Indole Pulse Signalling Regulates the Cytoplasmic pH of E. coli in a Memory-Like Manner

Zarkan, Ashraf; Caño-Muñiz, Santiago; Zhu, Jinbo; Nahas, Kareem Al; Cama, Jehangir; Keyser, Ulrich F.; Summers, David

doi:10.1038/s41598-019-40560-3

Cited by 28 publications

(57 citation statements)

References 54 publications

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“…The average error was 0.01. repellent response (37). As indole at high concentrations reportedly permeates the membrane and decreases the cytoplasmic pH (38,39), we tested whether the biphasic response to indole occurs through the known pH-mediated signaling mechanism. To do this, we expressed a pH-sensitive fluorescent protein in the wild-type strain (Materials and Methods).…”

Section: Resultsmentioning

confidence: 99%

Biphasic chemotaxis of Escherichia coli to the microbiota metabolite indole

Yang

Chawla

Rhee

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Bacterial chemotaxis to prominent microbiota metabolites such as indole is important in the formation of microbial communities in the gastrointestinal (GI) tract. However, the basis of chemotaxis to indole is poorly understood. Here, we exposedEscherichia colito a range of indole concentrations and measured the dynamic responses of individual flagellar motors to determine the chemotaxis response. Below 1 mM indole, a repellent-only response was observed. At 1 mM indole and higher, a time-dependent inversion from a repellent to an attractant response was observed. The repellent and attractant responses were mediated by the Tsr and Tar chemoreceptors, respectively. Also, the flagellar motor itself mediated a repellent response independent of the receptors. Chemotaxis assays revealed that receptor-mediated adaptation to indole caused a bipartite response—wild-type cells were attracted to regions of high indole concentration if they had previously adapted to indole but were otherwise repelled. We propose that indole spatially segregates cells based on their state of adaptation to repel invaders while recruiting beneficial resident bacteria to growing microbial communities within the GI tract.

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Section: Resultsmentioning

confidence: 99%

Biphasic chemotaxis of Escherichia coli to the microbiota metabolite indole

Yang

Chawla

Rhee

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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“…Indole can diffuse across bacterial membranes but may also partition into them, which could lead to elevated levels of indole in the vicinity of trans-membrane proteins, even if the extracellular levels are relatively low (Piñero-Fernandez et al, 2011). Intriguingly, it has also been shown recently that indole has a role in the regulation of the internal pH of E. coli, with the stationary phase pulse of indole signaling setting the internal pH to 7.2, as opposed to 7.8 in the absence of indole (Zarkan et al, 2019). The concentration of indole and how it varies in the human gut is unknown, but high levels (250-1000 µM) are typically found in stool samples (Karlin et al, 1985).…”

Section: Discussionmentioning

confidence: 99%

The Signaling Molecule Indole Inhibits Induction of the AR2 Acid Resistance System in Escherichia coli

et al. 2020

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Induction of the AR2 acid response system of Escherichia coli occurs at a moderately low pH (pH 5.5) and leads to high levels of resistance to pH levels below 2.5 in the presence of glutamate. Induction is mediated in part by the EvgAS two component system. Here, we show that the bacterial signaling molecule indole inhibits the induction of key promoters in the AR2 system and blocks the development of glutamatedependent acid resistance. The addition of tryptophan, the precursor for indole biosynthesis, had the same effects, and this block was relieved in a tnaA mutant, which is unable to synthesize indole. Expression of a constitutively active EvgS protein was able to relieve the inhibition caused by indole, consistent with EvgS being inhibited directly or indirectly by indole. Indole had no effect on autophosphorylation of the isolated cytoplasmic domain of EvgS. This is consistent with a model where indole directly or indirectly affects the ability of EvgS to detect its inducing signal or to transduce this information across the cytoplasmic membrane. The inhibitory activity of indole on the AR2 system is not related to its ability to act as an ionophore, and, conversely, the ionophore CCCP had no effect on acid-induced AR2 promoter activity, showing that the proton motive force is unlikely to be a signal for induction of the AR2 system.

