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Clark KB. Ownership psychology as a "cognitive cell" adaptation: A minimalist model of microbial goods theory. Behav Brain Sci 2023; 46:e330. [PMID: 37813404 DOI: 10.1017/s0140525x23001498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Microbes perfect social interactions with intuitive logics and goal-directed reciprocity. These multilevel, cognition-resembling adaptations in Dictyostelid cellular molds enable individual-to-group viability through public/private bacterial farming and dynamic marketspaces. Like humans and animals, Dictyostelid livestock-ownership depends on environmental sensing, cooperation, and competition. Moreover, social-norm policing of cosmopolitan colonies coordinates farmer decisions, phenotypes, and ownership identities with bacteria herding, privatization, and consumption.
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Affiliation(s)
- Kevin B Clark
- Cures Within Reach, Chicago, IL, USA ; www.linkedin.com/pub/kevin-clark/58/67/19a; https://access-ci.org
- Felidae Conservation Fund, Mill Valley, CA, USA
- Expert Network, Penn Center for Innovation, University of Pennsylvania, Philadelphia, PA, USA
- Network for Life Detection (NfoLD), NASA Astrobiology Program, NASA Ames Research Center, Mountain View, CA, USA
- Multi-Omics and Systems Biology & Artificial Intelligence and Machine Learning Analysis Working Groups, NASA GeneLab, NASA Ames Research Center, Mountain View, CA, USA
- Frontier Development Lab, NASA Ames Research Center, Mountain View, CA, USA
- SETI Institute, Mountain View, CA, USA
- Peace Innovation Institute, Netherlands & Stanford University, Palo Alto, CA, USA
- Shared Interest Group for Natural and Artificial Intelligence (sigNAI), Max Planck Alumni Association, Berlin, Germany
- Biometrics and Nanotechnology Councils, Institute for Electrical and Electronics Engineers, New York, NY, USA
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2
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Kippenberger S, Pipa G, Steinhorst K, Zöller N, Kleemann J, Özistanbullu D, Kaufmann R, Scheller B. Learning in the Single-Cell Organism Physarum polycephalum: Effect of Propofol. Int J Mol Sci 2023; 24:ijms24076287. [PMID: 37047260 PMCID: PMC10094176 DOI: 10.3390/ijms24076287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Propofol belongs to a class of molecules that are known to block learning and memory in mammals, including rodents and humans. Interestingly, learning and memory are not tied to the presence of a nervous system. There are several lines of evidence indicating that single-celled organisms also have the capacity for learning and memory which may be considered as basal intelligence. Here, we introduce a new experimental model for testing the learning ability of Physarum polycephalum, a model organism frequently used to study single-celled “intelligence”. In this study, the impact of propofol on Physarum’s “intelligence” was tested. The model consists of a labyrinth of subsequent bifurcations in which food (oat flakes soaked with coconut oil-derived medium chain triglycerides [MCT] and soybean oil-derived long chain triglycerides [LCT]) or propofol in MCT/LCT) is placed in one of each Y-branch. In this setting, it was tested whether Physarum memorized the rewarding branch. We saw that Physarum was a quick learner when capturing the first bifurcations of the maze; thereafter, the effect decreased, perhaps due to reaching a state of satiety. In contrast, when oat flakes were soaked with propofol, Physarum’s preference for oat flakes declined significantly. Several possible actions, including the blocking of gamma-aminobutyric acid (GABA) receptor signaling, are suggested to account for this behavior, many of which can be tested in our new model.
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3
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Aqeel M, Ran J, Hu W, Irshad MK, Dong L, Akram MA, Eldesoky GE, Aljuwayid AM, Chuah LF, Deng J. Plant-soil-microbe interactions in maintaining ecosystem stability and coordinated turnover under changing environmental conditions. CHEMOSPHERE 2023; 318:137924. [PMID: 36682633 DOI: 10.1016/j.chemosphere.2023.137924] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/07/2023] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Ecosystem functions directly depend upon biophysical as well as biogeochemical reactions occurring at the soil-microbe-plant interface. Environment is considered as a major driver of any ecosystem and for the distributions of living organisms. Any changes in climate may potentially alter the composition of communities i.e., plants, soil microbes and the interactions between them. Since the impacts of global climate change are not short-term, it is indispensable to appraise its effects on different life forms including soil-microbe-plant interactions. This article highlights the crucial role that microbial communities play in interacting with plants under environmental disturbances, especially thermal and water stress. We reviewed that in response to the environmental changes, actions and reactions of plants and microbes vary markedly within an ecosystem. Changes in environment and climate like warming, CO2 elevation, and moisture deficiency impact plant and microbial performance, their diversity and ultimately community structure. Plant and soil feedbacks also affect interacting species and modify community composition. The interactive relationship between plants and soil microbes is critically important for structuring terrestrial ecosystems. The anticipated climate change is aggravating the living conditions for soil microbes and plants. The environmental insecurity and complications are not short-term and limited to any particular type of organism. We have appraised effects of climate change on the soil inhabiting microbes and plants in a broader prospect. This article highlights the unique qualities of tripartite interaction between plant-soil-microbe under climate change.
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Affiliation(s)
- Muhammad Aqeel
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China
| | - Jinzhi Ran
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China
| | - Weigang Hu
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China
| | - Muhammad Kashif Irshad
- Department of Environmental Sciences, Government College University Faisalabad, (38000), Pakistan
| | - Longwei Dong
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China
| | - Muhammad Adnan Akram
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China; Department of Materials Engineering, KU Leuven, Kasteelpark Arenberg 44, Leuven 3001, Belgium
| | - Gaber E Eldesoky
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Ahmed Muteb Aljuwayid
- Department of Chemistry, College of Science, King Saud University, P. O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Lai Fatt Chuah
- Faculty of Maritime Studies, Universiti Malaysia Terengganu, Terengganu, Malaysia.
| | - Jianming Deng
- State Key Laboratory of Grassland Agro-Ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, PR China.
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4
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Sims M. Self-Concern Across Scales: A Biologically Inspired Direction for Embodied Artificial Intelligence. Front Neurorobot 2022; 16:857614. [PMID: 35574229 PMCID: PMC9106101 DOI: 10.3389/fnbot.2022.857614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/16/2022] [Indexed: 12/02/2022] Open
Abstract
Intelligence in current AI research is measured according to designer-assigned tasks that lack any relevance for an agent itself. As such, tasks and their evaluation reveal a lot more about our intelligence than the possible intelligence of agents that we design and evaluate. As a possible first step in remedying this, this article introduces the notion of “self-concern,” a property of a complex system that describes its tendency to bring about states that are compatible with its continued self-maintenance. Self-concern, as argued, is the foundation of the kind of basic intelligence found across all biological systems, because it reflects any such system's existential task of continued viability. This article aims to cautiously progress a few steps closer to a better understanding of some necessary organisational conditions that are central to self-concern in biological systems. By emulating these conditions in embodied AI, perhaps something like genuine self-concern can be implemented in machines, bringing AI one step closer to its original goal of emulating human-like intelligence.
