki, and Yuji Inagaki
- Subjects
0301 basic medicine ,Polyadenylation ,Molecular biology ,lcsh:Medicine ,Artificial Gene Amplification and Extension ,Genome ,Biochemistry ,Polymerase Chain Reaction ,Trans-Splicing ,Database and Informatics Methods ,0302 clinical medicine ,DNA library construction ,Paulinella ,Photosynthesis ,lcsh:Science ,Phylogeny ,Genetics ,Protozoans ,Multidisciplinary ,biology ,Messenger RNA ,Eukaryota ,Biodiversity ,Genomics ,Genomic Library Construction ,Nucleic acids ,Sequence Analysis ,Research Article ,RNA, Spliced Leader ,Genome evolution ,Symbiogenesis ,Trypanosoma ,Gene Transfer, Horizontal ,Bioinformatics ,DNA construction ,Research and Analysis Methods ,Evolution, Molecular ,03 medical and health sciences ,Sequence Motif Analysis ,Chromatophores ,Cercozoa ,Symbiosis ,Gene ,Sequence Assembly Tools ,cDNA library ,lcsh:R ,Organisms ,RNA ,Biology and Life Sciences ,Computational Biology ,DNA, Protozoan ,biology.organism_classification ,Genome Analysis ,Parasitic Protozoans ,030104 developmental biology ,Molecular biology techniques ,lcsh:Q ,Genome, Protozoan ,Sequence Alignment ,030217 neurology & neurosurgery - Abstract
Paulinella micropora is a rhizarian thecate amoeba, belonging to a photosynthetic Paulinella species group that has a unique organelle termed chromatophore, whose cyanobacterial origin is distinct from that of plant and algal chloroplasts. Because acquisition of the chromatophore was quite a recent event compared with that of the chloroplast ancestor, the Paulinella species are thought to be model organisms for studying the early process of primary endosymbiosis. To obtain insight into how endosymbiotically transferred genes acquire expression competence in the host nucleus, here we analyzed the 5′ end sequences of the mRNAs of P. micropora MYN1 strain with the aid of a cap-trapper cDNA library. As a result, we found that mRNAs of 27 genes, including endosymbiotically transferred genes, possessed the common 5′ end sequence of 28–33 bases that were posttranscriptionally added by spliced leader (SL) trans-splicing. We also found two subtypes of SL RNA genes encoded by the P. micropora MYN1 genome. Differing from the other SL trans-splicing organisms that usually possess poly(A)-less SL RNAs, this amoeba has polyadenylated SL RNAs. In this study, we characterize the SL trans-splicing of this unique organism and discuss the putative merits of SL trans-splicing in functional gene transfer and genome evolution.
- Published
- 2018
44. Early photosynthetic eukaryotes inhabited low-salinity habitats
- Author
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Davide Pisani, Andrew H. Knoll, Patricia Sánchez-Baracaldo, and John A. Raven
- Subjects
0106 biological sciences ,0301 basic medicine ,Cyanobacteria ,Salinity ,Chloroplasts ,Lineage (evolution) ,Origin of Life ,relaxed molecular clock ,01 natural sciences ,Evolution, Molecular ,03 medical and health sciences ,chloroplast ,Chlorophyta ,Botany ,primary endosymbiotic event ,Plastids ,Paulinella ,Plastid ,Great Oxidation Event ,Photosynthesis ,Symbiosis ,Genome, Chloroplast ,Ecosystem ,Phylogeny ,Photosynthetic eukaryotes ,Multidisciplinary ,biology ,Endosymbiosis ,Archaeplastida ,Eukaryota ,phylogenomics ,Bayes Theorem ,biology.organism_classification ,Biological Evolution ,Chloroplast ,030104 developmental biology ,Phytoplankton ,Rhodophyta ,Green algae ,Precambrian ,010606 plant biology & botany - Abstract
© 2017, National Academy of Sciences. All rights reserved. The early evolutionary history of the chloroplast lineage remains an open question. It is widely accepted that the endosymbiosis that established the chloroplast lineage in eukaryotes can be traced back to a single event, in which a cyanobacterium was incorporated into a protistan host. It is still unclear, however, which Cyanobacteria are most closely related to the chloroplast, when the plastid lineage first evolved, and in what habitats this endosymbiotic event occurred. We present phylogenomic and molecular clock analyses, including data from