Genomics of Eukaryotes and Lateral Gene Transfer

Genomics of Eukaryotes and Lateral Gene Transfer

doc. Mgr. Vladimír Hampl, Ph.D.

doc. Mgr. Vladimír Hampl, Ph.D. — Project head

About us

We are a research team based at Charles University in Prague. We are evolutionary protistologists which means our interest is nothing less than origin and evolution of eukaryotic life. Our research focuses on two groups of organisms: Euglenida and Preaxostyla, both of which are members of Excavata supergroup.

We are particularly interested in the evolution of their unusual semi-autonomous organelles: highly reduced or even completely lost mitochondrion-like organelles of anaerobic Preaxostyla and secondary plastids of photosynthetic euglenids.

Both of these areas of research provide insight into organelle origin and evolution of their structure, molecular biology, transport, targeting, biogenesis, genome composition, molecular genetics mechanisms and biochemical pathways. We also study the phenomenon of lateral gene transfer, which plays an important role in some of these processes.

Preaxostyla

Preaxostyla, living exclusively in oxygen-depleted environments, are one of the least studied protist lineages. We believe these organisms can give us priceless insights into the reductive evolution of mitochondria. Paratrimastix pyriformis belongs to a basal assemblage of free-living Preaxostyla, formerly grouped under a single genus "Trimastix". We study the reduced mitochondrion of Paratrimastix in order to expose the physiological role of the organelle. Our second organisms of interest are oxymonads, which are all living inside the guts of various animals and are the largest known group of eukaryotes without any evidence of mitochondrion or related structures. Our investigation of the species Monocercomonoides exilis is focused on the intriguing possibility that this organism indeed completely lost the mitochondrion, a cellular structure that has been long thought to be essential for all eukaryotic organisms. 

In our lab we focus on:

  • transcriptomics and genomics of oxymonads and Paratrimastix
  • cellular localization of potentially mitochondrial proteins
  • metabolism connected with anaerobiosis and the putative loss of mitochondrion
  • iron-sulfur clusters assembly pathways
  • the symbiosis of oxymonads and their ecto- and endosymbiotic prokaryotes
  • diversity of oxymonads

Preaxostyla

 

Euglenids

Euglenids are a group of mostly freshwater flagellates. Their mitochondria are unusual in both structure and molecular genetics. Many euglenids have firm but flexible pellicle and are capable of metaboly, a typical euglenoid movement. Euglenids are well known for their nutritional modes of diversity. The ancestral and most widespread mode of nutrition among euglenids is heterotrophy (bacteriovory, eukaryovory and primary osmotrophy). However, one monophyletic group, the euglenophytes, acquired a green secondary plastid and use photosynthesis as the main energy source. This plastid is derived from prasinophyte alga and has three envelope membranes. Light perceiving eyespot of unclear evolutionary origin is present in these organisms. The euglenophytes are still able to survive in dark by switching temporarily to heterotrophy; this feature enabled the origin of several secondarily osmotrophic species with non-photosynthetic colourless plastids. Rapaza viridis, recently discovered mixotrophic lineage requires both photosynthesis and eukaryotic prey for survival. 

In our lab we focus on:

  • transcriptomics and plastid genomics of euglenids and plastid-related algae
  • lateral gene transfer that accompanied the origin of the plastid
  • plastid proteomics and protein import in Euglena gracilis
  • lipid analysis of euglenid chloroplast
  • environmental sequencing in search for relatives of the plastid ancestor
  • heterotrophic euglenids diversity

 

Currently, our research is conducted in these areas:

Eukaryotes with no mitochondria

  • In 2016 we discovered that Monocercomonoides exilis cells lack mitochondria completely. It happens to be the very first eukaryotic organism, which provably lacks this organelle. Now we are trying to uncover the inner workings of such cells, and we are particularly interested in the synthesis of iron-sulfur clusters, which is a process closely related to mitochondria.
  • We would like to characterize electron carrier proteins which take part in redox reactions in oxymonads and their relatives.
  • We are also interested in the diversity of oxymonads and we would like to acquire a phylogenetic tree of oxymonads (as complete as possible). For this reason, we are collecting and sequencing oxymonads from their habitats.
  • We want to try using the amitochondriate cells for "evolutionary" experiments to simulate the event of mitochondrial origin. For example, we are interested in what happens when we mix the cytosolic fraction of amitochondriate oxymonads with the isolated mitochondria of other organisms. Which proteins will be imported to the isolated mitochondria? 
  • Oxymonads might not be the only organisms without mitochondria. In collaboration with our colleague Ivan Čepička, we are investigating two other groups, which are potentially amitochondriate. Some of these are amoebas of the genus Pelomyxa and flagellates of the genus Retortamonas.

