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Article ; Online: Beyond force generation: Why is a dynamic ring of FtsZ polymers essential for bacterial cytokinesis?

Coltharp, Carla / Xiao, Jie

BioEssays : news and reviews in molecular, cellular and developmental biology

2017 Volume 39, Issue 1, Page(s) 1–11

Abstract: We propose that the essential function of the most highly conserved protein in bacterial cytokinesis, FtsZ, is not to generate a mechanical force to drive cell division. Rather, we suggest that FtsZ acts as a signal-processing hub to coordinate cell wall ...

Abstract	We propose that the essential function of the most highly conserved protein in bacterial cytokinesis, FtsZ, is not to generate a mechanical force to drive cell division. Rather, we suggest that FtsZ acts as a signal-processing hub to coordinate cell wall synthesis at the division septum with a diverse array of cellular processes, ensuring that the cell divides smoothly at the correct time and place, and with the correct septum morphology. Here, we explore how the polymerization properties of FtsZ, which have been widely attributed to force generation, can also be advantageous in this signal processing role. We suggest mechanisms by which FtsZ senses and integrates both mechanical and biochemical signals, and conclude by proposing experiments to investigate how FtsZ contributes to the remarkable spatial and temporal precision of bacterial cytokinesis.
Language	English
Publishing date	2017-01
Publishing country	United States
Document type	Journal Article
ZDB-ID	50140-2
ISSN	1521-1878 ; 0265-9247
ISSN (online)	1521-1878
ISSN	0265-9247
DOI	10.1002/bies.201600179
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Article ; Online: Influence of FtsZ GTPase activity and concentration on nanoscale Z-ring structure in vivo revealed by three-dimensional Superresolution imaging.

Lyu, Zhixin / Coltharp, Carla / Yang, Xinxing / Xiao, Jie

Biopolymers

2016 Volume 105, Issue 10, Page(s) 725–734

Abstract: FtsZ is an essential bacterial cytoskeletal protein that assembles into a ring-like structure (Z-ring) at midcell to carry out cytokinesis. In vitro, FtsZ exhibits polymorphism in polymerizing into different forms of filaments based on its GTPase ... ...

Abstract	FtsZ is an essential bacterial cytoskeletal protein that assembles into a ring-like structure (Z-ring) at midcell to carry out cytokinesis. In vitro, FtsZ exhibits polymorphism in polymerizing into different forms of filaments based on its GTPase activity, concentration, and buffer condition. In vivo, the Z-ring appeared to be punctate and heterogeneously organized, although continuous, homogenous Z-ring structures have also been observed. Understanding how the Z-ring is organized in vivo is important because it provides a structural basis for the functional role of the Z-ring in cytokinesis. Here, we assess the effects of both GTPase activity and FtsZ concentration on the organization of the Z-ring in vivo using three-dimensional (3D) superresolution microscopy. We found that the Z-ring became more homogenous when assembled in the presence of a GTPase-deficient mutant, and upon overexpression of either wt or mutant FtsZ. These results suggest that the in vivo organization of the Z-ring is largely dependent on the intrinsic polymerization properties of FtsZ, which are significantly influenced by the GTPase activity and concentration of FtsZ. Our work provides a unifying theme to reconcile previous observations of different Z-ring structures, and supports a model in which the wt Z-ring comprises loosely associated, heterogeneously distributed FtsZ clusters. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 725-734, 2016.
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Cytoskeletal Proteins/genetics ; Cytoskeletal Proteins/metabolism ; Escherichia coli/enzymology ; Escherichia coli/genetics ; Escherichia coli/ultrastructure ; GTP Phosphohydrolases/genetics ; GTP Phosphohydrolases/metabolism ; Multienzyme Complexes/genetics ; Multienzyme Complexes/metabolism ; Multienzyme Complexes/ultrastructure ; Mutation
Chemical Substances	Bacterial Proteins ; Cytoskeletal Proteins ; FtsZ protein, Bacteria ; Multienzyme Complexes ; GTP Phosphohydrolases (EC 3.6.1.-)
Language	English
Publishing date	2016-06-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	1123-x
ISSN	1097-0282 ; 0006-3525
ISSN (online)	1097-0282
ISSN	0006-3525
DOI	10.1002/bip.22895
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Article ; Online: Superresolution microscopy for microbiology.

Coltharp, Carla / Xiao, Jie

Cellular microbiology

2012 Volume 14, Issue 12, Page(s) 1808–1818

Abstract: This review provides a practical introduction to superresolution microscopy from the perspective of microbiological research. Because of the small sizes of bacterial cells, superresolution methods are particularly powerful and suitable for revealing ... ...

