scholarly journals Genetic Analysis, Using P22 Challenge Phage, of the Nitrogen Activator Protein DNA-Binding Site in the Klebsiella aerogenes put Operon

1998 ◽  
Vol 180 (3) ◽  
pp. 571-577 ◽  
Author(s):  
Li-Mei Chen ◽  
Thomas J. Goss ◽  
Robert A. Bender ◽  
Simon Swift ◽  
Stanley Maloy
Keyword(s):  
Escherichia Coli ◽  
Dna Binding ◽  
Genetic Analysis ◽  
Nitrogen Assimilation ◽  
Regulatory Protein ◽  
Klebsiella Aerogenes ◽  
Dna Binding Site ◽  
Control Protein

ABSTRACT The nac gene product is a LysR regulatory protein required for nitrogen regulation of several operons fromKlebsiella aerogenes and Escherichia coli. We used P22 challenge phage carrying the put control region from K. aerogenes to identify the nucleotide residues important for nitrogen assimilation control protein (NAC) binding in vivo. Mutations in an asymmetric 30-bp region prevented DNA binding by NAC. Gel retardation experiments confirmed that NAC specifically binds to this sequence in vitro, but NAC does not bind to the corresponding region from the put operon of Salmonella typhimurium, which is not regulated by NAC.

scholarly journals The Amino-Terminal 100 Residues of the Nitrogen Assimilation Control Protein (NAC) Encode All Known Properties of NAC from Klebsiella aerogenes and Escherichia coli

1999 ◽  
Vol 181 (3) ◽  
pp. 934-940 ◽  
Author(s):  
Wilson B. Muse ◽  
Robert A. Bender
Keyword(s):  
Escherichia Coli ◽  
Amino Acids ◽  
Nitrogen Assimilation ◽  
Factor Xa ◽  
Klebsiella Aerogenes ◽  
Reading Frame ◽  
Amino Terminal ◽  
Control Protein

ABSTRACT The nitrogen assimilation control protein (NAC) fromKlebsiella aerogenes or Escherichia coli(NACK or NACE, respectively) is a transcriptional regulator that is both necessary and sufficient to activate transcription of the histidine utilization (hut) operon and to repress transcription of the glutamate dehydrogenase (gdh) operon in K. aerogenes. Truncated NAC polypeptides, generated by the introduction of stop codons within thenac open reading frame, were tested for the ability to activate hut and repress gdh in vivo. Most of the NACK and NACE fragments with 100 or more amino acids (wild-type NACK and NACE both have 305 amino acids) were functional in activating hut and repressing gdh expression in vivo. Full-length NACK and NACE were isolated as chimeric proteins with the maltose-binding protein (MBP). NACK and NACE released from such chimeras were able to activatehut transcription in a purified system in vitro, as were NACK129 and NACE100 (a NACKfragment of 129 amino acids and a NACE fragment of 100 amino acids) released from comparable chimeras. A set of NACE and NACK fragments carrying nickel-binding histidine tags (his6) at their C termini were also generated. All such constructs derived from NACE were insoluble, as was NACE itself. Of the his6-tagged constructs derived from NACK, NACK100 was inactive, but NACK120 was active. Several NAC fragments were tested for dimerization. NACK120-his6 and NACK100-his6 were dimers in solution. MBP-NACK and MBP-NACK129 were monomers in solution but dimerized when the MBP was released by cleavage with factor Xa. MBP-NACE was readily cleaved by factor Xa, but the resulting NACE was also degraded by the protease. However, MBP-NACE-his6 was completely resistant to cleavage by factor Xa, suggesting an interaction between the C and N termini of this protein.

scholarly journals Nitrogen Regulation of the codBA (Cytosine Deaminase) Operon from Escherichia coli by the Nitrogen Assimilation Control Protein, NAC

2003 ◽  
Vol 185 (9) ◽  
pp. 2920-2926 ◽  
Author(s):  
Wilson B. Muse ◽  
Christopher J. Rosario ◽  
Robert A. Bender
Keyword(s):  
Escherichia Coli ◽  
Nitrogen Assimilation ◽  
Cytosine Deaminase ◽  
In Vitro Transcription ◽  
Dependent Manner ◽  
E Coli ◽  
Different Response ◽  
Control Protein

ABSTRACT Transcription of the cytosine deaminase (codBA) operon of Escherichia coli is regulated by nitrogen, with about three times more codBA expression in cells grown in nitrogen-limiting medium than in nitrogen-excess medium. β-Galactosidase expression from codBp-lacZ operon fusions showed that the nitrogen assimilation control protein NAC was necessary for this regulation. In vitro transcription from the codBA promoter with purified RNA polymerase was stimulated by the addition of purified NAC, confirming that no other factors are required. Gel mobility shifts and DNase I footprints showed that NAC binds to a site centered at position −59 relative to the start site of transcription and that mutants that cannot bind NAC there cannot activate transcription. When a longer promoter region (positions −120 to +67) was used, a double footprint was seen with a second 26-bp footprint separated from the first by a hypersensitive site. When a shorter fragment was used (positions −83 to +67), only the primary footprint was seen. Nevertheless, both the shorter and longer fragments showed NAC-mediated regulation in vivo. Cytosine deaminase expression in Klebsiella pneumoniae was also regulated by nitrogen in a NAC-dependent manner. K. pneumoniae differs from E. coli in having two cytosine deaminase genes, an intervening open reading frame between the codB and codA orthologs, and a different response to hypoxanthine which increased cod expression in K. pneumoniae but decreased it in E. coli.