Euglenid plastids

  • It is now clear, that the origin of the plastid of green euglenids is from secondary endosymbiosis with a green alga. It is also known that this alga was a relative to the genus Pyramimonas. Euglenid phylogeny suggests this event took place in marine environment. We do not know the age of such event, but it is evident that this endosymbiosis is younger than most of other endosymbiotic events.
  • Our team wants to investigate the details of this event. We are interested in the evolution of plastid genomes, which is why we sequence these genomes in green algae and euglenids, which are phylogenetically closest to the endosymbiotic event. It's becoming apparent that the diversity of marine green and non-green euglenids is mapped only superficially, therefore we want to research it in depth. We hope for the discovery of new euglenid lineages.
  • We are also interested in how the euglenid plastids function. In particular, we want to find out the origin of euglenid plastid membranes. These plastids have only three membranes (the ancestral number is four) and we want to know which membrane was lost in the evolution of euglenids. The mechanism of protein transport to euglenid plastids is also unclear. We selected several proteins, which could take part in the transport, however, their localisation has not been determined and we don't know their interacting partners. 
  • We would also like to learn how to transfect euglenas and suppress their gene expression by RNAi.

Protist cytoskeleton

  • There is not much known about the protein composition of non-actin and non-tubulin cytoskeleton (intermediate and striated fibres) of protists. This knowledge might help us homologise morphological structures through divergent groups and help us answer some questions, such as how the last eukaryotic common ancestor (LECA) looked. Preliminary experiments show that we are able to prepare an enriched cytoskeleton fraction of oxymonad cytoskeleton and its subsequent proteomic analysis can tell us more about its composition.

News

Publications

2019

Lukešová S, Karlicki M, Tomečková Hadariová L, Szabová J, Karnkowska A, Hampl V. Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments. Environ Microbiol Rep. 2020 Feb;12(1):78-91. doi: 10.1111/1758-2229.12817. Epub 2019 Dec 26. PubMed PMID: 31845515.

Treitli, SC; Kolisko, M; Husnik, F; Keeling, PJ; Hampl, V. Revealing the metabolic capacity of Streblomastix strix and its bacterial symbionts using single-cell metagenomics. PNAS. 2019, 116(39), 19675-19684. DOI: https://doi.org/10.1073/pnas.1910793116.

Anna Karnkowska, Sebastian C Treitli, Ondřej Brzoň, Lukáš Novák, Vojtěch Vacek, Petr Soukal, Lael D Barlow, Emily K Herman, Shweta V Pipaliya, Tomáš Pánek, David Žihala, Romana Petrželková, Anzhelika Butenko, Laura Eme, Courtney W Stairs, Andrew J Roger, Marek Eliáš, Joel B Dacks, Vladimír Hampl, The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion, Molecular Biology and Evolution, Volume 36, Issue 10, October 2019, Pages 2292–2312, https://doi.org/10.1093/molbev/msz147

Vesteg M, Hadariová L, Horváth A, Estraño CE, Schwartzbach SD, Krajčovič J. Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa. Biol Rev Camb Philos Soc. 2019 Oct;94(5):1701-1721. doi: 10.1111/brv.12523.

Ebenezer, T.E., Zoltner, M., Burrell, A. et al. Transcriptome, proteome and draft genome of Euglena gracilis. BMC Biol 17, 11 (2019) doi:10.1186/s12915-019-0626-8

Hampl, V., Čepička, I., Eliáš, M. Was the Mitochondrion Necessary to Start Eukaryogenesis? Trends in Microbiology. 2019, 27(2):96-104. https://doi.org/10.1016/j.tim.2018.10.005

Adl, S.M., Bass, D., Lane, C.E., Lukeš, J., Schoch, C.L., Smirnov, A., Agatha, S., Berney, C., Brown, M.W., Burki, F., Cárdenas, P., Čepička, I., Chistyakova, L., del, Campo, J., Dunthorn, M., Edvardsen, B., Eglit, Y., Guillou, L., Hampl, V., Heiss, A.A., Hoppenrath, M., James, T.Y., Karnkowska, A., Karpov, S., Kim, E., Kolisko, M., Kudryavtsev, A., Lahr, D.J., Lara, E., Le Gall, L., Lynn, D.H., Mann, D.G., Massana, R., Mitchell, E.A., Morrow, C., Park, J.S., Pawlowski, J.W., Powell, M.J., Richter, D.J., Rueckert, S., Shadwick, L., Shimano, S., Spiegel, F.W., Torruella, G., Youssef, N., Zlatogursky, V. and Zhang, Q. (2019), Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. J. Eukaryot. Microbiol., 66: 4-119. https://doi.org/10.1111/jeu.12691

2018

Záhonová, K., Füssy, Z., Birčák, E. et al. Peculiar features of the plastids of the colourless alga Euglena longa and photosynthetic euglenophytes unveiled by transcriptome analyses. Sci Rep 8, 17012 (2018) doi:10.1038/s41598-018-35389-1

Vacek, V., Novák, L. V. F., Treitli, S. C., Táborský, P., Čepička, I., Kolísko, M., Keeling, P. J., Hampl, V. Fe–S Cluster assembly in oxymonads and related protists. Molecular Biology and Evolution. 2018, 35(11), 2712–2718. DOI: 10.1093/molbev/msy168.

