Supplementary Information Supplementary Figures

The ubiquitous sliding clamp facilitates processivity of the replicative polymerase and acts as a platform to recruit proteins involved in replication, recombination and repair. While the dynamics of the E. coli β2-sliding clamp have been characterized in vitro, its in vivo stoichiometry and dynamics remain unclear. To probe both β2-clamp dynamics and stoichiometry in live E. coli cells, we use custom-built microfluidics in combination with single-molecule fluorescence microscopy and photoactivated fluorescence microscopy. We quantify the recruitment, binding and turnover of β2-sliding clamps on DNA during replication. These quantitative in vivo results demonstrate that numerous β2-clamps in E. coli remain on the DNA behind the replication fork for a protracted period of time, allowing them to form a docking platform for other enzymes involved in DNA metabolism.

[1]  M. O’Donnell,et al.  The δ Subunit of DNA Polymerase III Holoenzyme Serves as a Sliding Clamp Unloader in Escherichia coli * , 2000, The Journal of Biological Chemistry.

[2]  J. Elf,et al.  Single molecule methods with applications in living cells. , 2013, Current opinion in biotechnology.

[3]  A. Grossman,et al.  Beta clamp directs localization of mismatch repair in Bacillus subtilis. , 2008, Molecular cell.

[4]  Gene Wijffels,et al.  Conservation of Eubacterial Replicases , 2005, IUBMB life.

[5]  John Kuriyan,et al.  Three-dimensional structure of the β subunit of E. coli DNA polymerase III holoenzyme: A sliding DNA clamp , 1992, Cell.

[6]  D. Sherratt,et al.  Independent Positioning and Action of Escherichia coli Replisomes in Live Cells , 2008, Cell.

[7]  C. McHenry,et al.  Cycling of the E. coli lagging strand polymerase is triggered exclusively by the availability of a new primer at the replication fork , 2013, Nucleic acids research.

[8]  F. J. López de Saro Regulation of Interactions with Sliding Clamps During DNA Replication and Repair , 2009, Current genomics.

[9]  D. Sherratt,et al.  Stoichiometry and Architecture of Active DNA Replication Machinery in Escherichia coli , 2010, Science.

[10]  Burak Okumus,et al.  Segregation of molecules at cell division reveals native protein localization , 2012, Nature Methods.

[11]  E. Isacoff,et al.  Subunit counting in membrane-bound proteins , 2007, Nature Methods.

[12]  Antoine M. van Oijen,et al.  Replication-fork dynamics. , 2014, Cold Spring Harbor perspectives in biology.

[13]  Nynke H. Dekker,et al.  Studying genomic processes at the single-molecule level: introducing the tools and applications , 2012, Nature Reviews Genetics.

[14]  J. Errington,et al.  The replicase sliding clamp dynamically accumulates behind progressing replication forks in Bacillus subtilis cells. , 2011, Molecular cell.

[15]  Suliana Manley,et al.  Photoactivatable mCherry for high-resolution two-color fluorescence microscopy , 2009, Nature Methods.

[16]  M. O’Donnell,et al.  A sliding-clamp toolbelt binds high- and low-fidelity DNA polymerases simultaneously. , 2005, Molecular cell.

[17]  A. M. Li,et al.  High-copy bacterial plasmids diffuse in the nucleoid-free space, replicate stochastically and are randomly partitioned at cell division , 2013, Nucleic acids research.

[18]  S. Kazmirski,et al.  The Mechanism of ATP-Dependent Primer-Template Recognition by a Clamp Loader Complex , 2009, Cell.

[19]  M. O’Donnell,et al.  Fidelity of Escherichia coli DNA Polymerase IV , 2002, The Journal of Biological Chemistry.

[20]  D. Sherratt,et al.  Single-molecule DNA repair in live bacteria , 2012, Proceedings of the National Academy of Sciences.

[21]  J. Kuriyan,et al.  Structure of a Sliding Clamp on DNA , 2008, Cell.

[22]  T. Katayama,et al.  A replicase clamp-binding dynamin-like protein promotes colocalization of nascent DNA strands and equipartitioning of chromosomes in E. coli. , 2013, Cell reports.

[23]  G. Jensen,et al.  The Helical MreB Cytoskeleton in Escherichia coli MC1000/pLE7 Is an Artifact of the N-Terminal Yellow Fluorescent Protein Tag , 2012, Journal of bacteriology.

[24]  M. O’Donnell,et al.  Cellular DNA replicases: components and dynamics at the replication fork. , 2005, Annual review of biochemistry.

[25]  A. Kornberg,et al.  The dnaN gene codes for the beta subunit of DNA polymerase III holoenzyme of escherichia coli. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[26]  N. Tanner,et al.  E. coli DNA replication in the absence of free β clamps , 2011, The EMBO journal.

[27]  M. Hingorani,et al.  DnaN clamp zones provide a platform for spatiotemporal coupling of mismatch detection to DNA replication , 2013, Molecular microbiology.

[28]  S. Benkovic,et al.  Replication clamps and clamp loaders. , 2013, Cold Spring Harbor perspectives in biology.

[29]  Andrew Wright,et al.  Robust Growth of Escherichia coli , 2010, Current Biology.

[30]  M. O’Donnell,et al.  Interaction of the β sliding clamp with MutS, ligase, and DNA polymerase I , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[31]  C. McHenry,et al.  Chaperoning of a replicative polymerase onto a newly assembled DNA-bound sliding clamp by the clamp loader. , 2010, Molecular cell.

[32]  M. O’Donnell,et al.  An explanation for lagging strand replication: Polymerase hopping among DNA sliding clamps , 1994, Cell.

