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Title: Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria

Abstract

Carboxysomes are protein-based bacterial organelles encapsulating key enzymes of the Calvin-Benson-Bassham cycle. Previous work has implicated a ParA-like protein (hereafter McdA) as important for spatially organizing carboxysomes along the longitudinal axis of the model cyanobacterium Synechococcus elongatus PCC 7942. Yet, how self-organization of McdA emerges and contributes to carboxysome positioning is unknown. Here, we identify a small protein, termed McdB that localizes to carboxysomes and drives emergent oscillatory patterning of McdA on the nucleoid. Our results demonstrate that McdB directly stimulates McdA ATPase activity and its release from DNA, driving carboxysome-dependent depletion of McdA locally on the nucleoid and promoting directed motion of carboxysomes towards increased concentrations of McdA. We propose that McdA and McdB are a previously unknown class of self-organizing proteins that utilize a Brownian-ratchet mechanism to position carboxysomes in cyanobacteria, rather than a cytoskeletal system. These results have broader implications for understanding spatial organization of protein mega-complexes and organelles in bacteria.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3];  [4];  [4]; ORCiD logo [5]; ORCiD logo [2]; ORCiD logo [6]
  1. Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States
  2. Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Michigan, United States
  3. Department of Biochemistry, Michigan State University, East Lansing, United States
  4. Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
  5. Department of Plant Biology, Michigan State University, East Lansing, United States
  6. Department of Biochemistry, Michigan State University, East Lansing, United States, MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, United States
Publication Date:
Research Org.:
Michigan State Univ., East Lansing (United States). MSU-DOE Plant Research Laboratory
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Science Foundation (NSF); University of Michigan
OSTI Identifier:
1484819
Alternate Identifier(s):
OSTI ID: 1484820; OSTI ID: 1603778
Grant/Contract Number:  
FG02-91ER20021; 1517241; 1817478
Resource Type:
Published Article
Journal Name:
eLife
Additional Journal Information:
Journal Name: eLife Journal Volume: 7; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

MacCready, Joshua S., Hakim, Pusparanee, Young, Eric J., Hu, Longhua, Liu, Jian, Osteryoung, Katherine W., Vecchiarelli, Anthony G., and Ducat, Daniel C. Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria. United States: N. p., 2018. Web. doi:10.7554/eLife.39723.
MacCready, Joshua S., Hakim, Pusparanee, Young, Eric J., Hu, Longhua, Liu, Jian, Osteryoung, Katherine W., Vecchiarelli, Anthony G., & Ducat, Daniel C. Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria. United States. doi:10.7554/eLife.39723.
MacCready, Joshua S., Hakim, Pusparanee, Young, Eric J., Hu, Longhua, Liu, Jian, Osteryoung, Katherine W., Vecchiarelli, Anthony G., and Ducat, Daniel C. Thu . "Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria". United States. doi:10.7554/eLife.39723.
@article{osti_1484819,
title = {Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria},
author = {MacCready, Joshua S. and Hakim, Pusparanee and Young, Eric J. and Hu, Longhua and Liu, Jian and Osteryoung, Katherine W. and Vecchiarelli, Anthony G. and Ducat, Daniel C.},
abstractNote = {Carboxysomes are protein-based bacterial organelles encapsulating key enzymes of the Calvin-Benson-Bassham cycle. Previous work has implicated a ParA-like protein (hereafter McdA) as important for spatially organizing carboxysomes along the longitudinal axis of the model cyanobacterium Synechococcus elongatus PCC 7942. Yet, how self-organization of McdA emerges and contributes to carboxysome positioning is unknown. Here, we identify a small protein, termed McdB that localizes to carboxysomes and drives emergent oscillatory patterning of McdA on the nucleoid. Our results demonstrate that McdB directly stimulates McdA ATPase activity and its release from DNA, driving carboxysome-dependent depletion of McdA locally on the nucleoid and promoting directed motion of carboxysomes towards increased concentrations of McdA. We propose that McdA and McdB are a previously unknown class of self-organizing proteins that utilize a Brownian-ratchet mechanism to position carboxysomes in cyanobacteria, rather than a cytoskeletal system. These results have broader implications for understanding spatial organization of protein mega-complexes and organelles in bacteria.},
doi = {10.7554/eLife.39723},
journal = {eLife},
number = ,
volume = 7,
place = {United States},
year = {2018},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.7554/eLife.39723

