1
|
Wirth NT, Rohr K, Danchin A, Nikel PI. Recursive genome engineering decodes the evolutionary origin of an essential thymidylate kinase activity in Pseudomonas putida KT2440. mBio 2023; 14:e0108123. [PMID: 37732760 PMCID: PMC10653934 DOI: 10.1128/mbio.01081-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/27/2023] [Indexed: 09/22/2023] Open
Abstract
IMPORTANCE Investigating fundamental aspects of metabolism is vital for advancing our understanding of the diverse biochemical capabilities and biotechnological applications of bacteria. The origin of the essential thymidylate kinase function in the model bacterium Pseudomonas putida KT2440, seemingly interrupted due to the presence of a large genomic island that disrupts the cognate gene, eluded a satisfactory explanation thus far. This is a first-case example of an essential metabolic function, likely acquired by horizontal gene transfer, which "landed" in a locus encoding the same activity. As such, foreign DNA encoding an essential dNMPK could immediately adjust to the recipient host-instead of long-term accommodation and adaptation. Understanding how these functions evolve is a major biological question, and the work presented here is a decisive step toward this direction. Furthermore, identifying essential and accessory genes facilitates removing those deemed irrelevant in industrial settings-yielding genome-reduced cell factories with enhanced properties and genetic stability.
Collapse
Affiliation(s)
- Nicolas T. Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | - Katja Rohr
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| | - Antoine Danchin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens, Lyngby, Denmark
| |
Collapse
|
2
|
Danchin A. Science, method and critical thinking. Microb Biotechnol 2023; 16:1888-1894. [PMID: 37462943 PMCID: PMC10527184 DOI: 10.1111/1751-7915.14315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 09/28/2023] Open
Abstract
Science is founded on a method based on critical thinking. A prerequisite for this is not only a sufficient command of language but also the comprehension of the basic concepts underlying our understanding of reality. This constraint implies an awareness of the fact that the truth of the World is not directly accessible to us, but can only be glimpsed through the construction of models designed to anticipate its behaviour. Because the relationship between models and reality rests on the interpretation of founding postulates and instantiations of their predictions (and is therefore deeply rooted in language and culture), there can be no demarcation between science and non-science. However, critical thinking is essential to ensure that the link between models and reality is gradually made more adequate to reality, based on what has already been established, thus guaranteeing that science progresses on this basis and excluding any form of relativism.
Collapse
Affiliation(s)
- Antoine Danchin
- School of Biomedical Sciences, Li KaShing Faculty of MedicineHong Kong UniversityPokfulamHong KongChina
| |
Collapse
|
3
|
Danchin A, Fenton AA. From Analog to Digital Computing: Is Homo sapiens’ Brain on Its Way to Become a Turing Machine? Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.796413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The abstract basis of modern computation is the formal description of a finite state machine, the Universal Turing Machine, based on manipulation of integers and logic symbols. In this contribution to the discourse on the computer-brain analogy, we discuss the extent to which analog computing, as performed by the mammalian brain, is like and unlike the digital computing of Universal Turing Machines. We begin with ordinary reality being a permanent dialog between continuous and discontinuous worlds. So it is with computing, which can be analog or digital, and is often mixed. The theory behind computers is essentially digital, but efficient simulations of phenomena can be performed by analog devices; indeed, any physical calculation requires implementation in the physical world and is therefore analog to some extent, despite being based on abstract logic and arithmetic. The mammalian brain, comprised of neuronal networks, functions as an analog device and has given rise to artificial neural networks that are implemented as digital algorithms but function as analog models would. Analog constructs compute with the implementation of a variety of feedback and feedforward loops. In contrast, digital algorithms allow the implementation of recursive processes that enable them to generate unparalleled emergent properties. We briefly illustrate how the cortical organization of neurons can integrate signals and make predictions analogically. While we conclude that brains are not digital computers, we speculate on the recent implementation of human writing in the brain as a possible digital path that slowly evolves the brain into a genuine (slow) Turing machine.
