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Chapter 5 : Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome

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Abstract:

This chapter focuses on the major nucleoid-associated proteins and summarizes one's current knowledge of how these proteins contribute to the structure of the nucleoid and function in specific reactions involving the chromosome. The current view is that the nucleoid is dominated by five different proteins: HU, integration host factor (IHF), H-NS, StpA and Fis under nutrient-rich exponential growth conditions. HU mutant cells display the most severe and varied phenotypes in comparison to strains containing mutations in the other major nucleoid proteins. Supercoiling of chromosomal and plasmid DNA is partially relaxed in mutants lacking HU, supporting an in vivo role for HU in regulating the degree of supercoiling. HU plays several interconnected roles in DNA replication and appears to be involved in several steps involving initiation of chromosomal DNA synthesis, chromosomal partitioning, and cell division. The genes that were differentially expressed were examined for putative IHF binding sites in the 500 bp upstream of the transcription initiation site. The criteria for identifying high-affinity sites were that the sites must have a 12 out of 13 bp match with the core consensus sequence and that at least 10 of the 15 bp 5' (upstream) to the core consensus must be dA-dT base pairs. The study identified 46 candidates that matched the criteria, some of which were documented in other studies. The study also identified seven genes, including , that were expressed only when IHF was present and eight genes that were expressed only in IHF-deficient cells.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5

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Gene Expression and Regulation
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Outer Membrane Proteins
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DNA Synthesis
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Chromosomal DNA
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Figures

Image of Figure 1.
Figure 1.

DAPI-stained cells highlighting the nucleoids. (A) MG1655 wild-type cells. (B) MG1655 mutants. Cells are often filamented with decondensed nucleoids ( ). Anucleated cells, which constitute about 10% of the population, are denoted with arrows. (C) MG1655 mutants expressing the HMGB protein NHP6A ( ). Cell and nucleoid morphology is similar to that of wild type. (D) MG1655 mutants. Cells are often elongated with multiple condensed nucleoids. The arrow points to a budding minicell, which has also been observed in mutant cell populations by Spaeny-Dekking et al. ( ). Cells grown in Luria broth were stained with DAPI by the method of Hiraga ( ). Similar preparations of or mutant cells do not show significant differences from wild type.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 2.
Figure 2.

Amino acid sequence alignment of members of the HU family. The sequences are identified by the species from whose genome they originated and their National Center for Biotechnology Information (NCBI) GenInfo Identifier (GI) number. The HU sequences were obtained by searching the SWISSPROT database for “DBH.” The NCBI PSI-BLAST program was used with HUα and HUβ query sequences to obtain additional HU sequences not contained in the SWISSPROT database. Sequences not described as HU, histonelike DNA binding protein, or DNA binding protein were discarded. The alignment is numbered according to the HU sequence. The sequences were aligned by using Blosum62-12-2 ( ) at the website http://prodes.toulouse.inra.fr/multalin/multalin.html. The following settings were used: the symbol comparison table was blosum 62, the gap weight was 12, and the gap length weight was 2. Overall consensus notation: a lowercase letter indicates the residue is found in 50 to 74% of sequences and is shaded gray where conserved. An uppercase letter indicates the residue is found in 75 to 100% of sequences overall, and the background is black where conserved. # indicates I or V residues are found in 75 to 100% of the sequences; the conserved sequences are boxed by a solid line. ¥ indicates that F, L, I, or V residues are found at this position 90 out of 97 times; the conserved sequences are boxed by a broken line. ^ indicates that T or K residues are found 60 out of 97 times at this position; the conserved sequences are boxed by a double line. § indicates that I, L, M, or V residues are found 94 out of 97 times at this position; the conserved sequence is boxed by a broken line. † indicates that P or A residues are found 72 out of 97 times at position 72, and 81 out of 97 times at position 81. The conserved sequences are boxed by a broken line and are white with a gray background. Local consensus notation: a lowercase letter indicates the residue is found in 50 to 74% of sequences locally. An uppercase letter indicates the residue is found in 75 to 100% of sequences locally. # indicates I or V residues are found in 75 to 100% of the sequences. $ indicates L or F residues are found in 75 to 100% of the sequences. % indicates I or M residues are found in 75 to 100% of the sequences. @ indicates V or A residues are found in 75 to 100% of the sequences. An asterisk below the residue in the local consensus indicates that residue is absolutely conserved in that local grouping. Secondary structure: the secondary structure cartoon shown below the alignments is based on the crystal structure of the HU homodimer performed by Tanaka et al. (414) (Protein Data Bank [PDB] accession code 1HUU). The secondary structure is as follows: a1 helix residues 3 to 13, α2 helix residues 21 to 37, β1-strand residues 40 to 44, β2-strand residues 48 to 51, “arm” region residues 52 to 77, β3-strand residues 78 to 83, and α3 helix residues 84 to 89.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 3.
Figure 3.