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“…The intracellular pH values we measured (Table 1) are higher than those commonly found in the literature (7.2-7.8 61,62 ). We assume these discrepancies originate from the fact that we constantly exchange the medium during the cell growth, removing from the environment metabolic waste products and any quorum sensing or signal molecules, which have previously been shown to influence cytoplasmic pH 63,72,73 . Indeed, when cells are kept in the original growth medium their cytoplasmic pH varies between 7.3 and 7.7, Fig.…”

Section: Growth Rate and Morphology Of Bacteria Do Not Depend On The mentioning

confidence: 99%

Comparison of Escherichia coli surface attachment methods for single-cell microscopy

Wang

Krasnopeeva

Lin

et al. 2019

Sci Rep

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for in vivo, single-cell imaging bacterial cells are commonly immobilised via physical confinement or surface attachment. Different surface attachment methods have been used both for atomic force and optical microscopy (including super resolution), and some have been reported to affect bacterial physiology. However, a systematic comparison of the effects these attachment methods have on the bacterial physiology is lacking. Here we present such a comparison for bacterium Escherichia coli, and assess the growth rate, size and intracellular pH of cells growing attached to different, commonly used, surfaces. We demonstrate that E. coli grow at the same rate, length and internal pH on all the tested surfaces when in the same growth medium. The result suggests that tested attachment methods can be used interchangeably when studying E. coli physiology. Microscopy has been a powerful tool for studying biological processes on the cellular level, ever since the first discovery of microorganisms by Antonie van Leeuwenhoek back in 17th century 1. Recently employed single-cell imaging allowed scientists to study population diversity 2 , physiology 3 , sub-cellular features 4 , and protein dynamics 5 in real-time. Single cell imaging of bacteria is particularly dependent on immobilisation, as majority of bacteria are small in size and capable of swimming. Immobilisation methods vary depending on the application, but typically fall into one of the two categories: use of physical confinement or attachment to the surface via specific molecules. The former group includes microfluidic platforms capable of mechanical trapping 6,7 , where some popular examples include the "mother machine" 8 , CellASIC 9 or MACS 10 devices, and porous membranes such as agarose gel pads 2,11-13. Physical confinement methods, while higher in throughput, can have drawbacks. For example, agarose gel pads do not allow fast medium exchange, and when mechanically confining bacteria the choice of enclosure dimensions should be done carefully in order to avoid influencing the growth and morphology with mechanical forces 14. Furthermore, mechanically confined bacteria cannot be used for studies of bacterial motility or energetics via detection of bacteria flagellar motor rotation 15-17. Chemical attachment methods rely on the interaction of various adhesive molecules, deposited on the cover glass surface, with the cell itself. Adhesion can be a result of electrostatic (polyethylenimine (PEI) 18,19 , poly-L-lysine (PLL) 15,17,19) or covalent interactions (3-aminopropyltriethoxysilane (APTES) 19), or a combination, such as with polyphenolic proteins (Cell-Tak) 19. Time scales on which researchers perform single-cell experiments vary. For example, scanning methods, like atomic force microscopy (AFM) or confocal laser scanning microscopy (CLSM) 19,20 , require enough time to probe each point of the sample, and stochastic approaches of super resolution microscopy (e.g. PALM and STORM) use low activation rate of fluorophores to achieve a single fluorophore localisati...

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Indole Pulse Signalling Regulates the Cytoplasmic pH of E. coli in a Memory-Like Manner

Cited by 28 publications

References 54 publications

Biphasic chemotaxis of Escherichia coli to the microbiota metabolite indole

Biphasic chemotaxis of Escherichia coli to the microbiota metabolite indole

The Signaling Molecule Indole Inhibits Induction of the AR2 Acid Resistance System in Escherichia coli

Comparison of Escherichia coli surface attachment methods for single-cell microscopy

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