scholarly journals In Vitro and in Vivo Function of the C-Terminus of Escherichia Coli Single-Stranded DNA Binding Protein

1996 ◽  
Vol 24 (14) ◽  
pp. 2706-2711 ◽  
Author(s):  
U. Curth ◽  
J. Genschel ◽  
C. Urbanke ◽  
J. Greipel
Keyword(s):  
Escherichia Coli ◽  
Dna Binding ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Single Stranded Dna ◽  
C Terminus

scholarly journals Separate physiological roles of specific and non-specific DNA binding of HU protein in Escherichia coli

2021 ◽  
Author(s):  
Sankar Adhya ◽  
Subhash Verma
Keyword(s):  
Escherichia Coli ◽  
Dna Binding ◽  
Protein Interactions ◽  
Specific Binding ◽  
Bacterial Genome ◽  
Dna Structure ◽  
Binding Modes ◽  
Chromosomal Dna

Conserved in bacteria, the histone-like protein HU is crucial for genome organization and expression of many genes. It binds DNA regardless of the sequence and exhibits two binding affinities in vitro, low-affinity to any B-DNA (non-specific) and high-affinity to DNA with distortions like kinks and cruciforms (structure-specific), but the physiological relevance of the two binding modes needed further investigation. We validated and defined the three conserved lysine residues, K3, K18, and K83, in Escherichia coli HU as critical amino acid residues for both non-specific and structure-specific binding and the conserved proline residue P63 additionally for only the structure-specific binding. By mutating these residues in vivo, we showed that two DNA binding modes of HU play separate physiological roles. The DNA structure-specific binding, occurring at specific sites in the E. coli genome, promotes higher-order DNA structure formation, regulating the expression of many genes, including those involved in chromosome maintenance and segregation. The non-specific binding participates in numerous associations of HU with the chromosomal DNA, dictating chromosome structure and organization. Our findings underscore the importance of DNA structure in transcription regulation and promiscuous DNA-protein interactions in a dynamic organization of a bacterial genome.

scholarly journals Transcriptional Control of the Mycobacterial embCAB Operon by PknH through a Regulatory Protein, EmbR, In Vivo

2006 ◽  
Vol 188 (8) ◽  
pp. 2936-2944 ◽  
Author(s):  
Kirti Sharma ◽  
Meetu Gupta ◽  
Monika Pathak ◽  
Nidhi Gupta ◽  
Anil Koul ◽  
...  
Keyword(s):  
Dna Binding ◽  
Transcriptional Control ◽  
Regulatory Protein ◽  
Binding Activity ◽  
In Vivo Studies ◽  
Promoter Regions ◽  
Signaling Mechanism ◽  
Dna Binding Activity

ABSTRACT EmbR, a putative transcriptional regulator from Mycobacterium tuberculosis, is homologous to the OmpR class of transcriptional regulators that possess winged helix-turn-helix DNA binding motifs. In contrast to other OmpR-like response regulators that are usually phosphorylated and controlled by histidine kinases, EmbR was recently shown to be phosphorylated by the cognate mycobacterial serine/threonine kinase PknH. Despite the in vitro evidence of phosphorylation and interaction between the kinase and regulator, the physiological function of the PknH-EmbR pair is still unknown. We identify the embCAB operon encoding arabinosyltransferases in M. tuberculosis as the cellular target of EmbR. Phosphorylation of EmbR enhances its DNA binding activity towards promoter regions of embCAB genes. In vivo studies involving expression of PknH in Mycobacterium smegmatis established its positive regulatory effect on transcription of the embCAB operon via phosphorylation of EmbR. Interestingly, increased transcription of embC, catalyzing arabinosylation of lipomannan (LM) to lipoarabinomannan (LAM), results in a high LAM/LM ratio, which in turn is a crucial factor in mycobacterial virulence. The PknH-mediated increase in the transcription of embAB genes significantly alters resistance to ethambutol, a frontline antituberculosis drug known to target embAB genes. These findings and in vivo upregulation of PknH inside the host macrophages suggest a functionally relevant signaling mechanism involving the PknH-EmbR-embCAB system.

scholarly journals Molecular and genetic analysis of the toxic effect of RAP1 overexpression in yeast.

