SUMMARY OF AN EXPLORATION IN BIOLOGY
Rolf LANDAUER
From deciphering genomes to synthetic biology: cells are information-gathering machines
Before summarizing the contribution to general knowledge of the work I developed over several decades, let me recall the last word of The Delphic Boat, to try and prevent misunderstandings: I am well aware that, in contrast to Art, Science should not have names. This short presentation is a way of explaining the « style » of a scientist's work, not to promote a narcissistic view. This is: while Science is universal, a style remains idiosyncratic.
The central question I have been exploring over the last few decades is this. Is there a general principle that explains that biological chemistry seems to be somehow 'animated'? This led to the second question. Is it possible to discover rules that explain that genes function as a whole in the cell and contribute to its consistent and reproducible development? If we isolate some of the important trends in this research, we get a picture that culminates in what can be considered as « symplectic biology », a biology in which the relations between objects have a greater conceptual importance than the objects themselves (see a view independently proposed by Murray Gell-Mann ***). This means that the material embodiment of abstraction is essential for understanding what life is. A critical consequence of this constraint is that, because the atoms of life have intrinsic properties reflected in the Mendeleiev table, which have nothing to do with the abstract world to which they are related in living things, many features of life will look like anecdotes. Consequently, life forms are very diverse. This makes it quite difficult to identify any possible underlying law. When this fact is understood, the idea that it will be possible to reconstruct life, and even to construct material objects with living properties, using building blocks different from those in existing living organisms, will gain ground. Synthetic biology is no longer a dream, it is becoming an unprecedented achievement. Yet this makes it even more important to identify what makes life so special.
Main exploration tracks (from present back to 1968)
Understanding what life is has been the main quest of philosophers, in particular since the time of the Presocratic philosophers. In his Lives of Illustrious Men, Plutarch described the return of Theseus—whose relationship with the temple of Apollo at Delphi is well known, hence my Delphic Boat—from Crete to Athens, and the fate of his ship made by the Athenians. To keep the ship operational the Athenians kept replacing the rotting boards with new ones. Philosophers, subsequently, used this example to discuss permanence and change, some claiming that the ship was no longer the same, while others said the opposite: "The ship wherein Theseus and the youth of Athens returned had thirty oars, and was preserved by the Athenians down even to the time of Demetrius Phalereus, for they took away the old planks as they decayed, putting in new and stronger timber in their place, insomuch that this ship became a standing example among the philosophers, for the logical question of things that grow; one side holding that the ship remained the same, and the other contending that it was not the same." (translated by John Dryden). Following the trend set by this profound question, the study of life must never be limited to the study of things, but must study their relationships. This is an abstract entity —the ship is able to float, whether it is built with oak, pine planks, or even metal boards—, which is represented by the physical currency we usually name information. How is this category of the physical reality handled in biological things?
Living organisms produce young offspring. However, their offspring come from parents that have already grown old. This implies that somehow the parents have recruited or created some kind of new information, restoring youth. Information is an essential currency of our world, it is physical. In 1961, Rolf Landauer established that computation is reversible, with the consequence that the creation of new information does not require energy dissipation. Yet, resetting the process used to create information again requires erasing the memory of past events. This is energy intensive. Charles Bennett, in 1988, illustrated reversible computing by showing how to construct a simple arithmetic operation, division, in a reversible way. He showed that the result of a division is obtained when the intermediate states are erased, leaving the remainder of the division as the prominent and 'valuable' result of the calculation. In this process, the erasure of memory dissipates energy. With this description, Bennett did not explain how the remainder of the division could be distinguished from the bits remaining from the computation procedure, that were to be erased. To make the choice, one needs some kind of additional (contextual) information: I have proposed that this is where energy dissipation comes in. Indeed, an agent must separate between the information forming the outcome of the operation (the remainder), and the information generated to reach this outcome. Energy is dissipated to prevent the remainder of the division from being erased, while erasing the remaining memory. This puts the remaining memory back into a state that can be used for other calculations. How does this process take place? The work developed here is an attempt to understand this process within cells, after explicitly identifying agents embodying the two main steps of the Landauer principle:
1/ An information-laden (or 'tense') step, associated with the loading of an energy source, without energy dissipation, and providing a quantum of information (typically the selection of a specific molecule, in an environment containing many related molecules). In the case of enzymes, this typically manifests itself as a functional step triggered upon binding to a non-hydrolyzable ATP analogue (APPNP or related molecules).
2 / A reset step, where energy is dissipated (usually the hydrolysis of an ATP or another nucleoside triphosphate to ADP and phosphate), so as to return the system to its ground state, allowing the process to start again.
Among these functions, we have highlighted the presence of ubiquitous but neglected functional categories. Cells are prone to accidents, errors and ageing. As a first key function, separation between clean and altered entities is indispensable. This process requires the management of information. For example, proteins age, sometimes very quickly. The cell must identify and then get rid of old proteins without destroying the young ones. These overlooked functions—which must be identified among the critical functions encoded in all genomes—play a role similar to that of Maxwell’s demons (MxDs). They can generate classes of material things among similar ones, identify a specific position in a 3D structure, or a particular time in a smooth set of events. Some fifty functions of this type could be identified in the minimal set required for an autonomous life. A dozen of those are used to direct the correct folding and assembly of the reading head of the genetic message, the ribosome. Indeed, this nanomachine is based on the spontaneous folding of a very long RNA by water, and as the number of incorrect conformations is very large, it requires agents capable of retaining only those that are finally functional by discarding or re-folding the others. There are also other functions that repair broken DNA molecules, calibrate the supercoiling of the double helix or export toxic components out of the cell while preserving essential ones, etc.