The crystal structure of HU from ( ). The α-helices (α1, α2, and α3) are indicated for the subunit shown in white, and the antiparallel β-sheet (β1-, β2-, and β3-strands) are indicated for the dark subunit. Residues 59 to 69 in the arms of the monomers are disordered and are not shown. (A and B) Two different views of the structure with the arms extended on each side. (Courtesy of P. Rice.)

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 4.
Figure 4.

The structure of the homodimeric HU from (K. Swinger and P. Rice, personal communication). The positions of the prolines that intercalate into the DNA are shown near the ends of the two β-ribbon arms. The α-helices of one subunit (α1, α2, and α3) are labeled. The β2'- and β3'-strands that are not visible in the HU structure are revealed in the HU-DNA complex. (Courtesy of P. Rice.)

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 5.
Figure 5.

The structure of HU bound to DNA (Swinger and Rice, personal communication). (A) The structure of three HU-DNA complexes as they are aligned in the crystal. Two thymines in each complex are flipped out. (B) A single HUDNA complex (dark shading) is superimposed over the IHF-DNA crystal structure (light shading) ( ). The T residues that are flipped out of the HU-DNA complex are shown. (Courtesy of P. Rice.)

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 6.
Figure 6.

Organization of the upstream regulatory sequences of the (top) and (bottom) genes ( ). The gene has three promoters designated P2, P3, and P4; the numbering is relative to the P3 start site ( ). An additional promoter (P1) initiating transcription at about -10 relative to the ATG of was described by Kohno et al. ( ) but not observed by Claret and Rouviere-Yaniv ( ). The four Fis binding sites (I, II, III, and IV [gray boxes]) upstream of the start of transcription of , the start site (indicated by an arrow), and the CRP site are shown. Transcription of is stimulated by CRP and repressed by Fis (sites I, II, III, and Ii). The Fis site I and the downstream site Ii are required for repression. Binding of CRP prevents Fis binding to site I and relieves repression of promoter P3.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 7.
Figure 7.

The HU-dependent repression loop complex of the operon ( ). In the presence of supercoiled DNA, GalR dimers bind to the O and O operators and form a DNA loop. Specific protein-protein interactions between HU and GalR facilitate recruitment of HU to the DNA complex. This association may be transient, or GalR and HU may continue to contact each other in the repression complex ( ).

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 8.
Figure 8.

Site-specific DNA inversion by the Hin and Gin recombinases. (A) Structures of the Hin-catalyzed flagellar phase variation control region from serovar Typhimurium ( ) and the Gin-catalyzed G inversion segment from phage Mu that controls tail fiber gene expression ( ). The recombination sites () are designated by triangles, and the coding regions are designated by gray bars. A recombinational enhancer sequence is located within the N-terminal segments of the and coding sequences. Fis binds to two essential sites within the enhancers. In the Hin system, and code for the H2 form of flagellin and a repressor of the unlinked flagellin gene, respectively. In this orientation of the invertible segment, the cell expresses the H2 flagellin, which is transcribed from the σ-dependent promoter located within the 996-bp invertible segment. In the Gin system, a constant 5' region is linked to the alternate forms of the 3' regions of the S gene, depending on the orientation of the 3,015-bp invertible segment. (B) Pathway leading to Hin-catalyzed site-specific DNA inversion ( ). Hin and Fis bind (ii) to their respective binding sites in the starting supercoiled plasmid substrate (i). (iii) An invertasome complex is assembled at the base of a supercoiled DNA branch. Within this complex Fis activates Hin to coordinately cleave both DNA strands within each recombination site. HU facilitates the looping of DNA between the recombination site and the enhancer, which are about 100 bp apart in their native context. (iv) DNA exchange is accompanied by a 180° clockwise rotation of duplex DNA strands to invert the internal segment (v).

