scholarly journals Positive transcriptional control of the pyridoxal phosphate biosynthesis genes pdxST by the MocR-type regulator PdxR of Corynebacterium glutamicum ATCC 13032

Microbiology ◽  
2011 ◽  
Vol 157 (1) ◽  
pp. 77-88 ◽  
Author(s):  
Nina Jochmann ◽  
Susanne Götker ◽  
Andreas Tauch
Keyword(s):  
Dna Binding ◽  
Corynebacterium Glutamicum ◽  
Transcriptional Control ◽  
Pyridoxal Phosphate ◽  
Specific Binding ◽  
Consensus Sequence ◽  
Regulatory Protein ◽  
Band Shift ◽  
Promoter Sequences ◽  
Amino Terminal

The pdxR (cg0897) gene of Corynebacterium glutamicum ATCC 13032 encodes a regulatory protein belonging to the MocR subfamily of GntR-type transcription regulators and consisting of an amino-terminal winged helix–turn–helix DNA-binding domain and a carboxy-terminal aminotransferase-like domain. A defined deletion in the pdxR gene resulted in the decreased expression of the divergently orientated pdxST genes coding for the subunits of pyridoxal 5′-phosphate synthase. The pdxST mutant C. glutamicum NJ0898 and the pdxR mutant C. glutamicum AMH17 showed vitamin B6 auxotrophy that was restored by supplementing the growth medium with either pyridoxal, pyridoxal 5′-phosphate or pyridoxamine. The genetic organization of the 89 bp pdxR–pdxST intergenic region was elucidated by mapping the 5′ ends of the respective transcripts, followed by detection of typical promoter sequences. Bioinformatic pattern searches and comparative genomics revealed three DNA motifs with the consensus sequence AAAGTGGW(−/T)CTA, overlapping the deduced promoter sequences and serving as candidate DNA-binding sites for PdxR. DNA band shift assays with the purified PdxR protein demonstrated the specific binding of the transcription regulator to double-stranded 40-mer sequences containing the detected motifs, thereby confirming the direct regulatory role of PdxR in activating the expression of the pdxST genes.

scholarly journals Identification of potential target genes for Adr1p through characterization of essential nucleotides in UAS1.

1994 ◽  
Vol 14 (6) ◽  
pp. 3842-3852 ◽  
Author(s):  
C Cheng ◽  
N Kacherovsky ◽  
K M Dombek ◽  
S Camier ◽  
S K Thukral ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Inverted Repeat ◽  
Target Genes ◽  
Consensus Sequence ◽  
Regulatory Protein ◽  
Yeast Saccharomyces Cerevisiae ◽  
Amino Terminal ◽  
Potential Target

Adr1p is a regulatory protein in the yeast Saccharomyces cerevisiae that binds to and activates transcription from two sites in a perfect 22-bp inverted repeat, UAS1, in the ADH2 promoter. Binding requires two C2H2 zinc fingers and a region amino terminal to the fingers. The importance for DNA binding of each position within UAS1 was deduced from two types of assays. Both methods led to an identical consensus sequence containing only four essential base pairs: GG(A/G)G. The preferred sequence, TTGG(A/G)GA, is found in both halves of the inverted repeat. The region of Adr1p amino terminal to the fingers is important for phosphate contacts in the central region of UAS1. However, no base-specific contacts in this portion of UAS1 are important for DNA binding or for ADR1-dependent transcription in vivo. When the central 6 bp were deleted, only a single monomer of Adr1p was able to bind in vitro and activation in vivo was severely reduced. On the basis of these results and previous knowledge about the DNA binding site requirements, including constraints on the spacing and orientation of sites that affect activation in vivo, a consensus binding site for Adr1p was derived. By using this consensus site, potential Adr1p binding sites were located in the promoters of genes known to show ADR1-dependent expression. In addition, this consensus allowed the identification of new potential target genes for Adr1p.

Identification of potential target genes for Adr1p through characterization of essential nucleotides in UAS1

1994 ◽  
Vol 14 (6) ◽  
pp. 3842-3852
Author(s):  
C Cheng ◽  
N Kacherovsky ◽  
K M Dombek ◽  
S Camier ◽  
S K Thukral ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Inverted Repeat ◽  
Target Genes ◽  
Consensus Sequence ◽  
Regulatory Protein ◽  
Yeast Saccharomyces Cerevisiae ◽  
Amino Terminal ◽  
Potential Target