Abstract	This review provides a practical introduction to superresolution microscopy from the perspective of microbiological research. Because of the small sizes of bacterial cells, superresolution methods are particularly powerful and suitable for revealing details of cellular structures that are not resolvable under conventional fluorescence light microscopy. Here we describe the methodological concepts behind three major categories of superresolution light microscopy: photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), structured illumination microscopy (SIM) and stimulated emission-depletion (STED) microscopy. We then present recent applications of each of these techniques to microbial systems, which have revealed novel conformations of cellular structures and described new properties of in vivo protein function and interactions. Finally, we discuss the unique issues related to implementing each of these superresolution techniques with bacterial specimens and suggest avenues for future development. The goal of this review is to provide the necessary technical background for interested microbiologists to choose the appropriate superresolution method for their biological systems, and to introduce the practical considerations required for designing and analysing superresolution imaging experiments.
MeSH term(s)	Biomedical Research/trends ; Microbiological Techniques/methods ; Microscopy/methods
Language	English
Publishing date	2012-10-04
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1468320-9
ISSN	1462-5822 ; 1462-5814
ISSN (online)	1462-5822
ISSN	1462-5814
DOI	10.1111/cmi.12024
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Article ; Online: Defining the rate-limiting processes of bacterial cytokinesis.

Coltharp, Carla / Buss, Jackson / Plumer, Trevor M / Xiao, Jie

Proceedings of the National Academy of Sciences of the United States of America

2016 Volume 113, Issue 8, Page(s) E1044–53

Abstract: Bacterial cytokinesis is accomplished by the essential 'divisome' machinery. The most widely conserved divisome component, FtsZ, is a tubulin homolog that polymerizes into the 'FtsZ-ring' ('Z-ring'). Previous in vitro studies suggest that Z-ring ... ...

Abstract	Bacterial cytokinesis is accomplished by the essential 'divisome' machinery. The most widely conserved divisome component, FtsZ, is a tubulin homolog that polymerizes into the 'FtsZ-ring' ('Z-ring'). Previous in vitro studies suggest that Z-ring contraction serves as a major constrictive force generator to limit the progression of cytokinesis. Here, we applied quantitative superresolution imaging to examine whether and how Z-ring contraction limits the rate of septum closure during cytokinesis in Escherichia coli cells. Surprisingly, septum closure rate was robust to substantial changes in all Z-ring properties proposed to be coupled to force generation: FtsZ's GTPase activity, Z-ring density, and the timing of Z-ring assembly and disassembly. Instead, the rate was limited by the activity of an essential cell wall synthesis enzyme and further modulated by a physical divisome-chromosome coupling. These results challenge a Z-ring-centric view of bacterial cytokinesis and identify cell wall synthesis and chromosome segregation as limiting processes of cytokinesis.
MeSH term(s)	Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Chromosomes, Bacterial/genetics ; Chromosomes, Bacterial/metabolism ; Cytokinesis/physiology ; Cytoskeletal Proteins/genetics ; Cytoskeletal Proteins/metabolism ; Escherichia coli/genetics ; Escherichia coli/metabolism
Chemical Substances	Bacterial Proteins ; Cytoskeletal Proteins ; FtsZ protein, Bacteria
Language	English
Publishing date	2016-02-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1514296113
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Article ; Online: Quantitative analysis of single-molecule superresolution images.

Coltharp, Carla / Yang, Xinxing / Xiao, Jie

Current opinion in structural biology

2014 Volume 28, Page(s) 112–121

Abstract: This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ... ...

Abstract	This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10-50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images.
MeSH term(s)	Fluorescent Dyes ; Microscopy/methods ; Microscopy/standards ; Molecular Imaging/methods ; Molecular Imaging/standards
Chemical Substances	Fluorescent Dyes
Language	English
Publishing date	2014-08-30
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1068353-7
ISSN	1879-033X ; 0959-440X
ISSN (online)	1879-033X
ISSN	0959-440X
DOI	10.1016/j.sbi.2014.08.008
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Article: Super-resolution imaging of the bacterial division machinery

Buss, Jackson / Coltharp, Carla / Xiao, Jie

Journal of visualized experiments. 2013 Jan. 21, , no. 71

2013

Abstract: Bacterial cell division requires the coordinated assembly of more than ten essential proteins at midcell1,2. Central to this process is the formation of a ring-like suprastructure (Z-ring) by the FtsZ protein at the division plan3,4. The Z-ring consists ... ...