Treitli, S. C., Kotyk, M., Yubuki, N., Jirounková, E., Vlásáková, J., Smejkalová, P., Šípek, P., Čepička, I., Hampl, V. Molecular and morphological diversity of the oxymonad genera Monocercomonoides and Blattamonas gen. nov. Protist. 2018, 169(5), 744-783. DOI: 10.1016/j.protis.2018.06.005.

Záhonová K., Petrželková R., Valach M., Yazaki E., Tikhonenkov D. V., Butenko A., Janouškovec J., Hrdá Š., Klimeš V., Burger G., Inagaki Y, Keeling P. J., Hampl V., Flegontov P., Yurchenko V., Eliáš M., Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase, https://doi.org/10.1038/s41598-018-23575-0 

2017

Hadariová L, Vesteg M, Hampl V, Krajčovič J. Reductive evolution of chloroplasts in non-photosynthetic plants, algae and protists. Curr Genet. 2017 doi: 10.1007/s00294-017-0761-0

Vanclová, AMG, Hadariová L, Hrdá Š, Hampl V. Secondary Plastids of Euglenophytes. In: Y. Hirakawa (ed.), Advances in Botanical Research, Academic Press 2017. doi: 10.1016/bs.abr.2017.06.008

2016

Hampl V. Preaxostyla. In: J.M. Archibald et al. (eds.), Handbook of the Protists, doi: 10.1007/978-3-319-32669-6_8-1. Springer 2016.

Klinger CM, Karnkowska A, Herman EK, Hampl V, Dacks JB. In the Light of Free-Living Relatives: Understanding the Phylogeny and Evolutionary Cell Biology of Parasites. In: Walochnik J and Duchêne M (eds.), Molecular Parasitology – Protozoan Parasites and their Molecules. Springer 2016.

Hrdá Š, Hroudová M, Vlček Č, Hampl V. Mitochondrial Genome of Prasinophyte Alga Pyramimonas parkeae. J Eukaryot Microbiol. 2016 Sep 28. 

Novák L, Zubáčová Z, Karnkowska A, Kolisko M, Hroudová M, Stairs CW, Simpson AGB, Keeling PJ, Roger AJ, Čepička I, Hampl V. Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. BMC Evol Biol. 2016 Oct 6;16(1):197.

Karnkowska A, Hampl V. The curious case of vanishing mitochondria. Microbial Cell 2016, 3, pp.361-364.

Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P, Hroudová M, Doležal P, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Vlček Č, Hampl V. A Eukaryote without a Mitochondrial Organelle. Curr Biol. 2016 May 11.

Zíková A, Hampl V, Paris Z, Týč J, Lukeš J. Aerobic mitochondria of parasitic protists: Diverse genomes and complex functions. Mol Biochem Parasitol. 2016 Feb 22.

2015

Rada P, Makki AR, Zimorski V, Garg S, Hampl V, Hrdý I, Gould SB, Tachezy J. N-Terminal Presequence-Independent Import of Phosphofructokinase into Hydrogenosomes of Trichomonas vaginalis. Eukaryot Cell. 2015 Dec;14(12):1264-75.

2014

Szabová J, Yubuki N, Leander BS, Triemer RE, Hampl V. The evolution of paralogous enzymes MAT and MATX within the Euglenida and beyond. BMC Evol Biol. 2014 Feb 11;14:25

2013

Zubáčová Z, Novák L, Bublíková J, Vacek V, Fousek J, Rídl J, Tachezy J, Doležal P, Vlček Č, Hampl V. The mitochondrion-like organelle of Trimastix pyriformis contains the complete glycine cleavage system. PLoS One. 2013;8(3):e55417.

2012

Krnáčová K, Vesteg M, Hampl V, Vlček Č, Horváth A. Euglena gracilis and Trypanosomatids Possess Common Patterns in Predicted Mitochondrial Targeting Presequences. J Mol Evol. 2012 Oct;75(3-4):119-29. doi: 10.1007/s00239-012-9523-2. Epub 2012 Oct 12.