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 9.
Figure 9.

Structure of the Mu transpososome ( ). MuA monomers bind to (L1, L2, and L3) sites and (R1, R2, and R3) sites to initiate transpososome assembly. The stabilization of a loop between the L1 and L2 sites by HU is believed to be required for assembly of the catalytically competent transpososome. The relative positions of the HU-α and HU-β subunits are shown. The MuA protomers at the L3 and R3 binding sites are loosely associated and not required for transpososome function.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 10.
Figure 10.

Alignment of the α and β subunits,members of the IHF family. The sequences are identified by the species fromwhose genome they originated and their NCBI GI number. The IHF sequences were obtained by searching the SWISSPROT database for “IHF” and for “integration host factor.” The NCBI PSI-BLAST program was used with IHFα and IHFβ query sequences to obtain additional IHF sequences not contained in the SWISSPROT database. Sequences not described as integration host factor were discarded. The alignments were performed as described in the legend to Fig. 2 and numbered according to the IHF sequences. Consensus notation: a lowercase letter indicates the residue is found in 50 to 74% of sequences overall and is shaded gray where conserved. An uppercase letter indicates the residue is found in 75 to 100% of sequences overall, and the background is black where conserved. The # indicates that I or V residues are found in 75 to 100%of the sequences and are boxed by a solid line. The indicates that I, L, orMis always found at this position, and the residues are boxed by a solid line. Secondary structure: the secondary structure cartoon shown below the alignments is based on the crystal structure of the IHF-DNA complex ( ) (PDB accession code, 1IHF). The secondary structure elements for the α subunit are as follows: α1 helix residues 5 to 14, α2 helix residues 20 to 39, β1-sheet residues 44 to 46, β2-sheet residues 50 to 57, β2'-sheet residues 60 to 63, β3'-sheet residues 70 to 73, β3- sheet residues 76 to 83, and α3 helix residues 85 to 91. The secondary structure elements for the b subunit are as follows: a1 helix residues 3 to 13, a2 helix residues 19 to 38, β1-sheet residues 43 to 45, β2-sheet residues 49 to 56, β2'-sheet residues 59 to 62, β3'-sheet residues 69 to 72, β3-sheet residues 75 to 82, and α3 helix residues 84 to 90.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 11.
Figure 11.

Structure of IHF bound to the H0 site ( ). (A) Crystal packing of IHF and DNA with seven asymmetric units shown ( ). The DNA forms a serpentinelike helix that zigzags through the crystal. (B) A single IHF-H' DNA complex. The α subunit (dark gray) and the β subunit (light gray) are shown. The six consecutive dT residues of the dA-dT-rich element are shown on the left. The WATCAA element (shown as the opposite strand: ATAGTT) is on the top of the complex and the TTR element (shown as AAC) is on the right. The arms of the α and β subunits interact with the minor groove of the DNA. The DNA is bent around the protein to generate a bend angle of more than 1608. (Courtesy of P. Rice.)

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 12.
Figure 12.

Site-specific recombination by bacteriophage l ( ). The 250-bp phage attachment site () contains multiple binding sites for Int and accessory proteins. Int binds to five arm sites (designated P1, P2, P'1, P'2, and P'3) and two core-type sites (designated C and C'). IHF binds to three sites (designated H1, H2, and H'). Xis binds to two sites (designated X1 and X2), and Fis binds to a single site (designated F). Binding of Fis to the F site and binding of Xis to the X2 site are mutually exclusive. Recombination between and the bacterial attachment site () generates the recombinant and sites. Int and IHF are required for integration, and Int, IHF, and Xis are required for excision. Excision is also stimulated by Fis.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 13.
Figure 13.