Adr1p is a regulatory protein in the yeast Saccharomyces cerevisiae that binds to and activates transcription from two sites in a perfect 22-bp inverted repeat, UAS1, in the ADH2 promoter. Binding requires two C2H2 zinc fingers and a region amino terminal to the fingers. The importance for DNA binding of each position within UAS1 was deduced from two types of assays. Both methods led to an identical consensus sequence containing only four essential base pairs: GG(A/G)G. The preferred sequence, TTGG(A/G)GA, is found in both halves of the inverted repeat. The region of Adr1p amino terminal to the fingers is important for phosphate contacts in the central region of UAS1. However, no base-specific contacts in this portion of UAS1 are important for DNA binding or for ADR1-dependent transcription in vivo. When the central 6 bp were deleted, only a single monomer of Adr1p was able to bind in vitro and activation in vivo was severely reduced. On the basis of these results and previous knowledge about the DNA binding site requirements, including constraints on the spacing and orientation of sites that affect activation in vivo, a consensus binding site for Adr1p was derived. By using this consensus site, potential Adr1p binding sites were located in the promoters of genes known to show ADR1-dependent expression. In addition, this consensus allowed the identification of new potential target genes for Adr1p.

trans activation of gene expression by v-myb

1990 ◽  
Vol 10 (5) ◽  
pp. 2285-2293 ◽  
Author(s):  
C E Ibanez ◽  
J S Lipsick
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Consensus Sequence ◽  
Amino Terminal ◽  
Multiple Copies ◽  
Vp16 Fusion ◽  
Acute Myelomonocytic Leukemia ◽  
Simplex Virus

The v-myb oncogene causes acute myelomonocytic leukemia in chickens and transforms avian myeloid cells in vitro. Its product, p48v-myb, is a short-lived nuclear protein which binds DNA. We demonstrate that p48v-myb can function as a trans activator of gene expression in transient DNA transfection assays. trans activation requires the highly conserved amino-terminal DNA-binding domain and the less highly conserved carboxyl-terminal domain of p48v-myb, both of which are required for transformation. Multiple copies of a consensus sequence for DNA binding by p48v-myb inserted upstream of a herpes simplex virus thymidine kinase promoter are strongly stimulatory for transcriptional activation by a v-myb-VP16 fusion protein but not by p48v-myb itself, suggesting that the binding of p48v-myb to DNA may not be sufficient for trans activation.

scholarly journals The proto-oncogene HLF and the related basic leucine zipper protein TEF display highly similar DNA-binding and transcriptional regulatory properties

Blood ◽  
1996 ◽  
Vol 87 (11) ◽  
pp. 4607-4617 ◽  
Author(s):  
SP Hunger ◽  
S Li ◽  
MZ Fall ◽  
L Naumovski ◽  
ML Cleary
Keyword(s):  
Amino Acid ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Leucine Zipper ◽  
Lymphoblastic Leukemia ◽  
Consensus Sequence ◽  
Basic Leucine Zipper ◽  
Amino Terminal ◽  
Transcriptional Regulatory ◽  
Regulatory Properties

Genes encoding transcription factors are frequently altered by chromosomal translocations in acute lymphoblastic leukemia (ALL), suggesting that aberrant transcriptional regulation plays a prominent role in leukemogenesis. E2A-hepatic leukemia factor (HLF), a chimeric transcription factor created by the t(17;19), consists of the amino terminal portion of E2A proteins, including two experimentally defined transcriptional activation domains (TADs), fused to the HLF DNA binding and protein dimerization basic leucine zipper (bZIP) domain. To understand the mechanisms by which E2A-HLF induces leukemia and the crucial functions contributed by each constituent of the chimera, it is essential to define the normal transcriptional regulatory properties of HLF and related bZIP proteins. To address these questions, we cloned the human homologue of TEF/VBP, a bZIP protein closely related to HLF. Using a binding site selection assay, we found that TEF bound preferentially to the consensus sequence 5′-GTTACGTAAT-3′, which is identical to the previously determined HLF recognition site. TEF and HLF activated transcription of consensus site-containing reporter genes in several different cell types with similar potencies. Using GAL4 chimeric proteins, a TAD was mapped to a discrete approximate 40 amino acid region of TEF and HLF within which they share 72% amino acid identity and 85% similarity. The TEF/HLF activation domain (THAD) has a predicted helical secondary structure, but shares no sequence homology with previously reported TADs. The THAD contained most, if not all, of the transcriptional activation properties present in both TEF and HLF and its deletion completely abrogated transcriptional activity of TEF and HLF in both mammalian cells and yeast. Thus, TEF and HLF share indistinguishable DNA-binding and transcriptional regulatory properties, whose alteration in leukemia may be pathogenetically important.

scholarly journals trans activation of gene expression by v-myb.