Before this hypothesis about the cause of the animation of life emerged, the research I developed followed several tracks, summarized in a series of articles, in particular derived from the genome sequencing programs I set up in 1987. They allow one to understand the conceptual and experimental leads that led to the hypothesis.
| A Danchin Information of the chassis and information of the program in synthetic cells Syst Synth Biol. (2009) 12: 210-242 doi: 10.1007/s11693-009-9036-5 |
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PM Binder, A Danchin Life's demons: information and order in biology. What subcellular machines gather and process the information necessary to sustain life? EMBO Reports (2011) 12: 495-499. In his seventeenth-century classic, Novum Organum, Francis Bacon wrote, “we cannot command nature except by obeying her” (Bacon, 2010). Although our knowledge of living systems is much improved since Bacon’s time, we are still far from understanding—or commanding—all the complex mechanisms of life. To take full advantage of living organisms for the benefit of mankind, we will need to understand those mechanisms to the furthest possible extent. To do so will require that the concept of information and the theories of information science take a more-prominent role in the understanding of living systems... |
| A Danchin, G Fang Unknown unknowns: essential genes in quest for function Microb Biotechnol. (2016) 9: 530-540 doi: 10.1111/1751-7915.12384 |
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| G Boël, O Danot, V de Lorenzo, A Danchin
Omnipresent Maxwell’s demons orchestrate information management in living cells Microb Biotechnol. (2019) 12: 210-242 doi: 10.1111/1751-7915.13378 |
Genomes cannot be considered as mere collections of genes. They are much more. How can we access this information? An obvious answer is to decipher the sequence of model genomes. This led me to set up the sequencing of the genome of Bacillus subtilis. At this time (beginning of 1987) this was the first project of this type launched for conceptual and not technological reasons. In 1991, —in parallel with the same result obtained by the consortium sequencing the genome of Saccharomyces cerevisiae— we discovered that many genes were completely unknown at the time, not only in their sequence but also in their function and in the structure of their product:
P Glaser, F
Kunst, M Arnaud, M-P Coudart, W Gonzales, M-F Hullo, M Ionescu, B
Lubochinsky, L Marcelino, I Moszer, E Presecan, M Santana, E
Schneider, J Schweizer, A Vertes, G Rapoport, A Danchin
Bacillus subtilis genome project: cloning and sequencing of the
97 Kb region from 325o to 333o
Mol Microbiol (1993) 10: 371-384
This utterly unexpected result (the opponents to genome sequencing projects had « demonstrated » that we knew at least 95% of all possible gene classes and published this demonstration in the most fashionable journals), presented with a similar conclusion from the sequencing of the yeast's chromosome III, at the first genomics symposium organised by the commission of European Communities in Elounda in Crete in 1991, revealed the first major discovery obtained by genome projects.
Performed by a consortium associating Europe and Japan, the sequencing of the B. subtilis genome was completed in 1997, at the same time as that of E. coli. As early as 1995 the total length of continuous fragments from the organism was significantly larger than that of the genomes sequenced at the date. This genome sequence remained for five years the only example of its domain (the genomes of the Firmicutes were particularly difficult to sequence, because their DNA is usually toxic in the universal host then used to construct DNA libraries, E. coli, for biochemical reasons well understood by the authors) :
F Kunst, N
Ogasawara, I Moszer, AM Albertini, G Alloni, V Azevedo, MG Bertero,
P Bessières, A Bolotin, S Borchert, R Borriss, L Boursier, A Brans,
M Braun, SC Brignell, S Bron, S Brouillet, CV Bruschi, B Caldwell, V
Capuano, NM Carter, SK Choi, JJ Codani, IF Connerton, NJ Cummings,
RA Daniel, F Denizot, KM Devine, A Düsterhöft, SD Ehrlich, PT
Emmerson, KD Entian, J Errington, C Fabret, E Ferrari, D Foulger, C
Fritz, M Fujita, Y Fujita, S Fuma, A Galizzi, N Galleron, SY Ghim, P
Glaser, A Goffeau, EJ Golightly, G Grandi, G Guiseppi, BJ Guy, K
Haga, J Haiech, CR Harwood, A Hénaut, H Hilbert, S Holsappel, S
Hosono, MF Hullo, M Itaya, L Jones, B Joris, D Karamata, Y Kasahara,
M Klaerr-Blanchard, C Klein, Y Kobayashi, P Koetter, G Koningstein,
S Krogh, M Kumano, K Kurita, A Lapidus, S Lardinois, J Lauber, V
Lazarevic, SM Lee, A Levine, H Liu, S Masuda, C Mauël, C Médigue, N
Medina, RP Mellado, M Mizuno, D Moesti, S Nakai, M Noback, D Noone,
M O'Reilly, K Ogawa, A Ogiwara, B Oudega, SH Park, V Parro, TM Pohl,
D Portetelle, S Porwollik, AM Prescott, E Presecan, P Pujic, B
purnelle, G Rapoport, M Rey, S Reynolds, M Rieger, C Rivolta, E
Rocha, B Roche, M Rose, Y Sadaie, T Sato, E Scalan, S Schleich, R
Schroeter, F Scoffone, J Sekiguchi, A Sekowska, SJ Seror, P Serror,
BS Shin, B Soldo, A Sorokin, E Tacconi, T Takagi, H Takahashi, K
Takemaru, M Takeuchi, A Tamakoshi, T Tanaka, P Terpstra, A Tognoni,
V Tosato, S Uchiyama, M Vandenbol, F Vannier, A Vassarotti, A Viari,
R Wambutt, E Wedler, T Weitzenegger, P Winters, A Wipat, H Yamamoto,
K Yamane, K Yasumoto, K Yata, K Yoshida, HF Yoshikawa, E Zumstein, H
Yoshikawa, A Danchin
The complete genome sequence of the gram-positive bacterium Bacillus
subtilis
Nature (1997) 390: 249-256
The sequence was further updated four times:
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V Barbe, S Cruveiller, F Kunst, P
Lenoble, G Meurice, A Sekowska, D Vallenet, TZ Wang, I Moszer,
C Médigue, A Danchin From a consortium sequence to a unified sequence: The Bacillus subtilis 168 reference genome a decade later Microbiology (2009) 155: 1758-1775 doi: 10.1099/mic.0.027839-0 
  
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E Belda, A Sekowska, F Le Fèvre, A
Morgat, D Mornico, C Ouzounis, D Vallenet, C Médigue, A
Danchin An updated metabolic view of the Bacillus subtilis 168 genome Microbiology (2013) 159: 757-770. doi: 10.1099/mic.0.064691-0 |