Collapse
|
4
|
Marijuán PC, Navarro J. The biological information flow: From cell theory to a new evolutionary synthesis. Biosystems 2022; 213:104631. [DOI: 10.1016/j.biosystems.2022.104631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 12/19/2022]
|
5
|
Marijuán PC, Navarro J. From Molecular Recognition to the "Vehicles" of Evolutionary Complexity: An Informational Approach. Int J Mol Sci 2021; 22:ijms222111965. [PMID: 34769394 PMCID: PMC8585065 DOI: 10.3390/ijms222111965] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 10/18/2021] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
Countless informational proposals and models have explored the singular characteristics of biological systems: from the initial choice of information terms in the early days of molecular biology to the current bioinformatic avalanche in this “omic” era. However, this was conducted, most often, within partial, specialized scopes or just metaphorically. In this paper, we attempt a consistent informational discourse, initially based on the molecular recognition paradigm, which addresses the main stages of biological organization in a new way. It considers the interconnection between signaling systems and information flows, between informational architectures and biomolecular codes, between controlled cell cycles and multicellular complexity. It also addresses, in a new way, a central issue: how new evolutionary paths are opened by the cumulated action of multiple variation engines or mutational ‘vehicles’ evolved for the genomic exploration of DNA sequence space. Rather than discussing the possible replacement, extension, or maintenance of traditional neo-Darwinian tenets, a genuine informational approach to evolutionary phenomena is advocated, in which systemic variation in the informational architectures may induce differential survival (self-construction, self-maintenance, and reproduction) of biological agents within their open ended environment.
Collapse
Affiliation(s)
- Pedro C. Marijuán
- Bioinformation Group, Aragon Health Sciences Institute (IACS), 50009 Zaragoza, Spain
- Correspondence:
| | - Jorge Navarro
- Department of Quantitative Methods for Business and Economy, University of Zaragoza, 50006 Zaragoza, Spain;
| |
Collapse
|
6
|
Budisa N, Kubyshkin V, Schmidt M. Xenobiology: A Journey towards Parallel Life Forms. Chembiochem 2020; 21:2228-2231. [PMID: 32323410 DOI: 10.1002/cbic.202000141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 03/29/2020] [Indexed: 12/11/2022]
Abstract
Xenobiology is the science of estranged life forms. More specifically, this is an emergent technoscience that combines advances in genetic engineering with the design of biological systems based on unusual biochemistries delivered by chemical compounds of mostly anthropogenic origin. Xenobiology enables us to create and study strange new life forms, "aliens", not in the way science fiction books do it, but in terms of enlightened science, design, and engineering.
Collapse
Affiliation(s)
- Nediljko Budisa
- Department of Chemistry, University of Manitoba, Dysart Road 144, Winnipeg, R2T 2N2, Canada.,Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin, 10623, Germany
| | - Vladimir Kubyshkin
- Department of Chemistry, University of Manitoba, Dysart Road 144, Winnipeg, R2T 2N2, Canada
| | - Markus Schmidt
- Biofaction KG, Kundmanngasse 39/12, 1030, Vienna, Austria
| |
Collapse
|
7
|
Jose AM. A framework for parsing heritable information. J R Soc Interface 2020; 17:20200154. [PMID: 32315573 PMCID: PMC7211480 DOI: 10.1098/rsif.2020.0154] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Living systems transmit heritable information using the replicating gene sequences and the cycling regulators assembled around gene sequences. Here, I develop a framework for heredity and development that includes the cycling regulators parsed in terms of what an organism can sense about itself and its environment by defining entities, their sensors and the sensed properties. Entities include small molecules (ATP, ions, metabolites, etc.), macromolecules (individual proteins, RNAs, polysaccharides, etc.) and assemblies of molecules. While concentration may be the only relevant property measured by sensors for small molecules, multiple properties that include concentration, sequence, conformation and modification may all be measured for macromolecules and assemblies. Each configuration of these entities and sensors that is recreated in successive generations in a given environment thus specifies a potentially vast amount of information driving complex development in each generation. This entity-sensor-property framework explains how sensors limit the number of distinguishable states, how distinct molecular configurations can be functionally equivalent and how regulation of sensors prevents detection of some perturbations. Overall, this framework is a useful guide for understanding how life evolves and how the storage of information has itself evolved with complexity since before the origin of life.
