1
|
Afonin DA, Gerasimov ES, Škodová-Sveráková I, Záhonová K, Gahura O, Albanaz ATS, Myšková E, Bykova A, Paris Z, Lukeš J, Opperdoes FR, Horváth A, Zimmer SL, Yurchenko V. Blastocrithidia nonstop mitochondrial genome and its expression are remarkably insulated from nuclear codon reassignment. Nucleic Acids Res 2024; 52:3870-3885. [PMID: 38452217 DOI: 10.1093/nar/gkae168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
The canonical stop codons of the nuclear genome of the trypanosomatid Blastocrithidia nonstop are recoded. Here, we investigated the effect of this recoding on the mitochondrial genome and gene expression. Trypanosomatids possess a single mitochondrion and protein-coding transcripts of this genome require RNA editing in order to generate open reading frames of many transcripts encoded as 'cryptogenes'. Small RNAs that can number in the hundreds direct editing and produce a mitochondrial transcriptome of unusual complexity. We find B. nonstop to have a typical trypanosomatid mitochondrial genetic code, which presumably requires the mitochondrion to disable utilization of the two nucleus-encoded suppressor tRNAs, which appear to be imported into the organelle. Alterations of the protein factors responsible for mRNA editing were also documented, but they have likely originated from sources other than B. nonstop nuclear genome recoding. The population of guide RNAs directing editing is minimal, yet virtually all genes for the plethora of known editing factors are still present. Most intriguingly, despite lacking complex I cryptogene guide RNAs, these cryptogene transcripts are stochastically edited to high levels.
Collapse
MESH Headings
- Genome, Mitochondrial
- RNA Editing
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
- Open Reading Frames/genetics
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Trypanosomatina/genetics
- Trypanosomatina/metabolism
- Codon/genetics
- Mitochondria/genetics
- Mitochondria/metabolism
- Codon, Terminator/genetics
- RNA, Guide, Kinetoplastida/genetics
- RNA, Guide, Kinetoplastida/metabolism
- Genetic Code
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
Collapse
Affiliation(s)
- Dmitry A Afonin
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Evgeny S Gerasimov
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV 252 50 Vestec, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, T6G 2R3 Edmonton, Alberta, Canada
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Amanda T S Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| | - Eva Myšková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Fred R Opperdoes
- De Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia
| | - Sara L Zimmer
- University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| |
Collapse
|
2
|
Kostygov AY, Albanaz ATS, Butenko A, Gerasimov ES, Lukeš J, Yurchenko V. Phylogenetic framework to explore trait evolution in Trypanosomatidae. Trends Parasitol 2024; 40:96-99. [PMID: 38065790 DOI: 10.1016/j.pt.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 11/23/2023] [Accepted: 11/23/2023] [Indexed: 02/10/2024]
Abstract
The number of sequenced trypanosomatid genomes has reached a critical point so that they are now available for almost all genera and subgenera. Based on this, we inferred a phylogenomic tree and propose it as a framework to study trait evolution together with some examples of how to do it.
Collapse
Affiliation(s)
- Alexei Yu Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia.
| | - Amanda T S Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia; Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice, Czechia; Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Evgeny S Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Julius Lukeš
- Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice, Czechia; Faculty of Sciences, University of South Bohemia, 370 05 České Budějovice, Czechia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czechia.
| |
Collapse
|
3
|
Albanaz ATS, Carrington M, Frolov AO, Ganyukova AI, Gerasimov ES, Kostygov AY, Lukeš J, Malysheva MN, Votýpka J, Zakharova A, Záhonová K, Zimmer SL, Yurchenko V, Butenko A. Shining the spotlight on the neglected: new high-quality genome assemblies as a gateway to understanding the evolution of Trypanosomatidae. BMC Genomics 2023; 24:471. [PMID: 37605127 PMCID: PMC10441713 DOI: 10.1186/s12864-023-09591-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023] Open
Abstract
BACKGROUND Protists of the family Trypanosomatidae (phylum Euglenozoa) have gained notoriety as parasites affecting humans, domestic animals, and agricultural plants. However, the true extent of the group's diversity spreads far beyond the medically and veterinary relevant species. We address several knowledge gaps in trypanosomatid research by undertaking sequencing, assembly, and analysis of genomes from previously overlooked representatives of this protistan group. RESULTS We assembled genomes for twenty-one trypanosomatid species, with a primary focus on insect parasites and Trypanosoma spp. parasitizing non-human hosts. The assemblies exhibit sizes consistent with previously sequenced trypanosomatid genomes, ranging from approximately 18 Mb for Obscuromonas modryi to 35 Mb for Crithidia brevicula and Zelonia costaricensis. Despite being the smallest, the genome of O. modryi has the highest content of repetitive elements, contributing nearly half of its total size. Conversely, the highest proportion of unique DNA is found in the genomes of Wallacemonas spp., with repeats accounting for less than 8% of the assembly length. The majority of examined species exhibit varying degrees of aneuploidy, with trisomy being the most frequently observed condition after disomy. CONCLUSIONS The genome of Obscuromonas modryi represents a very unusual, if not unique, example of evolution driven by two antidromous forces: i) increasing dependence on the host leading to genomic shrinkage and ii) expansion of repeats causing genome enlargement. The observed variation in somy within and between trypanosomatid genera suggests that these flagellates are largely predisposed to aneuploidy and, apparently, exploit it to gain a fitness advantage. High heterogeneity in the genome size, repeat content, and variation in chromosome copy numbers in the newly-sequenced species highlight the remarkable genome plasticity exhibited by trypanosomatid flagellates. These new genome assemblies are a robust foundation for future research on the genetic basis of life cycle changes and adaptation to different hosts in the family Trypanosomatidae.
Collapse
Affiliation(s)
- Amanda T S Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Alexander O Frolov
- Zoological Institute of the Russian Academy of Sciences, 199034, St. Petersburg, Russia
| | - Anna I Ganyukova
- Zoological Institute of the Russian Academy of Sciences, 199034, St. Petersburg, Russia
| | - Evgeny S Gerasimov
- Faculty of Biology, M. V. Lomonosov Moscow State University, 119991, Moscow, Russia
- Martsinovsky Institute of Medical Parasitology, Sechenov University, 119435, Moscow, Russia
| | - Alexei Y Kostygov
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Faculty of Sciences, University of South Bohemia, 370 05, České Budějovice, Czech Republic
| | - Marina N Malysheva
- Zoological Institute of the Russian Academy of Sciences, 199034, St. Petersburg, Russia
| | - Jan Votýpka
- Institute of Parasitology, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Department of Parasitology, Faculty of Science, Charles University, 128 44, Prague, Czech Republic
| | - Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic
- Institute of Parasitology, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, T6G 2G3, Canada
| | - Sara L Zimmer
- Duluth Campus, University of Minnesota Medical School, Duluth, MN, 55812, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic.