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Cited by: 10 works
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Works referenced in this record:

Light Modulates the Biosynthesis and Organization of Cyanobacterial Carbon Fixation Machinery through Photosynthetic Electron Flow
journal, March 2016

  • Sun, Yaqi; Casella, Selene; Fang, Yi
  • Plant Physiology, Vol. 171, Issue 1
  • DOI: 10.1104/pp.16.00107

Engineering the Bacterial Microcompartment Domain for Molecular Scaffolding Applications
journal, July 2017


Bacterial microcompartments and the modular construction of microbial metabolism
journal, January 2015


Brownian Ratchet Mechanism for Faithful Segregation of Low-Copy-Number Plasmids
journal, April 2017

  • Hu, Longhua; Vecchiarelli, Anthony G.; Mizuuchi, Kiyoshi
  • Biophysical Journal, Vol. 112, Issue 7
  • DOI: 10.1016/j.bpj.2017.02.039

Mini-P1 plasmid partitioning: excess ParB protein destabilizes plasmids containing the centromere parS.
journal, February 1988


Movement and equipositioning of plasmids by ParA filament disassembly
journal, November 2009

  • Ringgaard, S.; van Zon, J.; Howard, M.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 46
  • DOI: 10.1073/pnas.0908347106

Interactions between the termini of lumen enzymes and shell proteins mediate enzyme encapsulation into bacterial microcompartments
journal, August 2012

  • Fan, C.; Cheng, S.; Sinha, S.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 37
  • DOI: 10.1073/pnas.1207516109

A Multiprotein Bicarbonate Dehydration Complex Essential to Carboxysome Function in Cyanobacteria
journal, November 2007

  • Cot, S. S. -W.; So, A. K. -C.; Espie, G. S.
  • Journal of Bacteriology, Vol. 190, Issue 3
  • DOI: 10.1128/JB.01283-07

Direct characterization of the native structure and mechanics of cyanobacterial carboxysomes
journal, January 2017

  • Faulkner, Matthew; Rodriguez-Ramos, Jorge; Dykes, Gregory F.
  • Nanoscale, Vol. 9, Issue 30
  • DOI: 10.1039/C7NR02524F

Membrane-bound MinDE complex acts as a toggle switch that drives Min oscillation coupled to cytoplasmic depletion of MinD
journal, February 2016

  • Vecchiarelli, Anthony G.; Li, Min; Mizuuchi, Michiyo
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 11
  • DOI: 10.1073/pnas.1600644113

Surfing biological surfaces: exploiting the nucleoid for partition and transport in bacteria: ParAs exploit the nucleoid for transport
journal, September 2012

  • Vecchiarelli, Anthony G.; Mizuuchi, Kiyoshi; Funnell, Barbara E.
  • Molecular Microbiology, Vol. 86, Issue 3
  • DOI: 10.1111/mmi.12017

Bacterial chromosome segregation: structure and DNA binding of the Soj dimer ? a conserved biological switch
journal, January 2005


Cell Biology of Prokaryotic Organelles
journal, August 2010


Protein Self-Organization: Lessons from the Min System
journal, June 2011


Oscillating focus of SopA associated with filamentous structure guides partitioning of F plasmid: Guidance of F-plasmid partitioning by SopA
journal, May 2007


Plasmid Partition Mechanisms
journal, December 2014


ParA-mediated plasmid partition driven by protein pattern self-organization
journal, February 2013

  • Hwang, Ling Chin; Vecchiarelli, Anthony G.; Han, Yong-Woon
  • The EMBO Journal, Vol. 32, Issue 9
  • DOI: 10.1038/emboj.2013.34