1990 ◽  
Vol 10 (5) ◽  
pp. 2285-2293 ◽  
Author(s):  
C E Ibanez ◽  
J S Lipsick
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Transcriptional Activation ◽  
Consensus Sequence ◽  
Amino Terminal ◽  
Multiple Copies ◽  
Vp16 Fusion ◽  
Acute Myelomonocytic Leukemia ◽  
Simplex Virus

The v-myb oncogene causes acute myelomonocytic leukemia in chickens and transforms avian myeloid cells in vitro. Its product, p48v-myb, is a short-lived nuclear protein which binds DNA. We demonstrate that p48v-myb can function as a trans activator of gene expression in transient DNA transfection assays. trans activation requires the highly conserved amino-terminal DNA-binding domain and the less highly conserved carboxyl-terminal domain of p48v-myb, both of which are required for transformation. Multiple copies of a consensus sequence for DNA binding by p48v-myb inserted upstream of a herpes simplex virus thymidine kinase promoter are strongly stimulatory for transcriptional activation by a v-myb-VP16 fusion protein but not by p48v-myb itself, suggesting that the binding of p48v-myb to DNA may not be sufficient for trans activation.

scholarly journals Four of the seven zinc fingers of the Evi-1 myeloid-transforming gene are required for sequence-specific binding to GA(C/T)AAGA(T/C)AAGATAA.

1993 ◽  
Vol 13 (7) ◽  
pp. 4291-4300 ◽  
Author(s):  
R Delwel ◽  
T Funabiki ◽  
B L Kreider ◽  
K Morishita ◽  
J N Ihle
Keyword(s):  
Dna Binding ◽  
Specific Binding ◽  
Zinc Fingers ◽  
Consensus Sequence ◽  
Myelogenous Leukemia ◽  
Chromosome Band ◽  
Aberrant Expression ◽  
Relative Specificity ◽  
Acute Myelogenous ◽  
Binding Sequence

Expression of the Evi-1 gene is activated in murine myeloid leukemias by retroviral insertions and in human acute myelogenous leukemia by translocations and inversions involving chromosome band 3q26 where the gene resides. Aberrant expression of the Evi-1 gene has been shown to interfere with myeloid differentiation, which is proposed to be the basis for its role in leukemias. The Evi-1 gene encodes a 145-kDa DNA-binding protein containing two domains of seven and three Cys2-His2 zinc fingers. Previous studies identified a portion of the consensus DNA-binding sequence for the first domain of zinc fingers. The experiments presented here extend these studies and demonstrate that the first domain recognizes a consensus of 15 nucleotides consisting of GA(C/T)AAGA(T/C)AAGATAA. The first three fingers of the first domain do not detectably bind DNA but contribute to the binding by conferring a relative specificity for GACAA verses GATAA in the first position. The first three fingers also contribute to optimal binding of the 15-nucleotide consensus sequence.

Genetic makeup of the Corynebacterium glutamicum LexA regulon deduced from comparative transcriptomics and in vitro DNA band shift assays

Microbiology ◽  
2009 ◽  
Vol 155 (5) ◽  
pp. 1459-1477 ◽  
Author(s):  
Nina Jochmann ◽  
Anna-Katharina Kurze ◽  
Lisa F. Czaja ◽  
Karina Brinkrolf ◽  
Iris Brune ◽  
...  
Keyword(s):  
Dna Damage ◽  
Corynebacterium Glutamicum ◽  
Intergenic Region ◽  
Binding Sites ◽  
Consensus Sequence ◽  
Differentially Expressed ◽  
Wild Type ◽  
Band Shift ◽  
Lexa Binding

The lexA gene of Corynebacterium glutamicum ATCC 13032 was deleted to create the mutant strain C. glutamicum NJ2114, which has an elongated cell morphology and an increased doubling time. To characterize the SOS regulon in C. glutamicum, the transcriptomes of NJ2114 and a DNA-damage-induced wild-type strain were compared with that of a wild-type control using DNA microarray hybridization. The expression data were combined with bioinformatic pattern searches for LexA binding sites, leading to the detection of 46 potential SOS boxes located upstream of differentially expressed transcription units. Binding of a hexahistidyl-tagged LexA protein to 40 double-stranded oligonucleotides containing the potential SOS boxes was demonstrated in vitro by DNA band shift assays. It turned out that LexA binds not only to SOS boxes in the promoter–operator region of upregulated genes, but also to SOS boxes detected upstream of downregulated genes. These results demonstrated that LexA controls directly the expression of at least 48 SOS genes organized in 36 transcription units. The deduced genes encode a variety of physiological functions, many of them involved in DNA repair and survival after DNA damage, but nearly half of them have hitherto unknown functions. Alignment of the LexA binding sites allowed the corynebacterial SOS box consensus sequence TcGAA(a/c)AnnTGTtCGA to be deduced. Furthermore, the common intergenic region of lexA and the differentially expressed divS-nrdR operon, encoding a cell division suppressor and a regulator of deoxyribonucleotide biosynthesis, was characterized in detail. Promoter mapping revealed differences in divS-nrdR expression during SOS response and normal growth conditions. One of the four LexA binding sites detected in the intergenic region is involved in regulating divS-nrdR transcription, whereas the other sites are apparently used for negative autoregulation of lexA expression.