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00, Ostrava, Czech Republic.
- Institute of Parasitology, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic.
- Faculty of Sciences, University of South Bohemia, 370 05, České Budějovice, Czech Republic.
| |
Collapse
|
4
|
Gerasimov ES, Novozhilova TS, Zimmer SL, Yurchenko V. Kinetoplast Genome of Leishmania spp. Is under Strong Purifying Selection. Trop Med Infect Dis 2023; 8:384. [PMID: 37624322 PMCID: PMC10458658 DOI: 10.3390/tropicalmed8080384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/26/2023] Open
Abstract
Instability is an intriguing characteristic of many protist genomes, and trypanosomatids are not an exception in this respect. Some regions of trypanosomatid genomes evolve fast. For instance, the trypanosomatid mitochondrial (kinetoplast) genome consists of fairly conserved maxicircle and minicircle molecules that can, nevertheless, possess high nucleotide substitution rates between closely related strains. Recent experiments have demonstrated that rapid laboratory evolution can result in the non-functionality of multiple genes of kinetoplast genomes due to the accumulation of mutations or loss of critical genomic components. An example of a loss of critical components is the reported loss of entire minicircle classes in Leishmania tarentolae during laboratory cultivation, which results in an inability to generate some correctly encoded genes. In the current work, we estimated the evolutionary rates of mitochondrial and nuclear genome regions of multiple natural Leishmania spp. We analyzed synonymous and non-synonymous substitutions and, rather unexpectedly, found that the coding regions of kinetoplast maxicircles are among the most variable regions of both genomes. In addition, we demonstrate that synonymous substitutions greatly predominate among maxicircle coding regions and that most maxicircle genes show signs of purifying selection. These results imply that maxicircles in natural Leishmania populations remain functional despite their high mutation rate.
Collapse
Affiliation(s)
- Evgeny S. Gerasimov
- Department of Molecular Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, 127051 Moscow, Russia
| | - Tatiana S. Novozhilova
- Department of Molecular Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Sara L. Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| |
Collapse
|
5
|
Kudryavtseva OA, Gerasimov ES, Glagoleva ES, Gasparyan AA, Agroskin SM, Belozersky MA, Dunaevsky YE. Dynamics of Podospora anserina Genome Evolution in a Long-Term Experiment. Int J Mol Sci 2023; 24:12009. [PMID: 37569385 PMCID: PMC10418817 DOI: 10.3390/ijms241512009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/16/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
The Podospora anserina long-term evolution experiment (PaLTEE) is the only running filamentous fungus study, which is still going on. The aim of our work is to trace the evolutionary dynamics of the accumulation of mutations in the genomes of eight haploid populations of P. anserina. The results of the genome-wide analysis of all of the lineages, performed 8 years after the start of the PaLTEE, are presented. Data analysis detected 312 single nucleotide polymorphisms (SNPs) and 39 short insertion-deletion mutations (indels) in total. There was a clear trend towards a linear increase in the number of SNPs depending on the experiment duration. Among 312 SNPs, 153 were fixed in the coding regions of P. anserina genome. Relatively few synonymous mutations were found, exactly 38; 42 were classified as nonsense mutations; 72 were assigned to missense mutations. In addition, 21 out of 39 indels identified were also localized in coding regions. Here, we also report the detection of parallel evolution at the paralog level in the P. anserina model system. Parallelism in evolution at the level of protein functions also occurs. The latter is especially true for various transcription factors, which may indicate selection leading to optimization of the wide range of cellular processes under experimental conditions.
Collapse
Affiliation(s)
- Olga A. Kudryavtseva
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.K.); (E.S.G.); (E.S.G.); (A.A.G.); (S.M.A.)
| | - Evgeny S. Gerasimov
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.K.); (E.S.G.); (E.S.G.); (A.A.G.); (S.M.A.)
| | - Elena S. Glagoleva
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.K.); (E.S.G.); (E.S.G.); (A.A.G.); (S.M.A.)
| | - Anna A. Gasparyan
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.K.); (E.S.G.); (E.S.G.); (A.A.G.); (S.M.A.)
| | - Saveliy M. Agroskin
- Faculty of Biology, Lomonosov Moscow State University, 119991 Moscow, Russia; (O.A.K.); (E.S.G.); (E.S.G.); (A.A.G.); (S.M.A.)
| | - Mikhail A. Belozersky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Yakov E. Dunaevsky
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia;
| |
Collapse
|
6
|
Novozhilova TS, Chistyakov DS, Akhmadishina LV, Lukashev AN, Gerasimov ES, Yurchenko V. Genomic analysis of Leishmania turanica strains from different regions of Central Asia. PLoS Negl Trop Dis 2023; 17:e0011145. [PMID: 36877735 PMCID: PMC10019736 DOI: 10.1371/journal.pntd.0011145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/16/2023] [Accepted: 02/06/2023] [Indexed: 03/07/2023] Open
Abstract
The evolution in Leishmania is governed by the opposite forces of clonality and sexual reproduction, with vicariance being an important factor. As such, Leishmania spp. populations may be monospecific or mixed. Leishmania turanica in Central Asia is a good model to compare these two types. In most areas, populations of L. turanica are mixed with L. gerbilli and L. major. Notably, co-infection with L. turanica in great gerbils helps L. major to withstand a break in the transmission cycle. Conversely, the populations of L. turanica in Mongolia are monospecific and geographically isolated. In this work, we compare genomes of several well-characterized strains of L. turanica originated from monospecific and mixed populations in Central Asia in order to shed light on genetic factors, which may drive evolution of these parasites in different settings. Our results illustrate that evolutionary differences between mixed and monospecific populations of L. turanica are not dramatic. On the level of large-scale genomic rearrangements, we confirmed that different genomic loci and different types of rearrangements may differentiate strains originated from mixed and monospecific populations, with genome translocations being the most prominent example. Our data suggests that L. turanica has a significantly higher level of chromosomal copy number variation between the strains compared to its sister species L. major with only one supernumerary chromosome. This suggests that L. turanica (in contrast to L. major) is in the active phase of evolutionary adaptation.