Collapse
Affiliation(s)
- Antony M. Jose
- Department of Cell Biology and Molecular Genetics, University of Maryland, Room 2136, Bioscience Research Building (Building #413), College Park, MD 20742, USA
| |
Collapse
|
8
|
Boël G, Danot O, de Lorenzo V, Danchin A. Omnipresent Maxwell's demons orchestrate information management in living cells. Microb Biotechnol 2019; 12:210-242. [PMID: 30806035 PMCID: PMC6389857 DOI: 10.1111/1751-7915.13378] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The development of synthetic biology calls for accurate understanding of the critical functions that allow construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy in an unanticipated way. Analysis of these functions shows that they are meant to manage information under conditions when discrimination of substrates in a noisy background is preferred over a simple recognition process. We show here that many of these functions, including transporters and the ribosome construction machinery, behave as would behave a material implementation of the information-managing agent theorized by Maxwell almost 150 years ago and commonly known as Maxwell's demon (MxD). A core gene set encoding these functions belongs to the minimal genome required to allow the construction of an autonomous cell. These MxDs allow the cell to perform computations in an energy-efficient way that is vastly better than our contemporary computers.
Collapse
Affiliation(s)
- Grégory Boël
- UMR 8261 CNRS‐University Paris DiderotInstitut de Biologie Physico‐Chimique13 rue Pierre et Marie Curie75005ParisFrance
| | - Olivier Danot
- Institut Pasteur25‐28 rue du Docteur Roux75724Paris Cedex 15France
| | - Victor de Lorenzo
- Molecular Environmental Microbiology LaboratorySystems Biology ProgrammeCentro Nacional de BiotecnologiaC/Darwin n° 3, Campus de Cantoblanco28049MadridEspaña
| | - Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'Hôpital75013ParisFrance
- The School of Biomedical SciencesLi Kashing Faculty of MedicineHong Kong University21, Sassoon RoadPokfulamSAR Hong Kong
| |
Collapse
|
9
|
de Lorenzo V. Evolutionary tinkering vs. rational engineering in the times of synthetic biology. LIFE SCIENCES, SOCIETY AND POLICY 2018; 14:18. [PMID: 30099657 PMCID: PMC6087506 DOI: 10.1186/s40504-018-0086-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 07/24/2018] [Indexed: 06/08/2023]
Abstract
Synthetic biology is not only a contemporary reformulation of the recombinant DNA technologies of the last 30 years, combined with descriptive language imported from electrical and industrial engineering. It is also a new way to interpret living systems and a statement of intent for the use and reprogramming of biological objects for human benefit. In this context, the notion of designer biology is often presented as opposed to natural selection following the powerful rationale formulated by François Jacob on evolution-as-tinkering. The onset of synthetic biology opens a different perspective by leaving aside the question about the evolutionary origin of biological phenomena and focusing instead on the relational logic and the material properties of the corresponding components that make biological system work as they do. Once a functional challenge arises, the solution space for the problem is not homogeneous but it has attractors that can be accessed either through random exploration (as evolution does) or rational design (as engineers do). Although these two paths (i.e. evolution and engineering) are essentially different, they can lead to solutions to specific mechanistic bottlenecks that frequently coincide or converge-and one can easily help to understand and improve the other. Alas, productive discussions on these matters are often contaminated by ideological preconceptions that prevent adoption of the engineering metaphor to understand and ultimately reshape living systems-as ambitioned by synthetic biology. Yet, some possible ways to overcome the impasse are feasible. In parallel to Monod's evolutionary paradox of teleo-logy (finality/purpose) vs. teleo-nomy (appearance of finality/purpose), a mechanistic paradox could be entertained between techno-logy (rational engineering) vs techno-nomy (appearance of rational engineering), all for the sake of understanding the relational logic that enables live systems to function as physico-chemical entities in time and space. This article thus proposes a radical vision of synthetic biology through the lens of the engineering metaphor.
