Universität zu Köln

Simsek, Ahmet Nihat ORCID: 0000-0002-5032-7189 (2021). Micromechanics of bacterial surface-migration. PhD thesis, Universität zu Köln.

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Abstract

Biochemical regulation of cellular micromechanics is fundamental for many aspects of life, including development and disease. A better understanding of the principles of cellular information processing is therefore desirable. This thesis investigates how the stochastic micromechanis of bacteria on surfaces and thereby also surface-migrating bacterial cells perceive and adjust to their mechanical environment. We study the subject systematically from the single-cell level to the collective through analytical models, experiments, and simulations. Twitching is a mode of bacterial migration on biotic and abiotic surfaces driven by extracellular appendages called Type IV pili (T4P) that can extend and retract. We study the physics of twitching migration and the impact of mechanical properties of the substrates. To begin with, we employ mathematical modeling to find the conditions under which substrate-rigidity-dependent stick-slip motion of bacteria occurs. An idealized cell model is constructed, focusing solely on the mechanics of the migration. Migration is driven by stochastic extension-retraction dynamics of an active appendage modeled after T4P. A passive adhesion at the back of the cell allows for tension build-up in the system. The analytical calculations show that the migration speed depends non-linearly on the substrate rigidity on the condition that the attachment rates are an order of magnitude higher than the stochastic detachment rates of the appendages. We extend the model in simulations which allows us to obtain speed distributions. The results provide generic criteria for the emergence of substrate-rigidity-dependent stick-slip migration. Twitching is an intrinsically complex biological process that is only partially understood. It has been recently found that the extension-retraction dynamics of Pseudomonas aeruginosa's T4P result from stochastic binding of motor ATPases to a molecular transmembrane complex forming the pilus base. We investigate how such stochastic dynamics mediate twitching and explore the impact of substrate rigidity on T4P and twitching. Experiments done in collaboration, employing fluorescently labeled bacteria on two hydrogels with different chemical and mechanical properties, reveal that bacteria produce slightly shorter but twice as many pili on surfaces compared to the bacteria suspended in a liquid medium. An in-depth analysis of the empirical data shows no statistically significant change of these effects with different substrate rigidities. The experimental data also shows that only a small fraction of pili contributes to the migration, and bacteria retract their pili regardless of surface attachment. The fluorescent movies also reveal that passive adhesions on the cell body hinder twitching migration. A stochastic model describing the T4P dynamics is developed to study surface-associated migration of P. aeruginosa further. The model captures all measured T4P statistics quantitatively. By extending the T4P model with stochastic surface-bond dynamics, we simulate twitching bacteria. The simulations quantitatively explain the migration statistics of the ensemble. Moreover, the analysis of the measured mean-squared displacements suggests that the number of passive adhesions attaching P. aeruginosa to the substrate varies strongly. Using shear-flow experiments and simulations, we show that bacteria employ pili and passive adhesions together to balance migration and adherence to surfaces. Bacterial aggregation is an essential step towards biofilm formation. Hence, understanding aggregation dynamics is essential. Since we have explained the twitching dynamics of the individuals quantitatively, the next step is to study the collective behavior of twitching bacteria by taking into account our findings regarding T4P activity. For this purpose, a simulation framework is developed. The code is extended for investigating different twitching species by allowing for different bacterial shapes and T4P parameters. Moreover, a simplified bacterial gliding mechanism is implemented for bacteria that can glide and twitch. For rigid-rod-like bacteria that are strictly unipolar the simulations reveal a phase separation into dense clusters and areas with few bacteria, as previously shown. However, if bacteria twitch with the pilus distribution found in the experiments, without reversing the leading pole, the motion does not lead to phase separation. Even with a reversal of the leading pole every ~30 minutes, migration alone does not lead to clustering. These findings suggest that clustering of P. aeruginosa on surfaces is not purely driven by migration but that cell division, secretion of extracellular matrix proteins, or regulatory processes are essential for clustering. Finally, we investigate the effect of hydrogel-substrate composition on the microcolony formation of twitching and dividing bacteria by combining simulations with experimental data.

Item Type:	Thesis (PhD thesis)
Creators:	Creators Email ORCID ORCID Put Code Simsek, Ahmet Nihat ahmet.n.simsek@gmail.com orcid.org/0000-0002-5032-7189 UNSPECIFIED
URN:	urn:nbn:de:hbz:38-542507
Date:	5 July 2021
Language:	English
Faculty:	Faculty of Mathematics and Natural Sciences
Divisions:	Außeruniversitäre Forschungseinrichtungen > Forschungszentrum Jülich
Subjects:	Natural sciences and mathematics Physics
Uncontrolled Keywords:	Keywords Language bacteria English stochastic process English twitching migration English type IV pili English Pseudomonas aeruginosa English
Date of oral exam:	6 September 2021
Referee:	Name Academic Title Gompper, Gerhard Prof. Dr. Maier, Berenike Prof. Dr.
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/54250