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5
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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6
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Bioluminescence and Photoreception in Unicellular Organisms: Light-Signalling in a Bio-Communication Perspective. Int J Mol Sci 2021; 22:ijms222111311. [PMID: 34768741 PMCID: PMC8582858 DOI: 10.3390/ijms222111311] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/12/2021] [Accepted: 10/13/2021] [Indexed: 12/13/2022] Open
Abstract
Bioluminescence, the emission of light catalysed by luciferases, has evolved in many taxa from bacteria to vertebrates and is predominant in the marine environment. It is now well established that in animals possessing a nervous system capable of integrating light stimuli, bioluminescence triggers various behavioural responses and plays a role in intra- or interspecific visual communication. The function of light emission in unicellular organisms is less clear and it is currently thought that it has evolved in an ecological framework, to be perceived by visual animals. For example, while it is thought that bioluminescence allows bacteria to be ingested by zooplankton or fish, providing them with favourable conditions for growth and dispersal, the luminous flashes emitted by dinoflagellates may have evolved as an anti-predation system against copepods. In this short review, we re-examine this paradigm in light of recent findings in microorganism photoreception, signal integration and complex behaviours. Numerous studies show that on the one hand, bacteria and protists, whether autotrophs or heterotrophs, possess a variety of photoreceptors capable of perceiving and integrating light stimuli of different wavelengths. Single-cell light-perception produces responses ranging from phototaxis to more complex behaviours. On the other hand, there is growing evidence that unicellular prokaryotes and eukaryotes can perform complex tasks ranging from habituation and decision-making to associative learning, despite lacking a nervous system. Here, we focus our analysis on two taxa, bacteria and dinoflagellates, whose bioluminescence is well studied. We propose the hypothesis that similar to visual animals, the interplay between light-emission and reception could play multiple roles in intra- and interspecific communication and participate in complex behaviour in the unicellular world.
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7
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Marunga J, Goo E, Kang Y, Hwang I. Identification of a Genetically Linked but Functionally Independent Two-Component System Important for Cell Division of the Rice Pathogen Burkholderia glumae. Front Microbiol 2021; 12:700333. [PMID: 34276634 PMCID: PMC8281045 DOI: 10.3389/fmicb.2021.700333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Bacterial two-component regulatory systems control the expression of sets of genes to coordinate physiological functions in response to environmental cues. Here, we report a genetically linked but functionally unpaired two-component system (TCS) comprising the sensor kinase GluS (BGLU_1G13350) and the response regulator GluR (BGLU_1G13360), which is critical for cell division in the rice pathogen Burkholderia glumae BGR1. The gluR null mutant, unlike the gluS mutant, formed filamentous cells in Lysogeny Broth medium and was sensitive to exposure to 42°C. Expression of genes responsible for cell division and cell-wall (dcw) biosynthesis in the gluR mutant was elevated at transcription levels compared with the wild type. GluR-His bound to the putative promoter regions of ftsA and ftsZ is involved in septum formation, indicating that repression of genes in the dcw cluster by GluR is critical for cell division in B. glumae. The gluR mutant did not form filamentous cells in M9 minimal medium, whereas exogenous addition of glutamine or glutamate to the medium induced filamentous cell formation. These results indicate that glutamine and glutamate influence GluR-mediated cell division in B. glumae, suggesting that GluR controls cell division of B. glumae in a nutrition-dependent manner. These findings provide insight into how the recognition of external signals by TCS affects the sophisticated molecular mechanisms involved in controlling bacterial cell division.
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Affiliation(s)
- Joan Marunga
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Eunhye Goo
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yongsung Kang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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8
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Pessione E. The Less Expensive Choice: Bacterial Strategies to Achieve Successful and Sustainable Reciprocal Interactions. Front Microbiol 2021; 11:571417. [PMID: 33584557 PMCID: PMC7873842 DOI: 10.3389/fmicb.2020.571417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/11/2020] [Indexed: 12/22/2022] Open
Abstract
Bacteria, the first organisms that appeared on Earth, continue to play a central role in ensuring life on the planet, both as biogeochemical agents and as higher organisms' symbionts. In the last decades, they have been employed both as bioremediation agents for cleaning polluted sites and as bioconversion effectors for obtaining a variety of products from wastes (including eco-friendly plastics and green energies). However, some recent reports suggest that bacterial biodiversity can be negatively affected by the present environmental crisis (global warming, soil desertification, and ocean acidification). This review analyzes the behaviors positively selected by evolution that render bacteria good models of sustainable practices (urgent in these times of climate change and scarcity of resources). Actually, bacteria display a tendency to optimize rather than maximize, to economize energy and building blocks (by using the same molecule for performing multiple functions), and to recycle and share metabolites, and these are winning strategies when dealing with sustainability. Furthermore, their ability to establish successful reciprocal relationships by means of anticipation, collective actions, and cooperation can also constitute an example highlighting how evolutionary selection favors behaviors that can be strategic to contain the present environmental crisis.
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Affiliation(s)
- Enrica Pessione
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
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9
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Hung TW. Nonhuman rationality: a predictive coding perspective. Cogn Process 2021; 22:353-362. [PMID: 33404900 DOI: 10.1007/s10339-020-01009-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
How can we rethink 'rationality' in the wake of animal and artificial intelligence studies? Can nonhuman systems be rational in any nontrivial sense? In this paper, we propose that all organisms, under certain circumstances, exhibit rationality to a diverse degree and aspect in the sense of the standard picture (SP): Their inferential processes conform to logic and probability rules. We first show that according to Calvo and Friston (J R Soc Interface 14(131):20170096, 2017) and Orlandi (2018), all biological systems must embody a top-down process (active inference) to minimize free energy. Next, based on Maddy's (Second philosophy, Oxford University Press, Oxford, 2007; The logical must: Wittgenstein on logic, Oxford University Press, Oxford, 2014) analysis, we argue that this inferential process conforms to logic and probability rules; thus, it satisfies the SP, which explains the rudimentary logic and arithmetic (e.g., categorizing and numbering) found among pigeons and mice. We also hold that the mammalian brain is only one among many ways of implementing rationality. Finally, we discuss data from microorganisms to support this view.
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Affiliation(s)
- Tzu-Wei Hung
- Institute of European and American Studies, Academia Sinica, Taipei City, Taiwan.
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10
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Brown AJP, Larcombe DE, Pradhan A. Thoughts on the evolution of Core Environmental Responses in yeasts. Fungal Biol 2020; 124:475-481. [PMID: 32389310 PMCID: PMC7232023 DOI: 10.1016/j.funbio.2020.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 12/18/2022]
Abstract
The model yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, display Core Environmental Responses (CERs) that include the induction of a core set of stress genes in response to diverse environmental stresses. CERs underlie the phenomenon of stress cross-protection, whereby exposure to one type of stress can provide protection against subsequent exposure to a second type of stress. CERs have probably arisen through the accumulation, over evolutionary time, of protective anticipatory responses (“adaptive prediction”). CERs have been observed in other evolutionarily divergent fungi but, interestingly, not in the pathogenic yeast, Candida albicans. We argue that this is because we have not looked in the right place. In response to specific host inputs, C. albicans does activate anticipatory responses that protect it against impending attack from the immune system. Therefore, we suggest that C. albicans has evolved a CER that reflects the environmental challenges it faces in host niches. We review Core Environmental Responses (CERs) in domesticated and pathogenic yeasts. CERs probably evolved through the accumulation of protective anticipatory responses. Evolutionarily diverse yeasts display CERs, but the pathogen, Candida albicans, does not. C. albicans has evolved an alternative CER that protects against immune clearance. This has implications for the investigation of CERs in other fungi.