Collapse
Affiliation(s)
- Víctor de Lorenzo
- Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, 28049, Madrid, Spain.
| |
Collapse
|
10
|
Schmidt M, Pei L, Budisa N. Xenobiology: State-of-the-Art, Ethics, and Philosophy of New-to-Nature Organisms. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:301-315. [PMID: 28567486 DOI: 10.1007/10_2016_14] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The basic chemical constitution of all living organisms in the context of carbon-based chemistry consists of a limited number of small molecules and polymers. Until the twenty-first century, biology was mainly an analytical science and has now reached a point where it merges with engineering science, paving the way for synthetic biology. One of the objectives of synthetic biology is to try to change the chemical compositions of living cells, that is, to create an artificial biological diversity, which in turn fosters a new sub-field of synthetic biology, xenobiology. In particular, the genetic code in living systems is based on highly standardized chemistry composed of the same "letters" or nucleotides as informational polymers (DNA, RNA) and the 20 amino acids which serve as basic building blocks for proteins. The universality of the genetic code enables not only vertical gene transfer within the same species but also horizontal gene transfer across biological taxa, which require a high degree of standardization and interconnectivity. Although some minor alterations of the standard genetic code are found in nature (e.g., proteins containing non-conical amino acids exist in nature, and some organisms use alternated coding systems), all structurally deep chemistry changes within living systems are generally lethal, making the creation of artificial biological system an extremely difficult challenge.In this context, one of the great challenges for bioscience is the development of a strategy for expanding the standard basic chemical repertoire of living cells. Attempts to alter the meaning of the genetic information stored in DNA as an informational polymer by changing the chemistry of the polymer (i.e., xeno-nucleic acids) or by changes in the genetic code have already yielded successful results. In the future this should enable the partial or full redirection of the biological information flow to generate "new" version(s) of the genetic code derived from the "old" biological world.In addition to the scientific challenges, the attempt to increase biochemical diversity also raises important ethical and philosophical issues. Although promotors of this branch of synthetic biology highlight the many potential applications to come (e.g., novel tools for diagnostics and fighting infection diseases), such developments could also bring risks affecting social, political, and other structures of nearly all societies.
Collapse
Affiliation(s)
- Markus Schmidt
- Biofaction KG, Kundmanngasse 39/12, Vienna, 1030, Austria.
| | - Lei Pei
- Biofaction KG, Kundmanngasse 39/12, Vienna, 1030, Austria
| | - Nediljko Budisa
- AK Biokatalyse, Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Straße 10, 10623, Berlin, Germany
| |
Collapse
|
11
|
The Cellular Chassis as the Basis for New Functionalities: Shortcomings and Requirements. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
|
12
|
de Lorenzo V, Sekowska A, Danchin A. Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 2014; 39:96-119. [PMID: 25227915 DOI: 10.1111/1574-6976.12089] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In this review, we examine how bacterial metabolism is shaped by chemical constraints acting on the material and dynamic layout of enzymatic networks and beyond. These are moulded not only for optimisation of given metabolic objectives (e.g. synthesis of a particular amino acid or nucleotide) but also for curbing the detrimental reactivity of chemical intermediates. Besides substrate channelling, toxicity is avoided by barriers to free diffusion (i.e. compartments) that separate otherwise incompatible reactions, along with ways for distinguishing damaging vs. harmless molecules. On the other hand, enzymes age and their operating lifetime must be tuned to upstream and downstream reactions. This time dependence of metabolic pathways creates time-linked information, learning and memory. These features suggest that the physical structure of existing biosystems, from operon assemblies to multicellular development may ultimately stem from the need to restrain chemical damage and limit the waste inherent to basic metabolic functions. This provides a new twist of our comprehension of fundamental biological processes in live systems as well as practical take-home lessons for the forward DNA-based engineering of novel biological objects.