Abstract	Bacterial cell division requires the coordinated assembly of more than ten essential proteins at midcell1,2. Central to this process is the formation of a ring-like suprastructure (Z-ring) by the FtsZ protein at the division plan3,4. The Z-ring consists of multiple single-stranded FtsZ protofilaments, and understanding the arrangement of the protofilaments inside the Z-ring will provide insight into the mechanism of Z-ring assembly and its function as a force generator5,6. This information has remained elusive due to current limitations in conventional fluorescence microscopy and electron microscopy. Conventional fluorescence microscopy is unable to provide a high-resolution image of the Z-ring due to the diffraction limit of light (~200 nm). Electron cryotomographic imaging has detected scattered FtsZ protofilaments in small C. crescentus cells7, but is difficult to apply to larger cells such as E. coli or B. subtilis. Here we describe the application of a super-resolution fluorescence microscopy method, Photoactivated Localization Microscopy (PALM), to quantitatively characterize the structural organization of the E. coli Z-ring8. PALM imaging offers both high spatial resolution (~35 nm) and specific labeling to enable unambiguous identification of target proteins. We labeled FtsZ with the photoactivatable fluorescent protein mEos2, which switches from green fluorescence (excitation = 488 nm) to red fluorescence (excitation = 561 nm) upon activation at 405 nm9. During a PALM experiment, single FtsZ-mEos2 molecules are stochastically activated and the corresponding centroid positions of the single molecules are determined with <20 nm precision. A super-resolution image of the Z-ring is then reconstructed by superimposing the centroid positions of all detected FtsZ-mEos2 molecules. Using this method, we found that the Z-ring has a fixed width of ~100 nm and is composed of a loose bundle of FtsZ protofilaments that overlap with each other in three dimensions. These data provide a springboard for further investigations of the cell cycle dependent changes of the Z-ring10 and can be applied to other proteins of interest.
Keywords	Bacillus subtilis ; Escherichia coli ; bacteria ; cell division ; electron microscopy ; fluorescence ; fluorescence microscopy ; fluorescent proteins ; image analysis
Language	English
Dates of publication	2013-0121
Size	p. e50048.
Publishing place	Journal of Visualized Experiments
Document type	Article
ZDB-ID	2259946-0
ISSN	1940-087X
ISSN	1940-087X
DOI	10.3791/50048
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Super-resolution imaging of the bacterial division machinery.

Buss, Jackson / Coltharp, Carla / Xiao, Jie

Journal of visualized experiments : JoVE

2013 , Issue 71

Abstract: Bacterial cell division requires the coordinated assembly of more than ten essential proteins at midcell. Central to this process is the formation of a ring-like suprastructure (Z-ring) by the FtsZ protein at the division plan. The Z-ring consists of ... ...

Abstract	Bacterial cell division requires the coordinated assembly of more than ten essential proteins at midcell. Central to this process is the formation of a ring-like suprastructure (Z-ring) by the FtsZ protein at the division plan. The Z-ring consists of multiple single-stranded FtsZ protofilaments, and understanding the arrangement of the protofilaments inside the Z-ring will provide insight into the mechanism of Z-ring assembly and its function as a force generator. This information has remained elusive due to current limitations in conventional fluorescence microscopy and electron microscopy. Conventional fluorescence microscopy is unable to provide a high-resolution image of the Z-ring due to the diffraction limit of light (~200 nm). Electron cryotomographic imaging has detected scattered FtsZ protofilaments in small C. crescentus cells, but is difficult to apply to larger cells such as E. coli or B. subtilis. Here we describe the application of a super-resolution fluorescence microscopy method, Photoactivated Localization Microscopy (PALM), to quantitatively characterize the structural organization of the E. coli Z-ring. PALM imaging offers both high spatial resolution (~35 nm) and specific labeling to enable unambiguous identification of target proteins. We labeled FtsZ with the photoactivatable fluorescent protein mEos2, which switches from green fluorescence (excitation = 488 nm) to red fluorescence (excitation = 561 nm) upon activation at 405 nm. During a PALM experiment, single FtsZ-mEos2 molecules are stochastically activated and the corresponding centroid positions of the single molecules are determined with <20 nm precision. A super-resolution image of the Z-ring is then reconstructed by superimposing the centroid positions of all detected FtsZ-mEos2 molecules. Using this method, we found that the Z-ring has a fixed width of ~100 nm and is composed of a loose bundle of FtsZ protofilaments that overlap with each other in three dimensions. These data provide a springboard for further investigations of the cell cycle dependent changes of the Z-ring and can be applied to other proteins of interest.
MeSH term(s)	Bacterial Physiological Phenomena ; Bacterial Proteins/analysis ; Cell Division/physiology ; Cytoskeletal Proteins/analysis ; Escherichia coli/chemistry ; Escherichia coli/cytology ; Image Processing, Computer-Assisted/methods ; Microscopy, Fluorescence/instrumentation ; Microscopy, Fluorescence/methods
Chemical Substances	Bacterial Proteins ; Cytoskeletal Proteins ; FtsZ protein, Bacteria
Language	English
Publishing date	2013-01-21
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Video-Audio Media
ZDB-ID	2259946-0
ISSN	1940-087X ; 1940-087X
ISSN (online)	1940-087X
ISSN	1940-087X
DOI	10.3791/50048
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Article ; Online: Accurate construction of photoactivated localization microscopy (PALM) images for quantitative measurements.