Genetics ◽  
1995 ◽  
Vol 141 (4) ◽  
pp. 1253-1262 ◽  
Author(s):  
K Freeman ◽  
M Gwadz ◽  
D Shore
Keyword(s):  
Dna Binding ◽  
Genetic Analysis ◽  
Toxic Effect ◽  
Transcriptional Activation ◽  
Ribosomal Proteins ◽  
Regulatory Protein ◽  
Point Mutations ◽  
Binding Domain ◽  
Dna Binding Domain

Abstract Rap1p is a context-dependent regulatory protein in yeast that functions as a transcriptional activator of many essential genes, including those encoding ribosomal proteins and glycolytic enzymes. Rap1p also participates in transcriptional silencing at HM mating-type loci and telomeres. Overexpression of RAP1 strongly inhibits cell growth, perhaps by interfering with essential transcriptional activation functions within the cell. Here we report a molecular and genetic analysis of the toxic effect of RAP1 overexpression. We show that toxicity does not require the previously defined Rap1p activation and silencing domains, but instead is dependent upon the DNA-binding domain and an adjacent region of unknown function. Point mutations were identified in the DNA-binding domain that relieve the toxic effect of overexpression. Two of these mutations can complement a RAP1 deletion yet cause growth defects and altered DNA-binding properties in vitro. However, a small deletion of the adjacent (downstream) region that abolishes overexpression toxicity has, by itself, no apparent effect on growth or DNA binding. SKO1/ACR1, which encodes a CREB-like repressor protein in yeast, was isolated as a high copy suppressor of the toxicity caused by RAP1 overexpression. Models related to the regulation of Rap1p activity are discussed.

scholarly journals Structural basis for DNA recognition by STAT6

2016 ◽  
Vol 113 (46) ◽  
pp. 13015-13020 ◽  
Author(s):  
Jing Li ◽  
Jose Pindado Rodriguez ◽  
Fengfeng Niu ◽  
Mengchen Pu ◽  
Jinan Wang ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Recognition ◽  
Dynamics Simulation ◽  
Structural Basis ◽  
Innate Immune Responses ◽  
Site Analysis ◽  
X Ray Scattering ◽  
Dna Binding Site

STAT6 participates in classical IL-4/IL-13 signaling and stimulator of interferon genes-mediated antiviral innate immune responses. Aberrations in STAT6-mediated signaling are linked to development of asthma and diseases of the immune system. In addition, STAT6 remains constitutively active in multiple types of cancer. Therefore, targeting STAT6 is an attractive proposition for treating related diseases. Although a lot is known about the role of STAT6 in transcriptional regulation, molecular details on how STAT6 recognizes and binds specific segments of DNA to exert its function are not clearly understood. Here, we report the crystal structures of a homodimer of phosphorylated STAT6 core fragment (STAT6CF) alone and bound with the N3 and N4 DNA binding site. Analysis of the structures reveals that STAT6 undergoes a dramatic conformational change on DNA binding, which was further validated by performing molecular dynamics simulation studies and small angle X-ray scattering analysis. Our data show that a larger angle at the intersection where the two protomers of STAT meet and the presence of a unique residue, H415, in the DNA-binding domain play important roles in discrimination of the N4 site DNA from the N3 site by STAT6. H415N mutation of STAT6CF decreased affinity of the protein for the N4 site DNA, but increased its affinity for N3 site DNA, both in vitro and in vivo. Results of our structure–function studies on STAT6 shed light on mechanism of DNA recognition by STATs in general and explain the reasons underlying STAT6’s preference for N4 site DNA over N3.

scholarly journals Modulation of DNA binding properties of CCAAT/enhancer binding protein epsilon by heterodimer formation and interactions with NFkappaB pathway

Blood ◽  
2007 ◽  
Vol 109 (10) ◽  
pp. 4209-4219 ◽  
Author(s):  
Alexey M. Chumakov ◽  
Agnes Silla ◽  
Elizabeth A. Williamson ◽  
H. Phillip Koeffler
Keyword(s):  
Dna Binding ◽  
Myeloid Cell ◽  
Enhancer Binding Protein ◽  
Dna Binding Site ◽  
Zip Family ◽  
Family Protein ◽  
The Family ◽  
Dna Binding Properties

Abstract C/EBP epsilon is a transcription factor involved in myeloid cell differentiation. Along with C/EBP-α, -β, -γ, -δ, and -ζ, C/EBP-ϵ belongs to the family of CCAAT/enhancer binding proteins that are implicated in control of growth and differentiation of several cell lineages in inflammation and stress response. We have previously shown that C/EBP-ϵ preferentially binds DNA as a heterodimer with other C/EBP family members such as C/EBP-δ, CHOP (C/EBP-ζ), and the b-zip family protein ATF4. In this study, we define the consensus binding sites for C/EBP-ϵ dimers and C/EBP-ϵ–ATF4 heterodimers. We show that the activated NFkappaB pathway promotes interaction of the C/EBP-ϵ subunit with its cognate DNA binding site via interaction with RelA. RelA-C/EBP interaction is enhanced by phosphorylation of threonine at amino acid 75 and results in increased DNA binding compared with the wild-type nonphosphorylated C/EBP both in vitro and in vivo. We suggest that interaction of the activated NFkappaB pathway and C/EBP-ϵ may be important in selective activation of a subset of C/EBP-ϵ–responsive genes.

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