Uncategorized

6 month Master’s student project

Background 

Horizontal gene transfer, also called lateral gene transfer or LGT, allows the acquisition of genetic material, and thus new functions, from distantly related organisms. This process is well known to be a major driver of evolution in prokaryotes, and is for example responsible for the acquisition of antibiotic resistance in bacteria. In contrast, the role and frequency of LGT in eukaryotes has been much less studied, although there are clear examples of its impact on the evolution of certain unicellular eukaryote parasites. When they exist, these recent studies often focus on gene transfer events from very distant organisms, such as from bacteria, because they are easier to detect with confidence. However, it has been shown in bacteria that LGTs more often occur among closer related lineages. This can be explained in part because horizontally acquired genes that use codons that better match the codon usage of their new host genome will be better optimized for expression within the context of that genome and will confer less of a fitness cost on their new host. . In eukaryotes, the extent to which closely related organisms exchange genetic material and how much this varies across the diversity of eukaryotic lineages is, in contrast, limited. 

Project 

This project aims to estimate the importance of LGT between closely related eukaryotic species. It consists of two parts: A) developing an approach that detects genes that are very likely to be derived laterally from a different, but closely related eukaryote, and B) using this approach to study which eukaryotic clades underwent many of such ‘short-distance’ LGTs andto identify the features (such as function or codon usage) of genes shared via LGT between closely related species. The developed approach will first be benchmarked with a set of published LGTs, and will then be applied to identify cases of LGTs in understudied lineages of unicellular eukaryotes (protists).  

Your profile 

Ideally, the candidate will have some knowledge in phylogenetics/molecular evolution and some knowledge or strong desire to learn scripting (Python or Perl) and working in a linux environment. Additional requirement: good level in English, good oral and written communication skills, autonomy, organization skills. 

Practicalities 

This is a 6 month internship that will take place between January and June 2021. A financial compensation of €577.50/mo is offered. 

The research unit of “Ecology, Systematics and Evolution” (ESE) is located in the University Paris-Sud campus in Orsay. This campus is 20 km south of Paris and well connected through commuter train. 

The student will work within the DEEM (Diversity, Ecology and Evolution of Microbes: http://www.deemteam.fr/en) team, which has a broad expertise in ecology and evolutionary biology, with a focus on microbes (prokaryotic and eukaryotic). This internship will be co-supervised by Dr. Laura Eme (laura.eme@universite-paris-saclay.fr), principal investigator, and Dr. Jolien van Hooff, postdoctoral fellow (jolien.van-hooff@universite-paris-saclay.fr).  

Note the possibility to apply for a PhD scholarship from the doctoral school at the end of the internship if you are interested in pursuing a PhD with us.  

Interested? 

If you are interested in genome evolution and pursuing a research project in bioinformatics and phylogenetics, please contact Dr Laura Eme (laura.eme@universite-paris-saclay.fr) for more information or apply directly by sending your CV and a cover letter explaining your motivation for undertaking this project.  

Uncategorized

Book chapters

2015 –  Sharpe SC*, Eme L*, Brown MW, Roger AJ. Timing the Origins of Multicellular Eukaryotes Through Phylogenomics and Relaxed Molecular Clock Analyses. Evolutionary Transitions to Multicellular Life. Springer, 2015. 3-29.
*These authors equally contributed to the manuscript.
[Link]

Invited contributions

2015 –  Eme L, Doolittle WF. Primer: Archaea. Current Biology 25 (19), R851-R855. Special issue “History of Life on Earth”. [Abstract]

2015 –  Eme L, Doolittle WF. Microbial Diversity: A Bonanza of Phyla. Current Biology 25 (6), R227–R230.
[Abstract]

Peer-reviewed papers

In revision – Karnkowska K, Vacek V, Zubáčová Z, Treitli S, Petrželková R, Eme L, Novák N, Žárský V, Barlow L, Herman H, Soukal P, Hroudová M, Doležal P, Stairs C, Roger AJ, Elias M, Dacks J, Vlček C, Hampl V. A eukaryote without a mitochondrial organelle. Current Biology.

Submitted – Cenci U, Moog D, Curtis BA, Tanifuji G, Eme L, Lukes J, Archibald JM. Heme pathway evolution in kinetoplastid protists. Mol Phyl Evol.

Submitted – Dacks JB, Field MC, Buick R, Eme L, Gribaldo S, Roger AJ, Brochier-Armanet C and Devos DP. Bridging the divide: major advances and emerging consensus for the origins of eukaryotes. Journal of Cell Science.

2015 – Groussin M, Boussau B, Szöllosi GJ, Eme L, Gouy M, Brochier-Armanet C, Daubin V. Gene acquisitions from bacteria at the origins of major archaeal clades are vastly overestimated. Molecular biology and evolution, msv249. [Abstract] [PDF]

2015 – Torruella G, de Mendoza A, Grau-Bové X, Antó M, Chaplin MA, del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R, Roger AJ, Sitjà-Bobadilla A, Donachie S, Ruiz-Trillo I. Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi. Current Biology, 10.1016/j.cub.2015.07.053. [Abstract] [PDF]

2015 –  Gawryluk R*, Eme L*, Roger AJ. Gene fusion, fission, lateral transfer, and loss: not-so-rare events in the evolution of eukaryotic ATP citrate lyase. Molecular Phylogenetics and Evolution. *These authors equally contributed to the manuscript.
[Abstract]

2015 – Leger MM, Petrů M, Žárský V, Eme L, Vlček Č, Harding T, Lang BF, Eliáš M, Doležal P, Roger AJ. An ancestral bacterial division system is widespread in eukaryotic mitochondria. PNAS 2015, 1421392112.
[Abstract]