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Affiliation(s)
- Alistair J P Brown
- MRC Centre for Medical Mycology, University of Exeter, Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
| | - Daniel E Larcombe
- MRC Centre for Medical Mycology, University of Exeter, Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| | - Arnab Pradhan
- MRC Centre for Medical Mycology, University of Exeter, Department of Biosciences, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
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11
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Regulatory rewiring through global gene regulations by PhoB and alarmone (p)ppGpp under various stress conditions. Microbiol Res 2019; 227:126309. [PMID: 31421713 DOI: 10.1016/j.micres.2019.126309] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/23/2019] [Accepted: 08/02/2019] [Indexed: 12/14/2022]
Abstract
The phosphorus availability in soil ranged from <0.01 to 1 ppm and found limiting for the utilization by plants. Hence, phosphate solubilizing bacteria (PSB) proficiently fulfill the phosphorus requirement of plants in an eco-friendly manner. The PSB encounter dynamic and challenging environmental conditions viz., high temperature, osmotic, acid, and climatic changes often hamper their activity and proficiency. The modern trend is shifting from isolation of the PSB to their genetic potentials and genome annotation not only for their better performance in the field trials but also to study their ability to cope up with stresses. In order to withstand environmental stress, bacteria need to restructure its metabolic network to ensure its survival. Pi starving condition response regulator (PhoB) and the mediator of stringent stress response alarmone (p)ppGpp known to regulate the global regulatory network of bacteria to provide balanced physiology under various stress condition. The current review discusses the global regulation and crosstalk of genes involved in phosphorus homeostasis, solubilization, and various stress response to fine tune the bacterial physiology. The knowledge of these network crosstalk help bacteria to respond efficiently to the challenging environmental parameters, and their physiological plasticity lead us to develop proficient long-lasting consortia for plant growth promotion.
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12
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Brown AJ, Gow NA, Warris A, Brown GD. Memory in Fungal Pathogens Promotes Immune Evasion, Colonisation, and Infection. Trends Microbiol 2019; 27:219-230. [DOI: 10.1016/j.tim.2018.11.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/19/2018] [Accepted: 11/01/2018] [Indexed: 12/20/2022]
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Biological evolution as defense of 'self'. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 142:54-74. [PMID: 30336184 DOI: 10.1016/j.pbiomolbio.2018.10.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 09/27/2018] [Accepted: 10/11/2018] [Indexed: 02/06/2023]
Abstract
Although the origin of self-referential consciousness is unknown, it can be argued that the instantiation of self-reference was the commencement of the living state as phenomenal experientiality. As self-referential cognition is demonstrated by all living organisms, life can be equated with the sustenance of cellular homeostasis in the continuous defense of 'self'. It is proposed that the epicenter of 'self' is perpetually embodied within the basic cellular form in which it was instantiated. Cognition-Based Evolution argues that all of biological and evolutionary development represents the perpetual autopoietic defense of self-referential basal cellular states of homeostatic preference. The means by which these states are attained and maintained is through self-referential measurement of information and its communication. The multicellular forms, either as biofilms or holobionts, represent the cellular attempt to achieve maximum states of informational distinction and energy efficiency through individual and collective means. In this frame, consciousness, self-consciousness and intelligence can be identified as forms of collective cellular phenotype directed towards the defense of fundamental cellular self-reference.
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Watahiki M, Trewavas A. Systems, variation, individuality and plant hormones. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 146:3-22. [PMID: 30312622 DOI: 10.1016/j.pbiomolbio.2018.10.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/06/2018] [Indexed: 02/02/2023]
Abstract
Inter-individual variation in plants and particularly in hormone content, figures strongly in evolution and behaviour. Homo sapiens and Arabidopsis exhibit similar and substantial phenotypic and molecular variation. Whereas there is a very substantial degree of hormone variation in mankind, reports of inter-individual variation in plant hormone content are virtually absent but are likely to be as large if not larger than that in mankind. Reasons for this absence are discussed. Using an example of inter-individual variation in ethylene content in ripening, the article shows how biological time is compressed by hormones. It further resolves an old issue of very wide hormone dose response that result directly from negative regulation in hormone (and light) transduction. Negative regulation is used because of inter-individual variability in hormone synthesis, receptors and ancillary proteins, a consequence of substantial genomic and environmental variation. Somatic mosaics have been reported for several plant tissues and these too contribute to tissue variation and wide variation in hormone response. The article concludes by examining what variation exists in gravitropic responses. There are multiple sensing systems of gravity vectors and multiple routes towards curvature. These are an aspect of the need for reliability in both inter-individual variation and unpredictable environments. Plant hormone inter-individuality is a new area for research and is likely to change appreciation of the mechanisms that underpin individual behaviour.
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Affiliation(s)
- Masaaki Watahiki
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Anthony Trewavas
- Institute of Plant Molecular Science, University of Edinburgh, Kings Buildings, Mayfield Road, Edinburgh, EH9 3 JH, Scotland, United Kingdom.
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15
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Baluška F, Miller, Jr WB. Senomic view of the cell: Senome versus Genome. Commun Integr Biol 2018; 11:1-9. [PMID: 30214674 PMCID: PMC6132427 DOI: 10.1080/19420889.2018.1489184] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/11/2018] [Indexed: 12/25/2022] Open
Abstract
In the legacy of Thomas Henry Huxley, and his 'epigenetic' philosophy of biology, cells are proposed to represent a trinity of three memory-storing media: Senome, Epigenome, and Genome that together comprise a cell-wide informational architecture. Our current preferential focus on the Genome needs to be complemented by a similar focus on the Epigenome and a here proposed Senome, representing the sum of all the sensory experiences of the cognitive cell and its sensing apparatus. Only then will biology be in a position to embrace the whole complexity of the eukaryotic cell, understanding its true nature which allows the communicative assembly of cells in the form of sentient multicellular organisms.
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Four domains: The fundamental unicell and Post-Darwinian Cognition-Based Evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 140:49-73. [PMID: 29685747 DOI: 10.1016/j.pbiomolbio.2018.04.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 04/12/2018] [Indexed: 02/07/2023]
Abstract
Contemporary research supports the viewpoint that self-referential cognition is the proper definition of life. From that initiating platform, a cohesive alternative evolutionary narrative distinct from standard Neodarwinism can be presented. Cognition-Based Evolution contends that biological variation is a product of a self-reinforcing information cycle that derives from self-referential attachment to biological information space-time with its attendant ambiguities. That information cycle is embodied through obligatory linkages among energy, biological information, and communication. Successive reiterations of the information cycle enact the informational architectures of the basic unicellular forms. From that base, inter-domain and cell-cell communications enable genetic and cellular variations through self-referential natural informational engineering and cellular niche construction. Holobionts are the exclusive endpoints of that self-referential cellular engineering as obligatory multicellular combinations of the essential Four Domains: Prokaryota, Archaea, Eukaryota and the Virome. Therefore, it is advocated that these Four Domains represent the perpetual object of the living circumstance rather than the visible macroorganic forms. In consequence, biology and its evolutionary development can be appraised as the continual defense of instantiated cellular self-reference. As the survival of cells is as dependent upon limitations and boundaries as upon any freedom of action, it is proposed that selection represents only one of many forms of cellular constraint that sustain self-referential integrity.