Structure of the λ intasome ( ). IHF binds to the H0 site located between the core C' site and the arm P'1 site. An Int monomer forms a bridge, where its N-terminal domain binds the P'1 site and the C-terminal domain binds the C0 core site. An Int monomer bound to the P'2 site forms a interaction with the partner site (not shown) (

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 14.
Figure 14.

Activation of the λ PL promoter by IHF ( ). Binding of IHF induces a bend in the DNA that brings the UP (thick gray line) sequence closer to the promoter. This allows the αCTD of RNA polymerase to make contact with the UP element and stimulate transcription.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 15.
Figure 15.

Activation of the promoter by IHF ( ). The dA+dT-rich region upstream of the IHF binding site is destabilized by superhelical stress. When IHF binds, the superhelical stress is transferred downstream to the promoter to facilitate destabilization of the duplex in the -10 region, thereby increasing the rate of open complex formation by RNA polymerase.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 16.
Figure 16.

Regulation of by IHF, Fis, and H-NS ( ). (Top) Organization of the Fis (I and II), IHF, NarL/P, and FNR binding sites within the promoter region. (Middle) Binding of IHF, H-NS, and Fis forms a complex that inhibits transcription initiation. (Bottom) It has been proposed that binding of phospho-NarL/NarP displaces IHF from the complex. This facilitates interactions between RNA polymerase and upstream sequences, resulting in activation of transcription.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 17.
Figure 17.

Organization of the origin of replication. The black boxes indicate the DnaA binding sites R1, R2, R3, R4, and R5(M). The gray boxes indicate the weaker DnaA-ATP binding sites I1, I2, and I3 that are detected by dimethyl sulfate footprinting in the presence of IHF ( ). (A) During the majority of the cell cycle DnaA is bound to the R1, R2, and R4 sites, and the Fis protein is also bound. (B) During prereplication a nucleoprotein complex is formed in which all the R sites and weaker I sites are bound by DnaA. At this time, IHF is bound and Fis is absent. HU or IHF facilitates the DnaA-ATP-dependent unwinding of the DNA duplex in the region of the 13-bp direct repeats, which then enables loading of the DnaBC helicase plus other replication proteins to form the replication competent complex ( ).

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 18.
Figure 18.

Alignment of H-NS family members. The sequences are identified by the species from whose genome they originated and their NCBI GI number. The H-NS sequences were obtained by searching the SWISSPROT database, excluding eukaryotic sequences, for “hns.” Also, the NCBI PSI-BLAST program was used with H-NS and StpA query sequences to obtain additional H-NS sequences not present in the SWISSPROT database. Sequences not described as H-NS, StpA, histonelike DNA binding protein, or DNA binding protein were discarded. Sequences identified as StpA are denoted as such. The sequences were aligned as described in the legend to Fig. 2 and numbered according to the H-NS sequence. Consensus notation: a lowercase letter indicates the residue is found in 50 to 74% of sequences overall and is shaded gray where conserved. An uppercase letter indicates the residue is found in 75 to 100% of sequences overall, and the background is black where conserved. £ indicates that I or L residues are found 16 out of 17 times at this position, and the conserved residues are boxed by a solid line. Secondary structure: the secondary structure cartoon shown below the alignments is based on the structures determined by Esposito et al. ( ) (PDB accession code 1LR1) and Shindo et al. ( ) (PDB accession codes 1HNR and 1HNS). The secondary structure elements are as follows: a-helixes at residues 2 to 7, 10 to 16, 22 to 49, 117 to 125, and 130 to 133 (3-helix), and β-strands at residues 97 to 101 and 106 to 109. The structure of the region between residues 50 and 96 is not known and is marked with a dotted line.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 19.
Figure 19.