2014 –  Eme L, Sharpe SC, Brown MW, Roger AJ. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. “Origin and evolution of eukaryotes”, Cold Spring Harbor Perspectives in Biology, 6(8), a016139.
[Abstract]

2014 – Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, van der Giezen M, Roger AJ. A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia. Current Biology 24 (11), 1176-1186.
[Abstract] [PDF]

2013 – Tsaousis AD*, Gentekaki E*., Eme L*, Gaston D, & Roger AJ (2014). Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes. Eukaryotic cell, 13(1), 143-153.
*These authors equally contributed to the manuscript.
[Abstract] [PDF]

2013 – Eme L,  Reigstad LJ, Spang A, Lanzén A, Weinmaier T, Rattei T, Schleper C, Brochier-Armanet C. Metagenomics of Kamchatkan hot spring filaments reveals two new major (hyper)thermophilic lineages related to Thaumarchaeota. Research in Microbiologoy (2013), doi:10.1016/j.resmic.2013.02.006.
[Abstract] [PDF]

2011 – Eme L, Trilles A, Moreira D, Brochier-Armanet C “The phylogenomic analysis of the Anaphase Promoting Complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes.” BMC Evolutionary Biology. 2011 Sep 23;11:265. doi:10.1186/1471-2148-11-265.
[Abstract] [PDF]

2011 – Boileau C, Eme L, Brochier-Armanet C, Janicki A, Zhang CC, Latifi A. A eukaryotic-like sulfiredoxin important for peroxiredoxin reduction and oxidative stress response in the cyanobacterium Anabaena PCC 7120. New Phytologist. 2011 Jun 8. doi:10.1111/j.1469-8137.2011.03774.x. Epub 2011 Jun 8.
[Abstract] [PDF]

2009 – Eme L, Moreira D, Talla E, Brochier-Armanet C. A Complex Cell Division Machinery was Present in the Last Common Ancestor of Eukaryotes. PLoS ONE 4(4): e5021. doi:10.1371/journal.pone.0005021.
[Abstract] [PDF]

 

Oral communications

2015 – Invited speaker. Company of Biologists Workshop “Eukaryo-/Archaeogenesis: Where Do We Stand?”. Pinpointing the root of extant eukaryotic diversity: advances, challenges and consequences.

2014 – ISOP/ISEP meeting 2014 (Banff, Canada). Eme L, Sharpe SC, Brown MW and Roger AJ. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.

2014 – Invited speaker. Microbe Evolution 2014 (Tsukuba, Japan). The role of Lateral Gene Transfer in adaptation of protists to new environments.

2013 – ICOP conference (Vancouver, Canada). Eme L, Gentekaki E, Curtis B, Archiblad JA, Roger AJ. Phylogenomic analyses of Blastocystis sp . subtype 1 reveals an important role for lateral gene transfer in adaptation to parasitism of the human gut. 

2013 – SMBE Satellite Eukaryotic-omics (Davis, US). Eme L, Gentekaki E, Curtis B, Archiblad JA, Roger AJ. Phylogenomic analyses of Blastocystis sp . subtype 1 reveals an important role for lateral gene transfer in adaptation to parasitism of the human gut. 

2012 – PROTIST conference (Oslo, Norway). Eme L, Roger AJ. Pinpointing the root of extant eukaryotic diversity

2011 – ALPHY meeting (Bioinformatics et evolutionary genomics) (Lyon, France).
Eme L, Moreira D, Brochier-Armanet C. The phylogenomic analysis of the ACP/C and its targets points to a complex and modern-like control of the cell cycle in LECA.

2009 – Invitation at the International Meeting “Archaea and the universal tree of life” (Fondation des Treilles, France). Eme L, Moreira D, Brochier-Armanet C. Phylogenomics of eukaryotic systems: tracing back the nature of the last eukaryotic common ancestor

2009 – ALPHY meeting (Montpellier, France). Eme L, Moreira D, Talla E., Brochier-Armanet C. A complex cell division machinery in the last common ancestor of eukaryotes

Poster presentations

2015 – ECOP (European Congress of Protistology) (Seville, Spain). Eme L, Stairs CW, Karnkowska A, Hampl V, Roger AJ. Lateral Gene Transfer is an overlooked mechanism in the adaptation of microbial eukaryotes to new environments.

2015 – SMBE (Society for Molecular Biology and Evolution) (Vienna, Austria). Eme L, Stairs CW, Karnkowska A, Hampl V, Roger AJ. Lateral Gene Transfer is an overlooked mechanism in the adaptation of microbial eukaryotes to new environments.

2010 – SMBE (Society for Molecular Biology and Evolution) (Lyon, France). Eme L, Moreira D, Talla E., Brochier-Armanet C. Tracing back the nature of cell division in the Last Common Ancestor of Eukaryotes.

2009 – EMBO 2009 conference Comparative Genomics of Eukaryotic Microorganisms. (San Feliu de Guixols, Spain). Eme L, Moreira D, Brochier-Armanet C Phylogenomic study of cytokinesis in Eukaryotes
Eukaryotic Cell Journal Outstanding Young Investigator Award.

2009 – Graduate School Meeting (Marseilles, France).
Eme L, Moreira D, Brochier-Armanet C A complex cell division machinery in the last common ancestor of eukaryotes. Best Poster Award.

2007 – JOBIM conference (Marseille, France). Eme L, Moreira D, Brochier-Armanet C Origin and evolution of the eukaryotic midbody: A phylogenomic approach

Uncategorized

June 2011 – to date Post-Doctoral Fellow
Centre for Comparative Genomics and Evolutionary Bioinformatics (Halifax, Canada). Supervisor: Dr. Andrew J. Roger.