Collapse
Affiliation(s)
| | - Daniil S. Chistyakov
- Martsinovsky Institute of Medical Parasitology, Sechenov University, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Evgeny S. Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (ESG); (VY)
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- * E-mail: (ESG); (VY)
| |
Collapse
|
7
|
Gerasimov ES, Ramirez-Barrios R, Yurchenko V, Zimmer SL. Trypanosoma cruzi strain and starvation-driven mitochondrial RNA editing and transcriptome variability. RNA 2022; 28:993-1012. [PMID: 35470233 PMCID: PMC9202582 DOI: 10.1261/rna.079088.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 04/07/2022] [Indexed: 05/09/2023]
Abstract
Trypanosoma cruzi is a unicellular protistan parasitic species that is comprised of strains and isolates exhibiting high levels of genetic and metabolic variability. In the insect vector, it is known to be highly responsive to starvation, a signal for progression to a life stage in which it can infect mammalian cells. Most mRNAs encoded in its mitochondrion require the targeted insertion and deletion of uridines to become translatable transcripts. This study defined differences in uridine-insertion/deletion RNA editing among three strains and established the mechanism whereby abundances of edited (and, thus, translatable) mitochondrial gene products increase during starvation. Our approach utilized our custom T-Aligner toolkit to describe transcriptome-wide editing events and reconstruct editing products from high-throughput sequencing data. We found that the relative abundance of mitochondrial transcripts and the proportion of mRNAs that are edited varies greatly between analyzed strains, a characteristic that could potentially impact metabolic capacity. Starvation typically led to an increase in overall editing activity rather than affecting a specific step in the process. We also determined that transcripts CR3, CR4, and ND3 produce multiple open reading frames that, if translated, would generate different proteins. Finally, we quantitated the inherent flexibility of editing in T. cruzi and found it to be higher relative to that in a related trypanosomatid lineage. Over time, new editing domains or patterns could prove advantageous to the organism and become more widespread within individual transcriptomes or among strains.
Collapse
Affiliation(s)
- Evgeny S Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Roger Ramirez-Barrios
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, Minnesota 55812, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow 119435, Russia
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, Minnesota 55812, USA
| |
Collapse
|
8
|
Zakharova A, Albanaz ATS, Opperdoes FR, Škodová-Sveráková I, Zagirova D, Saura A, Chmelová L, Gerasimov ES, Leštinová T, Bečvář T, Sádlová J, Volf P, Lukeš J, Horváth A, Butenko A, Yurchenko V. Leishmania guyanensis M4147 as a new LRV1-bearing model parasite: Phosphatidate phosphatase 2-like protein controls cell cycle progression and intracellular lipid content. PLoS Negl Trop Dis 2022; 16:e0010510. [PMID: 35749562 PMCID: PMC9232130 DOI: 10.1371/journal.pntd.0010510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/17/2022] [Indexed: 12/11/2022] Open
Abstract
Leishmaniasis is a parasitic vector-borne disease caused by the protistan flagellates of the genus Leishmania. Leishmania (Viannia) guyanensis is one of the most common causative agents of the American tegumentary leishmaniasis. It has previously been shown that L. guyanensis strains that carry the endosymbiotic Leishmania RNA virus 1 (LRV1) cause more severe form of the disease in a mouse model than those that do not. The presence of the virus was implicated into the parasite’s replication and spreading. In this respect, studying the molecular mechanisms of cellular control of viral infection is of great medical importance. Here, we report ~30.5 Mb high-quality genome assembly of the LRV1-positive L. guyanensis M4147. This strain was turned into a model by establishing the CRISPR-Cas9 system and ablating the gene encoding phosphatidate phosphatase 2-like (PAP2L) protein. The orthologue of this gene is conspicuously absent from the genome of an unusual member of the family Trypanosomatidae, Vickermania ingenoplastis, a species with mostly bi-flagellated cells. Our analysis of the PAP2L-null L. guyanensis showed an increase in the number of cells strikingly resembling the bi-flagellated V. ingenoplastis, likely as a result of the disruption of the cell cycle, significant accumulation of phosphatidic acid, and increased virulence compared to the wild type cells. Worldwide, over one million people are getting infected by the parasitic flagellates of the genus Leishmania annually leading to ~30,000 deaths. Notably, there is still no approved vaccine against human leishmaniases. A range of methods of forward and reverse genetics has recently been developed for several model Leishmania species. Unfortunately, these methods are often not transferrable to non-model species, which may be of even greater medical importance. Leishmania guyanensis is one of such cases. It frequently carries a symbiotic RNA virus that contributes to the development of a more aggressive form of leishmaniasis in an experimental murine model. In order to establish and optimize the system for genetic manipulations in L. guyanensis, we sequenced and annotated its genome. Next, we applied the CRISPR-Cas9 technology to target a gene of interest. This approach was validated by ablating a gene encoding a protein involved in lipid metabolism. In this work, we document that deletion of this gene leads to the disturbance of cell cycle and affects the ratio of critical intracellular lipids. We believe that our study will facilitate research into more effective treatment of leishmaniases.
Collapse
Affiliation(s)
- Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Amanda T. S. Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R. Opperdoes
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Diana Zagirova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Lˇubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Evgeny S. Gerasimov
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Tereza Leštinová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomáš Bečvář
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Anton Horváth
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- * E-mail:
| |
Collapse
|
9
|
Poláková E, Albanaz ATS, Zakharova A, Novozhilova TS, Gerasimov ES, Yurchenko V. Ku80 is involved in telomere maintenance but dispensable for genomic stability in Leishmania mexicana. PLoS Negl Trop Dis 2021; 15:e0010041. [PMID: 34965251 PMCID: PMC8716037 DOI: 10.1371/journal.pntd.0010041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Telomeres are indispensable for genome stability maintenance. They are maintained by the telomere-associated protein complex, which include Ku proteins and a telomerase among others. Here, we investigated a role of Ku80 in Leishmania mexicana. Leishmania is a genus of parasitic protists of the family Trypanosomatidae causing a vector-born disease called leishmaniasis. METHODOLOGY/PRINCIPAL FINDINGS We used the previously established CRISPR/Cas9 system to mediate ablation of Ku80- and Ku70-encoding genes in L. mexicana. Complete knock-outs of both genes were confirmed by Southern blotting, whole-genome Illumina sequencing, and RT-qPCR. Resulting telomeric phenotypes were subsequently investigated using Southern blotting detection of terminal restriction fragments. The genome integrity in the Ku80- deficient cells was further investigated by whole-genome sequencing. Our work revealed that telomeres in the ΔKu80 L. mexicana are elongated compared to those of the wild type. This is a surprising finding considering that in another model trypanosomatid, Trypanosoma brucei, they are shortened upon ablation of the same gene. A telomere elongation phenotype has been documented in other species and associated with a presence of telomerase-independent alternative telomere lengthening pathway. Our results also showed that Ku80 appears to be not involved in genome stability maintenance in L. mexicana. CONCLUSION/SIGNIFICANCE Ablation of the Ku proteins in L. mexicana triggers telomere elongation, but does not have an adverse impact on genome integrity.