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R Borriss, A Danchin,
CR Harwood, C Médigue, EPC Rocha, A Sekowska, D Vallenet Bacillus subtilis, the model Gram-positive bacterium: 20 years of annotation refinement Microb Biotechnol. (2018) 11: 3-17 |
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Bremer E, Calteau A, Danchin A, Harwood
C, Helmann JD, Médigue C, Palsson BO, Sekowska A, Vallenet D,
Zuniga A, Zuniga C A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century Microb biotechnol (2023)16: 1203-1231 |
The distribution of the corresponding sequence and annotations to the international community was displayed in the form of a specialized database with no counterpart until now. Unfortunately, this endeavour was suspended in 2010.
C Médigue, A
Viari, A Hénaut, A Danchin
Colibri: a functional data base for the Escherichia coli
genome
Microbiol Rev (1993) 57: 623-654
I Moszer, P
Glaser, A Danchin
SubtiList: a relational database for the Bacillus subtilis
genome
Microbiology (1995) 141 (Pt 2): 261-268
I Moszer, LM Jones, S Moreira, C Fabry, A
Danchin
SubtiList: the reference database for the Bacillus subtilis genome
Nucleic Acids Res (2002) 30: 62-65
Several genome projects followed: Leptospira interrogans and Staphylococcus epidermidis, in collaboration with the Shanghai Genome Center, Photorhabdus luminescens, at the Institut Pasteur, and, to try and understand the impact of the temperature constraints on genomes, the genome of the Antarctica bacteria Pseudoalteromonas haloplanktis TAC125, in collaboration with the Genoscope and several universities in the world. Sequencing of the genome of Psychromonas ingrahamii followed as a collaboration with Monica Riley and her colleagues.
Looking at the flow of published genomic sequences, two contrasting pictures emerge: at first glance, genes appear to be randomly distributed along the chromosome. On the other hand, their organization into operons (or islands of pathogenicity) suggests that, at least locally, related functions are physically close. In an attempt to understand the organization of the genome, it is therefore necessary to explore the distribution of genes along the chromosome. This asks for generalizing the concept of neighbourhood to many other types of vicinities than the simple succession of genes in the genomic text. From the methodological standpoint this view for inductive research requires construction of neighborhoods tables (conveniently available to scientists in databases: a field of choice for bioinformatics). Finally, systematic investigation of history will identify literature neighborhoods, not only using title and abstracts, but the whole content of articles: "in biblio" analysis is an essential component of inductive reasoning. We do not possess heuristics permitting direct access to unknown functions, and apart from preliminary studies there does not exist many places where such in silico work is developed. There exists however an excellent illustration of the concept of neighbourhood, the software Entrez, created by David Lipman and colleagues at the NCBI.
Inductive exploration will consist in finding all neighbors of each given gene. "Neighbour" has here the largest possible meaning. This is not simply a geometrical or structural notion. Each neighbourhood is meant to shed specific light on a gene, looking for its function as bringing together the objects of the neighborhood. A natural neighborhood is proximity on the chromosome. Another interesting neighborhood is similarity between genes or gene products. The isoelectric point often gives a first idea of a gene product compartmentalization. Also, a gene may have been studied by scientists in laboratories all over the world. And it can display features that refer to other genes: its neighbors will be the genes found together with it in the literature. Finally, there exists more complex neighborhoods, the study of which gives particularly revealing results: two genes may be neighbors because they use the genetic code in the same way. One can also study all genes that belong to the same neighborhood in the cloud of points describing codon usage of all the genes of the organism. I proposed this approach at the symposium for the 20th anniversary of the EMBO at the EMBL in Heidelberg in 1994, with the example of the possible role of a major enzyme, polynucleotide phosphorylase.
All this has some flavour of a then fashionable field, Artificial Intelligence, a highly contentious but fascinating domain. This should also make clear to us that in silico analysis will never replace validation in vivo and in vitro: let us hope that propagation of erroneous assignments of functions by automatic interpretation of the genomic texts will not hinder discoveries. Knowing genome sequences is a marvelous feat, but it is the starting point, not the end. The first observations of my laboratory at the Institut Pasteur (Regulation of Gene Expression and Genetics of Bacterial Genomes) were interpreted as establishing that this order was far from random, but was linked to the function of genes, in relation with the cell's architecture. These results were fragmentary, so they needed to be experimentally substantiated, combining in silico analysis of the genome (bioinformatics) of model organisms, such as Escherichia coli or Bacillus subtilis, with their study in vivo (reverse genetics and physiological biochemistry, in particular using transcription expression profiling and two-dimensions protein electrophoresis), as well as comparative studies with other genomes, with biochemical and structural analyses. If indeed the map of the cell is in the chromosome, this asks for some physical principle linking the succession of the genes - a symbolic text, carrying an information - and the cell's architecture - concrete (i.e. massive or inert) matter. We do not need to resort to the existence of a divine principle of organization. This should be the consequence of a simple physical principle. The winning trio of darwinian natural selection (variation / selection / amplification) shows that evolution creates functions, that functions « capture » (recruit) structures (acquisitive evolution), so that structural analysis becomes the most relevant when functions are understood.