[33]  Roger Woodgate,et al.  Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis , 2000, Nature.

[34]  M. O’Donnell,et al.  Characterization of a triple DNA polymerase replisome. , 2007, Molecular cell.

[35]  B. Dalrymple,et al.  Interaction of the Sliding Clamp β-Subunit and Hda, a DnaA-Related Protein , 2004 .

[36]  Mike O'Donnell,et al.  Single‐molecule analysis of the Escherichia coli replisome and use of clamps to bypass replication barriers , 2010, FEBS letters.

[37]  D. Sherratt,et al.  Visualizing genetic loci and molecular machines in living bacteria. , 2008, Biochemical Society transactions.

[38]  Paul J. Choi,et al.  Quantifying E. coli Proteome and Transcriptome with Single-molecule Sensitivity in Single Cells , 2011 .

[39]  James M. Berger,et al.  DNA replication initiation: mechanisms and regulation in bacteria , 2007, Nature Reviews Microbiology.

[40]  B. Dalrymple,et al.  A universal protein–protein interaction motif in the eubacterial DNA replication and repair systems , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[41]  M. O’Donnell,et al.  Interaction of the beta sliding clamp with MutS, ligase, and DNA polymerase I. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[42]  M. O’Donnell,et al.  Replisome Assembly Reveals the Basis for Asymmetric Function in Leading and Lagging Strand Replication , 1996, Cell.

[43]  Z. Kelman,et al.  The internal workings of a DNA polymerase clamp‐loading machine , 1999, EMBO Journal.

[44]  Z. Kelman,et al.  Clamp loading, unloading and intrinsic stability of the PCNA, β and gp45 sliding clamps of human, E. coli and T4 replicases , 1996, Genes to cells : devoted to molecular & cellular mechanisms.

[45]  Nynke H Dekker,et al.  Electron beam fabrication of a microfluidic device for studying submicron-scale bacteria , 2013, Journal of Nanobiotechnology.

[46]  T. Katayama,et al.  The Initiator Function of DnaA Protein Is Negatively Regulated by the Sliding Clamp of the E. coli Chromosomal Replicase , 1998, Cell.

[47]  T. Katayama,et al.  Protein Associations in DnaA-ATP Hydrolysis Mediated by the Hda-Replicase Clamp Complex* , 2005, Journal of Biological Chemistry.

[48]  A direct proofreader–clamp interaction stabilizes the Pol III replicase in the polymerization mode , 2013, The EMBO journal.

[49]  O. Sliusarenko,et al.  High‐throughput, subpixel precision analysis of bacterial morphogenesis and intracellular spatio‐temporal dynamics , 2011, Molecular microbiology.

[50]  K. Marians,et al.  The Interaction between Helicase and Primase Sets the Replication Fork Clock* , 1996, The Journal of Biological Chemistry.

[51]  L. Bloom,et al.  The β Sliding Clamp Closes around DNA prior to Release by the Escherichia coli Clamp Loader γ Complex* , 2012, The Journal of Biological Chemistry.

[52]  C. McHenry DNA replicases from a bacterial perspective. , 2011, Annual review of biochemistry.

[53]  Michael D. Mason,et al.  Ultra-high resolution imaging by fluorescence photoactivation localization microscopy. , 2006, Biophysical journal.

[54]  B. Michel,et al.  Polymerase Exchange During Okazaki Fragment Synthesis Observed in Living Cells , 2012, Science.

[55]  Z. Kelman,et al.  The diverse spectrum of sliding clamp interacting proteins , 2003, FEBS letters.

[56]  W. E. Moerner,et al.  Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging , 2013, Nature Reviews Microbiology.

[57]  M. J. Teixeira de Mattos,et al.  Precise determinations of C and D periods by flow cytometry in Escherichia coli K-12 and B/r. , 2003, Microbiology.

[58]  T. Katayama,et al.  Hda, a novel DnaA‐related protein, regulates the replication cycle in Escherichia coli , 2001, The EMBO journal.

[59]  Jean-Christophe Olivo-Marin,et al.  Extraction of spots in biological images using multiscale products , 2002, Pattern Recognit..

[60]  N. Costantino,et al.  E. coli genome manipulation by P1 transduction. , 2007, Current protocols in molecular biology.

[61]  J. Lippincott-Schwartz,et al.  Imaging Intracellular Fluorescent Proteins at Nanometer Resolution , 2006, Science.

[62]  Valerie C. Coffman,et al.  Counting protein molecules using quantitative fluorescence microscopy. , 2012, Trends in biochemical sciences.

[63]  R. Singer,et al.  Calibrating excitation light fluxes for quantitative light microscopy in cell biology , 2008, Nature Protocols.

[64]  K. Marians Prokaryotic DNA replication. , 1992, Annual review of biochemistry.

[65]  X. Fang,et al.  Single-molecule fluorescence imaging in living cells. , 2013, Annual review of physical chemistry.

[66]  T. Okazaki,et al.  Discontinuous DNA replication. , 1980, Annual review of biochemistry.

[67]  J. Wagner,et al.  The beta clamp targets DNA polymerase IV to DNA and strongly increases its processivity. , 2000, EMBO reports.

[68]  Patrick S Daugherty,et al.  Evolutionary optimization of fluorescent proteins for intracellular FRET , 2005, Nature Biotechnology.

[69]  Stanley R. Sternberg,et al.  Biomedical Image Processing , 1983, Computer.

[70]  B. Wanner,et al.  One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[71]  J. Wagner,et al.  All three SOS‐inducible DNA polymerases (Pol II, Pol IV and Pol V) are involved in induced mutagenesis , 2000, The EMBO journal.