Root of the Eukaryotic Tree 
One of my major interests lies in the investigation of the relationships amongst eukaryotic lineages as well as the position of the root of the eukaryote tree. Eukaryotes are usually divided in six ‘super-groups’, but this hypothesis is still controversial. One of my postdoctoral projects aims to revisit the problem of robustly rooting the tree of eukaryotes through the investigation of three kinds of untapped phylogenetic markers.

Adaptation of eukaryotic microbes to anaerobiosis 
Since I’ve joined the Roger Lab I have been interested in the evolutionary transition from aerobic to microaerobic/anaerobic conditions that occurred several times independently across the tree of eukaryotes. In particular, I am interested in how this transition has affected mitochondrial functions and has reshaped the proteomes and biochemical abilities of the mitochondrial-related organelles (MROs) found in anaerobic protists.

Evolution of parasitic protists 
I am also interested in the genomic adaptations occuring during the transition from free-living to parasitic lifestyles, and in particular the ones in relation with the acquisition (through lateral gene transfers) and expansion of genes  involved in anaerobiosis, pathogenicity, nutrient acquisition and response to host defense mechanisms.

Eukaryotic microbes in the human microbiome 
Recently, I have been interested in the impact of eukaryotic microbes (parasites and commensals) on the human gut microbiome. Since the prevalence and roles of microbial eukaryotes has been rarely studied, we aim to obtain a better understanding of the relationships between particular parasitic infections and pathologies such as inflammatory bowel disease (IBD).

Archaeal biodiversity and evolution 

 

October 2007 – June 2011 PhD in Phylogeny, Evolution and Bioinformatics.
Team Genome, Evolution and Bioinformatics (Laboratoire de Chimie Bactérienne, CNRS, Marseilles, France). Supervisor: Dr. Céline Brochier-Armanet.

Characterization of LECA — Evolution of eukaryotic multiprotein complexes
The development of high throughput techniques, especially in proteomics and genomics has yielded extensive data that can be used in evolutionary analyses. In this context, eukaryotic multiprotein structures (EMS) are objects of interest. Indeed, these large protein complexes are involved in many fundamental processes of eukaryotic cells, and have no homologues in prokaryotes (even if the functions in which they are involved may exist) and therefore have certainly played a major role in the eukaryogenesis.
During my PhD, I carried out the phylogenomic analysis of two EMS involved in cell division (the midbody and the APC/C) and showed that these systems have an ancient evolutionary origin and were already present in the last common ancestor of eukaryotes (LECA), while resulting from eukaryotic innovations. This implies that the emergence of these two EMS occurred after the divergence of the eukaryotic lineage and before the diversification that gave rise to the current lineages.
Beyond these evolutionary questions, analyses of these EMS uncover some biological aspects of these systems. Indeed, if these systems were generally well conserved during the diversification of eukaryotes, their analysis shows a high plasticity of composition in some protist lineages. This suggests recent changes regarding certain phases of these organisms cell cycle which would be interesting to explore experimentally.

Eukaryotic tree of life
Concomitantly, this work showed that, although being operational protein, components of these EMS carry a phylogenetic signal usable for inferring phylogenetic relationships among eukaryotic lineages. Construction of supermatrixes from these proteins led to the inference of phylogenies of high quality. Combining these data with those from analyses based on informational proteins showed a significant progress on the resolution of inferred trees. These results open the field of possibilities to find other markers among the untapped operational proteins.

Uncategorized

6 month Master’s student project

Background 

Horizontal gene transfer, also called lateral gene transfer or LGT, allows the acquisition of genetic material, and thus new functions, from distantly related organisms. This process is well known to be a major driver of evolution in prokaryotes, and is for example responsible for the acquisition of antibiotic resistance in bacteria. In contrast, the role and frequency of LGT in eukaryotes has been much less studied, although there are clear examples of its impact on the evolution of certain unicellular eukaryote parasites. When they exist, these recent studies often focus on gene transfer events from very distant organisms, such as from bacteria, because they are easier to detect with confidence. However, it has been shown in bacteria that LGTs more often occur among closer related lineages. This can be explained in part because horizontally acquired genes that use codons that better match the codon usage of their new host genome will be better optimized for expression within the context of that genome and will confer less of a fitness cost on their new host. . In eukaryotes, the extent to which closely related organisms exchange genetic material and how much this varies across the diversity of eukaryotic lineages is, in contrast, limited. 

Project 

This project aims to estimate the importance of LGT between closely related eukaryotic species. It consists of two parts: A) developing an approach that detects genes that are very likely to be derived laterally from a different, but closely related eukaryote, and B) using this approach to study which eukaryotic clades underwent many of such ‘short-distance’ LGTs andto identify the features (such as function or codon usage) of genes shared via LGT between closely related species. The developed approach will first be benchmarked with a set of published LGTs, and will then be applied to identify cases of LGTs in understudied lineages of unicellular eukaryotes (protists).  

Your profile 

Ideally, the candidate will have some knowledge in phylogenetics/molecular evolution and some knowledge or strong desire to learn scripting (Python or Perl) and working in a linux environment. Additional requirement: good level in English, good oral and written communication skills, autonomy, organization skills. 

Practicalities 

This is a 6 month internship that will take place between January and June 2021. A financial compensation of €577.50/mo is offered. 

The research unit of “Ecology, Systematics and Evolution” (ESE) is located in the University Paris-Sud campus in Orsay. This campus is 20 km south of Paris and well connected through commuter train. 