Collapse
Affiliation(s)
- Ester Poláková
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Amanda T. S. Albanaz
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | | | - Evgeny S. Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| |
Collapse
|
10
|
Gerasimov ES, Gasparyan AA, Afonin DA, Zimmer SL, Kraeva N, Lukeš J, Yurchenko V, Kolesnikov A. Complete minicircle genome of Leptomonas pyrrhocoris reveals sources of its non-canonical mitochondrial RNA editing events. Nucleic Acids Res 2021; 49:3354-3370. [PMID: 33660779 PMCID: PMC8034629 DOI: 10.1093/nar/gkab114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 02/03/2021] [Accepted: 02/09/2021] [Indexed: 01/24/2023] Open
Abstract
Uridine insertion/deletion (U-indel) editing of mitochondrial mRNA, unique to the protistan class Kinetoplastea, generates canonical as well as potentially non-productive editing events. While the molecular machinery and the role of the guide (g) RNAs that provide required information for U-indel editing are well understood, little is known about the forces underlying its apparently error-prone nature. Analysis of a gRNA:mRNA pair allows the dissection of editing events in a given position of a given mitochondrial transcript. A complete gRNA dataset, paired with a fully characterized mRNA population that includes non-canonically edited transcripts, would allow such an analysis to be performed globally across the mitochondrial transcriptome. To achieve this, we have assembled 67 minicircles of the insect parasite Leptomonas pyrrhocoris, with each minicircle typically encoding one gRNA located in one of two similar-sized units of different origin. From this relatively narrow set of annotated gRNAs, we have dissected all identified mitochondrial editing events in L. pyrrhocoris, the strains of which dramatically differ in the abundance of individual minicircle classes. Our results support a model in which a multitude of editing events are driven by a limited set of gRNAs, with individual gRNAs possessing an inherent ability to guide canonical and non-canonical editing.
Collapse
Affiliation(s)
- Evgeny S Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow 119435, Russia
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Anna A Gasparyan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Dmitry A Afonin
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 55812, USA
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow 119435, Russia
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Alexander Kolesnikov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| |
Collapse
|
11
|
Sádlová J, Podešvová L, Bečvář T, Bianchi C, Gerasimov ES, Saura A, Glanzová K, Leštinová T, Matveeva NS, Chmelová Ľ, Mlacovská D, Spitzová T, Vojtková B, Volf P, Yurchenko V, Kraeva N. Catalase impairs Leishmania mexicana development and virulence. Virulence 2021; 12:852-867. [PMID: 33724149 PMCID: PMC7971327 DOI: 10.1080/21505594.2021.1896830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Catalase is one of the most abundant enzymes on Earth. It decomposes hydrogen peroxide, thus protecting cells from dangerous reactive oxygen species. The catalase-encoding gene is conspicuously absent from the genome of most representatives of the family Trypanosomatidae. Here, we expressed this protein from the Leishmania mexicana Β-TUBULIN locus using a novel bicistronic expression system, which relies on the 2A peptide of Teschovirus A. We demonstrated that catalase-expressing parasites are severely compromised in their ability to develop in insects, to be transmitted and to infect mice, and to cause clinical manifestation in their mammalian host. Taken together, our data support the hypothesis that the presence of catalase is not compatible with the dixenous life cycle of Leishmania, resulting in loss of this gene from the genome during the evolution of these parasites.
Collapse
Affiliation(s)
- Jovana Sádlová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Lucie Podešvová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Tomáš Bečvář
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Claretta Bianchi
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Evgeny S Gerasimov
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Kristýna Glanzová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tereza Leštinová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Nadezhda S Matveeva
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Ľubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Denisa Mlacovská
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Tatiana Spitzová
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Barbora Vojtková
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Volf
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Moscow, Russia
| | - Natalya Kraeva
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| |
Collapse
|
12
|
Opperdoes FR, Butenko A, Zakharova A, Gerasimov ES, Zimmer SL, Lukeš J, Yurchenko V. The Remarkable Metabolism of Vickermania ingenoplastis: Genomic Predictions. Pathogens 2021; 10:pathogens10010068. [PMID: 33466586 PMCID: PMC7828693 DOI: 10.3390/pathogens10010068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
A recently redescribed two-flagellar trypanosomatid Vickermania ingenoplastis is insensitive to the classical inhibitors of respiration and thrives under anaerobic conditions. Using genomic and transcriptomic data, we analyzed its genes of the core metabolism and documented that subunits of the mitochondrial respiratory complexes III and IV are ablated, while those of complexes I, II, and V are all present, along with an alternative oxidase. This explains the previously reported conversion of glucose to acetate and succinate by aerobic fermentation. Glycolytic pyruvate is metabolized to acetate and ethanol by pyruvate dismutation, whereby a unique type of alcohol dehydrogenase (shared only with Phytomonas spp.) processes an excess of reducing equivalents formed under anaerobic conditions, leading to the formation of ethanol. Succinate (formed to maintain the glycosomal redox balance) is converted to propionate by a cyclic process involving three enzymes of the mitochondrial methyl-malonyl-CoA pathway, via a cyclic process, which results in the formation of additional ATP. The unusual structure of the V. ingenoplastis genome and its similarity with that of Phytomonas spp. imply their relatedness or convergent evolution. Nevertheless, a critical difference between these two trypanosomatids is that the former has significantly increased its genome size by gene duplications, while the latter streamlined its genome.
Collapse
Affiliation(s)
- Fred R. Opperdoes
- De Duve Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
- Correspondence: (F.R.O.); (V.Y.)
| | - Anzhelika Butenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (A.B.); (A.Z.)
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic;
| | - Alexandra Zakharova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (A.B.); (A.Z.)
| | - Evgeny S. Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia;
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia
| | - Sara L. Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth Campus, Duluth, MN 558812, USA;
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, 370 05 České Budějovice (Budweis), Czech Republic;
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice (Budweis), Czech Republic
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic; (A.B.); (A.Z.)
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, 119435 Moscow, Russia
- Correspondence: (F.R.O.); (V.Y.)
| |
Collapse
|
13
|
Penin AA, Kasianov AS, Klepikova AV, Kirov IV, Gerasimov ES, Fesenko AN, Logacheva MD. High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum. Front Plant Sci 2021; 12:612382. [PMID: 33815435 PMCID: PMC8010679 DOI: 10.3389/fpls.2021.612382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/03/2021] [Indexed: 05/06/2023]
Abstract
Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop and a prospective component of functional food. Despite this, the genomic resources for this species and for the whole family Polygonaceae, to which it belongs, are scarce. Here, we report the assembly of the buckwheat genome using long-read technology and a high-resolution expression atlas including 46 organs and developmental stages. We found that the buckwheat genome has an extremely high content of transposable elements, including several classes of recently (0.5-1 Mya) multiplied TEs ("transposon burst") and gradually accumulated TEs. The difference in TE content is a major factor contributing to the three-fold increase in the genome size of F. esculentum compared with its sister species F. tataricum. Moreover, we detected the differences in TE content between the wild ancestral subspecies F. esculentum ssp. ancestrale and buckwheat cultivars, suggesting that TE activity accompanied buckwheat domestication. Expression profiling allowed us to test a hypothesis about the genetic control of petaloidy of tepals in buckwheat. We showed that it is not mediated by B-class gene activity, in contrast to the prediction from the ABC model. Based on a survey of expression profiles and phylogenetic analysis, we identified the MYB family transcription factor gene tr_18111 as a potential candidate for the determination of conical cells in buckwheat petaloid tepals. The information on expression patterns has been integrated into the publicly available database TraVA: http://travadb.org/browse/Species=Fesc/. The improved genome assembly and transcriptomic resources will enable research on buckwheat, including practical applications.