cyanobacterial and chloroplast genomes using a Bayesian approach, with the aim of estimating the age for the primary endosymbiotic event, the ages of crown groups for photosynthetic eukaryotes, and the independent incorporation of a cyanobacterial endosymbiont by Paulinella. Our analyses include both broad taxon sampling (119 taxa) and 18 fossil calibrations across all Cyanobacteria and photosynthetic eukaryotes. Phylogenomic analyses support the hypothesis that the chloroplast lineage diverged from its closet relative Gloeomargarita, a basal cyanobacterial lineage, ~2.1 billion y ago (Bya). Our analyses suggest that the Archaeplastida, consisting of glaucophytes, red algae, green algae, and land plants, share a common ancestor that lived ~1.9 Bya. Whereas crown group Rhodophyta evolved in the Mesoproterozoic Era (1,600–1,000 Mya), crown groups Chlorophyta and Streptophyta began to radiate early in the Neoproterozoic (1,000–542 Mya). Stochastic mapping analyses indicate that the first endosymbiotic event occurred in low-salinity environments. Both red and green algae colonized marine environments early in their histories, with prasinophyte green phytoplankton diversifying 850–650 Mya.
- Published
- 2017
45. Massive Protein Import into the Early-Evolutionary-Stage Photosynthetic Organelle of the Amoeba Paulinella chromatophora
- Author
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Cecilio Valadez-Cano, Vanessa Hüren, Anna Singer, Cornelia Mühlich, Sebastian Hänsch, Gereon Poschmann, Stefan A. Rensing, Kai Stühler, and Eva C. M. Nowack
- Subjects
0301 basic medicine ,Gene Transfer, Horizontal ,Proteome ,Protozoan Proteins ,medicine.disease_cause ,General Biochemistry, Genetics and Molecular Biology ,Mass Spectrometry ,Evolution, Molecular ,03 medical and health sciences ,Chloroplast localization ,Sequence Analysis, Protein ,Protein targeting ,Organelle ,medicine ,Chromatophores ,Paulinella ,Plastid ,Cercozoa ,Symbiosis ,biology ,Endosymbiosis ,biology.organism_classification ,Cell biology ,030104 developmental biology ,Eukaryote ,General Agricultural and Biological Sciences ,Metabolic Networks and Pathways - Abstract
The endosymbiotic acquisition of mitochondria and plastids more than 1 Ga ago profoundly impacted eukaryote evolution. At the heart of understanding organelle evolution is the re-arrangement of the endosymbiont proteome into a host-controlled organellar proteome. However, early stages in this process as well as the timing of events that underlie organelle integration remain poorly understood. The amoeba Paulinella chromatophora contains cyanobacterium-derived photosynthetic organelles, termed "chromatophores," that were acquired more recently (around 100 Ma ago). To explore the re-arrangement of an organellar proteome during its integration into a eukaryotic host cell, here we characterized the chromatophore proteome by protein mass spectrometry. Apparently, genetic control over the chromatophore has shifted substantially to the nucleus. Two classes of nuclear-encoded proteins-which differ in protein length-are imported into the chromatophore, most likely through independent pathways. Long imported proteins carry a putative, conserved N-terminal targeting signal, and many specifically fill gaps in chromatophore-encoded metabolic pathways or processes. Surprisingly, upon heterologous expression in a plant cell, the putative chromatophore targeting signal conferred chloroplast localization. This finding suggests common features in the protein import pathways of chromatophores and plastids, two organelles that evolved independently and more than 1 Ga apart from each other. By combining experimental data with in silico predictions, we provide a comprehensive catalog of almost 450 nuclear-encoded, chromatophore-targeted proteins. Interestingly, most imported proteins seem to derive from ancestral host genes, suggesting that the re-targeting of nuclear-encoded proteins that resulted from endosymbiotic gene transfers plays only a minor role at the onset of chromatophore integration.
