Modes of Escherichia coli Dps Interaction with DNA as Revealed by Atomic Force Microscopy

Multifunctional protein Dps plays an important role in iron assimilation and a crucial role in bacterial genome packaging. Its monomers form dodecameric spherical particles accumulating ~400 molecules of oxidized iron ions within the protein cavity and applying a flexible N-terminal ends of each subunit for interaction with DNA. Deposition of iron is a well-studied process by which cells remove toxic Fe2+ ions from the genetic material and store them in an easily accessible form. However, the mode of interaction with linear DNA remained mysterious and binary complexes with Dps have not been characterized so far. It is widely believed that Dps binds DNA without any sequence or structural preferences but several lines of evidence have demonstrated its ability to differentiate gene expression, which assumes certain specificity. Here we show that Dps has a different affinity for the two DNA fragments taken from the dps gene regulatory region. We found by atomic force microscopy that Dps predominantly occupies thermodynamically unstable ends of linear double-stranded DNA fragments and has high affinity to the central part of the branched DNA molecule self-assembled from three single-stranded oligonucleotides. It was proposed that Dps prefers binding to those regions in DNA that provide more contact pads for the triad of its DNA-binding bundle associated with one vertex of the protein globule. To our knowledge, this is the first study revealed the nucleoid protein with an affinity to branched DNA typical for genomic regions with direct and inverted repeats. As a ubiquitous feature of bacterial and eukaryotic genomes, such structural elements should be of particular care, but the protein system evolutionarily adapted for this function is not yet known, and we suggest Dps as a putative component of this system.

[1]  Yuri A. Purtov,et al.  Promoter islands as a platform for interaction with nucleoid proteins and transcription factors , 2014, J. Bioinform. Comput. Biol..

[2]  C. Day,et al.  Campylobacter jejuni Dps Protein Binds DNA in the Presence of Iron or Hydrogen Peroxide , 2013, Journal of bacteriology.

[3]  Julio Collado-Vides,et al.  RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more , 2012, Nucleic Acids Res..

[4]  I. Serdyuk,et al.  Investigation of site-specific DNA binding with nicking endonuclease Nt.BspD6I at single molecule level by atomic force microscopy , 2012, Biofizika.

[5]  K. Zeth.  Dps biomineralizing proteins: multifunctional architects of nature. , 2012, The Biochemical journal.

[6]  J. Song,et al.  THE DNA-BINDING PROTEIN DPS FUNCTIONS AS A GLOBAL REGULATOR IN STARVED SALMONELLA ENTERICA SEROVAR ENTERITIDIS DURING STARVATION , 2011 .

[7]  O. Ozoline,et al.  Bacterioferritin: Properties, structural and functional organization of the dps gene regulatory region , 2011, Biofizika.

[8]  C. Griesinger,et al.  Indirect DNA Readout by an H-NS Related Protein: Structure of the DNA Complex of the C-Terminal Domain of Ler , 2011, PLoS pathogens.

[9]  F. Dahlquist,et al.  The design involved in PapI and Lrp regulation of the pap operon. , 2011, Journal of molecular biology.

[10]  D. Chatterji,et al.  Unveiling the Role of Dps in the Organization of Mycobacterial Nucleoid , 2011, PloS one.

[11]  E. Chiancone,et al.  The multifaceted capacity of Dps proteins to combat bacterial stress conditions: Detoxification of iron and hydrogen peroxide and DNA binding. , 2010, Biochimica et biophysica acta.

[12]  O. Ozoline,et al.  Antisense transcription within the hns locus of Escherichia coli , 2010, Molecular Biology.

[13]  Reid C. Johnson,et al.  The shape of the DNA minor groove directs binding by the DNA-bending protein Fis. , 2010, Genes & development.

[14]  Christian L. Barrett,et al.  Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli , 2008, Proceedings of the National Academy of Sciences.

[15]  Byung-Kwan Cho,et al.  Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. , 2008, Genome research.

[16]  M. Vijayan,et al.  Structural studies on the second Mycobacterium smegmatis Dps: invariant and variable features of structure, assembly and function. , 2008, Journal of molecular biology.

[17]  I. Yamashita,et al.  Cadmium Sulfide Nanoparticle Synthesis in Dps Protein from Listeria innocua , 2007 .

[18]  M. Buckle,et al.  H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing , 2007, Nature Structural &Molecular Biology.

[19]  E. Chiancone,et al.  The neutrophil-activating Dps protein of Helicobacter pylori, HP-NAP, adopts a mechanism different from Escherichia coli Dps to bind and condense DNA , 2007, Nucleic acids research.

[20]  J. Perona,et al.  Structure of the Escherichia coli leucine-responsive regulatory protein Lrp reveals a novel octameric assembly. , 2007, Journal of molecular biology.

[21]  A. Minsky,et al.  Nucleoid organization and the maintenance of DNA integrity in E. coli, B. subtilis and D. radiodurans. , 2006, Journal of structural biology.

