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Title: Integrative visualization of the molecular structure of a cellular microdomain

Journal Article · · Protein Science
DOI: https://doi.org/10.1002/pro.4577 · OSTI ID:1924563
ORCiD logo [1]; ORCiD logo [2]
  1. Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla California USA, Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey Piscataway New Jersey USA, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey Piscataway New Jersey USA, Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey New Brunswick New Jersey USA
  2. Department of Integrative Structural and Computational Biology The Scripps Research Institute La Jolla California USA

Abstract An integrative approach to visualization is used to create a visual snapshot of the structural biology of the polar microdomain of Caulobacter crescentus . The visualization is based on the current state of molecular and cellular knowledge of the microdomain and its cellular context. The collaborative process of researching and executing the visualization has identified aspects that are well determined and areas that require further study. The visualization is useful for dissemination, education, and outreach, and the study lays the groundwork for future 3D modeling and simulation of this well‐studied example of a cellular condensate.

Research Organization:
Rutgers University, Piscataway, NJ (United States)
Sponsoring Organization:
National Institutes of Health (NIH); National Science Foundation (NSF); USDOE; USDOE Office of Science (SC)
Grant/Contract Number:
SC0019749
OSTI ID:
1924563
Journal Information:
Protein Science, Journal Name: Protein Science Journal Issue: 3 Vol. 32; ISSN 0961-8368
Publisher:
Wiley Blackwell (John Wiley & Sons)Copyright Statement
Country of Publication:
United Kingdom
Language:
English

References (94)