Adl SM, Simpson AG, Lane CE, Lukeš J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Le Gall L, Lynn DH, McManus H, Mitchell EA, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick L, Schoch CL, Smirnov A, Spiegel FW. The revised classification of eukaryotes. J Eukaryot Microbiol. 2012 Sep;59(5):429-93. 

Huňová K, Kašný M, Hampl V, Leontovyč R, Kuběna A, Mikeš L, Horák P. Radix spp.: Identification of trematode intermediate hosts in the Czech Republic. Acta Parasitol. 2012 Sep;57(3):273-84. Epub 2012 Aug 9.

Hampl V. Kontroverzní a nebojácná dáma. Vesmír 91, 103, 2012/2.

Hrdá Š, Fousek J, Szabová J, Hampl V, Vlček Č. The plastid genome of Eutreptiella provides a window into the process of secondary endosymbiosis of plastid in euglenids. PLoS One. 2012;7(3):e33746

2011

Hampl V, Stairs CW, Roger AJ. The Tangled Past Of Eukaryotic Enzymes Involved In Anaerobic Metabolism. Mobile Genetic Elements Volume 1 Issue 1.

Stairs CW, Roger AJ, Hampl V. Eukaryotic pyruvate formate lyase and its activating enzyme were acquired laterally from a firmicute. Mol Biol Evol. 2011 28(7):2087-2099.

Morada M, Šmíd O, Hampl V, Šuťák R, Lam B, Rappelli P, Dessi D, Fiori PL, Tachezy J, Yarlett N. Hydrogenosome-localization of arginine deiminase in Trichomonas vaginalis. Mol Biochem Parasitol. 2011; 176(1): 51-54.

Teaching

If you found any of our research topics interesting, we offer the possibility to work on your bachelor, master or doctoral thesis in our lab. In case you're interested contact our boss Vladimír Hampl at vlada@natur.cuni.cz. Below you can find a list of previously defended work in our lab.

Alumni

thesis author thesis name thesis type term
Vojtěch Vacek Iron-Sulfur cluster assembly in Monocercomonoides exilis PhD 2020
Štěpánka Hrdá Evolution of nuclear and plastid genomes in euglenids PhD 2020
Lukáš Novák Genomics of Preaxostyla flagellates PhD 2020
Anna Novák Vanclová Evolution of euglenid plastid proteome PhD 2019
Sebastian Cristian Treitli Genomics and cell biology of oxymonads PhD 2019
Jana Szabová The complicated evolution of methionine adenosyltransferase in euglenids and eukaryotes in general PhD 2015
Aneta Kubánková Phylogenetic position of genus Polymastix and its prokaryotic symbionts MSc 2020
Marie Zelená Functional study of the SUF pathway in the cell of Monocercomonoides exilis and Paratrimastix pyriformis MSc 2020
Martina Kornalíková Analyses of Monocercomonoides genome sizes, ploidies and karyotypes MSc 2019
Ondřej Brzoň Analysis of gene regulatory regions in the genome of oxymonad Monocercomonoides MSc 2016
Soňa Lukešová Diversity of prasinophyte algae related to the euglenid plastid MSc 2016
Jitka Vlasáková Diversity of the genus Monocercomonoides MSc 2014
Anna Novák Vanclová Membrane proteome of euglenid plastid MSc 2014
Lukáš Novák Mitochondrion of Trimastix pyriformis MSc 2013
Petr Soukal Search for the remnant of plastid in the cell of Rhabdomonas sp. MSc 2013
Eliška Šrámová Evolution of the genetic code and classification of oxymonads MSc 2012
Vojtěch Vacek Mitochondrion of oxymonads MSc 2011
Eva Švagr Protein composition of the cytoskeleton of protists BSc 2020
Marie Zelená Iron-sulphur cluster synthesis in anaerobic protists BSc 2018
David Trokšiar Losses of mitochondria and plastids in the evolution of eukaryotes BSc 2017
Aneta Kubánková Prokaryotic symbionts of protists living in the intestine of wood eating cockroaches and termites BSc 2017
Martina Kornalíková FISH method and its use in protistology BSc 2015
Soňa Lukešová The use of environmental sequencing in the studies on eukaryotic diversity BSc 2014
Ondřej Brzoň Regulation of gene expression in anaerobic parasitic protist and practical application of knowledge BSc 2014
Anna Novák Vanclová Transport of proteins into secondary plastids BSc 2012
Petr Soukal Transfer of genetic information between parasite and its host BSc 2011
Lukáš Novák Lateral gene transfer and its utilisation for the phylogeny of eukaryotes BSc 2011
Vojtěch Vacek Anaerobic mitochondrion-like organelles of Excavata BSc 2009