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Kippenberger S, Kleemann J, Kaufmann R, Meissner M. Acting without Central Agent—Considerations for a Self-Model at the Cellular Level. Front Hum Neurosci 2017; 11:191. [PMID: 28469568 PMCID: PMC5395625 DOI: 10.3389/fnhum.2017.00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/31/2017] [Indexed: 11/18/2022] Open
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Boisseau RP, Vogel D, Dussutour A. Habituation in non-neural organisms: evidence from slime moulds. Proc Biol Sci 2016; 283:20160446. [PMID: 27122563 PMCID: PMC4855389 DOI: 10.1098/rspb.2016.0446] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 04/06/2016] [Indexed: 11/12/2022] Open
Abstract
Learning, defined as a change in behaviour evoked by experience, has hitherto been investigated almost exclusively in multicellular neural organisms. Evidence for learning in non-neural multicellular organisms is scant, and only a few unequivocal reports of learning have been described in single-celled organisms. Here we demonstrate habituation, an unmistakable form of learning, in the non-neural organism Physarum polycephalum In our experiment, using chemotaxis as the behavioural output and quinine or caffeine as the stimulus, we showed that P. polycephalum learnt to ignore quinine or caffeine when the stimuli were repeated, but responded again when the stimulus was withheld for a certain time. Our results meet the principle criteria that have been used to demonstrate habituation: responsiveness decline and spontaneous recovery. To distinguish habituation from sensory adaptation or motor fatigue, we also show stimulus specificity. Our results point to the diversity of organisms lacking neurons, which likely display a hitherto unrecognized capacity for learning, and suggest that slime moulds may be an ideal model system in which to investigate fundamental mechanisms underlying learning processes. Besides, documenting learning in non-neural organisms such as slime moulds is centrally important to a comprehensive, phylogenetic understanding of when and where in the tree of life the earliest manifestations of learning evolved.
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Affiliation(s)
- Romain P Boisseau
- Research Center on Animal Cognition (CRCA), Center for Integrative Biology (CBI), Toulouse University, CNRS, UPS, 31062 Toulouse, France Ecole Normale Supérieure, 75005 Paris, France
| | - David Vogel
- Research Center on Animal Cognition (CRCA), Center for Integrative Biology (CBI), Toulouse University, CNRS, UPS, 31062 Toulouse, France Unit of Social Ecology, Université Libre de Bruxelles, 1050 Bruxelles, France
| | - Audrey Dussutour
- Research Center on Animal Cognition (CRCA), Center for Integrative Biology (CBI), Toulouse University, CNRS, UPS, 31062 Toulouse, France
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(Actino)Bacterial “intelligence”: using comparative genomics to unravel the information processing capacities of microbes. Curr Genet 2016; 62:487-98. [DOI: 10.1007/s00294-016-0569-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/20/2016] [Accepted: 01/22/2016] [Indexed: 01/24/2023]
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Calvo P, Baluška F. Conditions for minimal intelligence across eukaryota: a cognitive science perspective. Front Psychol 2015; 6:1329. [PMID: 26388822 PMCID: PMC4558474 DOI: 10.3389/fpsyg.2015.01329] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/19/2015] [Indexed: 11/29/2022] Open
Affiliation(s)
- Paco Calvo
- MINT Lab, Department of Philosophy, University of Murcia Murcia, Spain
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Lyon P. The cognitive cell: bacterial behavior reconsidered. Front Microbiol 2015; 6:264. [PMID: 25926819 PMCID: PMC4396460 DOI: 10.3389/fmicb.2015.00264] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 03/16/2015] [Indexed: 01/28/2023] Open
Abstract
Research on how bacteria adapt to changing environments underlies the contemporary biological understanding of signal transduction (ST), and ST provides the foundation of the information-processing approach that is the hallmark of the ‘cognitive revolution,’ which began in the mid-20th century. Yet cognitive scientists largely remain oblivious to research into microbial behavior that might provide insights into problems in their own domains, while microbiologists seem equally unaware of the potential importance of their work to understanding cognitive capacities in multicellular organisms, including vertebrates. Evidence in bacteria for capacities encompassed by the concept of cognition is reviewed. Parallels exist not only at the heuristic level of functional analogue, but also at the level of molecular mechanism, evolution and ecology, which is where fruitful cross-fertilization among disciplines might be found.
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Affiliation(s)
- Pamela Lyon
- Southgate Institute for Health, Society and Equity, School of Medicine, Flinders University Adelaide, SA, Australia
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Li J, Zheng X, Guo X, Qi L, Dong X. Characterization of an archaeal two-component system that regulates methanogenesis in Methanosaeta harundinacea. PLoS One 2014; 9:e95502. [PMID: 24748383 PMCID: PMC3991700 DOI: 10.1371/journal.pone.0095502] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Accepted: 03/27/2014] [Indexed: 02/02/2023] Open
Abstract
Two-component signal transduction systems (TCSs) are a major mechanism used by bacteria in response to environmental changes. Although many sequenced archaeal genomes encode TCSs, they remain poorly understood. Previously, we reported that a methanogenic archaeon, Methanosaeta harundinacea, encodes FilI, which synthesizes carboxyl-acyl homoserine lactones, to regulate transitions of cellular morphology and carbon metabolic fluxes. Here, we report that filI, the cotranscribed filR2, and the adjacent filR1 constitute an archaeal TCS. FilI possesses a cytoplasmic kinase domain (histidine kinase A and histidine kinase-like ATPase) and its cognate response regulator. FilR1 carries a receiver (REC) domain coupled with an ArsR-related domain with potential DNA-binding ability, while FilR2 carries only a REC domain. In a phosphorelay assay, FilI was autophosphorylated and specifically transferred the phosphoryl group to FilR1 and FilR2, confirming that the three formed a cognate TCS. Through chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR) using an anti-FilR1 antibody, FilR1 was shown to form in vivo associations with its own promoter and the promoter of the filI-filR2 operon, demonstrating a regulatory pattern common among TCSs. ChIP-qPCR also detected FilR1 associations with key genes involved in acetoclastic methanogenesis, acs4 and acs1. Electrophoretic mobility shift assays confirmed the in vitro tight binding of FilR1 to its own promoter and those of filI-filR2, acs4, and mtrABC. This also proves the DNA-binding ability of the ArsR-related domain, which is found primarily in Archaea. The archaeal promoters of acs4, filI, acs1, and mtrABC also initiated FilR1-modulated expression in an Escherichia coli lux reporter system, suggesting that FilR1 can up-regulate both archaeal and bacterial transcription. In conclusion, this work identifies an archaeal FilI/FilRs TCS that regulates the methanogenesis of M. harundinacea.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaopeng Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lei Qi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
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Clark KB. Biotic activity of Ca(2+)-modulating non-traditional antimicrobial and -viral agents. Front Microbiol 2013; 4:381. [PMID: 24376441 PMCID: PMC3859912 DOI: 10.3389/fmicb.2013.00381] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 11/24/2013] [Indexed: 01/23/2023] Open
Affiliation(s)
- Kevin B Clark
- Research and Development Service, Veterans Affairs Greater Los Angeles Healthcare System Los Angeles, CA, USA
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Baluska F, Mancuso S. Deep evolutionary origins of neurobiology: Turning the essence of 'neural' upside-down. Commun Integr Biol 2011; 2:60-5. [PMID: 19513267 DOI: 10.4161/cib.2.1.7620] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 12/15/2008] [Indexed: 01/17/2023] Open
Abstract
It is generally assumed, both in common-sense argumentations and scientific concepts, that brains and neurons represent late evolutionary achievements which are present only in more advanced animals. Here we overview recently published data clearly revealing that our understanding of bacteria, unicellular eukaryotic organisms, plants, brains and neurons, rooted in the Aristotelian philosophy is flawed. Neural aspects of biological systems are obvious already in bacteria and unicellular biological units such as sexual gametes and diverse unicellular eukaryotic organisms. Altogether, processes and activities thought to represent evolutionary 'recent' specializations of the nervous system emerge rather to represent ancient and fundamental cell survival processes.