- Published
- 2017
46. Exploring Biotic Interactions Within Protist Cell Populations Using Network Methods
- Author
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Slim Karkar, Dana C. Price, Shu Cheng, and Debashish Bhattacharya
- Subjects
Genome ,biology ,Protein family ,Assortativity ,Eukaryota ,Protist ,Genomics ,biology.organism_classification ,medicine.disease_cause ,Microbiology ,chemistry.chemical_compound ,chemistry ,Evolutionary biology ,Bigelowiella natans ,Botany ,medicine ,Paulinella ,Cercozoa ,DNA - Abstract
The study of diseased human cells and of cells isolated from the natural environment will likely be revolutionized by single cell genomics (SCG). Here, we used protein similarity networks to explore within- and between-cell DNA differences from SCG data derived from six individual rhizarian cells related to Paulinella ovalis and proteins from the complete genome of another rhizarian, Bigelowiella natans. We identified shared and distinct DNA components within our SCG data and between P. ovalis and B. natans. We show that network properties such as assortativity and degree effectively discriminate genome features between SCG assemblies and that SCG data follow the power law with a small number of protein families dominating networks.
- Published
- 2014
47. Applications of next-generation sequencing to unravelling the evolutionary history of algae
- Author
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Hwan Su Yoon, Jun-Hyung Park, Debashish Bhattacharya, and Kyeong Mi Kim
- Subjects
Symbiogenesis ,medicine.disease_cause ,Microbiology ,Algae ,Chlorophyta ,Botany ,medicine ,Plastids ,Viridiplantae ,Photosynthesis ,Paulinella ,Plastid ,Genome, Chloroplast ,Symbiosis ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,biology ,Endosymbiosis ,Protist ,Genomics ,Sequence Analysis, DNA ,General Medicine ,biology.organism_classification ,Biological Evolution ,Chloroplast ,Evolutionary biology ,Genome, Mitochondrial ,Rhodophyta ,Transcriptome - Abstract
First-generation Sanger DNA sequencing revolutionized science over the past three decades and the current next-generation sequencing (NGS) technology has opened the doors to the next phase in the sequencing revolution. Using NGS, scientists are able to sequence entire genomes and to generate extensive transcriptome data from diverse photosynthetic eukaryotes in a timely and cost-effective manner. Genome data in particular shed light on the complicated evolutionary history of algae that form the basis of the food chain in many environments. In the Eukaryotic Tree of Life, the fact that photosynthetic lineages are positioned in four supergroups has important evolutionary consequences. We now know that the story of eukaryotic photosynthesis unfolds with a primary endosymbiosis between an ancestral heterotrophic protist and a captured cyanobacterium that gave rise to the glaucophytes, red algae and Viridiplantae (green algae and land plants). These primary plastids were then transferred to other eukaryotic groups through secondary endosymbiosis. A red alga was captured by the ancestor(s) of the stramenopiles, alveolates (dinoflagellates, apicomplexa, chromeridae), cryptophytes and haptophytes, whereas green algae were captured independently by the common ancestors of the euglenophytes and chlorarachniophytes. A separate case of primary endosymbiosis is found in the filose amoeba Paulinella chromatophora, which has at least nine heterotrophic sister species. Paulinella genome data provide detailed insights into the early stages of plastid establishment. Therefore, genome data produced by NGS have provided many novel insights into the taxonomy, phylogeny and evolutionary history of photosynthetic eukaryotes.
