Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
Genome sequencing reveals metabolic and cellular interdependence in an amoeba-kinetoplastid symbiosis.
Tanifuji G
,
Cenci U
,
Moog D
,
Dean S
,
Nakayama T
,
David V
,
Fiala I
,
Curtis BA
,
Sibbald SJ
,
Onodera NT
,
Colp M
,
Flegontov P
,
Johnson-MacKinnon J
,
McPhee M
,
Inagaki Y
,
Hashimoto T
,
Kelly S
,
Gull K
,
Lukeš J
,
Archibald JM
.
???displayArticle.abstract???
Endosymbiotic relationships between eukaryotic and prokaryotic cells are common in nature. Endosymbioses between two eukaryotes are also known; cyanobacterium-derived plastids have spread horizontally when one eukaryote assimilated another. A unique instance of a non-photosynthetic, eukaryotic endosymbiont involves members of the genus Paramoeba, amoebozoans that infect marine animals such as farmed fish and sea urchins. Paramoeba species harbor endosymbionts belonging to the Kinetoplastea, a diverse group of flagellate protists including some that cause devastating diseases. To elucidate the nature of this eukaryote-eukaryote association, we sequenced the genomes and transcriptomes of Paramoeba pemaquidensis and its endosymbiont Perkinsela sp. The endosymbiont nuclear genome is ~9.5 Mbp in size, the smallest of a kinetoplastid thus far discovered. Genomic analyses show that Perkinsela sp. has lost the ability to make a flagellum but retains hallmark features of kinetoplastid biology, including polycistronic transcription, trans-splicing, and a glycosome-like organelle. Mosaic biochemical pathways suggest extensive ''cross-talk'' between the two organisms, and electron microscopy shows that the endosymbiont ingests amoeba cytoplasm, a novel form of endosymbiont-host communication. Our data reveal the cell biological and biochemical basis of the obligate relationship between Perkinsela sp. and its amoeba host, and provide a foundation for understanding pathogenicity determinants in economically important Paramoeba.
Figure 1.
Paramoeba and its kinetoplastid endosymbiont Perkinsela. (a) Paramoeba sp. cells stained with haematoxylin and eosin in histological sections of gill tissue of Salmo salar (NP = nucleus of the host amoeba; En = Perkinsela sp. endosymbiont). (b) Trophozoites of P. pemaquidensis in hanging drop preparations under Nomarski differential interference contrast microscopy. (c) High-pressure freezing scanning electron microscopy (SEM) of a P. pemaquidensis cell with prominent endosymbiont (MP = plasma membrane of P. pemaquidensis). (d) SEM of the host amoeba nucleus and associated endosymbiont with surface invaginations (arrows). (e–i). Transmission electron microscopy (TEM) of P. pemaquidensis and Perkinsela sp. (e and f) TEMs showing close association of the P. pemaquidensis nucleus (NP) and the endosymbiont Perkinsela sp., the kinetoplast (K) of the endosymbiont, the endosymbiont nucleus (N), vesicles within the endosymbiont cytoplasm (Ve), and mitochondria (M) within P. pemaquidensis. (g–i) TEMs showing ultrastructure of plasma membrane-associated putative endocytotic vesicles within the cytoplasm of Perkinsela sp. White arrows indicate the vesicle membrane, black arrows highlight glycoprotein-rich material on the inner surface of the vesicle, which is continuous with the outer surface of the plasma membrane.
Figure 2. Functional diversity of proteins in Perkinsela sp. compared to other kinetoplastids. (a) Venn diagram shows overlap in the number of proteins assigned a KOG ID encoded in the nuclear genome of Perkinsela sp. CCMP1560/4, the free-living flagellate Bodo saltans
25, the human pathogen Trypanosoma brucei
27, and the plant pathogen Phytomonas sp.26. Functions were assigned based on the euKaryotic Orthologous Groups (KOG) database29. The total number of proteins predicted from the nuclear genome of each organism is also shown. (b) Histogram showing the unique numbers of KOG IDs found in Perkinsela sp., Phytomonas sp., T. brucei and B. saltans. KOG categories are as follows: A, RNA processing and modification; B, chromatin structure and dynamics; C, energy production and conversion; D, cell cycle control, cell division and chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation, ribosomal structure and biogenesis; K, transcription; L, replication, recombination and repair; M, cell wall, membrane or envelope biogenesis; N, cell motility; O, post-translational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; R, general function prediction only; S, function unknown; T, signal transduction; U, intracellular trafficking, secretion and vesicular transport; V, defence mechanisms; W, extracellular structures; Y, nuclear structure; Z, cytoskeleton. Higher KOG categories are as follows: CP, cellular processing and signalling; Hyp, poorly characterized; Inf, information storage and processing; Met, metabolism.