Collapse
Affiliation(s)
- Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Ilya V. Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia
| | | | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
- *Correspondence: Maria D. Logacheva,
| |
Collapse
|
14
|
Vakhrusheva OA, Mnatsakanova EA, Galimov YR, Neretina TV, Gerasimov ES, Naumenko SA, Ozerova SG, Zalevsky AO, Yushenova IA, Rodriguez F, Arkhipova IR, Penin AA, Logacheva MD, Bazykin GA, Kondrashov AS. Genomic signatures of recombination in a natural population of the bdelloid rotifer Adineta vaga. Nat Commun 2020; 11:6421. [PMID: 33339818 PMCID: PMC7749112 DOI: 10.1038/s41467-020-19614-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 10/23/2020] [Indexed: 01/08/2023] Open
Abstract
Sexual reproduction is almost ubiquitous among extant eukaryotes. As most asexual lineages are short-lived, abandoning sex is commonly regarded as an evolutionary dead end. Still, putative anciently asexual lineages challenge this view. One of the most striking examples are bdelloid rotifers, microscopic freshwater invertebrates believed to have completely abandoned sexual reproduction tens of Myr ago. Here, we compare whole genomes of 11 wild-caught individuals of the bdelloid rotifer Adineta vaga and present evidence that some patterns in its genetic variation are incompatible with strict clonality and lack of genetic exchange. These patterns include genotype proportions close to Hardy-Weinberg expectations within loci, lack of linkage disequilibrium between distant loci, incongruent haplotype phylogenies across the genome, and evidence for hybridization between divergent lineages. Analysis of triallelic sites independently corroborates these findings. Our results provide evidence for interindividual genetic exchange and recombination in A. vaga, a species previously thought to be anciently asexual.
Collapse
Affiliation(s)
- Olga A Vakhrusheva
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation.
| | - Elena A Mnatsakanova
- Department of General Ecology and Hydrobiology, Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
| | - Yan R Galimov
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russian Federation
| | - Tatiana V Neretina
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
| | - Evgeny S Gerasimov
- Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- Martsinovsky Institute of Medical Parasitology, Tropical and Vector-Borne Diseases, Sechenov University, Moscow, 119435, Russian Federation
| | - Sergey A Naumenko
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- Department of Biostatistics, Harvard Chan School of Public Health, Boston, MA, 02115, USA
| | - Svetlana G Ozerova
- Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, 119334, Russian Federation
- Medkvadrat, Moscow, 115409, Russian Federation
| | - Arthur O Zalevsky
- Faculty of Bioengineering and Bioinformatics, M. V. Lomonosov Moscow State University, Moscow, 119234, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation
| | - Irina A Yushenova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Irina R Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, 02543, USA
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
| | - Maria D Logacheva
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
| | - Georgii A Bazykin
- Skolkovo Institute of Science and Technology, Moscow, 121205, Russian Federation
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, 127051, Russian Federation
| | - Alexey S Kondrashov
- A. N. Belozersky Institute of Physico-Chemical Biology, M. V. Lomonosov Moscow State University, Moscow, 119992, Russian Federation
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| |
Collapse
|
15
|
Shtratnikova VY, Rudenskaya YA, Gerasimov ES, Schelkunov MI, Logacheva MD, Kolesnikov AA. Complete genome assembly data of paenibacillus sp. RUD330, a hypothetical symbiont of euglena gracilis. Data Brief 2020; 32:106070. [PMID: 32793774 PMCID: PMC7408339 DOI: 10.1016/j.dib.2020.106070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 12/03/2022] Open
Abstract
An unknown bacterial strain was detected in the cytostome of Euglena gracilis and on the cell surface of Euglena gracilis using transmission electron microscopy. To identify the unknown bacterium and its function, we performed isolation experiments. Here we present the genome sequence of the isolate that was determined to be Paenibacillus sp. The genome of the bacterium was sequenced four times using Illumina technology with pair-end reads, Illumina technology with mate pair reads (inserts 3–4 and 6–8 Kb), and Nanopore technology with long reads (tens of thousands of nucleotides). Assemblies based on Illumina reads including mate-pair reads could not resolve issues caused by long tandem copies of rRNA, other tandem repeats, and extremely GC-rich regions (90–100%). Only long Nanopore reads resolved those gaps and made it possible to complete the entire genome; moreover, we found one plasmid. The length of the genome is 5.56 Mbp, and the average GC content is 59%. The genome of Paenibacillus sp. RUD330 included 8 copies of all the rRNA genes (23S; 16S; 5S), the length of the plasmid was 8.3 Kb. We hope that our genome assembly and the methods used can help other investigators in the assembly of complex genomes. Our reliable assembly could be a good basis for further physiological and genetic engineering studies of similar strains.