Coltharp, Carla / Kessler, Rene P / Xiao, Jie

PloS one

2012 Volume 7, Issue 12, Page(s) e51725

Abstract: Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical ... ...

Abstract	Localization-based superresolution microscopy techniques such as Photoactivated Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) have allowed investigations of cellular structures with unprecedented optical resolutions. One major obstacle to interpreting superresolution images, however, is the overcounting of molecule numbers caused by fluorophore photoblinking. Using both experimental and simulated images, we determined the effects of photoblinking on the accurate reconstruction of superresolution images and on quantitative measurements of structural dimension and molecule density made from those images. We found that structural dimension and relative density measurements can be made reliably from images that contain photoblinking-related overcounting, but accurate absolute density measurements, and consequently faithful representations of molecule counts and positions in cellular structures, require the application of a clustering algorithm to group localizations that originate from the same molecule. We analyzed how applying a simple algorithm with different clustering thresholds (t(Thresh) and d(Thresh)) affects the accuracy of reconstructed images, and developed an easy method to select optimal thresholds. We also identified an empirical criterion to evaluate whether an imaging condition is appropriate for accurate superresolution image reconstruction with the clustering algorithm. Both the threshold selection method and imaging condition criterion are easy to implement within existing PALM clustering algorithms and experimental conditions. The main advantage of our method is that it generates a superresolution image and molecule position list that faithfully represents molecule counts and positions within a cellular structure, rather than only summarizing structural properties into ensemble parameters. This feature makes it particularly useful for cellular structures of heterogeneous densities and irregular geometries, and allows a variety of quantitative measurements tailored to specific needs of different biological systems.
MeSH term(s)	Algorithms ; Cluster Analysis ; Computer Simulation ; Escherichia coli/cytology ; Fluorescent Dyes/metabolism ; Image Processing, Computer-Assisted ; Imaging, Three-Dimensional ; Kinetics ; Light ; Microscopy/methods
Chemical Substances	Fluorescent Dyes
Language	English
Publishing date	2012-12-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0051725
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Article ; Online: Multi-institutional TSA-amplified Multiplexed Immunofluorescence Reproducibility Evaluation (MITRE) Study.

Taube, Janis M / Roman, Kristin / Engle, Elizabeth L / Wang, Chichung / Ballesteros-Merino, Carmen / Jensen, Shawn M / McGuire, John / Jiang, Mei / Coltharp, Carla / Remeniuk, Bethany / Wistuba, Ignacio / Locke, Darren / Parra, Edwin R / Fox, Bernard A / Rimm, David L / Hoyt, Cliff

Journal for immunotherapy of cancer

2021 Volume 9, Issue 7

Abstract: Background: Emerging data suggest predictive biomarkers based on the spatial arrangement of cells or coexpression patterns in tissue sections will play an important role in precision immuno-oncology. Multiplexed immunofluorescence (mIF) is ideally ... ...

