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The nucleoid as a smart polymer

Abstract : Science has a close but very complex relationship with technology (Latour, 1987). A simple phenomenon is that technology enables science by offering tools that provide new data or new kinds of data. In other cases, aspects or views of the empirical world may remain invisible until technology builds something that unveils them to the eyes of the scientific community. On a deeper level, building something may be a form of understanding. For example " complex networks " became prominent in all sectors of science in the late 1990s, at the time that the Internet became a common tool for research and for society at large. Before then, networks had been restricted for decades to smaller niches. This change was accompanied by a thrust of high throughput technologies to collect new data, but arguably many of the " network " data had already been available for many years. On a smaller scale, we want to suggest here that so called " smart polymers " (Galaev and Mattiasson, 1999; Kumar et al., 2007) could be a promising technological metaphor for the behavior of the bacterial nucleoid. We want to explore the analogy with the similarly " intelligent " behavior shaped into bacterial nucleoids by natural selection. But first, what is a smart polymer, and what does it do? In soft-matter physics, " smart, " or " stimulus-responsive, " polymers are technological polymer systems designed to effect a variety of responsive behaviors to external stimuli (Figure 1). Smart polymers respond to the environment they are in. They are engineered to be sensitive to a number of factors, such as solvency, temperature, humidity, pH, light, electrical and magnetic field, and to effect mechanical and chemical changes (Galaev and Mattiasson, 1999; Kumar et al., 2007; Chen and Chang, 2014). They can be realized as linear free chains in solution, or as surface-grafted brushes or gels. Usually, response to stimuli is achieved through the addition of specific reactive functional groups and side chains, or by the use of graft-and-block copolymers (two different polymers grafted together) with different chemical properties (e.g., hydrophyly). Effective smart polymers typically undergo large changes (e.g., conformational transitions) in response to just small changes in the environment (e.g., pH, temperature, ionic strength). One way to achieve this behavior is through the introduction of " pre-programmed " phase transitions. For example, the polymer undergoes a reversible collapse after an external stimulus is applied. The reversibility of this change may also be an important property, allowing to detect changes in both directions. To fix the ideas, a prevalent use for smart polymers is targeted drug delivery. A smart-polymer system may control the release of drugs until the desired target is reached, and it is sensed by either a chemical or physical response triggering the release of the drug by " uncaging " it. For example, a polymer site-specific conjugation to specific amino acid sites may induce a trigger in the concentration of a targeted protein (Hoffman et al., 2000). It is then evident that the bacterial nucleoid can be seen as a smart polymer (Dillon and Dorman, 2010; Muskhelishvili et al., 2010; Benza et al., 2012; Kleckner et al., 2014). Its degree of compaction and conformation are modulated by the cell's growth conditions and in response to specific external cues (Figure 1). It is a complex system made of a long DNA polymer associated with RNA and proteins that may play at least two roles: adapt the shape of the nucleoid through both specific and non-specific DNA binding, and change the physical properties of DNA through dynamic changes in DNA topology.
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Vittore F. Scolari, Bianca Sclavi, Marco Cosentino Lagomarsino. The nucleoid as a smart polymer. Frontiers in Microbiology, Frontiers Media, 2015, 6, pp.UNSP 424. ⟨10.3389/fmicb.2015.00424⟩. ⟨hal-01221224⟩

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