Escherichia coli journal November 2009
An essential single domain response regulator required for normal cell division and differentiation in Caulobacter crescentus. journal August 1995
Cell Cycle Signal Transduction and Proteolysis in Caulobacter book January 2022
Partition of unit-copy miniplasmids to daughter cells journal September 1985
Structure and function of the F plasmid genes essential for partitioning journal November 1986
Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity journal November 1991
Inside a living cell journal January 1991
Partition of unit-copy miniplasmids to daughter cells journal September 1983
Cell Type-Specific Phosphorylation and Proteolysis of a Transcriptional Regulator Controls the G1-to-S Transition in a Bacterial Cell Cycle journal August 1997
Cell Cycle–Dependent Polar Localization of an Essential Bacterial Histidine Kinase that Controls DNA Replication and Cell Division journal April 1999
ParB-Stimulated Nucleotide Exchange Regulates a Switch in Functionally Distinct ParA Activities journal August 2002
The Asymmetric Spatial Distribution of Bacterial Signal Transduction Proteins Coordinates Cell Cycle Events journal July 2003
Cytokinesis Monitoring during Development journal September 2004
A Dynamically Localized Protease Complex and a Polar Specificity Factor Control a Cell Cycle Master Regulator journal February 2006
A Polymeric Protein Anchors the Chromosomal Origin/ParB Complex at a Bacterial Cell Pole journal September 2008
A Self-Associating Protein Critical for Chromosome Attachment, Division, and Polar Organization in Caulobacter journal September 2008
An Adaptor Hierarchy Regulates Proteolysis during a Bacterial Cell Cycle journal October 2015
A Bacterial Chromosome Structuring Protein Binds Overtwisted DNA to Stimulate Type II Topoisomerases and Enable DNA Replication journal October 2018
SMC Progressively Aligns Chromosomal Arms in Caulobacter crescentus but Is Antagonized by Convergent Transcription journal August 2017
Caulobacter crescentus: model system extraordinaire journal October 2020
A Dynamic Complex of Signaling Proteins Uses Polar Localization to Regulate Cell-Fate Asymmetry in Caulobacter crescentus journal March 2011
Activation of a signaling pathway by the physical translocation of a chromosome journal August 2021
Regulation of the activity of the bacterial histidine kinase PleC by the scaffolding protein PodJ journal April 2022
Intrinsically Disordered Bacterial Polar Organizing Protein Z, PopZ, Interacts with Protein Binding Partners Through an N-terminal Molecular Recognition Feature journal November 2020
Building Structural Models of a Whole Mycoplasma Cell journal January 2022
In vivo Architecture of the Polar Organizing Protein Z (PopZ) Meshwork in the Alphaproteobacteria Magnetospirillum gryphiswaldense and Caulobacter crescentus journal March 2022
Polarity and cell fate asymmetry in Caulobacter crescentus journal December 2012
Interplay between flagellation and cell cycle control in Caulobacter journal December 2015
An intracellular compass spatially coordinates cell cycle modules in Caulobacter crescentus journal October 2016
More than a Tad: spatiotemporal control of Caulobacter pili journal April 2018
Branched Signal Wiring of an Essential Bacterial Cell-Cycle Phosphotransfer Protein journal September 2013
Quantitative Multicolor Subdiffraction Imaging of Bacterial Protein Ultrastructures in Three Dimensions journal February 2013
How to shape a productive scientist–artist collaboration journal February 2021
Regulation of the bacterial cell cycle by an integrated genetic circuit journal November 2006
Cyclic di-GMP acts as a cell cycle oscillator to drive chromosome replication journal May 2015
A spindle-like apparatus guides bacterial chromosome segregation journal July 2010
A cell cycle kinase with tandem sensory PAS domains integrates cell fate cues journal April 2016
Biomolecular condensates: organizers of cellular biochemistry journal February 2017
Chromosome organization by a conserved condensin-ParB system in the actinobacterium Corynebacterium glutamicum journal March 2020
The material properties of a bacterial-derived biomolecular condensate tune biological function in natural and synthetic systems journal September 2022
Selective sequestration of signalling proteins in a membraneless organelle reinforces the spatial regulation of asymmetry in Caulobacter crescentus journal January 2020
Highly accurate protein structure prediction with AlphaFold journal July 2021
Art as a tool for science journal May 2021
Bacterial chromosome segregation: structure and DNA binding of the Soj dimer ? a conserved biological switch journal January 2005
Multilayered control of chromosome replication in Caulobacter crescentus journal January 2019
Productive interaction between the chromosome partitioning proteins, ParA and ParB, is required for the progression of the cell cycle in Caulobacter crescentus journal February 2003
Role of the GGDEF regulator PleD in polar development of Caulobacter crescentus: PleD control of polar development journal March 2003
Recruitment of a cytoplasmic response regulator to the cell pole is linked to its cell cycle-regulated proteolysis journal April 2004
Dynamic localization of a cytoplasmic signal transduction response regulator controls morphogenesis during the Caulobacter cell cycle journal March 2001
A phospho-signaling pathway controls the localization and activity of a protease complex critical for bacterial cell cycle progression journal July 2006
Genes directly controlled by CtrA, a master regulator of the Caulobacter cell cycle journal April 2002
A bacterial control circuit integrates polar localization and proteolysis of key regulatory proteins with a phospho-signaling cascade journal October 2008
Bacterial scaffold directs pole-specific centromere segregation journal April 2014
Cell cycle-dependent adaptor complex for ClpXP-mediated proteolysis directly integrates phosphorylation and second messenger signals journal September 2014
Caulobacter PopZ forms an intrinsically disordered hub in organizing bacterial cell poles journal October 2016
Dynamic translation regulation in Caulobacter cell cycle control journal October 2016
Integration of cell cycle signals by multi-PAS domain kinases journal July 2018
Identification of a localization factor for the polar positioning of bacterial structural and regulatory proteins journal October 2002
Cryogenic single-molecule fluorescence annotations for electron tomography reveal in situ organization of key proteins in Caulobacter journal June 2020
A localized adaptor protein performs distinct functions at the Caulobacter cell poles journal March 2021
Negative control of bacterial DNA replication by a cell cycle regulatory protein that binds at the chromosome origin journal January 1998
The Caulobacter crescentus smc gene is required for cell cycle progression and chromosome segregation journal September 1999
Spatiotemporal control of PopZ localization through cell cycle–coupled multimerization journal June 2013
Bacterial chromosome segregation by the ParABS system journal June 2020
Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain journal March 2004
Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression journal January 2009
Dissection of functional domains of the polar localization factor PodJ in Caulobacter crescentus journal January 2006
Whole-genome analysis of the chromosome partitioning and sporulation protein Spo0J (ParB) reveals spreading and origin-distal sites on the Bacillus subtilis chromosome journal May 2007
Caulobacter PopZ forms a polar subdomain dictating sequential changes in pole composition and function journal April 2010
The scaffolding and signalling functions of a localization factor impact polar development journal April 2012
Regulated proteolysis of a transcription factor complex is critical to cell cycle progression in Caulobacter crescentus: Cell cycle regulated proteolysis in Caulobacter journal February 2013
Oligomerization and higher-order assembly contribute to sub-cellular localization of a bacterial scaffold: Mutational analysis of PopZ journal October 2013
In situ structure of the Caulobacter crescentus flagellar motor and visualization of binding of a CheY‐homolog journal May 2020
Relief of ParB autoinhibition by parS DNA catalysis and recycling of ParB by CTP hydrolysis promote bacterial centromere assembly journal October 2021
Asymmetrical Distribution of the Second Messenger c-di-GMP upon Bacterial Cell Division journal June 2010
Liquid phase condensation in cell physiology and disease journal September 2017
DivL Performs Critical Cell Cycle Functions in Caulobacter crescentus Independent of Kinase Activity journal September 2007
Polar Localization of the CckA Histidine Kinase and Cell Cycle Periodicity of the Essential Master Regulator CtrA in Caulobacter crescentus journal January 2010
Dynamics of Two Phosphorelays Controlling Cell Cycle Progression in Caulobacter crescentus journal December 2009
Distribution of Centromere-Like parS Sites in Bacteria: Insights from Comparative Genomics journal September 2007
Getting in the Loop: Regulation of Development in Caulobacter crescentus journal March 2010
Identification of a novel response regulator required for the swarmer-to-stalked-cell transition in Caulobacter crescentus journal November 1995
Regulated Proteolysis in Bacteria: Caulobacter journal November 2016
ArtScience: Integrative Collaboration to Create a Sustainable Future journal June 2011
Proteolysis dependent cell cycle regulation in Caulobacter crescentus journal April 2022
Cell Fate Regulation Governed by a Repurposed Bacterial Histidine Kinase journal October 2014
Bi-modal Distribution of the Second Messenger c-di-GMP Controls Cell Fate and Asymmetry during the Caulobacter Cell Cycle journal September 2013
Regional Control of Chromosome Segregation in Pseudomonas aeruginosa journal November 2016
Integrative illustration of a JCVI-syn3A minimal cell journal June 2022
Art and science journal December 2018
The Protein Quality Control Network in Caulobacter crescentus journal April 2021
Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem journal July 2021
Cellular Landscapes in Watercolor journal February 2016
Modularity and determinants of a (bi-)polarization control system from free-living and obligate intracellular bacteria journal December 2016