Collapse
Affiliation(s)
- Victoria Yu Shtratnikova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gory, b.1, h. 40, Moscow, 119991, Russian Federation
| | - Yulia A Rudenskaya
- Biological faculty, Lomonosov Moscow State University, Leninskie gory, b.1, h. 12, Moscow, 119991, Russian Federation
| | - Evgeny S Gerasimov
- Biological faculty, Lomonosov Moscow State University, Leninskie gory, b.1, h. 12, Moscow, 119991, Russian Federation.,Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per., h. 19, b. 1, Moscow, 127051, Russian Federation.,Martsinovsky Institute of Medical Parasitology, Tropical and Vector Borne Diseases, Sechenov University, Trubetskaya str., h. 8, b.2, Moscow, 119991, Russian Federation
| | - Mikhail I Schelkunov
- Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russian Federation.,Institute for Information Transmission Problems, Russian Academy of Sciences, Bolshoy Karetny per., h. 19, b. 1, Moscow, 127051, Russian Federation
| | - Maria D Logacheva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gory, b.1, h. 40, Moscow, 119991, Russian Federation.,Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow 143026, Russian Federation
| | - Alexander A Kolesnikov
- Biological faculty, Lomonosov Moscow State University, Leninskie gory, b.1, h. 12, Moscow, 119991, Russian Federation
| |
Collapse
|
16
|
Gerasimov ES, Gasparyan AA, Kaurov I, Tichý B, Logacheva MD, Kolesnikov AA, Lukeš J, Yurchenko V, Zimmer SL, Flegontov P. Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool. Nucleic Acids Res 2019; 46:765-781. [PMID: 29220521 PMCID: PMC5778460 DOI: 10.1093/nar/gkx1202] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/20/2017] [Indexed: 12/22/2022] Open
Abstract
RNA editing by targeted insertion and deletion of uridine is crucial to generate translatable mRNAs from the cryptogenes of the mitochondrial genome of kinetoplastids. This type of editing consists of a stepwise cascade of reactions generally proceeding from 3′ to 5′ on a transcript, resulting in a population of partially edited as well as pre-edited and completely edited molecules for each mitochondrial cryptogene of these protozoans. Often, the number of uridines inserted and deleted exceed the number of nucleotides that are genome-encoded. Thus, analysis of kinetoplastid mitochondrial transcriptomes has proven frustratingly complex. Here we present our analysis of Leptomonas pyrrhocoris mitochondrial cDNA deep sequencing reads using T-Aligner, our new tool which allows comprehensive characterization of RNA editing, not relying on targeted transcript amplification and on prior knowledge of final edited products. T-Aligner implements a pipeline of read mapping, visualization of all editing states and their coverage, and assembly of canonical and alternative translatable mRNAs. We also assess T-Aligner functionality on a more challenging deep sequencing read input from Trypanosoma cruzi. The analysis reveals that transcripts of cryptogenes of both species undergo very complex editing that includes the formation of alternative open reading frames and whole categories of truncated editing products.
Collapse
Affiliation(s)
- Evgeny S Gerasimov
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.,Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
| | - Anna A Gasparyan
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Iosif Kaurov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Boris Tichý
- Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Maria D Logacheva
- Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.,Russia Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia.,Skolkovo Institute of Science and Technology, Moscow, 14326, Russia
| | | | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice 370 05, Czech Republic
| | - Vyacheslav Yurchenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic.,Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic.,Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Sara L Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth, MN 55812-3031, USA
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic.,Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow 119991, Russia.,Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava 710 00, Czech Republic
| |
Collapse
|
17
|
Penin AA, Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD. Comparative Analysis of Developmental Transcriptome Maps of Arabidopsis thaliana and Solanum lycopersicum. Genes (Basel) 2019; 10:genes10010050. [PMID: 30650673 PMCID: PMC6356586 DOI: 10.3390/genes10010050] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/04/2018] [Indexed: 11/26/2022] Open
Abstract
The knowledge of gene functions in model organisms is the starting point for the analysis of gene function in non-model species, including economically important ones. Usually, the assignment of gene functions is based on sequence similarity. In plants, due to a highly intricate gene landscape, this approach has some limitations. It is often impossible to directly match gene sets from one plant species to another species based only on their sequences. Thus, it is necessary to use additional information to identify functionally similar genes. Expression patterns have great potential to serve as a source of such information. An important prerequisite for the comparative analysis of transcriptomes is the existence of high-resolution expression maps consisting of comparable samples. Here, we present a transcriptome atlas of tomato (Solanum lycopersicum) consisting of 30 samples of different organs and developmental stages. The samples were selected in a way that allowed for side-by-side comparison with the Arabidopsis thaliana transcriptome map. Newly obtained data are integrated in the TraVA database and are available online, together with tools for their analysis. In this paper, we demonstrate the potential of comparing transcriptome maps for inferring shifts in the expression of paralogous genes.
Collapse
Affiliation(s)
- Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, 127051 Moscow, Russia.
- Lomonosov Moscow State University, Leninskye Gory, 119992 Moscow, Russia.
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, 127051 Moscow, Russia.
- Skolkovo Institute of Science and Technology, Center for Data-Intensive Biology and Biomedicine, Nobelya Ulitsa 3, 121205 Moscow, Russia.
| | - Artem S Kasianov
- Skolkovo Institute of Science and Technology, Center for Data-Intensive Biology and Biomedicine, Nobelya Ulitsa 3, 121205 Moscow, Russia.
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina 3, 119991 Moscow, Russia.
| | - Evgeny S Gerasimov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, 127051 Moscow, Russia.
- Lomonosov Moscow State University, Leninskye Gory, 119992 Moscow, Russia.
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Bolshoy Karetny per. 19, build. 1, 127051 Moscow, Russia.
- Lomonosov Moscow State University, Leninskye Gory, 119992 Moscow, Russia.
- Skolkovo Institute of Science and Technology, Center for Data-Intensive Biology and Biomedicine, Nobelya Ulitsa 3, 121205 Moscow, Russia.
| |
Collapse
|
18
|
Kalem MC, Gerasimov ES, Vu PK, Zimmer SL. Gene expression to mitochondrial metabolism: Variability among cultured Trypanosoma cruzi strains. PLoS One 2018; 13:e0197983. [PMID: 29847594 PMCID: PMC5976161 DOI: 10.1371/journal.pone.0197983] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/11/2018] [Indexed: 11/18/2022] Open
Abstract
The insect-transmitted protozoan parasite Trypanosoma cruzi experiences changes in nutrient availability and rate of flux through different metabolic pathways across its life cycle. The species encompasses much genetic diversity of both the nuclear and mitochondrial genomes among isolated strains. The genetic or expression variation of both genomes are likely to impact metabolic responses to environmental stimuli, and even steady state metabolic function, among strains. To begin formal characterization these differences, we compared aspects of metabolism between genetically similar strains CL Brener and Tulahuen with less similar Esmeraldo and Sylvio X10 strains in a culture environment. Epimastigotes of all strains took up glucose at similar rates. However, the degree of medium acidification that could be observed when glucose was absent from the medium varied by strain, indicating potential differences in excreted metabolic byproducts. Our main focus was differences related to electron transport chain function. We observed differences in ATP-coupled respiration and maximal respiratory capacity, mitochondrial membrane potential, and mitochondrial morphology between strains, despite the fact that abundances of two nuclear-encoded proteins of the electron transport chain are similar between strains. RNA sequencing reveals strain-specific differences in abundances of mRNAs encoding proteins of the respiratory chain but also other metabolic processes. From these differences in metabolism and mitochondrial phenotypes we have generated tentative models for the differential metabolic fluxes or differences in gene expression that may underlie these results.
