SMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome

Abstract Single-particle (molecule) tracking (SPT/SMT) is a powerful method to study dynamic processes in living cells at high spatial and temporal resolution. Even though SMT is becoming a widely used method in bacterial cell biology, there is no program employing different analytical tools for the...

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Autores principales:	Thomas C. Rösch, Luis M. Oviedo-Bocanegra, Georg Fritz, Peter L. Graumann
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Single-molecule Tracking (SMT) Average Diffusion Constant State Diffusion Spatial Distribution Analysis (SDA) Superdiffusive Behavior Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d106bd58e63e4a429a6263860e33f984
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spelling	oai:doaj.org-article:d106bd58e63e4a429a6263860e33f9842021-12-02T15:08:43ZSMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome10.1038/s41598-018-33842-92045-2322https://doaj.org/article/d106bd58e63e4a429a6263860e33f9842018-10-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-33842-9https://doaj.org/toc/2045-2322Abstract Single-particle (molecule) tracking (SPT/SMT) is a powerful method to study dynamic processes in living cells at high spatial and temporal resolution. Even though SMT is becoming a widely used method in bacterial cell biology, there is no program employing different analytical tools for the quantitative evaluation of tracking data. We developed SMTracker, a MATLAB-based graphical user interface (GUI) for automatically quantifying, visualizing and managing SMT data via five interactive panels, allowing the user to interactively explore tracking data from several conditions, movies and cells on a track-by-track basis. Diffusion constants are calculated a) by a Gaussian mixture model (GMM) panel, analyzing the distribution of positional displacements in x- and y-direction using a multi-state diffusion model (e.g. DNA-bound vs. freely diffusing molecules), and inferring the diffusion constants and relative fraction of molecules in each state, or b) by square displacement analysis (SQD), using the cumulative probability distribution of square displacements to estimate the diffusion constants and relative fractions of up to three diffusive states, or c) through mean-squared displacement (MSD) analyses, allowing the discrimination between Brownian, sub- or superdiffusive behavior. A spatial distribution analysis (SDA) panel analyzes the subcellular localization of molecules, summarizing the localization of trajectories in 2D- heat maps. Using SMTracker, we show that the global transcriptional repressor AbrB performs highly dynamic binding throughout the Bacillus subtilis genome, with short dwell times that indicate high on/off rates in vivo. While about a third of AbrB molecules are in a DNA-bound state, 40% diffuse through the chromosome, and the remaining molecules freely diffuse through the cells. AbrB also forms one or two regions of high intensity binding on the nucleoids, similar to the global gene silencer H-NS in Escherichia coli, indicating that AbrB may also confer a structural function in genome organization.Thomas C. RöschLuis M. Oviedo-BocanegraGeorg FritzPeter L. GraumannNature PortfolioarticleSingle-molecule Tracking (SMT)Average Diffusion ConstantState DiffusionSpatial Distribution Analysis (SDA)Superdiffusive BehaviorMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-12 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Single-molecule Tracking (SMT) Average Diffusion Constant State Diffusion Spatial Distribution Analysis (SDA) Superdiffusive Behavior Medicine R Science Q
spellingShingle	Single-molecule Tracking (SMT) Average Diffusion Constant State Diffusion Spatial Distribution Analysis (SDA) Superdiffusive Behavior Medicine R Science Q Thomas C. Rösch Luis M. Oviedo-Bocanegra Georg Fritz Peter L. Graumann SMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome
description	Abstract Single-particle (molecule) tracking (SPT/SMT) is a powerful method to study dynamic processes in living cells at high spatial and temporal resolution. Even though SMT is becoming a widely used method in bacterial cell biology, there is no program employing different analytical tools for the quantitative evaluation of tracking data. We developed SMTracker, a MATLAB-based graphical user interface (GUI) for automatically quantifying, visualizing and managing SMT data via five interactive panels, allowing the user to interactively explore tracking data from several conditions, movies and cells on a track-by-track basis. Diffusion constants are calculated a) by a Gaussian mixture model (GMM) panel, analyzing the distribution of positional displacements in x- and y-direction using a multi-state diffusion model (e.g. DNA-bound vs. freely diffusing molecules), and inferring the diffusion constants and relative fraction of molecules in each state, or b) by square displacement analysis (SQD), using the cumulative probability distribution of square displacements to estimate the diffusion constants and relative fractions of up to three diffusive states, or c) through mean-squared displacement (MSD) analyses, allowing the discrimination between Brownian, sub- or superdiffusive behavior. A spatial distribution analysis (SDA) panel analyzes the subcellular localization of molecules, summarizing the localization of trajectories in 2D- heat maps. Using SMTracker, we show that the global transcriptional repressor AbrB performs highly dynamic binding throughout the Bacillus subtilis genome, with short dwell times that indicate high on/off rates in vivo. While about a third of AbrB molecules are in a DNA-bound state, 40% diffuse through the chromosome, and the remaining molecules freely diffuse through the cells. AbrB also forms one or two regions of high intensity binding on the nucleoids, similar to the global gene silencer H-NS in Escherichia coli, indicating that AbrB may also confer a structural function in genome organization.
format	article
author	Thomas C. Rösch Luis M. Oviedo-Bocanegra Georg Fritz Peter L. Graumann
author_facet	Thomas C. Rösch Luis M. Oviedo-Bocanegra Georg Fritz Peter L. Graumann
author_sort	Thomas C. Rösch
title	SMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome
title_short	SMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome
title_full	SMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome
title_fullStr	SMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome
title_full_unstemmed	SMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome
title_sort	smtracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of b. subtilis global repressor abrb throughout the genome
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/d106bd58e63e4a429a6263860e33f984
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SMTracker: a tool for quantitative analysis, exploration and visualization of single-molecule tracking data reveals highly dynamic binding of B. subtilis global repressor AbrB throughout the genome

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