From bioputing to bactoputing: computing with bacteria

The relevance of certain biological materials and processes to computing or bioputing has been explored for decades. These materials include DNA, RNA, enzymes and other proteins whilst the processes include transcription and translation (as well as the control of these processes by protein and by small RNA) and signal transduction. Recently, other directions have been envisaged using bacteria themselves as living computers. Generally, these uses of bacteria fall within the classical paradigm of computing. Computer scientists, however, have a variety of problems to which they seek solutions whilst microbiologists are having new insights into the problems bacteria are solving and how they are solving them. Here, we envisage that bacteria might be used for new sorts of computing. These might be based on the capacity of bacteria to grow, move and adapt to a myriad different fickle environments as both individuals and as populations of both bacteria and bacteriophage. This new computing may extend to developing a new high level language appropriate to using populations of bacteria and bacteriophage. Such new principles might be based on the way that bacteria explore phenotype space via hyperstructure dynamics and the fundamental nature of the cell cycle. Here we offer a speculative tour of what we term bactoputing, namely the use of the natural behaviour of bacteria and other cells for calculating.

[1]  Franck Molina,et al.  Hyperstructures , genome analysis and I-cell , 2008 .

[2]  M. Laub,et al.  Specificity in two-component signal transduction pathways. , 2007, Annual review of genetics.

[3]  J. Stock,et al.  Signal Transduction: Networks and Integrated Circuits in Bacterial Cognition , 2007, Current Biology.

[4]  S. Carmeli,et al.  A Linear Pentapeptide Is a Quorum-Sensing Factor Required for mazEF-Mediated Cell Death in Escherichia coli , 2007, Science.

[5]  Emmanuelle Le Chatelier,et al.  Genetic Evidence for a Link Between Glycolysis and DNA Replication , 2007, PloS one.

[6]  T. Mančal,et al.  Evidence for wavelike energy transfer through quantum coherence in photosynthetic systems , 2007, Nature.

[7]  A. Grossman,et al.  Nutritional Control of Elongation of DNA Replication by (p)ppGpp , 2007, Cell.

[8]  Ivan Mijakovic,et al.  Tyrosine phosphorylation: an emerging regulatory device of bacterial physiology. , 2007, Trends in biochemical sciences.

[9]  Hajime Ishikawa,et al.  The 160-Kilobase Genome of the Bacterial Endosymbiont Carsonella , 2006, Science.

[10]  Patrick Amar,et al.  Steady‐state kinetic behaviour of functioning‐dependent structures , 2006, The FEBS journal.

[11]  Simon V. Avery,et al.  Microbial cell individuality and the underlying sources of heterogeneity , 2006, Nature Reviews Microbiology.

[12]  Ian Grainge,et al.  Tracking of controlled Escherichia coli replication fork stalling and restart at repressor‐bound DNA in vivo , 2006, The EMBO journal.

[13]  F. Blattner,et al.  Emergent Properties of Reduced-Genome Escherichia coli , 2006, Science.

[14]  Matthias Platzer,et al.  The analysis of cell division and cell wall synthesis genes reveals mutationally inactivated ftsQ and mraY in a protoplast-type L-form of Escherichia coli. , 2006, FEMS microbiology letters.

[15]  Doron Lancet,et al.  Compositional complementarity and prebiotic ecology in the origin of life , 2006, BioEssays : news and reviews in molecular, cellular and developmental biology.

[16]  Klaus-Peter Zauner,et al.  Robot Control: From Silicon Circuitry to Cells , 2006, BioADIT.

[17]  E. Ben-Jacob,et al.  Self-engineering capabilities of bacteria , 2006, Journal of The Royal Society Interface.

[18]  V. Norris,et al.  Poly-(R)-3-hydroxybutyrate and the pioneering work of Rosetta Natoli Reusch. , 2005, Cellular and molecular biology.

[19]  Vincent Noireaux,et al.  Toward an artificial cell based on gene expression in vesicles , 2005, Physical biology.

[20]  Georgios Skretas,et al.  A bacterial biosensor of endocrine modulators. , 2005, Journal of molecular biology.

[21]  Monya Baker,et al.  Better living through microbes , 2005, Nature Biotechnology.

[22]  S. Porwollik,et al.  Sensing wetness: a new role for the bacterial flagellum , 2005, The EMBO journal.