Figure 3. Metabolic maps for Paramoeba pemaquidensis (host) and Perkinsela sp. (endosymbiont). (a) Global metabolic maps. Nodes represent metabolic compounds and lines represent enzyme-catalyzed biochemical reactions. Metabolic maps were based on KEGG annotations and generated using the interactive Pathways Explorer (iPath 2.0). Colored lines indicate enzymes/reactions predicted to be present in one or both organisms. (b–d) Close-ups of trypanothione, heme and ubiquinone metabolism, respectively. Color-coding corresponds to part a.
Figure 4. Schematic diagram of Paramoeba pemaquidensis and its endosymbiont Perkinsela sp. The number of protein-coding genes in each genome is shown. Arrows show possible host-endosymbiont exchange of metabolites via endocytosis and exocytosis by Perkinsela sp. Abbreviation: MT, mitochondrion.
Abeel,
GenomeView: a next-generation genome browser.
2012, Pubmed
Abeel,
GenomeView: a next-generation genome browser.
2012,
Pubmed
Aslett,
TriTrypDB: a functional genomic resource for the Trypanosomatidae.
2010,
Pubmed
Barrett,
The trypanosomiases.
2003,
Pubmed
Bennett,
Heritable symbiosis: The advantages and perils of an evolutionary rabbit hole.
2015,
Pubmed
Berriman,
The genome of the African trypanosome Trypanosoma brucei.
2005,
Pubmed
Boetzer,
Scaffolding pre-assembled contigs using SSPACE.
2011,
Pubmed
Boisvert,
Ray Meta: scalable de novo metagenome assembly and profiling.
2012,
Pubmed
Broadhead,
Flagellar motility is required for the viability of the bloodstream trypanosome.
2006,
Pubmed
Butter,
Comparative proteomics of two life cycle stages of stable isotope-labeled Trypanosoma brucei reveals novel components of the parasite's host adaptation machinery.
2013,
Pubmed
Callahan,
Molecular taxonomy of the suborder Bodonina (Order Kinetoplastida), including the important fish parasite, Ichthyobodo necator.
2002,
Pubmed
Capella-Gutiérrez,
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
2009,
Pubmed
Caraguel,
Microheterogeneity and coevolution: an examination of rDNA sequence characteristics in Neoparamoeba pemaquidensis and its prokinetoplastid endosymbiont.
2007,
Pubmed
Cenci,
Heme pathway evolution in kinetoplastid protists.
2016,
Pubmed
Chikhi,
Informed and automated k-mer size selection for genome assembly.
2014,
Pubmed
Crosbie,
In vitro cultured Neoparamoeba perurans causes amoebic gill disease in Atlantic salmon and fulfils Koch's postulates.
2012,
Pubmed
David,
Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid.
2015,
Pubmed
Dean,
Host control and nutrient trading in a photosynthetic symbiosis.
2016,
Pubmed
Dean,
Cilium transition zone proteome reveals compartmentalization and differential dynamics of ciliopathy complexes.
2016,
Pubmed
Dyková,
Neoparamoeba spp. and their eukaryotic endosymbionts similar to Perkinsela amoebae (Hollande, 1980): coevolution demonstrated by SSU rRNA gene phylogenies.
2008,
Pubmed
Dyková,
Neoparamoeba branchiphila n. sp., and related species of the genus Neoparamoeba Page, 1987: morphological and molecular characterization of selected strains.
2005,
Pubmed
Edgar,
MUSCLE: multiple sequence alignment with high accuracy and high throughput.
2004,
Pubmed
El-Sayed,
Comparative genomics of trypanosomatid parasitic protozoa.
2005,
Pubmed
Emms,
OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy.
2015,
Pubmed
Fairlamb,
Metabolism and functions of trypanothione in the Kinetoplastida.
1992,
Pubmed
Fiebig,
SLaP mapper: a webserver for identifying and quantifying spliced-leader addition and polyadenylation site usage in kinetoplastid genomes.
2014,
Pubmed
Field,
The trypanosome flagellar pocket.
2009,
Pubmed
Gawryluk,
Morphological Identification and Single-Cell Genomics of Marine Diplonemids.
2016,
Pubmed
Gluenz,
Beyond 9+0: noncanonical axoneme structures characterize sensory cilia from protists to humans.
2010,
Pubmed
Grabherr,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
2011,
Pubmed
Gunasekera,
Proteome remodelling during development from blood to insect-form Trypanosoma brucei quantified by SILAC and mass spectrometry.
2012,
Pubmed
Güther,
High-confidence glycosome proteome for procyclic form Trypanosoma brucei by epitope-tag organelle enrichment and SILAC proteomics.
2014,
Pubmed
Haas,
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
2003,
Pubmed
Herman,
Autophagy and related processes in trypanosomatids: insights from genomic and bioinformatic analyses.