The student will work within the DEEM (Diversity, Ecology and Evolution of Microbes: http://www.deemteam.fr/en) team, which has a broad expertise in ecology and evolutionary biology, with a focus on microbes (prokaryotic and eukaryotic). This internship will be co-supervised by Dr. Laura Eme (laura.eme@universite-paris-saclay.fr), principal investigator, and Dr. Jolien van Hooff, postdoctoral fellow (jolien.van-hooff@universite-paris-saclay.fr).  

Note the possibility to apply for a PhD scholarship from the doctoral school at the end of the internship if you are interested in pursuing a PhD with us.  

Interested? 

If you are interested in genome evolution and pursuing a research project in bioinformatics and phylogenetics, please contact Dr Laura Eme (laura.eme@universite-paris-saclay.fr) for more information or apply directly by sending your CV and a cover letter explaining your motivation for undertaking this project.  

Uncategorized

Book chapters

2015 –  Sharpe SC*, Eme L*, Brown MW, Roger AJ. Timing the Origins of Multicellular Eukaryotes Through Phylogenomics and Relaxed Molecular Clock Analyses. Evolutionary Transitions to Multicellular Life. Springer, 2015. 3-29.
*These authors equally contributed to the manuscript.
[Link]

Invited contributions

2015 –  Eme L, Doolittle WF. Primer: Archaea. Current Biology 25 (19), R851-R855. Special issue “History of Life on Earth”. [Abstract]

2015 –  Eme L, Doolittle WF. Microbial Diversity: A Bonanza of Phyla. Current Biology 25 (6), R227–R230.
[Abstract]

Peer-reviewed papers

In revision – Karnkowska K, Vacek V, Zubáčová Z, Treitli S, Petrželková R, Eme L, Novák N, Žárský V, Barlow L, Herman H, Soukal P, Hroudová M, Doležal P, Stairs C, Roger AJ, Elias M, Dacks J, Vlček C, Hampl V. A eukaryote without a mitochondrial organelle. Current Biology.

Submitted – Cenci U, Moog D, Curtis BA, Tanifuji G, Eme L, Lukes J, Archibald JM. Heme pathway evolution in kinetoplastid protists. Mol Phyl Evol.

Submitted – Dacks JB, Field MC, Buick R, Eme L, Gribaldo S, Roger AJ, Brochier-Armanet C and Devos DP. Bridging the divide: major advances and emerging consensus for the origins of eukaryotes. Journal of Cell Science.

2015 – Groussin M, Boussau B, Szöllosi GJ, Eme L, Gouy M, Brochier-Armanet C, Daubin V. Gene acquisitions from bacteria at the origins of major archaeal clades are vastly overestimated. Molecular biology and evolution, msv249. [Abstract] [PDF]

2015 – Torruella G, de Mendoza A, Grau-Bové X, Antó M, Chaplin MA, del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R, Roger AJ, Sitjà-Bobadilla A, Donachie S, Ruiz-Trillo I. Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi. Current Biology, 10.1016/j.cub.2015.07.053. [Abstract] [PDF]

2015 –  Gawryluk R*, Eme L*, Roger AJ. Gene fusion, fission, lateral transfer, and loss: not-so-rare events in the evolution of eukaryotic ATP citrate lyase. Molecular Phylogenetics and Evolution. *These authors equally contributed to the manuscript.
[Abstract]

2015 – Leger MM, Petrů M, Žárský V, Eme L, Vlček Č, Harding T, Lang BF, Eliáš M, Doležal P, Roger AJ. An ancestral bacterial division system is widespread in eukaryotic mitochondria. PNAS 2015, 1421392112.
[Abstract]

2014 –  Eme L, Sharpe SC, Brown MW, Roger AJ. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. “Origin and evolution of eukaryotes”, Cold Spring Harbor Perspectives in Biology, 6(8), a016139.
[Abstract]

2014 – Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, van der Giezen M, Roger AJ. A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia. Current Biology 24 (11), 1176-1186.
[Abstract] [PDF]

2013 – Tsaousis AD*, Gentekaki E*., Eme L*, Gaston D, & Roger AJ (2014). Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes. Eukaryotic cell, 13(1), 143-153.
*These authors equally contributed to the manuscript.
[Abstract] [PDF]

2013 – Eme L,  Reigstad LJ, Spang A, Lanzén A, Weinmaier T, Rattei T, Schleper C, Brochier-Armanet C. Metagenomics of Kamchatkan hot spring filaments reveals two new major (hyper)thermophilic lineages related to Thaumarchaeota. Research in Microbiologoy (2013), doi:10.1016/j.resmic.2013.02.006.
[Abstract] [PDF]

2011 – Eme L, Trilles A, Moreira D, Brochier-Armanet C “The phylogenomic analysis of the Anaphase Promoting Complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes.” BMC Evolutionary Biology. 2011 Sep 23;11:265. doi:10.1186/1471-2148-11-265.
[Abstract] [PDF]

2011 – Boileau C, Eme L, Brochier-Armanet C, Janicki A, Zhang CC, Latifi A. A eukaryotic-like sulfiredoxin important for peroxiredoxin reduction and oxidative stress response in the cyanobacterium Anabaena PCC 7120. New Phytologist. 2011 Jun 8. doi:10.1111/j.1469-8137.2011.03774.x. Epub 2011 Jun 8.
[Abstract] [PDF]

2009 – Eme L, Moreira D, Talla E, Brochier-Armanet C. A Complex Cell Division Machinery was Present in the Last Common Ancestor of Eukaryotes. PLoS ONE 4(4): e5021. doi:10.1371/journal.pone.0005021.
[Abstract] [PDF]

 

Oral communications

2015 – Invited speaker. Company of Biologists Workshop “Eukaryo-/Archaeogenesis: Where Do We Stand?”. Pinpointing the root of extant eukaryotic diversity: advances, challenges and consequences.