[23]  S. Basu,et al.  A synthetic multicellular system for programmed pattern formation , 2005, Nature.

[24]  T. den Blaauwen,et al.  Maturation of the Escherichia coli divisome occurs in two steps , 2005, Molecular microbiology.

[25]  Hiroshi Mizoguchi,et al.  Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome , 2004, Molecular microbiology.

[26]  Pasquale Stano,et al.  Approaches to semi-synthetic minimal cells: a review , 2005, Naturwissenschaften.

[27]  Vincent Noireaux,et al.  A vesicle bioreactor as a step toward an artificial cell assembly. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[28]  E. Winfree,et al.  Algorithmic Self-Assembly of DNA Sierpinski Triangles , 2004, PLoS biology.

[29]  Yaneer Bar-Yam,et al.  Theory predicts the uneven distribution of genetic diversity within species , 2004, Nature.

[30]  S. Leibler,et al.  Bacterial Persistence as a Phenotypic Switch , 2004, Science.

[31]  A. Moya,et al.  Determination of the Core of a Minimal Bacterial Gene Set , 2004, Microbiology and Molecular Biology Reviews.

[32]  H. Levine,et al.  Bacterial linguistic communication and social intelligence. , 2004, Trends in microbiology.

[33]  Roy H. Doi,et al.  Cellulosomes: plant-cell-wall-degrading enzyme complexes , 2004, Nature Reviews Microbiology.

[34]  K. Skarstad,et al.  Replication fork and SeqA focus distributions in Escherichia coli suggest a replication hyperstructure dependent on nucleotide metabolism , 2004, Molecular microbiology.

[35]  F. Taddei,et al.  Survival versus maintenance of genetic stability: a conflict of priorities during stress. , 2004, Research in microbiology.

[36]  E. Shapiro,et al.  An autonomous molecular computer for logical control of gene expression , 2004, Nature.

[37]  Zdena Palková,et al.  Multicellular microorganisms: laboratory versus nature , 2004, EMBO reports.

[38]  Camille Ripoll,et al.  Ion condensation and signal transduction. , 2004, BioEssays : news and reviews in molecular, cellular and developmental biology.

[39]  R. Weiss,et al.  Programmed population control by cell–cell communication and regulated killing , 2004, Nature.

[40]  J. Liao,et al.  Design of artificial cell-cell communication using gene and metabolic networks. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[41]  Ertugrul M. Ozbudak,et al.  Multistability in the lactose utilization network of Escherichia coli , 2004, Nature.

[42]  D. Raine,et al.  A Fission-Fusion Origin for Life , 1998, Origins of life and evolution of the biosphere.

[43]  Gilles Bernot,et al.  Questions for cell cyclists , 2004 .

[44]  M. Wall,et al.  Design of gene circuits: lessons from bacteria , 2004, Nature Reviews Genetics.

[45]  J. E. Cabrera,et al.  The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues , 2003, Molecular microbiology.

[46]  Yoichiro Ito,et al.  On the relation between fluctuation and response in biological systems , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[47]  Antoine Danchin,et al.  A strand‐specific model for chromosome segregation in bacteria , 2003, Molecular microbiology.

[48]  Eshel Ben-Jacob,et al.  Bacterial self–organization: co–enhancement of complexification and adaptability in a dynamic environment , 2003, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[49]  A. Ninfa,et al.  Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli , 2003, Cell.

[50]  S. Ehrlich,et al.  Essential Bacillus subtilis genes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Andrew Adamatzky,et al.  Collision-free path planning in the Belousov-Zhabotinsky medium assisted by a cellular automaton , 2002, Naturwissenschaften.

[52]  I. Booth,et al.  Stress and the single cell: intrapopulation diversity is a mechanism to ensure survival upon exposure to stress. , 2002, International journal of food microbiology.

[53]  Alessandra Carbone,et al.  Circuits and programmable self-assembling DNA structures , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[54]  J. Caballero,et al.  Ribonucleoside diphosphate reductase is a component of the replication hyperstructure in Escherichia coli , 2002, Molecular microbiology.

[55]  Franck Molina,et al.  Hyperstructures, Genome Analysis and I-Cells , 2002, Acta biotheoretica.

[56]  E. Shimoni,et al.  Stress, order and survival , 2002, Nature Reviews Molecular Cell Biology.