Structural Determinants of the Outer Shell of β-Carboxysomes in Synechococcus elongatus PCC 7942: Roles for CcmK2, K3-K4, CcmO, and CcmL
journal, August 2012


The Phyre2 web portal for protein modeling, prediction and analysis
journal, May 2015

  • Kelley, Lawrence A.; Mezulis, Stefans; Yates, Christopher M.
  • Nature Protocols, Vol. 10, Issue 6
  • DOI: 10.1038/nprot.2015.053

Functional Cyanobacterial β -Carboxysomes Have an Absolute Requirement for Both Long and Short Forms of the CcmM Protein
journal, March 2010

  • Long, Benedict M.; Tucker, Loraine; Badger, Murray R.
  • Plant Physiology, Vol. 153, Issue 1
  • DOI: 10.1104/pp.110.154948

Functions, Compositions, and Evolution of the Two Types of Carboxysomes: Polyhedral Microcompartments That Facilitate CO2 Fixation in Cyanobacteria and Some Proteobacteria
journal, September 2013

  • Rae, B. D.; Long, B. M.; Badger, M. R.
  • Microbiology and Molecular Biology Reviews, Vol. 77, Issue 3
  • DOI: 10.1128/MMBR.00061-12

A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method
journal, October 2014


Directed and persistent movement arises from mechanochemistry of the ParA/ParB system
journal, December 2015

  • Hu, Longhua; Vecchiarelli, Anthony G.; Mizuuchi, Kiyoshi
  • Proceedings of the National Academy of Sciences
  • DOI: 10.1073/pnas.1505147112

Prokaryotic cytoskeletons: protein filaments organizing small cells
journal, January 2018


Live-cell imaging of cyanobacteria
journal, November 2014


Assembly Dynamics of the Bacterial MinCDE System and Spatial Regulation of the Z Ring
journal, June 2007


JPred4: a protein secondary structure prediction server
journal, April 2015

  • Drozdetskiy, Alexey; Cole, Christian; Procter, James
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv332

Engineering Bacterial Microcompartment Shells: Chimeric Shell Proteins and Chimeric Carboxysome Shells
journal, July 2014

  • Cai, Fei; Sutter, Markus; Bernstein, Susan L.
  • ACS Synthetic Biology, Vol. 4, Issue 4
  • DOI: 10.1021/sb500226j

Deletion of the parA (soj) Homologue in Pseudomonas aeruginosa Causes ParB Instability and Affects Growth Rate, Chromosome Segregation, and Motility
journal, June 2007

  • Lasocki, K.; Bartosik, A. A.; Mierzejewska, J.
  • Journal of Bacteriology, Vol. 189, Issue 15
  • DOI: 10.1128/JB.00371-07

A propagating ATPase gradient drives transport of surface-confined cellular cargo
journal, February 2014

  • Vecchiarelli, Anthony G.; Neuman, Keir C.; Mizuuchi, Kiyoshi
  • Proceedings of the National Academy of Sciences, Vol. 111, Issue 13
  • DOI: 10.1073/pnas.1401025111

Assembly, function and evolution of cyanobacterial carboxysomes
journal, June 2016


The ParA/MinD family puts things in their place
journal, September 2012


Atomic-Level Models of the Bacterial Carboxysome Shell
journal, February 2008


F plasmid partition depends on interaction of SopA with non-specific DNA
journal, November 2008


Spatially Ordered Dynamics of the Bacterial Carbon Fixation Machinery
journal, March 2010


Bacterial partition complexes segregate within the volume of the nucleoid
journal, July 2016

  • Le Gall, Antoine; Cattoni, Diego I.; Guilhas, Baptiste
  • Nature Communications, Vol. 7, Issue 1
  • DOI: 10.1038/ncomms12107

Ultrastructure of compacted DNA in cyanobacteria by high-voltage cryo-electron tomography
journal, October 2016

  • Murata, Kazuyoshi; Hagiwara, Sayuri; Kimori, Yoshitaka
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep34934

A dynamically localized histidine kinase controls the asymmetric distribution of polar pili proteins
journal, September 2002


Enzymatic assembly of DNA molecules up to several hundred kilobases
journal, April 2009

  • Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan
  • Nature Methods, Vol. 6, Issue 5, p. 343-345
  • DOI: 10.1038/nmeth.1318

Reconstitution of self-organizing protein gradients as spatial cues in cell-free systems
journal, October 2014


Soj (ParA) DNA binding is mediated by conserved arginines and is essential for plasmid segregation
journal, December 2007

  • Hester, C. M.; Lutkenhaus, J.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 51
  • DOI: 10.1073/pnas.0705196105

Engineering Cyanobacterial Cell Morphology for Enhanced Recovery and Processing of Biomass
journal, February 2017

  • Jordan, Adam; Chandler, Jenna; MacCready, Joshua S.
  • Applied and Environmental Microbiology, Vol. 83, Issue 9
  • DOI: 10.1128/AEM.00053-17

Collaboration of FlhF and FlhG to regulate polar-flagella number and localization in Vibrio alginolyticus
journal, May 2008


Elucidating Essential Role of Conserved Carboxysomal Protein CcmN Reveals Common Feature of Bacterial Microcompartment Assembly
journal, March 2012

  • Kinney, James N.; Salmeen, Annette; Cai, Fei
  • Journal of Biological Chemistry, Vol. 287, Issue 21
  • DOI: 10.1074/jbc.M112.355305

Biogenesis of a Bacterial Organelle: The Carboxysome Assembly Pathway
journal, November 2013


Theophylline-Dependent Riboswitch as a Novel Genetic Tool for Strict Regulation of Protein Expression in Cyanobacterium Synechococcus elongatus PCC 7942
journal, September 2013

  • Nakahira, Yoichi; Ogawa, Atsushi; Asano, Hiroyuki
  • Plant and Cell Physiology, Vol. 54, Issue 10
  • DOI: 10.1093/pcp/pct115

DNA-relay mechanism is sufficient to explain ParA-dependent intracellular transport and patterning of single and multiple cargos
journal, October 2016

  • Surovtsev, Ivan V.; Campos, Manuel; Jacobs-Wagner, Christine
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 46
  • DOI: 10.1073/pnas.1616118113

Stoichiometry of P1 Plasmid Partition Complexes
journal, March 2000

  • Bouet, Jean-Yves; Surtees, Jennifer A.; Funnell, Barbara E.
  • Journal of Biological Chemistry, Vol. 275, Issue 11
  • DOI: 10.1074/jbc.275.11.8213

Cell cycle coordination and regulation of bacterial chromosome segregation dynamics by polarly localized proteins
journal, August 2010

  • Schofield, Whitman B.; Lim, Hoong Chuin; Jacobs-Wagner, Christine
  • The EMBO Journal, Vol. 29, Issue 18
  • DOI: 10.1038/emboj.2010.207

Robust M in‐system oscillation in the presence of internal photosynthetic membranes in cyanobacteria
journal, November 2016

  • MacCready, Joshua S.; Schossau, Jory; Osteryoung, Katherine W.
  • Molecular Microbiology, Vol. 103, Issue 3
  • DOI: 10.1111/mmi.13571

A spindle-like apparatus guides bacterial chromosome segregation
journal, July 2010

  • Ptacin, Jerod L.; Lee, Steven F.; Garner, Ethan C.
  • Nature Cell Biology, Vol. 12, Issue 8
  • DOI: 10.1038/ncb2083

Analysis of a genomic DNA region from the cyanobacterium Synechococcus sp. strain PCC7942 involved in carboxysome assembly and function.
journal, May 1993


Noise-Induced Min Phenotypes in E. coli
journal, January 2006


Spatial Regulators for Bacterial Cell Division Self-Organize into Surface Waves in Vitro
journal, May 2008


Identification of cyanobacterial cell division genes by comparative and mutational analyses: Identification of cyanobacterial cell division genes
journal, February 2005


Dual Role of DNA in Regulating ATP Hydrolysis by the SopA Partition Protein
journal, September 2009