2014 – ISOP/ISEP meeting 2014 (Banff, Canada). Eme L, Sharpe SC, Brown MW and Roger AJ. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.

2014 – Invited speaker. Microbe Evolution 2014 (Tsukuba, Japan). The role of Lateral Gene Transfer in adaptation of protists to new environments.

2013 – ICOP conference (Vancouver, Canada). Eme L, Gentekaki E, Curtis B, Archiblad JA, Roger AJ. Phylogenomic analyses of Blastocystis sp . subtype 1 reveals an important role for lateral gene transfer in adaptation to parasitism of the human gut. 

2013 – SMBE Satellite Eukaryotic-omics (Davis, US). Eme L, Gentekaki E, Curtis B, Archiblad JA, Roger AJ. Phylogenomic analyses of Blastocystis sp . subtype 1 reveals an important role for lateral gene transfer in adaptation to parasitism of the human gut. 

2012 – PROTIST conference (Oslo, Norway). Eme L, Roger AJ. Pinpointing the root of extant eukaryotic diversity

2011 – ALPHY meeting (Bioinformatics et evolutionary genomics) (Lyon, France).
Eme L, Moreira D, Brochier-Armanet C. The phylogenomic analysis of the ACP/C and its targets points to a complex and modern-like control of the cell cycle in LECA.

2009 – Invitation at the International Meeting “Archaea and the universal tree of life” (Fondation des Treilles, France). Eme L, Moreira D, Brochier-Armanet C. Phylogenomics of eukaryotic systems: tracing back the nature of the last eukaryotic common ancestor

2009 – ALPHY meeting (Montpellier, France). Eme L, Moreira D, Talla E., Brochier-Armanet C. A complex cell division machinery in the last common ancestor of eukaryotes

Poster presentations

2015 – ECOP (European Congress of Protistology) (Seville, Spain). Eme L, Stairs CW, Karnkowska A, Hampl V, Roger AJ. Lateral Gene Transfer is an overlooked mechanism in the adaptation of microbial eukaryotes to new environments.

2015 – SMBE (Society for Molecular Biology and Evolution) (Vienna, Austria). Eme L, Stairs CW, Karnkowska A, Hampl V, Roger AJ. Lateral Gene Transfer is an overlooked mechanism in the adaptation of microbial eukaryotes to new environments.

2010 – SMBE (Society for Molecular Biology and Evolution) (Lyon, France). Eme L, Moreira D, Talla E., Brochier-Armanet C. Tracing back the nature of cell division in the Last Common Ancestor of Eukaryotes.

2009 – EMBO 2009 conference Comparative Genomics of Eukaryotic Microorganisms. (San Feliu de Guixols, Spain). Eme L, Moreira D, Brochier-Armanet C Phylogenomic study of cytokinesis in Eukaryotes
Eukaryotic Cell Journal Outstanding Young Investigator Award.

2009 – Graduate School Meeting (Marseilles, France).
Eme L, Moreira D, Brochier-Armanet C A complex cell division machinery in the last common ancestor of eukaryotes. Best Poster Award.

2007 – JOBIM conference (Marseille, France). Eme L, Moreira D, Brochier-Armanet C Origin and evolution of the eukaryotic midbody: A phylogenomic approach

Uncategorized

June 2011 – to date Post-Doctoral Fellow
Centre for Comparative Genomics and Evolutionary Bioinformatics (Halifax, Canada). Supervisor: Dr. Andrew J. Roger.

Root of the Eukaryotic Tree 
One of my major interests lies in the investigation of the relationships amongst eukaryotic lineages as well as the position of the root of the eukaryote tree. Eukaryotes are usually divided in six ‘super-groups’, but this hypothesis is still controversial. One of my postdoctoral projects aims to revisit the problem of robustly rooting the tree of eukaryotes through the investigation of three kinds of untapped phylogenetic markers.

Adaptation of eukaryotic microbes to anaerobiosis 
Since I’ve joined the Roger Lab I have been interested in the evolutionary transition from aerobic to microaerobic/anaerobic conditions that occurred several times independently across the tree of eukaryotes. In particular, I am interested in how this transition has affected mitochondrial functions and has reshaped the proteomes and biochemical abilities of the mitochondrial-related organelles (MROs) found in anaerobic protists.

Evolution of parasitic protists 
I am also interested in the genomic adaptations occuring during the transition from free-living to parasitic lifestyles, and in particular the ones in relation with the acquisition (through lateral gene transfers) and expansion of genes  involved in anaerobiosis, pathogenicity, nutrient acquisition and response to host defense mechanisms.

Eukaryotic microbes in the human microbiome 
Recently, I have been interested in the impact of eukaryotic microbes (parasites and commensals) on the human gut microbiome. Since the prevalence and roles of microbial eukaryotes has been rarely studied, we aim to obtain a better understanding of the relationships between particular parasitic infections and pathologies such as inflammatory bowel disease (IBD).

Archaeal biodiversity and evolution 

 

October 2007 – June 2011 PhD in Phylogeny, Evolution and Bioinformatics.
Team Genome, Evolution and Bioinformatics (Laboratoire de Chimie Bactérienne, CNRS, Marseilles, France). Supervisor: Dr. Céline Brochier-Armanet.

