Microbial genetics

One of our areas of study is to understand the synthesis and mobilization pathways of storage polysaccharides in general with a particular emphasis on the study of alpha-glucan storage compounds such as starch and glycogen.

Glycogen metabolism in fungi and mammalian cells has received much attention and has been extensively studied. In comparison, starch metabolism in plants, glycogen metabolism in other non-fungal lower eukaryotes, and glycogen metabolism in bacteria and archaea have all received much less attention and are rather poorly understood.

Our initial research focused on elaborating key aspects of starch metabolism through the study of mutants affected at different stages of the pathway. In the late 80's and early 90's, we chose the unicellular green alga Chlamydomonas as our main model for this purpose. Indeed Chlamydomonas defined at that time, the ideal system for the isolation and rapid study of mutants.

Ten loci affecting starch synthesis have been thoroughly studied over the years. Our group has made essential contributions to the understanding of starch metabolism that are familiar to most specialists in this field. These contributions can be summarized as the understanding of the major steps responsible for the distinction of starch and glycogen synthesis, the elaboration of the detailed mechanism of amylose synthesis, contributing to the understanding of the precise function of the multiple forms of enzymes responsible for amylopectin synthesis.

At the end of this decade of research, it appeared to us that functional approaches in Chlamydomonas would soon be surpassed by reverse genetic approaches in Arabidopsis. Indeed, the Arabidopsis genome sequence was first obtained with a complete collection of mutants marked for almost all loci of the plant genome. We therefore embarked on large-scale research programs involving the functional genomics of Arabidopsis around 1999-2000. Christophe d'Hulst, a former member of the microbial genetics research group, took over these aspects and is now independently pursuing this very productive direction as the leader of the "Plant Storage Polysaccharides" group.

However, our group is now much more attracted by another biological question, the evolutionary pathway followed by the starch metabolism gene network. Indeed, evo-devo approaches have stimulated research in many different areas of developmental biology. We believe that the same kind of approaches and reasoning could be fruitfully applied to biochemical pathways. However, true evo-devo approaches are within a time scale of events ranging from a few million years to a few hundred million years at most. Moreover, the phylogenetic origin of the species studied for this purpose is generally well understood. The problem with the important and widespread biochemical pathways is that they are comparatively much older and go back hundreds of millions and often billions of years. Moreover, the context of the events that shaped them is almost completely unknown. Although many fascinating theories can be put forward regarding the origin of eukaryotic archaea or bacteria, there is currently no consensus on these questions. With such unknowns, tracing the evolutionary steps that generated the major biochemical pathways can be a very difficult and speculative exercise.

As for the origin of the main plant-specific pathways, the situation is fortunately much clearer. Indeed, there is now a very broad consensus regarding the origin of plants and their monophyletic origin has been accepted. Plants (i.e., red algae, green algae, and land plants and glaucophytes) originated from a single endosymbiotic event involving a cyanobacterial symbiont and a heterotrophic eukaryotic host. While some plant pathways are still completely cyanobacterial or eukaryotic in their essence (e.g., photosynthesis or mitosis), others result from the fusion of pre-existing pathways while others result from later acquisition and evolution.

Starch is at first sight an ancient plant-specific pathway. Indeed this polysaccharide is only found in plants or their endosymbiotic derivatives (such as cryptophytes, dinoflagellates and apicomplexan parasites). Our recent goal has been to understand how the polysaccharide storage pathways of the cyanobacterial symbiont and its eukaryotic host fused to generate starch.

This involves studying in detail through a combination of biochemical and genetic approaches a number of species located at phylogenetically relevant positions in the tree of life, including cyanobacteria, dinoflagellates, glaucophytes, rhodophytes and cryptophytes. A major distinction in our new approaches is that we do not rely solely on bioinformatics studies of complete genomic sequences, but rather on functional mutant studies aimed at understanding how a similar enzyme has evolved and changed to perform different functions in the same polysaccharide metabolism enzyme network. . A good example of this is our recent approaches comparing the phenotype of defective mutants of the debranching enzyme or phosphorylase in bacteria and algae. While working on these aspects, we recently stumbled upon what we believe explains major aspects of plastid endosymbiosis and the birth of the plant kingdom. This contribution is now published as the "ménage à trois" hypothesis. Our current working hypothesis is that symbiotic carbon flow at the beginning of plastid endosymbiosis involved glycogen metabolism through the encoding by 3 genomes of enzymes necessary for the establishment of the flow. These genomes consisted of the nascent cyanobacterium (the cyanobiont), a symbiont or helper chlamydial pathogen and the eukaryotic host. This proposal has major implications for our view of organelle biogenesis and underscores the importance of phagocytosis and energetic parasites (rickettsiae and chlamydia) as major drivers of eukaryotic evolution.