Abstract	Background: Emerging data suggest predictive biomarkers based on the spatial arrangement of cells or coexpression patterns in tissue sections will play an important role in precision immuno-oncology. Multiplexed immunofluorescence (mIF) is ideally suited to such assessments. Standardization and validation of an end-to-end workflow that supports multisite trials and clinical laboratory processes are vital. Six institutions collaborated to: (1) optimize an automated six-plex assay focused on the PD-1/PD-L1 axis, (2) assess intersite and intrasite reproducibility of staining using a locked down image analysis algorithm to measure tumor cell and immune cell (IC) subset densities, %PD-L1 expression on tumor cells (TCs) and ICs, and PD-1/PD-L1 proximity assessments. Methods: A six-plex mIF panel (PD-L1, PD-1, CD8, CD68, FOXP3, and CK) was rigorously optimized as determined by quantitative equivalence to immunohistochemistry (IHC) chromogenic assays. Serial sections from tonsil and breast carcinoma and non-small cell lung cancer (NSCLC) tissue microarrays (TMAs), TSA-Opal fluorescent detection reagents, and antibodies were distributed to the six sites equipped with a Leica Bond Rx autostainer and a Vectra Polaris multispectral imaging platform. Tissue sections were stained and imaged at each site and delivered to a single site for analysis. Intersite and intrasite reproducibility were assessed by linear fits to plots of cell densities, including %PDL1 expression by TCs and ICs in the breast and NSCLC TMAs. Results: Comparison of the percent positive cells for each marker between mIF and IHC revealed that enhanced amplification in the mIF assay was required to detect low-level expression of PD-1, PD-L1, FoxP3 and CD68. Following optimization, an average equivalence of 90% was achieved between mIF and IHC across all six assay markers. Intersite and intrasite cell density assessments showed an average concordance of R Conclusions: Assay optimization yielded highly sensitive, reproducible mIF characterization of the PD-1/PD-L1 axis across multiple sites. High concordance was observed across sites for measures of density of specific IC subsets, measures of coexpression and proximity with single-cell resolution.
MeSH term(s)	Biomarkers, Tumor/metabolism ; Female ; Fluorescent Antibody Technique/methods ; Humans ; Immunohistochemistry/methods ; Laboratories, Clinical/standards ; Male ; Tissue Array Analysis/methods
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2021-07-13
Publishing country	England
Document type	Journal Article ; Multicenter Study ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2719863-7
ISSN	2051-1426 ; 2051-1426
ISSN (online)	2051-1426
ISSN	2051-1426
DOI	10.1136/jitc-2020-002197
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Article ; Online: A multi-layered protein network stabilizes the Escherichia coli FtsZ-ring and modulates constriction dynamics.

Buss, Jackson / Coltharp, Carla / Shtengel, Gleb / Yang, Xinxing / Hess, Harald / Xiao, Jie

PLoS genetics

2015 Volume 11, Issue 4, Page(s) e1005128

Abstract: The prokaryotic tubulin homolog, FtsZ, forms a ring-like structure (FtsZ-ring) at midcell. The FtsZ-ring establishes the division plane and enables the assembly of the macromolecular division machinery (divisome). Although many molecular components of ... ...

Abstract	The prokaryotic tubulin homolog, FtsZ, forms a ring-like structure (FtsZ-ring) at midcell. The FtsZ-ring establishes the division plane and enables the assembly of the macromolecular division machinery (divisome). Although many molecular components of the divisome have been identified and their interactions extensively characterized, the spatial organization of these proteins within the divisome is unclear. Consequently, the physical mechanisms that drive divisome assembly, maintenance, and constriction remain elusive. Here we applied single-molecule based superresolution imaging, combined with genetic and biophysical investigations, to reveal the spatial organization of cellular structures formed by four important divisome proteins in E. coli: FtsZ, ZapA, ZapB and MatP. We show that these interacting proteins are arranged into a multi-layered protein network extending from the cell membrane to the chromosome, each with unique structural and dynamic properties. Further, we find that this protein network stabilizes the FtsZ-ring, and unexpectedly, slows down cell constriction, suggesting a new, unrecognized role for this network in bacterial cell division. Our results provide new insight into the structure and function of the divisome, and highlight the importance of coordinated cell constriction and chromosome segregation.
MeSH term(s)	Bacterial Proteins/metabolism ; Carrier Proteins/metabolism ; Cell Cycle Proteins/metabolism ; Cell Division ; Chromosomal Proteins, Non-Histone/metabolism ; Cytoskeletal Proteins/metabolism ; Escherichia coli/metabolism ; Escherichia coli/physiology ; Escherichia coli/ultrastructure ; Escherichia coli Proteins/metabolism ; Motion
Chemical Substances	Bacterial Proteins ; Carrier Proteins ; Cell Cycle Proteins ; Chromosomal Proteins, Non-Histone ; Cytoskeletal Proteins ; Escherichia coli Proteins ; FtsZ protein, Bacteria ; MatP protein, E coli ; ZapA protein, E coli ; ZapB protein, E coli
Language	English
Publishing date	2015-04-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1005128
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