scholarly journals P64, a Novel Major Virion DNA-Binding Protein Potentially Involved in Condensing the Spodoptera frugiperda Ascovirus 1a Genome

2009 ◽  
Vol 83 (6) ◽  
pp. 2708-2714 ◽  
Author(s):  
Yeping Tan ◽  
Tatsinda Spears ◽  
Dennis K. Bideshi ◽  
Jeffrey J. Johnson ◽  
Robert Hice ◽  
...  
Keyword(s):  
Dna Binding ◽  
Spodoptera Frugiperda ◽  
Consensus Sequence ◽  
Structural Protein ◽  
Mobility Shift ◽  
Virion Assembly ◽  
Amino Terminal ◽  
Ultrathin Sections ◽  
Carboxy Terminal ◽  
Electrophoretic Mobility Shift Assays

ABSTRACT We recently identified 21 structural proteins in the virion of Spodoptera frugiperda ascovirus 1a (SfAV1a), a virus with a large, double-stranded DNA genome of 157 kbp, which attacks species of the lepidopteran family Noctuidae. The two most abundant virion proteins were the major capsid protein and a novel protein (P64) of 64 kDa that contained two distinct domains not known previously to occur together. The amino-terminal half of P64 (residues 1 to 263) contained four repeats (a recently recognized motif with an unknown function) of a virus-specific two-cysteine adaptor. Adjoined to this, the carboxy-terminal half of P64 (residues 279 to 455) contained 14 copies of a highly basic, tandemly repeated motif rich in arginine and serine, having an 11- to 13-amino-acid consensus sequence, SPSQRRSTS(V/K)(A/S)RR, yielding a predicted isoelectric point of 12.2 for this protein. In the present study, we demonstrate by Southwestern analysis that SfAV1a P64 was the only virion structural protein that bound DNA. Additional electrophoretic mobility shift assays showed that P64 bound SfAV1a as well as non-SfAV1a DNA. Furthermore, we show through immunogold labeling of ultrathin sections that P64 is a component of virogenic stroma and appears to be progressively incorporated into the SfAV1a DNA core during virion assembly. As no other virion structural protein bound DNA and no basic DNA-binding proteins of lower mass are encoded by the SfAV1a genome or were identified by proteomic analysis, our results suggest that P64's function is to condense the large genome of this virus and assist in packaging this genome into its virion.

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 Characterization of the Pathway-Specific Positive Transcriptional Regulator for Actinorhodin Biosynthesis inStreptomyces coelicolor A3(2) as a DNA-Binding Protein

1999 ◽  
Vol 181 (22) ◽  
pp. 6958-6968 ◽  
Author(s):  
Paloma Arias ◽  
Miguel A. Fernández-Moreno ◽  
Francisco Malpartida
Keyword(s):  
Dna Binding ◽  
Binding Protein ◽  
Consensus Sequence ◽  
Regulatory Protein ◽  
Dna Binding Protein ◽  
Binding Activity ◽  
Wild Type ◽  
Biosynthetic Genes ◽  
Dna Binding Activity ◽  
Orf4 Protein

ABSTRACT The ActII-ORF4 protein has been characterized as a DNA-binding protein that positively regulates the transcription of the actinorhodin biosynthetic genes. The target regions for the ActII-ORF4 protein were located within the act cluster. These regions, at high copy number, generate a nonproducer strain by in vivo titration of the regulator. The mutant phenotype could be made to revert with extra copies of the wild-type actII-ORF4 gene but not with theactII-ORF4-177 mutant. His-tagged recombinant wild-type ActII-ORF4 and mutant ActII-ORF4-177 proteins were purified fromEscherichia coli cultures; both showed specific DNA-binding activity for the actVI-ORF1–ORFA andactIII-actI intergenic regions. DNase I footprinting assays clearly located the DNA-binding sites within the −35 regions of the corresponding promoters, showing the consensus sequence 5′-TCGAG-3′. Although both gene products (wild-type and mutant ActII-ORF4) showed DNA-binding activity, only the wild-type gene was capable of activating transcription of the actgenes; thus, two basic functions can be differentiated within the regulatory protein: a specific DNA-binding activity and a transcriptional activation of the act biosynthetic genes.

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