EPC Rocha, A
Danchin, A Viari
Universal replication biases in bacteria
Mol Microbiol (1999) 32: 11-16
A Danchin, P
Guerdoux-Jamet, I Moszer, P Nitschké
Mapping
the bacterial cell architecture into the chromosome
Philos Trans R Soc Lond B Biol Sci (2000) 355:
179-190
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EPC Rocha, A Danchin |
| Ongoing evolution of strand composition in bacterial genomes | |
| Mol Biol Evol (2001) 18: 1789-1799 |
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EPC Rocha, A Danchin |
| Essentiality, not expressiveness, drives gene-strand bias in bacteria | |
| Nature Genetics (2003) 34: 377-378 |
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EPC Rocha, A Danchin |
| Gene essentiality determines chromosome organisation in bacteria | |
| Nucleic Acids Res (2003) 31: 6570-6577 |
Looking at genomes as whole entities, we have long known that there is a 10-11.5 period in the distribution of nucleotides, and this is true from prokaryotes to eukaryotes. This bias is present throughout a given genome, in both coding and non-coding sequences. Using a linear projection-based auto-correlation analysis technique, the sequences responsible for this bias were identified. These ubiquitous motifs were termed "flexible class A motifs". Each motif consists of up to ten conserved nucleotides or dinucleotides distributed in a discontinuous pattern. Each occurrence spans a region of up to 50 bp in length. There is limited fluctuation in the distances between the nucleotides comprising each occurrence of a given motif, suggesting that they are constrained by supercoiling and/or bending of the DNA. Taken together, these motifs cover up to half the genome in most prokaryotes. They generate the previously recognised 11 bp periodic bias. Based on the structure of the motifs, it has been suggested that they may define a dense network of protein interaction sites in chromosomes:
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E Larsabal, A Danchin |
| Genomes are covered with ubiquitous 11bp periodic patterns, the "class A flexible patterns" | |
BMC Bioinformatics (2005) 6: 206  |
The corresponding constraints are visible in the amino-acid sequence of the proteins, suggesting that the sequence is more constrained by the genome organisation than by the protein function. These novel observations have considerable implications in terms of phylogenetic profiles when one analyses protein sequences:
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G Pascal, C Médigue, A Danchin |
| Universal biases in protein composition of model prokaryotes | |
Proteins (2005) 60: 27-35 
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This latter work characterizes “orphan” proteins which form approximately 10% of any genome of a new species. These proteins are characterized by their enrichment in aromatic amino-acids. This work proposes that many among the represent the "self" of the species, by behaving as “gluons” which bring about an extra contribution is the stability of multi-protein complexes in the cell. This would bring an essential contribution to the functional stabilization of complex intracellular structures. More generally the approach thus defined allowed the investigators to define the essentiality of a gene in a real context, by measuring its persistence in many species, not only in sequence but also in its place in the genome:
G
Fang, EPC Rocha, A Danchin
How essential are non-essential genes? Mol Biol Evol (2005) 22:
2147-2156
In summary, it appears that bacterial genomes are highly organised entities, contrary to a widely spread idea of a random « fluidity » of genomes. What are the selective constraints that support this organisation?
A general analysis of the conservation of syntenies in a large number of complete bacterial genomes has shown that two classes of genes tend to stay together. The way the class of persistent genes keep remaining grouped is organized in a way that is reminiscent of a scenario of the origin of life. This is why the corresponding set has been named the paleome. In the same way, genes that are rarely found in genomes make clusters that are easily horizontally transferred. The corresponding genes allow the bacteria to live in a specific niche. They are named, for this reason, the cenome (to indicate the fact that they are shared by a community living in a particular environment, and prone to be transferred):
G Fang, EP Rocha, A Danchin
Persistence drives gene clustering in bacterial genomes
BMC Genomics (2008) 9: 4
A Danchin
Natural
selection and immortality
Biogerontology (2009) 10: 503-516
A Danchin
A phylogenetic view of bacterial ribonucleases
Prog Nucleic Acid Res Mol Biol (2009) 85: 1-41
Furthermore, the nature of DNA polymerase III plays a role in the overall organisation of the genome. Firmicutes, which have two such polymerases (DnaE and PolC), show a strong bias in gene distribution. Analysis of the genes co-evolving with these polymerases shows that the different bacterial clades have different origins. This has a consequence of considerable importance for the question of the origins of life, as it shows that there is no single ancestor, no LUCA, but a population of progenotes that merged and divided several times before giving rise to the species we know today.
The simplest way to evolve is to follow the arrow of time, to increase the overall entropy of the system. In water, this is the driving force behind the construction of many biological structures: it is the origin of the universal formation of helices, it is what allows the folding of proteins and the formation of viral capsids. And it should not escape us that the greatest increase in entropy of a molecular complex in water occurs when the surface/volume ratio is the highest: when a planar structure is formed, it orders the water molecules on both sides. Consequently, if this plane meets another, it will lose a layer of water molecules, and stick to it. The formation of flat layers should therefore be a very strong organizing principle. Is it possible to know, simply by knowing the genomic text, whether a gene product will form such layers, if it simply forms hexagons, for example? This is even more unlikely than the fact that an amino acid sequence can tell us exactly how a protein folds, without knowing the pre-existing folds: pancreatic RNase would indeed fold, because selection has isolated it to do so (it is secreted in bile salts), but this would never be accepted as the paradigm for protein folding.
