Laboratory equipment in the MICALIS quantitative metagenomics (MetaQuant) experimental facility. © INRA, INRA

How synthetic biology could benefit from the social sciences

INRA research: finding the minimal genome

 In 2012, INRA researchers were co-authors on major publications that described gene regulation mechanisms in the model bacterial species Bacillus subtilis; this research aimed to uncover the minimal genome.

By Pascale Mollier, translated by Jessica Pearce
Updated on 01/16/2015
Published on 10/14/2014

Loading a DNA sequencer. DNA sequencers automatically sequence DNA fragments via gel electrophoresis. © INRA, MAITRE Christophe
Loading a DNA sequencer. DNA sequencers automatically sequence DNA fragments via gel electrophoresis © INRA, MAITRE Christophe

Bacillus subtilis is a bacterium whose genome comprises approximately 4,200 genes. In nature, it lives in the soil, but it is widely used in lab research projects and is exploited commercially. For instance, it is used to produce vitamins or the enzymes found in laundry detergents. It was also utilized as a model organism in two European research programmes headed by INRA teams (1). The first was focused on how the bacterium functions (BaSysBio). The second was looking to drastically reduce the size of B. subtilis’ genome while simultaneously striving to understand and dissect the bacterium’s biological systems (BaSynthec).

Characterizing the mechanisms underlying environmental adaptation

Certain adaptive mechanisms employed by the bacterium were described in two articles published in March 2012 in Science (see sidebar). The authors were scientists from eight European countries and Australia who were collaborating on the BaSysBio project. The articles describe how B. subtilis manages to live in its ever-changing natural environment; they provide an unprecedented level of detail with regards to how all the genes in the bacterium’s genome were expressed under around 100 different experimental conditions (involving changes in temperature, humidity, salinity, nutrient levels, etc.). In addition to the sheer amount of new knowledge they yielded—novel information is crucial to promoting scientific discoveries in the research community as a whole—these studies also showed that a significant proportion of the bacterium’s “programming” involves transcription and the subtle interplay that exists between RNA polymerase and one of its subunits, the sigma factor. Indeed, nearly 2/3 of the changes in gene expression that took place under the experimental conditions were tied to changes in the sigma factor.

Predictable programming

Vincent Fromion, a control engineer in INRA’s MIG research unit (1), feels that it is appropriate to use the term programming when discussing bacteria, because there are clear similarities between what we see going on in bacteria and the systems that engineers design to control advanced technological devices, such as airplanes. The similarity actually runs deeper because the programming system in bacteria is very modular and seems to result from a general principle that can be described in mathematical terms and that can predict how the bacterium will behave under a large number of conditions with astounding accuracy. This was one of the findings of the BaSynthec project. Philippe Noirot, deputy director of the MICALIS Institute and coordinator of the BaSysBio and BaSynthec research programs, comments, “These are major discoveries in the field of synthetic biology. Understanding cell systems and modeling how they function under natural conditions are the first steps in being able to predict cell behavior in other situations, like when you want a bacterium to produce certain target compounds.”

Uncovering the minimal genome

The BaSynthec programme, which began in 2010, was focused on finding the minimal genome; to this end, it used the technique of progressively eliminating parts of the genome in order to identify the regions that are necessary for basic functions, such as reproduction and survival. Noirot summarizes, “We were identifying the parts of the genome that could and could not be removed.”

In a laboratory environment, under controlled conditions (e.g., stable temperature and humidity), bacterial strains can survive without certain genes. Fromion notes, “Even when they are missing large chunks of their genomes, certain strains are very robust, which confirms that there are underlying mechanisms contributing to robustness that would be very interesting to study.” As a consequence, thanks to this variety of strains, it has become possible to imagine creating bacteria with minimal genomes that can be used to produce proteins. Fromion explains, “Using a minimal genome offers two-fold benefits. First, by removing ‘useless’ genes, we prevent any unanticipated interactions. Second, the bacterium would be rather inept at surviving in nature, which would limit its potential to spread through the environment by accident.”

The minimal genome is a relative concept

Because the minimal genome varies in size depending on the organism, Thomas Heams (2) has suggested that it is necessary “to do away with the approach of focusing solely on the number of genes that make up a minimal genome.” He recommends that it would be better to study “minimal cellular metabolism” to understand what is necessary for cells to function. Michel Morange (3) and Carole Lartigue (4) both “wonder about the relevance of the assumption that there is a bare minimum for life, because it is very likely that the search for life’s bare minimum will yield not one but several convergent solutions” (5).

(1) The Systems and Synthetic Biology Research Team, part of the INRA MICALIS Joint Research Unit, and the BioSysResearch Team, part of the Mathematics, Informatics and Genome Unit (MIG) at INRA,Jouy-en-Josas
(2) Thomas Heams, “De quoi la biologie synthétique est-elle le nom ?” (“Defining Synthetic Biology”), in the non-fiction anthology « “Les mondes darwiniens” (“Darwinian Worlds), originally published by Syllepse in 2009, new edition printed by Matériologiques in 2011.
(3) Professor at Université de Paris VI and Ecole Normale Supérieure. Taken from his book “La vie expliquée” (“Life Explained”), Editions Odile Jacob, 2008, p.142.
(4) INRA researcher who has previously collaborated with Craig Venter.
(5) Excerpt from the 2012 OPECST report.

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Animal Physiology and Livestock Systems
Associated Centre(s):
Jouy-en-Josas

References

- Basysbio:

Buescher J-M., ...and Aymerich S., Sauer U. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 2012 March 2:335(6072):1099-1103. DOI: 10.1126/science.1206871.

Nicolas P., ...and Noirot P. Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis. Science 2012 March 2:335 (6072):1103-1106, DOI:10.1126/science.1206848.

- BaSynthec:

Tanaka K., ...and Noirot P. 2013. Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. Nucleic Acids Res. 41(1):687-99. DOI: 10.1093/nar/gks963. Epub 2012 Oct 29.

Prior seminal work

Findings obtained by the Craig Venter Institute related to the minimal genome:

• 2005: Research by Glass et al. aims to identify the minimal genome for the bacterial species Mycoplasma genitalium, which has the smallest known genome for a culturable bacterium. Around 400 genes are found to be essential for its survival.
• 2006: Discovery of a bacterial species (Candidatus carsonella ruddii) whose genome comprises 180 genes.