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Dobrzyński M, Bernatowicz P, Kloc M, Kubiak JZ. Evolution of bet-hedging mechanisms in cell cycle and embryo development stimulated by weak linkage of stochastic processes. Results Probl Cell Differ 2011; 53:11-30. [PMID: 21630139 DOI: 10.1007/978-3-642-19065-0_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Our current understanding of the origin and evolution of the cell cycle is largely filled with gaps and unresolved questions. Numerous similarities between the processes comprising the cell cycle in distant organisms from the Pro- and Eukaryota kingdoms provide some clues about the course that evolution has taken. Contemporary Prokaryotes and Eukaryotes regulate their cell cycles in a quite similar way, using a master oscillator that regulates cell division. Despite this striking similarity, they use entirely different molecules for this purpose. The necessity to keep the master oscillator intact for the survival of every cell/organism allows evolutionary changes in only the secondary mechanisms and processes of the cell cycle. This is especially clear in oocytes and embryos, which have a direct impact on the reproductive success of an adult organism. Here, we present examples of cues driving such mild evolutionary changes of certain aspects of cell cycle progression in oocytes and early embryos. We suggest that weak linkages between core processes that rely on randomness (stochasticity) have led to the evolution of strategies increasing fitness similar to bet-hedging, a stochastic-based survival strategy of risk minimization widely implemented by populations of bacteria, yeast, arthropods, and birds. Stochastic diversification of phenotypes by isogenic cells increases their fitness in unpredictable environments and improves their survival rate upon exposure to stress, a trait beneficial in evading antibiotic treatment by bacteria or withstanding chemotherapy by cancer cells. The evolution of bet-hedging has been observed experimentally for bacteria and attributed to specific molecular mechanisms involved in this strategy. In this chapter, we set out to answer whether similar strategies could have evolved at the level of oocytes and embryos. We indicate possible evolutionary cues capable of realizing bet-hedging-like mechanisms.
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Affiliation(s)
- Maciej Dobrzyński
- Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland
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Sirota-Madi A, Olender T, Helman Y, Ingham C, Brainis I, Roth D, Hagi E, Brodsky L, Leshkowitz D, Galatenko V, Nikolaev V, Mugasimangalam RC, Bransburg-Zabary S, Gutnick DL, Lancet D, Ben-Jacob E. Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments. BMC Genomics 2010; 11:710. [PMID: 21167037 PMCID: PMC3012674 DOI: 10.1186/1471-2164-11-710] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 12/17/2010] [Indexed: 12/05/2022] Open
Abstract
Background The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae) have been sequenced. However, no genomic data is available on the Paenibacillus species with pattern-forming and complex social motility. Here we report the de novo genome sequence of this Gram-positive, soil-dwelling, sporulating bacterium. Results The complete P. vortex genome was sequenced by a hybrid approach using 454 Life Sciences and Illumina, achieving a total of 289× coverage, with 99.8% sequence identity between the two methods. The sequencing results were validated using a custom designed Agilent microarray expression chip which represented the coding and the non-coding regions. Analysis of the P. vortex genome revealed 6,437 open reading frames (ORFs) and 73 non-coding RNA genes. Comparative genomic analysis with 500 complete bacterial genomes revealed exceptionally high number of two-component system (TCS) genes, transcription factors (TFs), transport and defense related genes. Additionally, we have identified genes involved in the production of antimicrobial compounds and extracellular degrading enzymes. Conclusions These findings suggest that P. vortex has advanced faculties to perceive and react to a wide range of signaling molecules and environmental conditions, which could be associated with its ability to reconfigure and replicate complex colony architectures. Additionally, P. vortex is likely to serve as a rich source of genes important for agricultural, medical and industrial applications and it has the potential to advance the study of social microbiology within Gram-positive bacteria.
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Affiliation(s)
- Alexandra Sirota-Madi
- The Sackler School of Physics and Astronomy, Tel Aviv University, PO Box 39040, Tel Aviv 69978, Israel
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Clark KB. Bose–Einstein condensates form in heuristics learned by ciliates deciding to signal ‘social’ commitments. Biosystems 2010; 99:167-78. [DOI: 10.1016/j.biosystems.2009.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Revised: 10/22/2009] [Accepted: 10/27/2009] [Indexed: 10/20/2022]
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29
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Clark KB. Origins of learned reciprocity in solitary ciliates searching grouped ‘courting’ assurances at quantum efficiencies. Biosystems 2010; 99:27-41. [DOI: 10.1016/j.biosystems.2009.08.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2009] [Revised: 08/11/2009] [Accepted: 08/11/2009] [Indexed: 10/20/2022]
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Hong Y, Velegol D, Chaturvedi N, Sen A. Biomimetic behavior of synthetic particles: from microscopic randomness to macroscopic control. Phys Chem Chem Phys 2009; 12:1423-35. [PMID: 20126754 DOI: 10.1039/b917741h] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Randomness is an inherent property of biological systems. In contrast, randomness has been mostly avoided in designing synthetic or artificial systems. Particularly, in designing micro/nano-motors, some researchers have successfully used external fields to gain deterministic control over the directionality of the objects, which otherwise move in completely random directions due to Brownian motion. However, a partial control that preserves a certain degree of randomness can be very useful in certain applications of micro/nano-motors. In this Perspective we review the current progress in establishing autonomous motion of micro/nano-particles that possess controlled randomness, provide insight into the phenomena where macroscopic order originates from microscopic disorder and discuss the resemblance between these artificial systems and biological emergent/collective behaviors.