Beginning with a summary of our view of the minimal functions required to make a cell alive revealed many genes coding for unknown functions.This work was followed by a series of developments combining identification of agents generating classes of things (i.e. protein complexes that dissipate energy during the process of separation between classes of material things, positions, or times) and the coordination of non-homothetic growth, mediated by the omnipresent control of cytidine triphosphate (CTP) synthesis.
Being abstract, information must nevertheless be embodied into material entities, with unavoidable idiosyncratic properties. This inevitably makes new unmet functional needs emerge. Thus, the growth of cells requires specific but clumsy material implementations "kludges" as a trite saying names them. Although difficult to identify this "tinkering" become essential in particular situations. Finally, a specific functional category characterizes the need for growth: metabolic implementations that allow the cell to organize the growth of its cytoplasm, membranes and genome, in different spatial dimensions (3D, 2D, 1D). Solving this metabolic dilemma, which is essential for the engineering of new synthetic biology chassis, has led us to discover an unexpected role for CTP synthetase as a coordinator of non-homothetic growth.
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EPC
Rocha, A Danchin Base composition bias might result from competition for metabolic resources Trends Genet (2002) 18: 291-294 |
 Le
contenu en GC des génomes varie chez les bactéries de 25 à
75%. Nous montrons dans ce travail que le génome des bactéries
qui dépendent d'un hôte pour survivre (pathogènes obligatoires
ou symbiontes) tendent à devenir riches en AT. Mieux,
l'analyse des bactériophages, des plasmides et des séquences
d'insertion, qui peuvent être considérés comme des pathogènes
intracellulaires, nous a montré qu'ils sont aussi bien plus
riches en AT que leurs hôtes. Nous interprétons ce fait par le
coût énergétique et la difficulté d'obtention de C et G par
rapport à T/U et A, en raison de la construction des voies
métaboliques. Ces conclusions s'appliquent aux virus
eucaryotes comme ceux de la grippe ou du Sida |
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A Danchin Comparison between the Escherichia coli and Bacillus subtilis genomes suggests that a major function of polynucleotide phosphorylase is to synthesize CDP DNA Res (1997) 4: 9-18 |
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P Nitschké, P Guerdoux-Jamet, H Chiapello, G Faroux, C Hénaut,
A Hénaut, A Danchin Indigo: a World-Wide-Web review of genomes and gene functions FEMS Microbiol Rev (1998) 22: 207-227 |
In particular, it explains the surprising observation that deoxyribonucleotide synthesis starts from ribonucleoside diphosphates, not triphosphates.
A consequence of non-homothetic growth is a huge pressure to make genome long, not short. This results in the multiplication of accidents — such as DNA sequence local duplications — or processes resulting in accretion of DNA sequences within genomes. Horizontal Gene Transfer, a process we discovered to be omnipresent, is therefore an inevitable consequence of this pressure.
When I decided in 1986 to explore the sequencing of a whole bacterial genome this was in an attempt to understand the basic principles of both its construction and its role. At the time, this undertaking was seen by most biologists as a waste of time and resources, unlikely to yield important new knowledge and the idea was received with reluctance in spring 1987. My idea was to explore the coupling between the coordination of gene expression and the physical organization of the genome, on the basis that a genome was not just a collection of genes. After a complex set of political obstacles, impossible to summarize here (see Why sequence genomes? The Escherichia coli imbroglio or The Delphic Boat) I was eventually driving the sequencing of a large segment of the Bacillus subtilis genome and, together with the late Frank Kunst, in the scientific co-ordination of an international team for sequencing the genome of strain 168 of this organism. This led me to try and organize genome bioinformatics in France with the help of several colleagues at Universities, and national research agencies, through the creation of a nation-wide group, GDR 1029 (1991-1995) and subsequently through the coordination of the bioinformatics programme of the Groupement de Recherche et d'Études des Génomes (1992-1996, headed by Piotr Slonimski), and subsequently at the Comité de Coordination des Sciences du Vivant (1998-2000). To describe this endeavour I coined the expression "in silico". Amusingly, this was so successful that it has now been accepted universally as a counterpart of in vivo and in vitro.
As the director of the Department Genomes and Genetics at the Institut Pasteur until june 2009, I put an final point to the project by re-sequencing and re-annotating afresh the sequence of the reference genome of B. subtilis, as a tribute to the whole international community working on this model organism. As discussed previously, in 1991 the B. subtilis program in parallel with that of Yeast, discovered that a considerable number of the genes making genomes were still of unknown function. This same year the analysis of this unknown gene complement of the E. coli genome led us to demonstrate, that, rather than be an anecdotal feature as previously thought, horizontal gene transfer accounted for a large proportion of bacterial genomes. Most of those unknown genes belonged to an original class that displayed a specific codon usage bias. Since then HGT has been found to be an essential component of the construction of most if not all, genomes. And indeed, the number of articles in the domain keeps increasing at a fast pace.
C Médigue, T Rouxel, P Vigier, A Hénaut, A
Danchin
Evidence for horizontal gene transfer in Escherichia coli
speciation
J Mol Biol (1991) 222: 851-856
 This
paper shows, for the very first time, that in the genome of
the best known bacterium, Escherichia coli, one
sixth of the genes originate elsewhere. This result, which
demonstrates the considerable importance of horizontal gene
transfer (HGT) in bacteria, also shows that replication
fidelity is not the primary characteristic of species, but
that error-correcting genes spread by horizontal transfer.