Characterization of LECA — Evolution of eukaryotic multiprotein complexes
The development of high throughput techniques, especially in proteomics and genomics has yielded extensive data that can be used in evolutionary analyses. In this context, eukaryotic multiprotein structures (EMS) are objects of interest. Indeed, these large protein complexes are involved in many fundamental processes of eukaryotic cells, and have no homologues in prokaryotes (even if the functions in which they are involved may exist) and therefore have certainly played a major role in the eukaryogenesis.
During my PhD, I carried out the phylogenomic analysis of two EMS involved in cell division (the midbody and the APC/C) and showed that these systems have an ancient evolutionary origin and were already present in the last common ancestor of eukaryotes (LECA), while resulting from eukaryotic innovations. This implies that the emergence of these two EMS occurred after the divergence of the eukaryotic lineage and before the diversification that gave rise to the current lineages.
Beyond these evolutionary questions, analyses of these EMS uncover some biological aspects of these systems. Indeed, if these systems were generally well conserved during the diversification of eukaryotes, their analysis shows a high plasticity of composition in some protist lineages. This suggests recent changes regarding certain phases of these organisms cell cycle which would be interesting to explore experimentally.

Eukaryotic tree of life
Concomitantly, this work showed that, although being operational protein, components of these EMS carry a phylogenetic signal usable for inferring phylogenetic relationships among eukaryotic lineages. Construction of supermatrixes from these proteins led to the inference of phylogenies of high quality. Combining these data with those from analyses based on informational proteins showed a significant progress on the resolution of inferred trees. These results open the field of possibilities to find other markers among the untapped operational proteins.

Uncategorized

6 month Master’s student project

Background 

Horizontal gene transfer, also called lateral gene transfer or LGT, allows the acquisition of genetic material, and thus new functions, from distantly related organisms. This process is well known to be a major driver of evolution in prokaryotes, and is for example responsible for the acquisition of antibiotic resistance in bacteria. In contrast, the role and frequency of LGT in eukaryotes has been much less studied, although there are clear examples of its impact on the evolution of certain unicellular eukaryote parasites. When they exist, these recent studies often focus on gene transfer events from very distant organisms, such as from bacteria, because they are easier to detect with confidence. However, it has been shown in bacteria that LGTs more often occur among closer related lineages. This can be explained in part because horizontally acquired genes that use codons that better match the codon usage of their new host genome will be better optimized for expression within the context of that genome and will confer less of a fitness cost on their new host. . In eukaryotes, the extent to which closely related organisms exchange genetic material and how much this varies across the diversity of eukaryotic lineages is, in contrast, limited. 

Project 

This project aims to estimate the importance of LGT between closely related eukaryotic species. It consists of two parts: A) developing an approach that detects genes that are very likely to be derived laterally from a different, but closely related eukaryote, and B) using this approach to study which eukaryotic clades underwent many of such ‘short-distance’ LGTs andto identify the features (such as function or codon usage) of genes shared via LGT between closely related species. The developed approach will first be benchmarked with a set of published LGTs, and will then be applied to identify cases of LGTs in understudied lineages of unicellular eukaryotes (protists).  

Your profile 

Ideally, the candidate will have some knowledge in phylogenetics/molecular evolution and some knowledge or strong desire to learn scripting (Python or Perl) and working in a linux environment. Additional requirement: good level in English, good oral and written communication skills, autonomy, organization skills. 

Practicalities 

This is a 6 month internship that will take place between January and June 2021. A financial compensation of €577.50/mo is offered. 

The research unit of “Ecology, Systematics and Evolution” (ESE) is located in the University Paris-Sud campus in Orsay. This campus is 20 km south of Paris and well connected through commuter train. 

The student will work within the DEEM (Diversity, Ecology and Evolution of Microbes: http://www.deemteam.fr/en) team, which has a broad expertise in ecology and evolutionary biology, with a focus on microbes (prokaryotic and eukaryotic). This internship will be co-supervised by Dr. Laura Eme (laura.eme@universite-paris-saclay.fr), principal investigator, and Dr. Jolien van Hooff, postdoctoral fellow (jolien.van-hooff@universite-paris-saclay.fr).  

Note the possibility to apply for a PhD scholarship from the doctoral school at the end of the internship if you are interested in pursuing a PhD with us.  

Interested? 

If you are interested in genome evolution and pursuing a research project in bioinformatics and phylogenetics, please contact Dr Laura Eme (laura.eme@universite-paris-saclay.fr) for more information or apply directly by sending your CV and a cover letter explaining your motivation for undertaking this project.  

Uncategorized

Book chapters

2015 –  Sharpe SC*, Eme L*, Brown MW, Roger AJ. Timing the Origins of Multicellular Eukaryotes Through Phylogenomics and Relaxed Molecular Clock Analyses. Evolutionary Transitions to Multicellular Life. Springer, 2015. 3-29.
*These authors equally contributed to the manuscript.
[Link]

Invited contributions

2015 –  Eme L, Doolittle WF. Primer: Archaea. Current Biology 25 (19), R851-R855. Special issue “History of Life on Earth”. [Abstract]

2015 –  Eme L, Doolittle WF. Microbial Diversity: A Bonanza of Phyla. Current Biology 25 (6), R227–R230.
[Abstract]

Peer-reviewed papers

In revision – Karnkowska K, Vacek V, Zubáčová Z, Treitli S, Petrželková R, Eme L, Novák N, Žárský V, Barlow L, Herman H, Soukal P, Hroudová M, Doležal P, Stairs C, Roger AJ, Elias M, Dacks J, Vlček C, Hampl V. A eukaryote without a mitochondrial organelle. Current Biology.