[22]  E. Chiancone,et al.  Reassessment of Protein Stability, DNA Binding, and Protection of Mycobacterium smegmatis Dps* , 2005, Journal of Biological Chemistry.

[23]  T. J. Stillman,et al.  The crystal structures of Lactococcus lactis MG1363 Dps proteins reveal the presence of an N‐terminal helix that is required for DNA binding , 2005, Molecular microbiology.

[24]  E. A. Rogulin,et al.  Plasmid pRARE as a Vector for Cloning to Construct a Superproducer of the Site-Specific Nickase N.BspD6I , 2004, Biochemistry (Moscow).

[25]  S. Wolf,et al.  Nucleoid restructuring in stationary‐state bacteria , 2004, Molecular microbiology.

[26]  E. Chiancone,et al.  The Dps Protein of Agrobacterium tumefaciens Does Not Bind to DNA but Protects It toward Oxidative Cleavage , 2003, Journal of Biological Chemistry.

[27]  E. Margeat,et al.  The H-NS dimerization domain defines a new fold contributing to DNA recognition , 2003, Nature Structural Biology.

[28]  D. Chatterji,et al.  Bimodal Protection of DNA by Mycobacterium smegmatis DNA-binding Protein from Stationary Phase Cells* , 2003, The Journal of Biological Chemistry.

[29]  Andrea Ilari,et al.  Iron Incorporation into Escherichia coli Dps Gives Rise to a Ferritin-like Microcrystalline Core* , 2002, The Journal of Biological Chemistry.

[30]  R. G. Lloyd,et al.  Holliday junction binding and processing by the RuvA protein of Mycoplasma pneumoniae. , 2002, European journal of biochemistry.

[31]  R. Kolter,et al.  Regulated phase transitions of bacterial chromatin: a non‐enzymatic pathway for generic DNA protection , 2001, The EMBO journal.

[32]  C. Higgins,et al.  The nucleoid-associated protein StpA binds curved DNA, has a greater DNA-binding affinity than H-NS and is present in significant levels in hns mutants. , 2001, Biochimie.

[33]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[34]  Akira Ishihama,et al.  Two types of localization of the DNA‐binding proteins within the Escherichia coli nucleoid , 2000, Genes to cells : devoted to molecular & cellular mechanisms.

[35]  A. Ishihama,et al.  Twelve Species of the Nucleoid-associated Protein from Escherichia coli , 1999, The Journal of Biological Chemistry.

[36]  S. Ueda,et al.  Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid , 1999, Journal of bacteriology.

[37]  R. Kolter,et al.  DNA protection by stress-induced biocrystallization , 1999, Nature.

[38]  Anca M. Segall,et al.  In Vitro Selection of Integration Host Factor Binding Sites , 1999, Journal of bacteriology.

[39]  R. Kolter,et al.  The crystal structure of Dps, a ferritin homolog that binds and protects DNA , 1998, Nature Structural Biology.

[40]  M. V. Petrova,et al.  Slipped loop structure of DNA: a specific nucleotide sequence forms only one unique conformer , 1998, FEBS letters.

[41]  A Martinez,et al.  Protection of DNA during oxidative stress by the nonspecific DNA-binding protein Dps , 1997, Journal of bacteriology.

[42]  Phoebe A Rice,et al.  Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn , 1996, Cell.

[43]  G. Shaw,et al.  Anatomy of a Flexer–DNA Complex inside a Higher-Order Transposition Intermediate , 1996, Cell.

[44]  B. Castaing,et al.  HU Protein of Escherichia coli Binds Specifically to DNA That Contains Single-strand Breaks or Gaps (*) , 1995, The Journal of Biological Chemistry.

[45]  E. Bonnefoy,et al.  DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. , 1994, Journal of molecular biology.

[46]  Roberto Kolter,et al.  The dps promoter is activated by OxyR during growth and by IHF and σs in stationary phase , 1994, Molecular microbiology.

[47]  T. Mizuno,et al.  An analogue of the DnaJ molecular chaperone in Escherichia coli. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[48]  R. Kolter,et al.  A novel DNA-binding protein with regulatory and protective roles in starved Escherichia coli. , 1992, Genes & development.

[49]  R. Dickerson,et al.  The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[50]  A. Ishihama,et al.  Bipartite functional map of the E. coli RNA polymerase α subunit: Involvement of the C-terminal region in transcription activation by cAMP-CRP , 1991, Cell.

[51]  C. Dorman.  Nucleoid-associated proteins and bacterial physiology. , 2009, Advances in applied microbiology.

[52]  E. Chiancone,et al.  DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. , 2004, Nucleic acids research.

[53]  P. Landini,et al.  S-Dependent Gene Expression at the Onset of Stationary Phase in Escherichia coli : Function of S-Dependent Genes and Identification of Their Promoter Sequences † , 2004 .

[54]  N. Guex,et al.  SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling , 1997, Electrophoresis.