H-NS domain structures. The structure of the Nterminal domain that mediates dimerization and is involved in the formation of higher-order H-NS oligomers is from the NMR study of residues 1 to 57 ( ). A recent NMR-based structure of residues 1 to 46 of the E. coli H-NS dimer peptide revealed that the long α3-helices are associated in an antiparallel orientation; a similar configuration was also observed in a crystal structure of the N-terminal domain of an H-NS homologue from (see Addendum in Proof). The structure of the C-terminal trypsinresistant domain (residues 90 to 137) that mediates DNA binding is from Shindo et al. ( ). The locations of residues implicated as being close to DNA by NMR chemical shift mapping ( ) or by the properties of mutant proteins ( ) are highlighted with spheres. The structurally undefined region between residues 57 and 90 that links the two domains is important for higher-order oligomerization ( ). Computer-based analysis predicts that this linker region is mostly a-helical with a centrally located unstructured region or b-turn.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 20.
Figure 20.

Bridging of DNA segments by H-NS. (A to C) Atomic force microscopy images of nicked pUC19 without (A) and with (B and C) addition of H-NS showing H-NS-mediated filaments associating two DNA segments ( ). (D to F) Atomic force microscopy images of a 1.2-kbDNAfragment containing the promoter region and RNA polymerase ( ). H-NS was added to the reactions in panels E and F. In the presence of H-NS, RNA polymerase is able to form open complexes that are competent for abortive initiation but not elongation ( ). (Images kindly provided by Remus Dame, Nora Goosen, and Claire Wyman.)

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 21.
Figure 21.

Examples of H-NS-regulated genes. Regulatory regions for the gene, operon, operon, operon, and gene are depicted; the transcription initiation sites are indicated with arrows. Centers of curved DNA are indicated with a caret (^). Primary H-NS control regions are shown with black boxes, and Fis binding sites are depicted with gray boxes. Binding sites were determined by DNase I footprinting in the (five of the seven Fis sites are shown) ( ), rrnB P1 ( ), and virF promoter regions ( ). The upstream and downstream regulatory regions required for H-NS regulation of bgl were determined by deletion analysis ( ). The negative regulatory element (NRE) in the proU operon control region is depicted, as determined by deletion analysis ( ). High-affinity H-NS binding occurs within multiple discrete regions throughout the negative regulatory element, particularly between about +60 and +180, and coating extends to cover the entire promoter region at higher concentrations of H-NS ( ).

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 22.
Figure 22.

Alignment of Fis homologues. The sequences are identified by the species from whose genome they originated and their NCBI GI number. The Fis sequences were obtained by searching the SWISSPROT database, excluding eukaryotic sequences, for “Fis” or “factor for inversion stimulation.” Also, the NCBI PSI-BLAST program was used with the Fis query sequence to obtain additional Fis sequences not contained in the SWISSPROT database. Sequences described as “Fislike” DNA binding protein are marked with an asterisk. Sequences not described as Fis or Fis-like DNA binding protein or DNA binding protein were discarded. The alignment was performed as described in the legend to Fig. 2 and is numbered according to the Fis sequence. Consensus notation: a lowercase letter indicates the residue is found in 50 to 74% of sequences overall and is shaded gray where conserved. An uppercase letter indicates the residue is found in 75 to 100% of sequences overall, and the background is black where conserved. # indicates that I or V residues are found in 75 to 100% of the sequences and are boxed by a solid line. ¢ indicates that L or M residues are found in 75 to 100% of the sequences and are boxed by a solid line. Secondary structure: the secondary structure designation shown below the alignment is based on the crystal structures of Fis by Kostrewa et al. ( ) (PDB accession code 1FIA), Yuan et al. ( ) (PDB accession code 3FIS), and Cheng et al. ( ) (PDB accession code 1ETY) and of Fis mutant K36E by Safo et al. ( ) (PDB accession code 1F36). The secondary structure elements are follows: β1-strand residues 12 to 16, β2-strand residues 22 to 26, αA-helix residues 27 to 40, αB-helix residues 50 to 70, αC-helix residues 74 to 81, and αD-helix residues 85 to 94.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 23.
Figure 23.