Collapse
Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología CSIC, Cantoblanco-Madrid, Spain
| | - Agnieszka Sekowska
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Antoine Danchin
- AMAbiotics SAS, Institut du Cerveau et de la Moëlle Épinière, Hôpital de la Pitié-Salpêtrière, Paris, France
| |
Collapse
|
13
|
Jiménez JI, Pérez-Pantoja D, Chavarría M, Díaz E, de Lorenzo V. A second chromosomal copy of thecatAgene endowsPseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environ Microbiol 2014; 16:1767-78. [DOI: 10.1111/1462-2920.12361] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 12/10/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Jose I. Jiménez
- Centro de Investigaciones Biológicas; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Danilo Pérez-Pantoja
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Max Chavarría
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Eduardo Díaz
- Centro de Investigaciones Biológicas; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| | - Víctor de Lorenzo
- Centro Nacional de Biotecnología; Consejo Superior de Investigaciones Científicas; 28049 Madrid Spain
| |
Collapse
|
14
|
Douglas CMW, Stemerding D. Special issue editorial: synthetic biology, global health, and its global governance. SYSTEMS AND SYNTHETIC BIOLOGY 2013; 7:63-6. [PMID: 24432143 DOI: 10.1007/s11693-013-9120-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 07/11/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Conor M W Douglas
- Technology Assessment, Rathenau Institute, 2593 HW The Hague, The Netherlands ; Collaborations for Outcomes Research and Evaluation, Faculty of Pharmaceutical Sciences, University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3 Canada
| | - Dirk Stemerding
- Technology Assessment, Rathenau Institute, 2593 HW The Hague, The Netherlands
| |
Collapse
|
15
|
|
16
|
Pei L, Bar‐Yam S, Byers‐Corbin J, Casagrande R, Eichler F, Lin A, Österreicher M, Regardh PC, Turlington RD, Oye KA, Torgersen H, Guan Z, Wei W, Schmidt M. Regulatory Frameworks for Synthetic Biology. Synth Biol (Oxf) 2012. [DOI: 10.1002/9783527659296.ch5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
17
|
de Las Heras A, Chavarría M, de Lorenzo V. Association of dnt genes of Burkholderia sp. DNT with the substrate-blind regulator DntR draws the evolutionary itinerary of 2,4-dinitrotoluene biodegradation. Mol Microbiol 2011; 82:287-99. [PMID: 21923773 DOI: 10.1111/j.1365-2958.2011.07825.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The regulation of the DNT pathway for biodegradation of 2,4-dinitrotoluene of Burkholderia sp. DNT has been examined by exporting each of its components to Pseudomonas putida KT2440. The cognate regulator DntR does not respond to the pathway substrate, but to the non-substrate salicylate. In order to examine whether such a response to an unrelated inducer was specific or rather a vestige of a previous evolutionary stage, the complete dnt complement or parts of it were expressed functionally for accumulation of various metabolic intermediates. Their effect on expression of dnt genes was then followed both biochemically and by means of a luminescent reporter engineered in the surrogate host. DntR was not only unresponsive to DNT biodegradation products, but it also failed to influence expression of dnt genes at all. Comparison of the dntR/dntA divergent promoter region with similar ones found in various catabolic systems indicated that the leading segment of the DNT biodegradation pathway evolved from a matching portion of naphthalene biodegradation routes existing in other bacteria. That a useless but still active transcriptional factor occurs along enzymes that have already evolved a new substrate specificity suggests that emergence of novel catalytic abilities precedes their submission to cognate regulatory devices, not vice versa.