This work highlights the role of mutator strains in the
environment, giving horizontal gene transfer a prominent role
in adaptation to a new niche, particularly during the
evolution from commensalism to pathogenicity. Amusingly,
the comment of the Assistant Editor of Nature to
exclude publication was: "I have discussed your manuscript
with my colleagues, and while we appreciate the interest of
your observation suggesting the existence of an apparent
'third class of genes', the inference of horizontal gene
transfer seems rather tentative, and for this reason we feel
that the manuscript would be better suited to publication in
a rather more specialized molecular evolution or
microbiology journal." And this is probably why this
same popular magazine had to re-publish an updated view of HGT
in year 2000 under the name of "lateral gene
transfer"... Nominalism is still relevant |
Cet
article montre, pour la première fois, que dans le génome de
la bactérie la mieux connue, Escherichia coli, un
sixième des gènes provient d'ailleurs. Ce résultat, qui
démontre l'importance considérable du transfert génétique
latéral chez les bactéries, montre aussi que la fidélité de la
réplication n'est pas le caractère premier des espèces, mais
que les gènes de correction des erreurs se propagent par
transfert horizontal. Ce travail met en évidence le rôle des
souches mutatrices dans l'environnement, donnant au transfert
génétique horizontal un rôle de premier plan pour l'adaptation
à une nouvelle niche, en particulier au cours de l'évolution
du commensalisme vers la pathogénicité |
C Médigue, A
Viari, A Hénaut, A Danchin
Escherichia coli molecular genetic map (1500 kbp): update II
Mol Microbiol (1991) 5: 2629-2640
Our work of genomics in silico demonstrated for the first time that a fraction (at least one sixth) of the genes of E. coli are derived from horizontal gene transfer. It also showed that antimutator genes were likely to be propagated by HGT, suggesting that bacteria in the environment are often in a highly mutable state and fixed in a much more rigid (invariable) form when they meet a stable biotope. Another observation from this study was the clustering of HGT genes in relation with particular cell processes, suggesting that genomes are organised entities:
P
Guerdoux-Jamet, A Hénaut, P Nitschké, JL Risler, A Danchin
Using codon usage to predict genes origin: is the Escherichia coli
outer membrane a patchwork of products from different genomes?
DNA Research (1997) 4: 257-265
That this observation is general would be demonstrated later on, with Bacillus subtilis. The importance of HGT is so well accepted nowadays that it has become common knowledge:
I Moszer, EPC Rocha, A Danchin
Our efforts have led to the identification of several rules, linked to the particularities of the building blocks of life:
1/ There is a universal bias in the composition of the genes present in the leading and lagging strands of DNA;
2/ Remarkably, the essential genes (identified experimentally after the B. subtilis sequencing project) are specifically encoded in the main DNA strand.
These rules must be implemented in synthetic biology constructs.
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V de Lorenzo, A Danchin Synthetic biology: discovering new worlds and new words EMBO Rep (2008) 9: 822-827. doi: 10.1038/embor.2008.159 |
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A Danchin Bacteria as computers making computers FEMS Microbiol Rev (2009) 33: 3-26. doi: 10.1111/j.1574-6976.2008.00137.x | ||
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A Danchin, A Sekowska Frustration: Physico-chemical prerequisites for the construction of a synthetic cell in: Systems Chemistry, May 26th - 30th, 2008, in Bozen, Italy Beilstein Institut for the Advancement of Chemical Sciences (2009) 1-13. |
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A Danchin, PM Binder, S Noria Antifragility and tinkering in biology (and in business): Flexibility provides an efficient epigenetic way to manage risk Genes (2011), 2: 998-1016; doi:10.3390/genes2040998 |
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M Porcar, A Danchin, V de Lorenzo, VA
dos Santos, N Krasnogor, S Rasmussen, A Moya The ten grand challenges of synthetic life Systems and Synthetic Biology (2011) 5:1-9. doi: 10.1007/s11693-011-9084-5 |
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A Danchin Scaling up synthetic biology: Do not forget the chassis FEBS Letters (2012) 586: 2129-2137. doi: 10.1016/j.febslet.2011.12.024 |
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A Danchin Synthetic biology's flywheel EMBO Reports (2012) 13: 92. doi: 10.1038/embor.2011.253 |
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CG Acevedo-Rocha, G Fang, M Schmidt, DW
Ussery, A Danchin From essential to persistent genes: a functional approach to constructing synthetic life Trends Genet. (2013) 29: 273-279. doi: 10.1016/j.tig.2012.11.001 |
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A Danchin, A Sekowska Constraints in the design of the synthetic bacterial chassis Methods in Microbiology (2013) 40: 39-68. doi: |
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A Danchin, A Sekowska, S Noria
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Danchin A Isobiology: A variational principle for exploring synthetic life Chembiochem (2020) 21: 1781-1792 doi: 10.1002/cbic.202000060 |
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Danchin A Biological innovation in the functional landscape of a model regulator, or the lactose operon repressor CR Biol (2021) 344: 111-126 doi: 10.5802/crbiol.52 |
My interest for biology stemmed from the idea that selection had a stabilizing role. I had discovered this during my travel through West Africa, where I collected butterflies (and frogs, for the laboratory of Zoology at the École Normale Supérieure) and the way Ivan Schmalhausen discussed the problems of Darwinism. In line with my interest in tise work and my involvement at the Centre Royaumont pour une Science de l'Homme, I organized in 1971 a weekly seminar, every wednesday's afternoon, at the Institut de Biologie Physico-Chimique. There, together with Philippe Courrège and Jean-Pierre Changeux we tried to delineate the limits of selection in biological processes. Our work explored the role of selective stabilization in learning and memory in the nervous system and in the immune system. This exploration predated the fashion for neuronal networks, but with a specific feature: synapses evolved in such a way that they could degenerate irreversibly. The outcome of the process was the carving of an image of the environment within the neuronal network.