  • Ah-Seng, Yoan; Lopez, Frederic; Pasta, Franck
  • Journal of Biological Chemistry, Vol. 284, Issue 44
  • DOI: 10.1074/jbc.M109.044800

The positioning of cytoplasmic protein clusters in bacteria
journal, May 2006

  • Thompson, S. R.; Wadhams, G. H.; Armitage, J. P.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 21
  • DOI: 10.1073/pnas.0600919103

The Structure of CcmP, a Tandem Bacterial Microcompartment Domain Protein from the β-Carboxysome, Forms a Subcompartment Within a Microcompartment
journal, April 2013

  • Cai, Fei; Sutter, Markus; Cameron, Jeffrey C.
  • Journal of Biological Chemistry, Vol. 288, Issue 22
  • DOI: 10.1074/jbc.M113.456897

A family of ParA-like ATPases promotes cell pole maturation by facilitating polar localization of chemotaxis proteins
journal, July 2011

  • Ringgaard, S.; Schirner, K.; Davis, B. M.
  • Genes & Development, Vol. 25, Issue 14
  • DOI: 10.1101/gad.2061811

Analysis of Carboxysomes from Synechococcus PCC7942 Reveals Multiple Rubisco Complexes with Carboxysomal Proteins CcmM and CcaA
journal, August 2007

  • Long, Benedict M.; Badger, Murray R.; Whitney, Spencer M.
  • Journal of Biological Chemistry, Vol. 282, Issue 40
  • DOI: 10.1074/jbc.M703896200

Subcellular Positioning of F Plasmid Mediated by Dynamic Localization of SopA and SopB
journal, March 2006


Insights from multiple structures of the shell proteins from the β-carboxysome
journal, January 2008

  • Tanaka, Shiho; Sawaya, Michael R.; Phillips, Martin
  • Protein Science
  • DOI: 10.1002/pro.14

Agrobacterium ParA/MinD-like VirC1 spatially coordinates early conjugative DNA transfer reactions
journal, May 2007

  • Atmakuri, Krishnamohan; Cascales, Eric; Burton, Oliver T.
  • The EMBO Journal, Vol. 26, Issue 10
  • DOI: 10.1038/sj.emboj.7601696

The Bacterial Carbon-Fixing Organelle Is Formed by Shell Envelopment of Preassembled Cargo
journal, September 2013


A bacterial two-hybrid system based on a reconstituted signal transduction pathway
journal, May 1998

  • Karimova, G.; Pidoux, J.; Ullmann, A.
  • Proceedings of the National Academy of Sciences, Vol. 95, Issue 10
  • DOI: 10.1073/pnas.95.10.5752

P1 Plasmid Segregation: Accurate Redistribution by Dynamic Plasmid Pairing and Separation
journal, November 2009

  • Sengupta, M.; Nielsen, H. J.; Youngren, B.
  • Journal of Bacteriology, Vol. 192, Issue 5
  • DOI: 10.1128/JB.01245-09

Coupling chemosensory array formation and localization
journal, October 2017


MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis
journal, June 2016


β-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints
journal, April 2017

  • Sommer, Manuel; Cai, Fei; Melnicki, Matthew
  • Journal of Experimental Botany, Vol. 68, Issue 14
  • DOI: 10.1093/jxb/erx115

Biochemical activities of the ParA partition protein of the P1 plasmid
journal, May 1992


Protein Structures Forming the Shell of Primitive Bacterial Organelles
journal, August 2005


Light-dependent governance of cell shape dimensions in cyanobacteria
journal, May 2015


Cell-free study of F plasmid partition provides evidence for cargo transport by a diffusion-ratchet mechanism
journal, March 2013

  • Vecchiarelli, A. G.; Hwang, L. C.; Mizuuchi, K.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 15
  • DOI: 10.1073/pnas.1302745110

Evidence for a DNA-relay mechanism in ParABS-mediated chromosome segregation
journal, May 2014

  • Lim, Hoong Chuin; Surovtsev, Ivan Vladimirovich; Beltran, Bruno Gabriel
  • eLife, Vol. 3
  • DOI: 10.7554/eLife.02758