Collapse
Affiliation(s)
- Murat C. Kalem
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, United States of America
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth campus, Duluth, Minnesota, United States of America
| | | | - Pamela K. Vu
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, United States of America
| | - Sara L. Zimmer
- Department of Biomedical Sciences, University of Minnesota Medical School, Duluth campus, Duluth, Minnesota, United States of America
| |
Collapse
|
19
|
Kasianov AS, Klepikova AV, Kulakovskiy IV, Gerasimov ES, Fedotova AV, Besedina EG, Kondrashov AS, Logacheva MD, Penin AA. High-quality genome assembly of Capsella bursa-pastoris reveals asymmetry of regulatory elements at early stages of polyploid genome evolution. Plant J 2017; 91:278-291. [PMID: 28387959 DOI: 10.1111/tpj.13563] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 03/01/2017] [Accepted: 03/31/2017] [Indexed: 05/22/2023]
Abstract
Polyploidization and subsequent sub- and neofunctionalization of duplicated genes represent a major mechanism of plant genome evolution. Capsella bursa-pastoris, a widespread ruderal plant, is a recent allotetraploid and, thus, is an ideal model organism for studying early changes following polyploidization. We constructed a high-quality assembly of C. bursa-pastoris genome and a transcriptome atlas covering a broad sample of organs and developmental stages (available online at http://travadb.org/browse/Species=Cbp). We demonstrate that expression of homeologs is mostly symmetric between subgenomes, and identify a set of homeolog pairs with discordant expression. Comparison of promoters within such pairs revealed emerging asymmetry of regulatory elements. Among them there are multiple binding sites for transcription factors controlling the regulation of photosynthesis and plant development by light (PIF3, HY5) and cold stress response (CBF). These results suggest that polyploidization in C. bursa-pastoris enhanced its plasticity of response to light and temperature, and allowed substantial expansion of its distribution range.
Collapse
Affiliation(s)
- Artem S Kasianov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia
| | - Anna V Klepikova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
| | - Ivan V Kulakovskiy
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkina str, Moscow, 119333, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova 32, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo Innovation Center, Building 3, Moscow, 143026, Russia
| | - Evgeny S Gerasimov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna V Fedotova
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Elizaveta G Besedina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Alexey S Kondrashov
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Department of Ecology and Evolution, University of Michigan, 830 North University, Ann Arbor, MI 48109-1048, MI, USA
| | - Maria D Logacheva
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, 18 Kremlevskaya str, Kazan, 420008, Russia
| | - Aleksey A Penin
- A. N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
20
|
Gerasimov ES, Gasparyan AA, Litus IA, Logacheva MD, Kolesnikov AA. Minicircle Kinetoplast Genome of Insect Trypanosomatid Leptomonas pyrrhocoris. Biochemistry (Mosc) 2017; 82:572-578. [PMID: 28601067 DOI: 10.1134/s0006297917050054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We present here the structure of a minicircle population based on transcriptome sequencing of Leptomonas pyrrhocoris. We show that minicircle DNA molecules are dimeric. As in dixenous species, the entire molecule of minicircle DNA is transcribed. This is the first minicircle transcriptome of monoxenous trypanosomatid species determined using NGS technology.
Collapse
Affiliation(s)
- E S Gerasimov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, 119991, Russia.
| | | | | | | | | |
Collapse
|
21
|
Kovina AP, Petrova NV, Gushchanskaya ES, Dolgushin KV, Gerasimov ES, Galitsyna AA, Penin AA, Flyamer IM, Ioudinkova ES, Gavrilov AA, Vassetzky YS, Ulianov SV, Iarovaia OV, Razin SV. Evolution of the Genome 3D Organization: Comparison of Fused and Segregated Globin Gene Clusters. Mol Biol Evol 2017; 34:1492-1504. [DOI: 10.1093/molbev/msx100] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
|
22
|
Klepikova AV, Kasianov AS, Gerasimov ES, Logacheva MD, Penin AA. A high resolution map of the Arabidopsis thaliana developmental transcriptome based on RNA-seq profiling. Plant J 2016; 88:1058-1070. [PMID: 27549386 DOI: 10.1111/tpj.13312] [Citation(s) in RCA: 388] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 05/18/2023]
Abstract
Arabidopsis thaliana is a long established model species for plant molecular biology, genetics and genomics, and studies of A. thaliana gene function provide the basis for formulating hypotheses and designing experiments involving other plants, including economically important species. A comprehensive understanding of the A. thaliana genome and a detailed and accurate understanding of the expression of its associated genes is therefore of great importance for both fundamental research and practical applications. Such goal is reliant on the development of new genetic and genomic resources, involving new methods of data acquisition and analysis. We present here the genome-wide analysis of A. thaliana gene expression profiles across different organs and developmental stages using high-throughput transcriptome sequencing. The expression of 25 706 protein-coding genes, as well as their stability and their spatiotemporal specificity, was assessed in 79 organs and developmental stages. A search for alternative splicing events identified 37 873 previously unreported splice junctions, approximately 30% of them occurred in intergenic regions. These potentially represent novel spliced genes that are not included in the TAIR10 database. These data are housed in an open-access web-based database, TraVA (Transcriptome Variation Analysis, http://travadb.org/), which allows visualization and analysis of gene expression profiles and differential gene expression between organs and developmental stages.
Collapse
Affiliation(s)
- Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
| | - Artem S Kasianov
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny S Gerasimov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Laboratory of Extreme Biology, Institute of Fundamental Biology and Medicine, Kazan Federal University, Kazan, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127051, Russia
- A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
23
|
Flegontov P, Changmai P, Zidkova A, Logacheva MD, Altınışık NE, Flegontova O, Gelfand MS, Gerasimov ES, Khrameeva EE, Konovalova OP, Neretina T, Nikolsky YV, Starostin G, Stepanova VV, Travinsky IV, Tříska M, Tříska P, Tatarinova TV. Genomic study of the Ket: a Paleo-Eskimo-related ethnic group with significant ancient North Eurasian ancestry. Sci Rep 2016; 6:20768. [PMID: 26865217 PMCID: PMC4750364 DOI: 10.1038/srep20768] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/07/2016] [Indexed: 01/11/2023] Open
Abstract
The Kets, an ethnic group in the Yenisei River basin, Russia, are considered the last nomadic hunter-gatherers of Siberia, and Ket language has no transparent affiliation with any language family. We investigated connections between the Kets and Siberian and North American populations, with emphasis on the Mal'ta and Paleo-Eskimo ancient genomes, using original data from 46 unrelated samples of Kets and 42 samples of their neighboring ethnic groups (Uralic-speaking Nganasans, Enets, and Selkups). We genotyped over 130,000 autosomal SNPs, identified mitochondrial and Y-chromosomal haplogroups, and performed high-coverage genome sequencing of two Ket individuals. We established that Nganasans, Kets, Selkups, and Yukaghirs form a cluster of populations most closely related to Paleo-Eskimos in Siberia (not considering indigenous populations of Chukotka and Kamchatka). Kets are closely related to modern Selkups and to some Bronze and Iron Age populations of the Altai region, with all these groups sharing a high degree of Mal'ta ancestry. Implications of these findings for the linguistic hypothesis uniting Ket and Na-Dene languages into a language macrofamily are discussed.