JP Changeux, A
Danchin
Selective stabilisation of developing synapses as a mechanism for the
specification of neuronal networks
Nature (1976) 264: 705-712
A Danchin
A selective theory for the epigenetic specification of the
monospecific antibody production in single cell lines
Ann Immunol (Paris) (1976) 127: 787-804
A Danchin
The specification of the immune response: a general selective model
Mol Immunol (1979) 16: 515-526
Subsequently I explored the general process of selective stabilization in the building up of cells as computers making computers. This process allows the embodiment of functional properties within material entities that will progressively be associated together as networks or organized in space, in operons, for example. This view led to emphasis on the role of information as an authentic currency of the physical world, and discovery of the key role of Landauer's principle in biology, as presented previously. More recently I summarized this old work together with André Fenton.
A Danchin, AA Fenton
From analog to digital computing: Is Homo sapiens’ brain on
its way to become a Turing Machine?
Front Ecol Evol (2022) 10: fevo.2022.796413
The functional organisation of the genes in genomes must result from the selection pressure of simple physico-chemical principles. Beside physical causes such as the structure of water (the study of the genome of P. haloplanktis is meant to have access to some of those), gasses and radicals, because they are highly diffusible, may play a major role in cellular compartmentalisation, and might be the cause of some of the organisation of the genes in genomes. Sulfur metabolism is particularly sensitive to gasses and radicals, and it is therefore important to understand how it is organised. A first study demonstrated that sulfur-related genes are organised into islands:
EPC Rocha, A
Sekowska, A Danchin
Sulphur islands in the Escherichia coli genome: markers of the
cell's architecture?
FEBS Lett (2000) 476: 8-11
and a detailed analysis, mainly developed during the creation of the HKU-Pasteur Research Centre in Hong Kong permitted them to uncover the details of the “methionine salvage pathway”:
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A Sekowska, HF Kung, A Danchin |
| Sulfur metabolism in Escherichia coli and related bacteria: facts and fiction | |
| J Mol Microbiol Biotechnol (2000) 2: 145-177 |
A Sekowska, JY
Coppée, JP Le Caer, I Martin-Verstraete, A Danchin
S-adenosylmethionine decarboxylase of Bacillus subtilis
is closely related to archaebacterial counterparts
Mol Microbiol (2000) 36: 1135-1147
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A Sekowska, L Mulard, S Krogh, JK Tse, A Danchin |
| MtnK, methylthioribose kinase, is a starvation-induced protein in Bacillus subtilis | |
| BMC Microbiol (2001) 1: 15 |
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A Sekowska, A Danchin |
| The methionine salvage pathway in Bacillus subtilis | |
| BMC Microbiol (2002) 2: 8 |
The following work makes a synthesis of the catalytic activities involved in this ubiquitous cycle (it is also present in man and plants), which has the interesting feature that it systematically recruited proteins of diverse structures to lead to the completion of the cycle. One of these proteins is likely to be related to the ancestor of ribulose-phosphate carboxylase/oxygenase (RuBisCO), the most abundant enzyme on the planet (this opens fascinating questions on the origin of catalytic activities):
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A Sekowska, V Dénervaud, H Ashida, K Michoud, D Haas, A Yokota, A Danchin |
| Bacterial variations on the methionine salvage pathway | |
| BMC Microbiol (2004) 4: 9 |
H
Ashida, A Danchin, A Yokota
Was photosynthetic RuBisCO recruited by acquisitive
evolution from RuBisCO-like proteins involved in sulfur
metabolism?
Res Microbiol (2005) 156: 611-618
This remarkable metabolic cycle has the surprising property as shown in ourwork, under particular conditions, to lead the cell to synthesize carbon monoxide. As this cycle exists in man, this opens interesting perspective about possible controls mediated by CO, a gas different from nitric oxide, in the immune system and in the nervous system.
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A Sekowska, H Ashida, A Danchin Revisiting the methionine salvage pathway and its paralogues Microb Biotechnol. (2019) 12: 77-97 doi: 10.1111/1751-7915.13324 |
Metabolism can be seen as a pre-requisite for any scenario of the origins of life. I have explored several features of the question, based on surface metabolism, as advocated by Samuel Granick, Freeman Dyson and Günter Wächtershäuser.