X-ray crystal structure of Fis. Shown is the structure of the Fis mutant K36E in which the β-arms (β1 and β2 plus connecting turn) are resolved ( ). The polypeptide chain for both subunits starts at residue 10. The locations of some of the functionally or structurally important side chains are shown and labeled for one of the subunits. The secondary structure elements are labeled for the other subunit.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 24.
Figure 24.

Fis consensus binding sequence. The 15-bp core recognition sequence is in bold capital letters, with the size reflecting the degree of conservation ( ). Y indicates C or T, R indicates A or G, W indicates A or T, and N is no obvious preference. Ten base pairs of flanking sequences denoted in lowercase letters are shown; the left flanking sequence is from the hin enhancer proximal site, where little bending is observed, and the right flanking sequence is from the λ F binding site, which displays a large amount of bending (see reference ). DNase I typically generates an interrupted protection pattern over the Fis binding site; the positions designated with an arrow are often hypersensitive to cleavage. Protections from dimethyl sulfate reactivity on guanines, when present in the sequence, are denoted by asterisks. Positions of oxidative cleavage by 1,10-phenanthroline–copper when tethered to Fis residues 71 or 73 are designated by solid triangles; on these flanking sequences, poor cleavage is obtained on the left side whereas strong cleavage is obtained on the right side ( ). Positions designated from below refer to locations in the bottom DNA strand, which is not shown.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 25.
Figure 25.

Models of Fis-DNA complexes ( ). (A) Fis binding to DNA without the sequences flanking the core binding site contacting the protein. A ribbon representation of residues 249 to 320 of the α subunit of RNA polymerase ( ) is also shown docked to the B-C turn region of Fis ( ). Residues 271 to 273 specifying the region contacted by Fis on the αCTD are light gray. (B) Fis binding to DNA where the flanking sequences are wrapped along the sides of Fis such that backbone contacts are made by Arg-71 and Asn-73.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 26.
Figure 26.

Examples of genes negatively regulated by Fis. Specific Fis binding sites are denoted as gray boxes. The extended region from contains six Fis binding sites ( ). Also shown is an IHF binding site that negatively regulates transcription ( ). Several low-affinity CRP binding sites are not shown ( ). In serovar Typhimurium, Fis binding sites corresponding to -83 and -143 are weaker than those in , and there is no high-affinity site around position -101 ( ). is expressed preferentially in stationary phase by the RpoS (σ) form of RNA polymerase. Fis represses whereas CRPcAMP activates transcription ( ). The 370-bp intercistronic region between the divergently transcribed and genes is depicted, and the Fis binding sites are numbered relative to the closest promoter (S. McLeod, J. Xu, and R. Johnson, unpublished data). Fis has been reported to repress transcription at a late step during transcription initiation, since open complex formation is not affected by Fis ( ).

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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Image of Figure 27.
Figure 27.

Examples of Fis-activated genes. (A) Fis binds to multiple sites upstream of the promoter regions in ( ), ( ), and ( ). Most of the activation at occurs from the promoter proximal site centered at -71 through a direct interaction with the aCTD of RNA polymerase ( ). In addition to the proximal site, the upstream sites are required for efficient activation at and ( ). Fis activation at the RpoS-dependent P2 promoter occurs from the binding site at -41 ( ). CRP bound at -121 coactivates P2 transcription in a Fis-dependent manner ( ). Transcription from the P1 promoter is strongly inhibited by CRP by an osmotically dependent mechanism ( ) and is weakly inhibited by Fis bound at -81. (B) Schematic models of the Fis-activated transcription initiation complexes at the P1 (left panel) and P2 (right panel) promoters ( ). There is a small preference for Fis activating through contacts with the αCTD over the αCTD at but a large preference at . Coactivation by CRP at P2 requires both αCTD subunits and the strong preference for Fis activation through the αCTD.

Citation: Johnson R, Johnson L, Schmidt J, Gardner J. 2005. Major Nucleoid Proteins in the Structure and Function of the Escherichia coli Chromosome, p 65-132. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch5
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