- Published
- 2014
48. Paulinella chromatophora – rethinking the transition from endosymbiont to organelle
- Author
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Eva C. M. Nowack
- Subjects
Genome evolution ,Symbiogenesis ,food.ingredient ,Plant Science ,Biology ,plastid evolution ,medicine.disease_cause ,Amoeba (genus) ,food ,cyanobacterium ,lcsh:Botany ,Organelle ,Botany ,Protein targeting ,protein targeting ,medicine ,Plastid ,Paulinella ,endosymbiosis ,photosynthesis ,chromatophore ,Endosymbiosis ,fungi ,organellogenesis ,biology.organism_classification ,lcsh:QK1-989 ,Rhizaria ,Evolutionary biology - Abstract
Eukaryotes co-opted photosynthetic carbon fixation from prokaryotes by engulfing a cyanobacterium and stably integrating it as a photosynthetic organelle (plastid) in a process known as primary endosymbiosis. The sheer complexity of interactions between a plastid and the surrounding cell that started to evolve over 1 billion years ago, make it challenging to reconstruct intermediate steps in organelle evolution by studying extant plastids. Recently, the photosynthetic amoeba Paulinella chromatophora was identified as a much sought-after intermediate stage in the evolution of a photosynthetic organelle. This article reviews the current knowledge on this unique organism. In particular it describes how the interplay of reductive genome evolution, gene transfers, and trafficking of host-encoded proteins into the cyanobacterial endosymbiont contributed to transform the symbiont into a nascent photosynthetic organelle. Together with recent results from various other endosymbiotic associations a picture emerges that lets the targeting of host-encoded proteins into bacterial endosymbionts appear as an early step in the establishment of an endosymbiotic relationship that enables the host to gain control over the endosymbiont.
- Published
- 2014
49. Protein translocons in photosynthetic organelles of Paulinella chromatophora
- Author
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Paweł Mackiewicz and Przemysław Gagat
- Subjects
Cyanobacteria ,endosymbiosis ,Nuclear gene ,Endosymbiosis ,biology ,Archaeplastida ,primary plastids ,Plant Science ,biology.organism_classification ,Translocon ,translocons ,lcsh:QK1-989 ,Cell biology ,chromatophores ,Essential gene ,lcsh:Botany ,protein import ,Plastid ,Paulinella ,Paulinella chromatophora - Abstract
The rhizarian amoeba Paulinella chromatophora harbors two photosynthetic cyanobacterial endosymbionts (chromatophores), acquired independently of primary plastids of glaucophytes, red algae and green plants. These endosymbionts have lost many essential genes, and transferred substantial number of genes to the host nuclear genome via endosymbiotic gene transfer (EGT), including those involved in photosynthesis. This indicates that, similar to primary plastids, Paulinella endosymbionts must have evolved a transport system to import their EGT-derived proteins. This system involves vesicular trafficking to the outer chromatophore membrane and presumably a simplified Tic-like complex at the inner chromatophore membrane. Since both sequenced Paulinella strains have been shown to undergo differential plastid gene losses, they do not have to possess the same set of Toc and Tic homologs. We searched the genome of Paulinella FK01 strain for potential Toc and Tic homologs, and compared the results with the data obtained for Paulinella CCAC 0185 strain, and 72 cyanobacteria, eight Archaeplastida as well as some other bacteria. Our studies revealed that chromatophore genomes from both Paulinella strains encode the same set of translocons that could potentially create a simplified but fully-functional Tic-like complex at the inner chromatophore membranes. The common maintenance of the same set of translocon proteins in two Paulinella strains suggests a similar import mechanism and/or supports the proposed model of protein import. Moreover, we have discovered a new putative Tic component, Tic62, a redox sensor protein not identified in previous comparative studies of Paulinella translocons.
- Published
- 2014
50. Symbionts into Organelles: Mitochondria, Plastids, and Their Kin
- Author
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Harold, Franklin M., author
- Published
- 2014
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