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Affiliation(s)
- Yiying Hong
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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31
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Emergence of Animals from Heat Engines – Part 1. Before the Snowball Earths. ENTROPY 2009. [DOI: 10.3390/e11030463] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Groban ES, Clarke EJ, Salis HM, Miller SM, Voigt CA. Kinetic buffering of cross talk between bacterial two-component sensors. J Mol Biol 2009; 390:380-93. [PMID: 19445950 DOI: 10.1016/j.jmb.2009.05.007] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Revised: 05/05/2009] [Accepted: 05/07/2009] [Indexed: 11/26/2022]
Abstract
Two-component systems are a class of sensors that enable bacteria to respond to environmental and cell-state signals. The canonical system consists of a membrane-bound sensor histidine kinase that autophosphorylates in response to a signal and transfers the phosphate to an intracellular response regulator. Bacteria typically have dozens of two-component systems. The key questions are whether these systems are linear and, if they are, how cross talk between systems is buffered. In this work, we studied the EnvZ/OmpR and CpxA/CpxR systems from Escherichia coli, which have been shown previously to exhibit slow cross talk in vitro. Using in vitro radiolabeling and a rapid quenched-flow apparatus, we experimentally measured 10 biochemical parameters capturing the cognate and non-cognate phosphotransfer reactions between the systems. These data were used to parameterize a mathematical model that was used to predict how cross talk is affected as different genes are knocked out. It was predicted that significant cross talk between EnvZ and CpxR only occurs for the triple mutant DeltaompR DeltacpxA DeltaactA-pta. All seven combinations of these knockouts were made to test this prediction and only the triple mutant demonstrated significant cross talk, where the cpxP promoter was induced 280-fold upon the activation of EnvZ. Furthermore, the behavior of the other knockouts agrees with the model predictions. These results support a kinetic model of buffering where both the cognate bifunctional phosphatase activity and the competition between regulator proteins for phosphate prevent cross talk in vivo.
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Affiliation(s)
- Eli S Groban
- University of California, San Francisco, 94158, USA
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Siryaporn A, Goulian M. Cross-talk suppression between the CpxA-CpxR and EnvZ-OmpR two-component systems in E. coli. Mol Microbiol 2008; 70:494-506. [PMID: 18761686 DOI: 10.1111/j.1365-2958.2008.06426.x] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many bacteria possess large numbers of two-component signalling systems, which are composed of histidine kinase-response regulator pairs. The high level of sequence similarity between some systems raises the possibility of undesired cross-talk between a histidine kinase and a non-cognate response regulator. Although molecular specificity ensures that phospho-transfer occurs primarily between correct partners, even a low level of inappropriate cross-talk could lead to unacceptable levels of noise or interference in signal transduction. To explore mechanisms that provide insulation against such interference, we have examined cross-talk between the histidine kinase CpxA and non-cognate response regulator OmpR in Escherichia coli. Our results show that there are two mechanisms that suppress cross-talk between these two proteins, which depend on the corresponding cognate partners CpxR and EnvZ and on the bifunctional nature of the histidine kinases CpxA and EnvZ. When cross-talk is detectable, we find it is independent of CpxA stimulus. We also show that cross-talk suppression leads to mutational robustness, i.e. it masks the effects of mutations that would otherwise lead to increased cross-talk. The mechanisms that provide insulation against interference described here may be applicable to many other two-component systems.
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Affiliation(s)
- Albert Siryaporn
- Department of Physics, University of Pennsylvania, Philadelphia, PA 19104, USA
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Denton AM, Wu J, Townsend MK, Sule P, Prüss BM. Relating gene expression data on two-component systems to functional annotations in Escherichia coli. BMC Bioinformatics 2008; 9:294. [PMID: 18578884 PMCID: PMC2478693 DOI: 10.1186/1471-2105-9-294] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Accepted: 06/25/2008] [Indexed: 11/30/2022] Open
Abstract
Background Obtaining physiological insights from microarray experiments requires computational techniques that relate gene expression data to functional information. Traditionally, this has been done in two consecutive steps. The first step identifies important genes through clustering or statistical techniques, while the second step assigns biological functions to the identified groups. Recently, techniques have been developed that identify such relationships in a single step. Results We have developed an algorithm that relates patterns of gene expression in a set of microarray experiments to functional groups in one step. Our only assumption is that patterns co-occur frequently. The effectiveness of the algorithm is demonstrated as part of a study of regulation by two-component systems in Escherichia coli. The significance of the relationships between expression data and functional annotations is evaluated based on density histograms that are constructed using product similarity among expression vectors. We present a biological analysis of three of the resulting functional groups of proteins, develop hypotheses for further biological studies, and test one of these hypotheses experimentally. A comparison with other algorithms and a different data set is presented. Conclusion Our new algorithm is able to find interesting and biologically meaningful relationships, not found by other algorithms, in previously analyzed data sets. Scaling of the algorithm to large data sets can be achieved based on a theoretical model.
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Affiliation(s)
- Anne M Denton
- Department of Computer Science and Operations Research, North Dakota State University, Fargo, ND 58105, USA.
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Wolf DM, Fontaine-Bodin L, Bischofs I, Price G, Keasling J, Arkin AP. Memory in microbes: quantifying history-dependent behavior in a bacterium. PLoS One 2008; 3:e1700. [PMID: 18324309 PMCID: PMC2264733 DOI: 10.1371/journal.pone.0001700] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Accepted: 01/28/2008] [Indexed: 11/19/2022] Open
Abstract
Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These “memory” effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesis and estimate the capacity of these systems and growth dynamics to ‘remember’ 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy.
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Affiliation(s)
- Denise M. Wolf
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- * To whom correspondence should be addressed. E-mail: (DW); (AA)
| | - Lisa Fontaine-Bodin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Ilka Bischofs
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Gavin Price
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Jay Keasling
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- Department of Chemical Engineering, University of California, Berkeley, California, United States of America
| | - Adam P. Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Department of Bioengineering, University of California, Berkeley, California, United States of America
- * To whom correspondence should be addressed. E-mail: (DW); (AA)
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Baluška F, Mancuso S. Plant neurobiology as a paradigm shift not only in the plant sciences. PLANT SIGNALING & BEHAVIOR 2007; 2:205-7. [PMID: 19516989 PMCID: PMC2634129 DOI: 10.4161/psb.2.4.4550] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2007] [Accepted: 06/07/2007] [Indexed: 05/07/2023]
Abstract
Plants are complex living beings, extremely sensitive to environmental factors, continuously adapting to the ever changing environment. Emerging research document that plants sense, memorize, and process experiences and use this information for their adaptive behavior and evolution. As any other living and evolving systems, plants act as knowledge accumulating systems. Neuronal informational systems are behind this concept of organisms as knowledge accumulating systems because they allow the most rapid and efficient adaptive responses to changes in environment. Therefore, it should not be surprising that neuronal computation is not limited to animal brains but is used also by bacteria and plants. The journal, Plant Signaling & Behavior, was launched as a platform for exchanging information and fostering research on plant neurobiology in order to allow our understanding of plants in their whole integrated, communicative, and behavioral complexity.I always go by official statistics because they are very carefully compounded and, even if they are false, we have no others ... approximately Jaroslav Hasek, 1911.
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Prosser JI, Bohannan BJM, Curtis TP, Ellis RJ, Firestone MK, Freckleton RP, Green JL, Green LE, Killham K, Lennon JJ, Osborn AM, Solan M, van der Gast CJ, Young JPW. The role of ecological theory in microbial ecology. Nat Rev Microbiol 2007; 5:384-92. [PMID: 17435792 DOI: 10.1038/nrmicro1643] [Citation(s) in RCA: 534] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.
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Affiliation(s)
- James I Prosser
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 3UU, Scotland, UK.