2006,
Pubmed
Hodges,
Reconstructing the evolutionary history of the centriole from protein components.
2010,
Pubmed
Huang,
Proteomic analysis of the acidocalcisome, an organelle conserved from bacteria to human cells.
2014,
Pubmed
Ivens,
The genome of the kinetoplastid parasite, Leishmania major.
2005,
Pubmed
Jackson,
Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism.
2016,
Pubmed
Jamdhade,
Comprehensive proteomics analysis of glycosomes from Leishmania donovani.
2015,
Pubmed
Johnson,
Hidden Markov model speed heuristic and iterative HMM search procedure.
2010,
Pubmed
Kanehisa,
KEGG as a reference resource for gene and protein annotation.
2016,
Pubmed
Keeling,
The number, speed, and impact of plastid endosymbioses in eukaryotic evolution.
2013,
Pubmed
Kodama,
Cell division and density of symbiotic Chlorella variabilis of the ciliate Paramecium bursaria is controlled by the host's nutritional conditions during early infection process.
2012,
Pubmed
Koonin,
A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.
2004,
Pubmed
Lane,
Novel nucleomorph genome architecture in the cryptomonad genus hemiselmis.
2006,
Pubmed
Langousis,
Motility and more: the flagellum of Trypanosoma brucei.
2014,
Pubmed
Lartillot,
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process.
2004,
Pubmed
Lee,
High yield and rapid growth of Neoparamoeba pemaquidensis in co-culture with a rainbow trout gill-derived cell line RTgill-W1.
2006,
Pubmed
Li,
Fast and accurate long-read alignment with Burrows-Wheeler transform.
2010,
Pubmed
Lowe,
Shining a Light on Exploitative Host Control in a Photosynthetic Endosymbiosis.
2016,
Pubmed
Lukes,
Kinetoplast DNA network: evolution of an improbable structure.
2002,
Pubmed
Lukeš,
Evolution of parasitism in kinetoplastid flagellates.
2014,
Pubmed
Maruyama,
Treetrimmer: a method for phylogenetic dataset size reduction.
2013,
Pubmed
McCutcheon,
Extreme genome reduction in symbiotic bacteria.
2011,
Pubmed
Mitchell,
A review of infectious gill disease in marine salmonid fish.
2011,
Pubmed
Molla-Herman,
The ciliary pocket: an endocytic membrane domain at the base of primary and motile cilia.
2010,
Pubmed
Moreira,
An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea.
2004,
Pubmed
Niemann,
Mitochondrial outer membrane proteome of Trypanosoma brucei reveals novel factors required to maintain mitochondrial morphology.
2013,
Pubmed
Peacock,
Identification of the meiotic life cycle stage of Trypanosoma brucei in the tsetse fly.
2011,
Pubmed
Perkins,
Ultrastructure of the Nebenkörper or "secondary nucleus" of the parasitic amoeba Paramoeba perniciosa (Amoebida, Paramoebidae).
1971,
Pubmed
Porcel,
The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants.
2014,
Pubmed
Price,
FastTree 2--approximately maximum-likelihood trees for large alignments.
2010,
Pubmed
Sant'Anna,
Subcellular proteomics of Trypanosoma cruzi reservosomes.
2009,
Pubmed
Sibbald,
Diversity and Evolution of Paramoeba spp. and their Kinetoplastid Endosymbionts.
2017,
Pubmed
,
Echinobase
Simpson,
The evolution and diversity of kinetoplastid flagellates.
2006,
Pubmed
Stamatakis,
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models.
2006,
Pubmed
Stanke,
Gene prediction with a hidden Markov model and a new intron submodel.
2003,
Pubmed
Stevens,
Kinetoplastid phylogenetics, with special reference to the evolution of parasitic trypanosomes.
2008,
Pubmed
Stuart,
RNA editing in kinetoplastid protozoa.
1997,
Pubmed
Szöör,
Evolution, dynamics and specialized functions of glycosomes in metabolism and development of trypanosomatids.
2014,
Pubmed
Tanifuji,
Genomic characterization of Neoparamoeba pemaquidensis (Amoebozoa) and its kinetoplastid endosymbiont.
2011,
Pubmed
Ter-Hovhannisyan,
Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training.
2008,
Pubmed
Timmis,
Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes.
2004,
Pubmed
Todal,
Ichthyobodo necator (Kinetoplastida)--a complex of sibling species.
2004,
Pubmed
Urbaniak,
Comparative SILAC proteomic analysis of Trypanosoma brucei bloodstream and procyclic lifecycle stages.
2012,
Pubmed
Wu,
WebMGA: a customizable web server for fast metagenomic sequence analysis.
2011,
Pubmed
Young,
Neoparamoeba perurans is a cosmopolitan aetiological agent of amoebic gill disease.
2008,
Pubmed