[57]  Philippe Marlière,et al.  Long term adaptation of a microbial population to a permanent metabolic constraint: overcoming thymineless death by experimental evolution of Escherichia coli , 2001, BMC biotechnology.

[58]  Daniel A. Wagenaar,et al.  The Neurally Controlled Animat: Biological Brains Acting with Simulated Bodies , 2001, Auton. Robots.

[59]  B. Bassler,et al.  Quorum sensing in bacteria. , 2001, Annual review of microbiology.

[60]  J. Vohradský,et al.  Genome resource utilization during prokaryotic development , 2001, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[61]  D. Bartel,et al.  Synthesizing life : Paths to unforeseeable science & technology , 2001 .

[62]  M Wakabayashi,et al.  Synthesis of functional protein in liposome. , 2001, Journal of bioscience and bioengineering.

[63]  D. Bartel,et al.  Synthesizing life , 2001, Nature.

[64]  H. McAdams,et al.  Global analysis of the genetic network controlling a bacterial cell cycle. , 2000, Science.

[65]  I. Sabanay,et al.  Ordered intracellular RecA-DNA assemblies: a potential site of in vivo RecA-mediated activities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[66]  L. Serrano,et al.  Engineering stability in gene networks by autoregulation , 2000, Nature.

[67]  W. R. Farmer,et al.  Improving lycopene production in Escherichia coli by engineering metabolic control , 2000, Nature Biotechnology.

[68]  P. Freestone,et al.  Effects of Calcium and Calcium Chelators on Growth and Morphology of Escherichia coli L-Form NC-7 , 2000, Journal of bacteriology.

[69]  M Conrad,et al.  Adaptive information processing in microtubule networks. , 2000, Bio Systems.

[70]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[71]  E Ben-Jacob,et al.  Lubricating bacteria model for branching growth of bacterial colonies. , 1998, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[72]  Akira Harata,et al.  Production of sound waves by bacterial cells and the response of bacterial cells to sound. , 1998, The Journal of general and applied microbiology.

[73]  Kim Holmstrøm,et al.  Non‐genetic population heterogeneity studied by in situ polymerase chain reaction , 1998, Molecular microbiology.

[74]  D. Seebach,et al.  Proof for a nonproteinaceous calcium-selective channel in Escherichia coli by total synthesis from (R)-3-hydroxybutanoic acid and inorganic polyphosphate. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[75]  Lov K. Grover Quantum Mechanics Helps in Searching for a Needle in a Haystack , 1997, quant-ph/9706033.

[76]  V. Norris,et al.  Do bacteria sing? Sonic intercellular communication between bacteria may reflect electromagnetic intracellular communication involving coherent collective vibrational modes that could integrate enzyme activities and gene expression , 1997, Molecular microbiology.

[77]  E. Koonin,et al.  A minimal gene set for cellular life derived by comparison of complete bacterial genomes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[78]  Tomohiko Kaneko,et al.  BACILLUS CARBONIPHILUS CELLS RESPOND TO GROWTH-PROMOTING PHYSICAL SIGNALS FROM CELLS OF HOMOLOGOUS AND HETEROLOGOUS BACTERIA , 1996 .

[79]  V. Norris,et al.  Autocatalytic gene expression occurs via transertion and membrane domain formation and underlies differentiation in bacteria: a model. , 1995, Journal of molecular biology.

[80]  M Conrad,et al.  Scaling of efficiency in programmable and non-programmable systems. , 1995, Bio Systems.

[81]  L M Adleman,et al.  Molecular computation of solutions to combinatorial problems. , 1994, Science.

[82]  D. Schomburg,et al.  Ribonucleoside-diphosphate reductase , 1994 .

[83]  R. Palmen,et al.  Physiological characterization of natural transformation in Acinetobacter calcoaceticus. , 1993, Journal of general microbiology.

[84]  D. Bray,et al.  Intracellular signalling as a parallel distributed process. , 1990, Journal of theoretical biology.

[85]  Peter J. Denning,et al.  Computing as a discipline , 1989, Computer.

[86]  René Thomas On the Relation Between the Logical Structure of Systems and Their Ability to Generate Multiple Steady States or Sustained Oscillations , 1981 .

[87]  P. Reichard,et al.  Ribonucleoside diphosphate reductase. Formation of active and inactive complexes of proteins B1 and B2. , 1969, Journal of molecular biology.

[88]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , 2022 .