Submitted – Cenci U, Moog D, Curtis BA, Tanifuji G, Eme L, Lukes J, Archibald JM. Heme pathway evolution in kinetoplastid protists. Mol Phyl Evol.

Submitted – Dacks JB, Field MC, Buick R, Eme L, Gribaldo S, Roger AJ, Brochier-Armanet C and Devos DP. Bridging the divide: major advances and emerging consensus for the origins of eukaryotes. Journal of Cell Science.

2015 – Groussin M, Boussau B, Szöllosi GJ, Eme L, Gouy M, Brochier-Armanet C, Daubin V. Gene acquisitions from bacteria at the origins of major archaeal clades are vastly overestimated. Molecular biology and evolution, msv249. [Abstract] [PDF]

2015 – Torruella G, de Mendoza A, Grau-Bové X, Antó M, Chaplin MA, del Campo J, Eme L, Pérez-Cordón G, Whipps CM, Nichols KM, Paley R, Roger AJ, Sitjà-Bobadilla A, Donachie S, Ruiz-Trillo I. Phylogenomics reveals convergent evolution of lifestyles in close relatives of animals and fungi. Current Biology, 10.1016/j.cub.2015.07.053. [Abstract] [PDF]

2015 –  Gawryluk R*, Eme L*, Roger AJ. Gene fusion, fission, lateral transfer, and loss: not-so-rare events in the evolution of eukaryotic ATP citrate lyase. Molecular Phylogenetics and Evolution. *These authors equally contributed to the manuscript.
[Abstract]

2015 – Leger MM, Petrů M, Žárský V, Eme L, Vlček Č, Harding T, Lang BF, Eliáš M, Doležal P, Roger AJ. An ancestral bacterial division system is widespread in eukaryotic mitochondria. PNAS 2015, 1421392112.
[Abstract]

2014 –  Eme L, Sharpe SC, Brown MW, Roger AJ. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. “Origin and evolution of eukaryotes”, Cold Spring Harbor Perspectives in Biology, 6(8), a016139.
[Abstract]

2014 – Stairs CW, Eme L, Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, van der Giezen M, Roger AJ. A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the anaerobic protist Pygsuia. Current Biology 24 (11), 1176-1186.
[Abstract] [PDF]

2013 – Tsaousis AD*, Gentekaki E*., Eme L*, Gaston D, & Roger AJ (2014). Evolution of the Cytosolic Iron-Sulfur Cluster Assembly Machinery in Blastocystis Species and Other Microbial Eukaryotes. Eukaryotic cell, 13(1), 143-153.
*These authors equally contributed to the manuscript.
[Abstract] [PDF]

2013 – Eme L,  Reigstad LJ, Spang A, Lanzén A, Weinmaier T, Rattei T, Schleper C, Brochier-Armanet C. Metagenomics of Kamchatkan hot spring filaments reveals two new major (hyper)thermophilic lineages related to Thaumarchaeota. Research in Microbiologoy (2013), doi:10.1016/j.resmic.2013.02.006.
[Abstract] [PDF]

2011 – Eme L, Trilles A, Moreira D, Brochier-Armanet C “The phylogenomic analysis of the Anaphase Promoting Complex and its targets points to complex and modern-like control of the cell cycle in the last common ancestor of eukaryotes.” BMC Evolutionary Biology. 2011 Sep 23;11:265. doi:10.1186/1471-2148-11-265.
[Abstract] [PDF]

2011 – Boileau C, Eme L, Brochier-Armanet C, Janicki A, Zhang CC, Latifi A. A eukaryotic-like sulfiredoxin important for peroxiredoxin reduction and oxidative stress response in the cyanobacterium Anabaena PCC 7120. New Phytologist. 2011 Jun 8. doi:10.1111/j.1469-8137.2011.03774.x. Epub 2011 Jun 8.
[Abstract] [PDF]

2009 – Eme L, Moreira D, Talla E, Brochier-Armanet C. A Complex Cell Division Machinery was Present in the Last Common Ancestor of Eukaryotes. PLoS ONE 4(4): e5021. doi:10.1371/journal.pone.0005021.
[Abstract] [PDF]

 

Oral communications

2015 – Invited speaker. Company of Biologists Workshop “Eukaryo-/Archaeogenesis: Where Do We Stand?”. Pinpointing the root of extant eukaryotic diversity: advances, challenges and consequences.

2014 – ISOP/ISEP meeting 2014 (Banff, Canada). Eme L, Sharpe SC, Brown MW and Roger AJ. On the age of eukaryotes: evaluating evidence from fossils and molecular clocks.

2014 – Invited speaker. Microbe Evolution 2014 (Tsukuba, Japan). The role of Lateral Gene Transfer in adaptation of protists to new environments.

2013 – ICOP conference (Vancouver, Canada). Eme L, Gentekaki E, Curtis B, Archiblad JA, Roger AJ. Phylogenomic analyses of Blastocystis sp . subtype 1 reveals an important role for lateral gene transfer in adaptation to parasitism of the human gut. 

2013 – SMBE Satellite Eukaryotic-omics (Davis, US). Eme L, Gentekaki E, Curtis B, Archiblad JA, Roger AJ. Phylogenomic analyses of Blastocystis sp . subtype 1 reveals an important role for lateral gene transfer in adaptation to parasitism of the human gut. 

2012 – PROTIST conference (Oslo, Norway). Eme L, Roger AJ. Pinpointing the root of extant eukaryotic diversity

2011 – ALPHY meeting (Bioinformatics et evolutionary genomics) (Lyon, France).
Eme L, Moreira D, Brochier-Armanet C. The phylogenomic analysis of the ACP/C and its targets points to a complex and modern-like control of the cell cycle in LECA.