Collapse
Affiliation(s)
- Aitor de Las Heras
- Systems Biology Program, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
| | | | | |
Collapse
|
18
|
Jaeger L, Calkins ER. Downward causation by information control in micro-organisms. Interface Focus 2011; 2:26-41. [PMID: 23386958 DOI: 10.1098/rsfs.2011.0045] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 08/30/2011] [Indexed: 11/12/2022] Open
Abstract
The concepts of functional equivalence classes and information control in living systems are useful to characterize downward (or top-down) causation by feedback information control in synthetic biology. Herein, we re-analyse published experiments of microbiology and synthetic biology that demonstrate the existence of several classes of functional equivalence in microbial organisms. Classes of functional equivalence from the bacterial operating system, which processes and controls the information encoded in the genome, can readily be interpreted as strong evidence, if not demonstration, of top-down causation (TDC) by information control. The proposed biological framework reveals how this type of causality is put in action in the cellular operating system. Considerations on TDC by information control and adaptive selection can be useful for synthetic biology by delineating the irreducible set of properties that characterizes living systems. Through a 'retro-synthetic' biology approach, these considerations could contribute to identifying the constraints behind the emergence of molecular complexity during the evolution of an ancient RNA/peptide world into a modern DNA/RNA/protein world. In conclusion, we propose TDCs by information control and adaptive selection as the two types of downward causality absolutely necessary for life.
Collapse
Affiliation(s)
- Luc Jaeger
- Department of Chemistry and Biochemistry , University of California , Santa Barbara, CA 93106-9510 , USA ; Biomolecular Science and Engineering Program , University of California , Santa Barbara, CA 93106-9510 , USA
| | | |
Collapse
|
19
|
Schmidt M, Pei L. Synthetic toxicology: where engineering meets biology and toxicology. Toxicol Sci 2010; 120 Suppl 1:S204-24. [PMID: 21068213 DOI: 10.1093/toxsci/kfq339] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
This article examines the implications of synthetic biology (SB) for toxicological sciences. Starting with a working definition of SB, we describe its current subfields, namely, DNA synthesis, the engineering of DNA-based biological circuits, minimal genome research, attempts to construct protocells and synthetic cells, and efforts to diversify the biochemistry of life through xenobiology. Based on the most important techniques, tools, and expected applications in SB, we describe the ramifications of SB for toxicology under the label of synthetic toxicology. We differentiate between cases where SB offers opportunities for toxicology and where SB poses challenges for toxicology. Among the opportunities, we identified the assistance of SB to construct novel toxicity testing platforms, define new toxicity-pathway assays, explore the potential of SB to improve in vivo biotransformation of toxins, present novel biosensors developed by SB for environmental toxicology, discuss cell-free protein synthesis of toxins, reflect on the contribution to toxic use reduction, and the democratization of toxicology through do-it-yourself biology. Among the identified challenges for toxicology, we identify synthetic toxins and novel xenobiotics, biosecurity and dual-use considerations, the potential bridging of toxic substances and infectious agents, and do-it-yourself toxin production.
Collapse
Affiliation(s)
- Markus Schmidt
- Organization for International Dialogue and Conflict Management, Biosafety Working Group, 1070 Vienna, Austria.
| | | |
Collapse
|
20
|
Danchin A. A challenge to vaccinology: living organisms trap information. Vaccine 2009; 27 Suppl 6:G13-6. [PMID: 20006133 PMCID: PMC7115390 DOI: 10.1016/j.vaccine.2009.10.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 10/11/2009] [Accepted: 10/14/2009] [Indexed: 11/03/2022]
Abstract
Life couples reproduction of the cell machinery with replication of the genetic program. Both processes are linked to the expression of some information. Over time, reproduction can enhance the information of the machine. We show that accumulation of valuable information results from degradative processes required to make room for novel entities. Degradation systems act as Maxwell's demons, using energy not to make room per se, but to prevent degradation of what has some functional features. This myopic process will accumulate information, whatever its source, in a ratchet-like manner. The consequence is that genes acquired by horizontal transfer as well as viruses will tend to perpetuate in niches where they are functional, creating recurrent conditions for emergence of diseases.
Collapse
Affiliation(s)
- Antoine Danchin
- CEA/Genoscope, Amabiotics, 2, rue Gaston Crémieux, 91057 Evry Cedex, France.
| |
Collapse
|
21
|
Affiliation(s)
- Manuel Porcar
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, València, Spain
| | | |
Collapse
|