Collapse
Affiliation(s)
- Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - Piya Changmai
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Anastassiya Zidkova
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Maria D. Logacheva
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - N. Ezgi Altınışık
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czech Republic
| | - Mikhail S. Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny S. Gerasimov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina E. Khrameeva
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Olga P. Konovalova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Neretina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Yuri V. Nikolsky
- Biomedical Cluster, Skolkovo Foundation, Skolkovo, Russia
- George Mason University, Fairfax, VA, USA
| | - George Starostin
- Russian State University for the Humanities, Moscow, Russia
- Russian Presidential Academy (RANEPA), Moscow, Russia
| | - Vita V. Stepanova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | | | - Martin Tříska
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
| | - Petr Tříska
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal
- Instituto de Ciências Biomédicas da Universidade do Porto (ICBAS), Porto, Portugal
| | - Tatiana V. Tatarinova
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Children’s Hospital Los Angeles, Los Angeles, CA, USA
- Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
24
|
Baranova MA, Logacheva MD, Penin AA, Seplyarskiy VB, Safonova YY, Naumenko SA, Klepikova AV, Gerasimov ES, Bazykin GA, James TY, Kondrashov AS. Extraordinary Genetic Diversity in a Wood Decay Mushroom. Mol Biol Evol 2015; 32:2775-83. [PMID: 26163667 PMCID: PMC4576712 DOI: 10.1093/molbev/msv153] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10−8 (95% CI: 1.1 × 10−8 to 4.1 × 10−8) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics.
Collapse
Affiliation(s)
- Maria A Baranova
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir B Seplyarskiy
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Yana Y Safonova
- Algorithmic Biology Lab, St. Petersburg Academic University of the Russian Academy of Sciences, St Petersburg, Russia
| | - Sergey A Naumenko
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny S Gerasimov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Georgii A Bazykin
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan
| | - Alexey S Kondrashov
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia Department of Ecology and Evolutionary Biology, University of Michigan
| |
Collapse
|
25
|
Leushkin EV, Logacheva MD, Penin AA, Sutormin RA, Gerasimov ES, Kochkina GA, Ivanushkina NE, Vasilenko OV, Kondrashov AS, Ozerskaya SM. Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages. BMC Genomics 2015; 16:400. [PMID: 25994131 PMCID: PMC4438637 DOI: 10.1186/s12864-015-1570-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/23/2015] [Indexed: 01/17/2023] Open
Abstract
Background Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology. Results We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments. We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100–10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree. Conclusions Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1570-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Evgeny V Leushkin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127994, Russia.
| | - Maria D Logacheva
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127994, Russia. .,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Aleksey A Penin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, 127994, Russia. .,Department of Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Roman A Sutormin
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Lawrence Berkeley National Laboratory, Berkeley, 94710, CA, USA.
| | - Evgeny S Gerasimov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Department of Biology, Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Galina A Kochkina
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia.
| | - Natalia E Ivanushkina
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia.
| | - Oleg V Vasilenko
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia.
| | - Alexey S Kondrashov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Leninskye Gory 1-73, Moscow, 119992, Russia. .,Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Svetlana M Ozerskaya
- G.K.Skryabin Institute of Biochemistry and Physiology of Microorganisms RAS, Pushchino, 142290, Russia.
| |
Collapse
|
26
|
Abstract
In this review, we discuss types of mitochondrial genome structural organization (architecture), which includes the following characteristic features: size and the shape of DNA molecule, number of encoded genes, presence of cryptogenes, and editing of primary transcripts.
Collapse
Affiliation(s)
- A A Kolesnikov
- Biological Faculty, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | | |
Collapse
|
27
|
Gerasimov ES, Efimova NS, Kolesnikov AA. [Three patterns of trypanosomatid cryptogene structural organization]. Mol Biol (Mosk) 2012; 46:612-621. [PMID: 23113350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We sequenced a number of cryptogenes from previously unstudied species of homoxenous trypanosomatids belonging to the different phylogenetic groups and found new examples of editing domain length reduction for A6 and COIII. The comparative analyzes of sequences allows to divide the cryptogenes in three groups (patterns) according to the degree of primary structure conservation and editing domain length variation. We discuss the possible factors which influence the cryptogene's structure and evolutionary behavior. Also we demonstrate alternative editing of rps12 transcript in Wallaceina sp. Wsd.
Collapse
|
28
|
Gerasimov ES, Kostygov AY, Yan S, Kolesnikov AA. From cryptogene to gene? ND8 editing domain reduction in insect trypanosomatids. Eur J Protistol 2011; 48:185-93. [PMID: 22014411 DOI: 10.1016/j.ejop.2011.09.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 09/08/2011] [Accepted: 09/09/2011] [Indexed: 11/17/2022]
Abstract
Mitochondrial ND8 gene is pan-edited in most known trypanosomatid species and 5'-edited only in a few trypanosomatid species. In this work, the ND8 nucleotide sequences from three species of insect trypanosomatids ("Wallaceina" sp. Wsd, Leptomonas rigidus and Leptomonas collosoma) were obtained and compared with previously known ND8 cryptogene sequences and mature mRNA sequences from other trypanosomatid species. We found a new pattern of editing: only 18 U residues are inserted in the 5' region of the primary transcript in all investigated species and the potential start codon is encoded on the DNA level. This is the first case when a pre-edited ND8 sequence is found to contain a putative ORF. Previously, a 5'-edited ND8 cryptogene was known only from Strigomonas oncopelti, but it contained only about half of the ORF and no start codon. Here we present the ND8 gene sequence from Angomonas deanei which has similar cryptogene structure. We also show that according to 18S rRNA phylogenetic analysis, the species with the encoded ORF group together and so do species with the 5'-edited and pan-edited forms of the gene. This result sheds light on the evolution of cryptogene structure which involved multiple events of editing domain length reduction.
Collapse
Affiliation(s)
- Evgeny S Gerasimov
- Dept Molecular Biology, MV Lomonosov Moscow State University, 119991 Moscow, Russia
| | | | | | | |
Collapse
|
29
|
Flegontov PN, Zhirenkina EN, Gerasimov ES, Ponirovsky EN, Strelkova MV, Kolesnikov AA. Selective amplification of maxicircle classes during the life cycle of Leishmania major. Mol Biochem Parasitol 2009; 165:142-52. [DOI: 10.1016/j.molbiopara.2009.01.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2008] [Revised: 01/23/2009] [Accepted: 01/26/2009] [Indexed: 10/21/2022]
|