A Danchin
Homeotopic transformation and the origin of translation
Progress in Biophysics and Molecular Biology (1989) 54:
81-86
A
Danchin
Archives or palimpsests? Bacterial genomes unveil a scenario for the
origin of life
Biological
Theory (2007) 2: 52-61
A
Danchin, G Fang, S Noria
The extant core bacterial proteome is an archive of the origin of life
Proteomics (2007) 7: 875-889
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A Danchin From chemical metabolism to life: the origin of the genetic coding process Beilstein J Org Chem. (2017) 13: 1119-1135 doi:10.3762/bjoc.13.111 |
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| A Danchin Multiple clocks in the evolution of living organisms pp. 101-118 In: Molecular Mechanisms of Microbial Evolution (2018) edited by Pabulo H. Rampelotto, Springer ISBN: 978-3-319-69078-0 |
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To answer this very general question, a genetic selection and screening procedure in the model bacterium Escherichia coli was meant to isolate mutants that would orient future experiments along a rewarding track. The idea was to explore whether some signals which appear to us as redundant (i.e. look somewhat "useless" for the unprepared human mind) in macromolecular syntheses could be separated (i.e. by selecting mutants that would grow with only one active signal instead of several). The idea was that there exists some "secundary punctuation" in the expression of the genetic message allowing coupling between macromolecular syntheses and the bulk metabolism of the cell. Emphasis on this linguistic analogy came from my contribution to the reflection on the role of selective processes at the root of memory and learning. The study of the process of initiation of translation, which, in Bacteria, associates two independent signals (a metabolic signal that labels the first methionine of the nascent polypeptide with a one-carbon residue, and the structure of a special transfer RNA) led me, through experiments using genetics, to the discovery of a ubiquitous anomaly in metabolism, coupling replication, transcription, translation and cell division. The mutants affected in that process were analysed in succession. They involved transcription termination, translation initiation, the “stringent” coupling between these processes, the one-carbon metabolism, synthesis of cyclic AMP, a protein long proposed to be a bacterial histone, H-NS, and the biosynthesis pathway of branched-chain amino-acids. This apparently haphazard list, derived from the outcome of genetic experiments, accounts for the threads followed, one by one, to attempt to unravel this complicated network of interactions, finally understood in january 2006 with the role of the serine amino acid (this common amino acid is toxic in excess because of at least two processes: production of hydroxypyruvate, that makes dead-end products with thiamine, and of aminoacrylate / iminopropionate when it enters pathways such as cysteine and tryptophan biosynthesis). Mid-1980 the time was now ripe to explore this same question not through the study of individual genes, but rather to develop a global study of the genes from the knowledge of the complete genome texts. This required introduction of a large component of computer sciences, and experiments “in silico” were proposed to complement in vivo or in vitro experiments (this term was used for the first time in 1988-1989, in discussions with the European commission, meant to justify the setting up of genome projects). The question then became a simple conjecture, based on a former reflection of von Neumann about Turing machines: is there a link between the architecture of the cell and that of the genome? Work from the Unit Genetics of Bacterial Genomes showed that indeed genes are not randomly distributed in genomes. Whether this indicates a link with the architecture of the cell remains however, of course, an open question.
The involvement of cyclic AMP in the "serine effect" (wild type strains are sensitive to serine, but cya and crp mutants are more resistant) led us to a thorough study both in terms of genetics and biochemistry of adenylate cyclases. After having been the first laboratory to isolate and characterise in full the gene of an adenylate cyclase (that of Escherichia coli), the work was extended to the identification of adenylate cyclase toxins, present in the etiologic agents of whooping cough and anthrax. Having invented a multipartner cloning technique, the ancestor of the technique now known as “double hybrid” (patent EP0301954), the genes from the corresponding toxins were isolated and sequenced, the proteins analysed biochemically and the secretion process of the cyclases was characterised:
P Glaser, D
Ladant, O Sezer, F Pichot, A Ullmann, A Danchin
The calmodulin-sensitive adenylate cyclase of Bordetella pertussis:
cloning and expression in Escherichia coli
Mol Microbiol (1988) 2: 19-30
P Glaser, H
Sakamoto, J Bellalou, A Ullmann, A Danchin
Secretion of cyclolysin, the calmodulin-sensitive adenylate
cyclase-haemolysin bifunctional protein of Bordetella pertussis
EMBO J (1988) 7: 3997-4004
A symmetrical approach was used to clone the cDNA of mammalian calmodulins, showing that the method (double hybrid) is of wide efficiency:
A Danchin, O
Sezer, P Glaser, P Chalon, D Caput
Cloning and expression of mouse-brain calmodulin as an activator of Bordetella
pertussis adenylate cyclase in Escherichia coli
Gene (1989) 80: 145-149
As early as 1988, this work asked a series of ethical problems (recently revived under the name of « bioterrorism ») discussed in:
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A Danchin |
| Not every truth is good. The dangers of publishing knowledge about potential bioweapons | |
| EMBO Rep (2002) 3: 102-104 |
This led me to be appointed as a member of the Centre Consultatif National pour la Biosécurité (CNCB).
An overview of this first work on adenylate cyclases is summarised in:
A Danchin
Phylogeny of adenylyl cyclases
Adv Second Messenger Phosphoprotein Res (1993) 27:
109-162
This article created the international reference for the classification of adenylate cyclases. Three classes from different phylogenetic descent (convergent evolution) were first identified: Class I, cyclases from enterobacteria and related bacteria; Class II, secreted toxic cyclases; Class III, "universal" class present in Bacteria and in Eukarya (including higher vertebrates). A fourth class, also from a completely different phylogenetic origin, and perhaps involved in promiscuous activities, was discovered several years later in our research Unit:
O Sismeiro, P
Trotot, F Biville, C Vivarès, A Danchin
Aeromonas hydrophila adenylyl cyclase 2: a new class of
adenylyl cyclases with thermophilic properties and sequence
similarities to proteins from hyperthermophilic archaebacteria
J Bacteriol (1998) 180: 3339-3344 
The "universal" cyclases class (class III) clusters together adenylate and guanylyl cyclases, and an original selection procedure allows one to go from one type of specificity to the other one (this was one of the very first experiments showing that it is possible to change the specificity of an enzyme for its substrate):
A Beuve, A
Danchin
From adenylate cyclase to guanylate cyclase. Mutational analysis of a
change in substrate specificity
J Mol Biol (1992) 225: 933-938
***
This text, which strictly follows the
rules we discussed in an article published in 2021, does not
seem to be available, which justifies making it available here.
Murray Gell-Mann [© Complexus 1 (5) 1995-1996 (Out of
print)]