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Inoue T, Shingaki R, Hirose S, Waki K, Mori H, Fukui K. Genome-wide screening of genes required for swarming motility in Escherichia coli K-12. J Bacteriol 2007; 189:950-7. [PMID: 17122336 PMCID: PMC1797309 DOI: 10.1128/jb.01294-06] [Citation(s) in RCA: 145] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 11/14/2006] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli K-12 has the ability to migrate on semisolid media by means of swarming motility. A systematic and comprehensive collection of gene-disrupted E. coli K-12 mutants (the Keio collection) was used to identify the genes involved in the swarming motility of this bacterium. Of the 3,985 nonessential gene mutants, 294 were found to exhibit a strongly repressed-swarming phenotype. Further, 216 of the 294 mutants displayed no significant defects in swimming motility; therefore, the 216 genes were considered to be specifically associated with the swarming phenotype. The swarming-associated genes were classified into various functional categories, indicating that swarming is a specialized form of motility that requires a wide variety of cellular activities. These genes include genes for tricarboxylic acid cycle and glucose metabolism, iron acquisition, chaperones and protein-folding catalysts, signal transduction, and biosynthesis of cell surface components, such as lipopolysaccharide, the enterobacterial common antigen, and type 1 fimbriae. Lipopolysaccharide and the enterobacterial common antigen may be important surface-acting components that contribute to the reduction of surface tension, thereby facilitating the swarm migration in the E. coli K-12 strain.
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MESH Headings
- Antigens, Bacterial/genetics
- Antigens, Bacterial/physiology
- Citric Acid Cycle/genetics
- Citric Acid Cycle/physiology
- Escherichia coli/genetics
- Escherichia coli/physiology
- Escherichia coli/ultrastructure
- Escherichia coli Proteins/chemistry
- Escherichia coli Proteins/genetics
- Escherichia coli Proteins/physiology
- Fimbriae, Bacterial/chemistry
- Fimbriae, Bacterial/genetics
- Fimbriae, Bacterial/physiology
- Gene Deletion
- Genes, Bacterial
- Genome, Bacterial
- Glucose/metabolism
- Microscopy, Electron, Transmission
- Molecular Chaperones/genetics
- Molecular Chaperones/physiology
- Polysaccharides, Bacterial/metabolism
- Protein Folding
- Signal Transduction/genetics
- Signal Transduction/physiology
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Affiliation(s)
- Tetsuyoshi Inoue
- Department of Oral Microbiology, Graduate School of Medicine, Dentistry, and Pharmaceutical Sciences, Okayama University, 2-5-1, Shikata, Okayama 700-8525, Japan.
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Tsang P, Merritt J, Shi W, Qi F. IrvA-dependent and IrvA-independent pathways for mutacin gene regulation in Streptococcus mutans. FEMS Microbiol Lett 2006; 261:231-4. [PMID: 16907725 DOI: 10.1111/j.1574-6968.2006.00351.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Streptococcus mutans is a primary pathogen associated with dental caries. Its bacteriocin (mutacin) production ability is thought to play an important role in maintaining competitiveness in the multispecies oral biofilm. Previous studies have demonstrated that the production of the lantibiotic, mutacin I, is responsive to multiple input signals and that a putative inducible repressor, irvA, seems to be involved in the luxS-mediated mutacin I gene regulation pathway. In this study, we demonstrate that these multiple inputs can be divided into two pathways: irvA-dependent and irvA-independent. Similar to luxS, signals mediated through vicK, pttB and hk03 exert their effect possibly through modulating irvA transcription, whereas signals mediated through ciaH, hrcA, adhE, and Smu1281 exert their effect through an unknown mechanism independent of irvA.
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Affiliation(s)
- Phoebe Tsang
- UCLA School of Dentistry, Los Angeles, CA 90095, USA
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Ashby MK. Distribution, structure and diversity of "bacterial" genes encoding two-component proteins in the Euryarchaeota. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2006; 2:11-30. [PMID: 16877318 PMCID: PMC2685588 DOI: 10.1155/2006/562404] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The publicly available annotated archaeal genome sequences (23 complete and three partial annotations, October 2005) were searched for the presence of potential two-component open reading frames (ORFs) using gene category lists and BLASTP. A total of 489 potential two-component genes were identified from the gene category lists and BLASTP. Two-component genes were found in 14 of the 21 Euryarchaeal sequences (October 2005) and in neither the Crenarchaeota nor the Nanoarchaeota. A total of 20 predicted protein domains were identified in the putative two-component ORFs that, in addition to the histidine kinase and receiver domains, also includes sensor and signalling domains. The detailed structure of these putative proteins is shown, as is the distribution of each class of two-component genes in each species. Potential members of orthologous groups have been identified, as have any potential operons containing two or more two-component genes. The number of two-component genes in those Euryarchaeal species which have them seems to be linked more to lifestyle and habitat than to genome complexity, with most examples being found in Methanospirillum hungatei, Haloarcula marismortui, Methanococcoides burtonii and the mesophilic Methanosarcinales group. The large numbers of two-component genes in these species may reflect a greater requirement for internal regulation. Phylogenetic analysis of orthologous groups of five different protein classes, three probably involved in regulating taxis, suggests that most of these ORFs have been inherited vertically from an ancestral Euryarchaeal species and point to a limited number of key horizontal gene transfer events.
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Affiliation(s)
- Mark K Ashby
- Department of Basic Medical Sciences, Biochemistry Section, University of the West Indies, Mona Campus, Kingston 7, Jamaica.
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Abstract
Under natural growth conditions, bacteria can utilize intricate communication capabilities (e.g. quorum-sensing, chemotactic signalling and plasmid exchange) to cooperatively form (self-organize) complex colonies with elevated adaptability-the colonial pattern is collectively engineered according to the encountered environmental conditions. Bacteria do not genetically store all the information required for creating all possible patterns. Instead, additional information is cooperatively generated as required for the colonial self-organization to proceed. We describe how complex colonial forms (patterns) emerge through the communication-based singular interplay between individual bacteria and the colony. Each bacterium is, by itself, a biotic autonomous system with its own internal cellular informatics capabilities (storage, processing and assessment of information). These afford the cell plasticity to select its response to biochemical messages it receives, including self-alteration and the broadcasting of messages to initiate alterations in other bacteria. Hence, new features can collectively emerge during self-organization from the intracellular level to the whole colony. The cells thus assume newly co-generated traits and abilities that are not explicitly stored in the genetic information of the individuals.
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Affiliation(s)
- Eshel Ben-Jacob
- School of Physics and Astronomy, Raymond and Beverly Sackler, Faculty of Exact Sciences, Tel-Aviv University, Israel.
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Ashby M, Houmard J. Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution. Microbiol Mol Biol Rev 2006; 70:472-509. [PMID: 16760311 PMCID: PMC1489541 DOI: 10.1128/mmbr.00046-05] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A survey of the already characterized and potential two-component protein sequences that exist in the nine complete and seven partially annotated cyanobacterial genome sequences available (as of May 2005) showed that the cyanobacteria possess a much larger repertoire of such proteins than most other bacteria. By analysis of the domain structure of the 1,171 potential histidine kinases, response regulators, and hybrid kinases, many various arrangements of about thirty different modules could be distinguished. The number of two-component proteins is related in part to genome size but also to the variety of physiological properties and ecophysiologies of the different strains. Groups of orthologues were defined, only a few of which have representatives with known physiological functions. Based on comparisons with the proposed phylogenetic relationships between the strains, the orthology groups show that (i) a few genes, some of them clustered on the genome, have been conserved by all species, suggesting their very ancient origin and an essential role for the corresponding proteins, and (ii) duplications, fusions, gene losses, insertions, and deletions, as well as domain shuffling, occurred during evolution, leading to the extant repertoire. These mechanisms are put in perspective with the different genetic properties that cyanobacteria have to achieve genome plasticity. This review is designed to serve as a basis for orienting further research aimed at defining the most ancient regulatory mechanisms and understanding how evolution worked to select and keep the most appropriate systems for cyanobacteria to develop in the quite different environments that they have successfully colonized.