2009 – Invitation at the International Meeting “Archaea and the universal tree of life” (Fondation des Treilles, France). Eme L, Moreira D, Brochier-Armanet C. Phylogenomics of eukaryotic systems: tracing back the nature of the last eukaryotic common ancestor

2009 – ALPHY meeting (Montpellier, France). Eme L, Moreira D, Talla E., Brochier-Armanet C. A complex cell division machinery in the last common ancestor of eukaryotes

Poster presentations

2015 – ECOP (European Congress of Protistology) (Seville, Spain). Eme L, Stairs CW, Karnkowska A, Hampl V, Roger AJ. Lateral Gene Transfer is an overlooked mechanism in the adaptation of microbial eukaryotes to new environments.

2015 – SMBE (Society for Molecular Biology and Evolution) (Vienna, Austria). Eme L, Stairs CW, Karnkowska A, Hampl V, Roger AJ. Lateral Gene Transfer is an overlooked mechanism in the adaptation of microbial eukaryotes to new environments.

2010 – SMBE (Society for Molecular Biology and Evolution) (Lyon, France). Eme L, Moreira D, Talla E., Brochier-Armanet C. Tracing back the nature of cell division in the Last Common Ancestor of Eukaryotes.

2009 – EMBO 2009 conference Comparative Genomics of Eukaryotic Microorganisms. (San Feliu de Guixols, Spain). Eme L, Moreira D, Brochier-Armanet C Phylogenomic study of cytokinesis in Eukaryotes
Eukaryotic Cell Journal Outstanding Young Investigator Award.

2009 – Graduate School Meeting (Marseilles, France).
Eme L, Moreira D, Brochier-Armanet C A complex cell division machinery in the last common ancestor of eukaryotes. Best Poster Award.

2007 – JOBIM conference (Marseille, France). Eme L, Moreira D, Brochier-Armanet C Origin and evolution of the eukaryotic midbody: A phylogenomic approach

Uncategorized

June 2011 – to date Post-Doctoral Fellow
Centre for Comparative Genomics and Evolutionary Bioinformatics (Halifax, Canada). Supervisor: Dr. Andrew J. Roger.

Root of the Eukaryotic Tree 
One of my major interests lies in the investigation of the relationships amongst eukaryotic lineages as well as the position of the root of the eukaryote tree. Eukaryotes are usually divided in six ‘super-groups’, but this hypothesis is still controversial. One of my postdoctoral projects aims to revisit the problem of robustly rooting the tree of eukaryotes through the investigation of three kinds of untapped phylogenetic markers.

Adaptation of eukaryotic microbes to anaerobiosis 
Since I’ve joined the Roger Lab I have been interested in the evolutionary transition from aerobic to microaerobic/anaerobic conditions that occurred several times independently across the tree of eukaryotes. In particular, I am interested in how this transition has affected mitochondrial functions and has reshaped the proteomes and biochemical abilities of the mitochondrial-related organelles (MROs) found in anaerobic protists.

Evolution of parasitic protists 
I am also interested in the genomic adaptations occuring during the transition from free-living to parasitic lifestyles, and in particular the ones in relation with the acquisition (through lateral gene transfers) and expansion of genes  involved in anaerobiosis, pathogenicity, nutrient acquisition and response to host defense mechanisms.

Eukaryotic microbes in the human microbiome 
Recently, I have been interested in the impact of eukaryotic microbes (parasites and commensals) on the human gut microbiome. Since the prevalence and roles of microbial eukaryotes has been rarely studied, we aim to obtain a better understanding of the relationships between particular parasitic infections and pathologies such as inflammatory bowel disease (IBD).

Archaeal biodiversity and evolution 

 

October 2007 – June 2011 PhD in Phylogeny, Evolution and Bioinformatics.
Team Genome, Evolution and Bioinformatics (Laboratoire de Chimie Bactérienne, CNRS, Marseilles, France). Supervisor: Dr. Céline Brochier-Armanet.

Characterization of LECA — Evolution of eukaryotic multiprotein complexes
The development of high throughput techniques, especially in proteomics and genomics has yielded extensive data that can be used in evolutionary analyses. In this context, eukaryotic multiprotein structures (EMS) are objects of interest. Indeed, these large protein complexes are involved in many fundamental processes of eukaryotic cells, and have no homologues in prokaryotes (even if the functions in which they are involved may exist) and therefore have certainly played a major role in the eukaryogenesis.
During my PhD, I carried out the phylogenomic analysis of two EMS involved in cell division (the midbody and the APC/C) and showed that these systems have an ancient evolutionary origin and were already present in the last common ancestor of eukaryotes (LECA), while resulting from eukaryotic innovations. This implies that the emergence of these two EMS occurred after the divergence of the eukaryotic lineage and before the diversification that gave rise to the current lineages.
Beyond these evolutionary questions, analyses of these EMS uncover some biological aspects of these systems. Indeed, if these systems were generally well conserved during the diversification of eukaryotes, their analysis shows a high plasticity of composition in some protist lineages. This suggests recent changes regarding certain phases of these organisms cell cycle which would be interesting to explore experimentally.

Eukaryotic tree of life
Concomitantly, this work showed that, although being operational protein, components of these EMS carry a phylogenetic signal usable for inferring phylogenetic relationships among eukaryotic lineages. Construction of supermatrixes from these proteins led to the inference of phylogenies of high quality. Combining these data with those from analyses based on informational proteins showed a significant progress on the resolution of inferred trees. These results open the field of possibilities to find other markers among the untapped operational proteins.