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 evolution of their unusual semi-autonomous organelles: highly reduced or even completely lost mitochondrion-like organelle of anaerobic Preaxostyla and secondary plastid 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 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 guts of various animals and are the largest known group of eukaryotes without any evidence of mitochondrion or related structures. Our investigation of genus  Monocercomonoides 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
  • 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 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 this feature enabled the origin of several secondarily osmotrophic species with non-photosynthetic colorless 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 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

 

News

Publications

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

Alumni

thesis author thesis name thesis type term
Naoji Yubuki The origin(s) of the euglenid plastid as inferred from the transcriptome and the genome of a mixotrophic euglenophyte Rapaza viridis Postdoc
Soňa Lukešová Diversity of pyramimonadales algae and evolution of euglenid plastid. MSc graduate
Anna Karnkowska Genomics of oxymonads and trimastix Postdoc
Jana Szabová The evolution of derived form of methionin adenosyltransferase (MATX) in euglenids. PhD graduate
Zuzana Zubáčová Genomes and mitochondrial organelles of preaxostyla Postdoc