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Affiliation(s)
- Mark
K. Ashby
- Department
of Basic Medical Sciences, Biochemistry Section, University of the West
Indies, Mona Campus, Kingston 7,
Jamaica, Ecole Normale
Supérieure, CNRS UMR 8541, Génétique
Moléculaire, 46 rue d'Ulm, 75230 Paris Cedex 05,
France
| | - Jean Houmard
- Department
of Basic Medical Sciences, Biochemistry Section, University of the West
Indies, Mona Campus, Kingston 7,
Jamaica, Ecole Normale
Supérieure, CNRS UMR 8541, Génétique
Moléculaire, 46 rue d'Ulm, 75230 Paris Cedex 05,
France
- Corresponding
author. Mailing address: Ecole Normale Supérieure, CNRS UMR 8541,
Génétique Moléculaire, 46 rue d'Ulm, 75230 Paris
Cedex 05, France. Phone: 33 1 44 32 35 19. Fax: 33 1 44 96 53 60.
E-mail:
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Bekker M, Teixeira De Mattos MJ, Hellingwerf KJ. The role of two-component regulation systems in the physiology of the bacterial cell. Sci Prog 2006; 89:213-42. [PMID: 17338439 PMCID: PMC10368358 DOI: 10.3184/003685006783238308] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Two-component regulation systems (TCRSs) are the dominant type of signal transduction system in prokaryotes that are used to inform the cellular trancriptional machinery (and additional targets for regulation, like the motility apparatus) about actual changes in the extracellular physicochemical conditions. We now review their molecular structure and enzymatic characteristics, their mutual interactions and its implications, and their role in cellular physiology. Specific emphasis is placed on the ArcB/A system, a representative of the phosphorelay type of TCRS, and a key player in the adjustment of the cellular make-up of enterobacteria in response to alterations in the oxygen availability. Also some applied aspects of the TCRSs are discussed, i.e. their role as a target to develop new anti-bacterials and their application in biotechnology (or: 'synthetic biology').
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Affiliation(s)
| | | | - Klaas J. Hellingwerf
- Laboratory for Microbiology, Swammerdam Institute for Life Sciences, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
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Trewavas A. Green plants as intelligent organisms. TRENDS IN PLANT SCIENCE 2005; 10:413-9. [PMID: 16054860 DOI: 10.1016/j.tplants.2005.07.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2005] [Revised: 06/24/2005] [Accepted: 07/15/2005] [Indexed: 05/03/2023]
Abstract
Intelligent behaviour, even in humans, is an aspect of complex adaptive behaviour that provides a capacity for problem solving. This article assesses whether plants have a capacity to solve problems and, therefore, could be classified as intelligent organisms. The complex molecular network that is found in every plant cell and underpins plant behaviour is described. The problems that many plants face and that need solution are briefly outlined, and some of the kinds of behaviour used to solve these problems are discussed. A simple way of comparing plant intelligence between two genotypes is illustrated and some of the objections raised against the idea of plant intelligence are considered but discarded. It is concluded that plants exhibit the simple forms of behaviour that neuroscientists describe as basic intelligence.
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Affiliation(s)
- Anthony Trewavas
- Institute of Molecular Plant Science, Kings Buildings, University of Edinburgh, Edinburgh, UK EH9 3JH.
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Galperin MY. A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts. BMC Microbiol 2005; 5:35. [PMID: 15955239 PMCID: PMC1183210 DOI: 10.1186/1471-2180-5-35] [Citation(s) in RCA: 320] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2005] [Accepted: 06/14/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction. RESULTS This paper presents results of a comprehensive census of signal transduction proteins--histidine kinases, methyl-accepting chemotaxis receptors, Ser/Thr/Tyr protein kinases, adenylate and diguanylate cyclases and c-di-GMP phosphodiesterases--encoded in 167 bacterial and archaeal genomes, sequenced by the end of 2004. The data have been manually checked to avoid false-negative and false-positive hits that commonly arise during large-scale automated analyses and compared against other available resources. The census data show uneven distribution of most signaling proteins among bacterial and archaeal phyla. The total number of signal transduction proteins grows approximately as a square of genome size. While histidine kinases are found in representatives of all phyla and are distributed according to the power law, other signal transducers are abundant in certain phylogenetic groups but virtually absent in others. CONCLUSION The complexity of signaling systems differs even among closely related organisms. Still, it usually can be correlated with the phylogenetic position of the organism, its lifestyle, and typical environmental challenges it encounters. The number of encoded signal transducers (or their fraction in the total protein set) can be used as a measure of the organism's ability to adapt to diverse conditions, the 'bacterial IQ', while the ratio of transmembrane receptors to intracellular sensors can be used to define whether the organism is an 'extrovert', actively sensing the environmental parameters, or an 'introvert', more concerned about its internal homeostasis. Some of the microorganisms with the highest IQ, including the current leader Wolinella succinogenes, are found among the poorly studied beta-, delta- and epsilon-proteobacteria. Among all bacterial phyla, only cyanobacteria appear to be true introverts, probably due to their capacity to conduct oxygenic photosynthesis, using a complex system of intracellular membranes. The census data, available at http://www.ncbi.nlm.nih.gov/Complete_Genomes/SignalCensus.html, can be used to get an insight into metabolic and behavioral propensities of each given organism and improve prediction of the organism's properties based solely on its genome sequence.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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El-Sharoud WM. Two-component signal transduction systems as key players in stress responses of lactic acid bacteria. Sci Prog 2005; 88:203-28. [PMID: 16961092 PMCID: PMC10361167 DOI: 10.3184/003685005783238381] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Lactic acid bacteria (LAB) continue as an important group of gram-positive bacteria that have been extensively exploited in food industries and various biotechnological applications. Some LAB species are, however, opportunistic pathogens and were reported to be associated with overwhelming number of human infections. During the use of LAB in industry or over the course of human infection, these bacteria are exposed to environmental stress. While LAB display adaptive mechanisms to cope with adverse conditions, the regulation of these mechanisms remains to be elucidated. Recent completion of genome sequencing of various LAB strains combined with the development of advanced molecular techniques have enabled the identification of a number of putative two-component signal transduction systems, also known as two-component regulatory systems (2CRS), in LAB. Examining the effect of deleting genes specifying putative 2CRS proteins in these organisms has revealed the involvement of 2CRS in the responses of LAB to different stresses. There are lines of evidence indicating that certain 2CRS may mediate a general stress response in Enterococcus faecalis and Streptococcus pyogenes. This review highlights the influence of 2CRS on the physiology of LAB during optimal growth and survival/growth on exposure to environmental stress.
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Affiliation(s)
- Walid M El-Sharoud
- Dairy Science and Technology Department, Faculty of Agriculture, Mansoura University, Egypt.
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