Jonathan Lombard
Microbial evolution and phylogeny


Current postdoctoral work will be updated soon! (March 2017 - present)

Previous postdoctoral work (December 2014 - November 2016)

Ancestral gene repertoires at the dawn and diversification of the eukaryotes

Tom Richards' lab, University of Exeter, in collaboration with Bill Wickstead's lab, University of Nottingham.

The eukaryotes are one of the three domains of life, namely the one characterized by nucleated cells, also containing features like mitochondria, a compartmented cytoplasm or a cytoskeleton. How eukaryotes first evolved from organisms that did not have these characteristics remains one of the most intriguing questions in evolutionary biology. For some time, the study of eukaryogenesis focused on the examination of seemingly amitochondriate eukaryotes or the evolution of independent genes. This has changed in more recent analyses as the necessity to tackle the origins and evolution of molecular complexes and cell functions has become more apparent. In this context, I currently participate in an extensive collaborative effort centered around Tom Richards' and Bill Wickstead's lab to reconstruct the set of genes present in the last common ancestor of eukaryotes. This information will be a step further to understand the origins of the cell biology and metabolism in early eukaryotes as well as to investigate the evolution of this repertoire in the derived, modern eukaryotic groups.

In this position I also intend to develop my previous interests in membrane evolution by examining the intriguing question of the origin of eukaryotic membranes and membrane functions.

Previous postdoctoral work (2013 - 2014)

Early membrane cellular functions: New insights from phylogenetic comparisons

National Evolutionary Synthesis Center (NESCent), Durham, NC, USA

The precise biological description of the last common ancestor of living organisms (the cenancestor) is necessary to understand the previous evolution from the origins of life and subsequent changes in modern lineages. Most early evolutionary studies examine the informational apparatus (replication, translation, etc), but the genome content in the cenancestor likely encoded many other metabolic and cellular functions. During my postdoctoral position at NESCent I tackled the infrequently addressed issue of the early evolution of membrane-related functions using innovative phylogenomic approaches. Publications related to this work are in preparation and should be available shortly.

This postdoctoral position was also the occasion for me to prepare a detailed historical account of the discovery of cell membranes that echos into our current reflexions on early membranes.

PhD dissertation (2009 - 2012)

Origins and evolution of the phospholipid biosynthetic pathways in the three domains of life. Implications for the nature the membranes in the cenancestor

Unité Ecologie, Systématique, Evolution (ESE) – Université Paris Sud / CNRS, Orsay, France

Supervisor: David Moreira

cenancestralmembranes All cells are surrounded by phospholipid bilayer membranes with embedded proteins in them. Nevertheless, archaeal phospholipids are synthesized by different means than their bacterial/eukaryotic counterparts. As a result, it had been suggested by the turn of the century that the cenancestor was not able to synthesize phospholipids and that the modern phospholipid biosynthesis pathways independently emerged in subsequent lineages. These hypotheses argued that the cenancestor had no lipid membranes, so it could not be a cellular organism although other indirect clues indicated the opposite. These contradictions raise the question of the presence in modern organisms of traces that the cenancestor had a phospholipid biosynthesis machinery.

During my PhD, I took advantage from the recent accumulation of genomic data to address this issue. Previous work had shown that the members of two universal protein superfamilies could be present in the cenancestor to carry out the respective non-specific synthesis of the glycerol phosphate enantiomers that are the backbones of modern phospholipids. Bacterial and eukaryotic phospholipids use fatty acids whereas archaeal phospholipids are made up of isoprenoids. Thus, I studied the evolution of the metabolic pathways that synthesize these molecules and build up the phospholipids from their components. My results showed that the eukaryotic isoprenoid biosynthesis pathway and a hypothetical archaeal fatty acid biosynthesis pathway are likely to have had ancestors in the cenancestor: However, these primitive pathways were probably less specific than those in modern mechanisms. In addition, the phospholipid assembly machinery was also probably present in the cenancestor.

These results suggest that the cenancestor was likely able to enzymatically synthesize its phospholipids by means less specific than modern ones. Dissimilarities in modern membrane phospholipids would result from the specialization of each biosynthesis system in each lineage. More generally, my work also stresses the fact that the cenancestor is a theoretical consequence of common ancestry. Therefore, it should be described on the basis of the comparison of modern organisms to avoid frequent confusions between this organism and the origins of life.

M.Sc. dissertation (2009)

Origins and evolution of the isoprenoid metabolism

Unité Ecologie, Systématique, Evolution (ESE) – Université Paris Sud /CNRS, Orsay, France

Supervisor: David Moreira

The isoprenoids are a very diverse family of compounds widespread in the three domains of Life. Although they are produced from the condensation of the same precursors in all organisms, the evolutionary origin of their biosynthesis remains controversial. Two independent non-homologous metabolic pathways are known: the mevalonate (MVA) pathway in eukaryotes and archaea, and the methylerythritol phosphate (MEP) pathway in bacteria. During my masters, I studied the origin and early evolution of all enzymes of these pathways using phylogenomic analyses. My results confirmed previous observations that the MEP pathway was widespread but limited to bacteria and plastid-bearing eukaryotes. They extended to archaea the observation that Methanococcus jannaschi likely had a partially different MVA pathway. And, surprisingly, they showed that the classical eukaryotic MVA pathway was likely ancestral to the three domains and, hence, present in the cenancestor.

Undergraduate research

Relationship between fitness and diversification in a model adaptive radiation of Pseudomonas fluorescens

University of Ottawa, Ottawa, ON, Canada

Supervisor: Rees Kassen

Evolutionary history of the Pseudouridine Synthases of the 55th position of the tRNAs

Laboratoire de Chimie Bactérienne, CNRS, Marseille, France

Supervisor: Céline Brochier-Armanet