scholarly journals ON THE NATURE OF CIS-ACTING REGULATORY PROTEINS AND GENETIC ORGANIZATION IN BACTERIOPHAGE: THE EXAMPLE OF GENE Q OF BACTERIOPHAGE Λ

Genetics ◽  
1976 ◽  
Vol 83 (1) ◽  
pp. 5-10
Author(s):  
Harrison Echols ◽  
Donald Court ◽  
Linda Green
Keyword(s):  
Dna Binding ◽  
Regulatory Protein ◽  
Dna Binding Protein ◽  
Regulatory Proteins ◽  
Bacteriophage Λ ◽  
Complete Spectrum ◽  
Cis Acting ◽  
Nonspecific Interactions ◽  
Q Gene ◽  
Linkage Of Genes

ABSTRACT We note the existence of a "partially cis-acting" regulatory protein of bacteriophage λ: the product of the phage Q gene. We suggest that there may be a complete spectrum from "all cis" to "all trans" for such regulatory proteins. This behavior might arise because a DNA-binding protein either acts at a nearby (cis) site soon after synthesis or becomes "lost" for its trans activity on another genome through nonspecific interactions with DNA. Our proposed explanation provides one evolutionary basis for the linkage of genes for regulatory proteins and the sites at which such proteins act; it also suggests a possible rationale for the "metabolic instability" of certain regulatory proteins.

scholarly journals Dissection of the bifunctional ARGRII protein involved in the regulation of arginine anabolic and catabolic pathways.

1991 ◽  
Vol 11 (4) ◽  
pp. 2169-2179 ◽  
Author(s):  
H F Qui ◽  
E Dubois ◽  
F Messenguy
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Regulatory Protein ◽  
Protein A ◽  
Regulatory Proteins ◽  
Dna Binding Domain ◽  
Zinc Finger Motif ◽  
Activation Domain ◽  
Catabolic Pathways ◽  
Lexa Protein

ARGRII is a regulatory protein which regulates the arginine anabolic and catabolic pathways in combination with ARGRI and ARGRIII. We have investigated, by deletion analysis and fusion to LexA protein, the different domains of ARGRII protein. In contrast to other yeast regulatory proteins, 92% of ARGRII is necessary for its anabolic repression function and 80% is necessary for its catabolic activator function. We can define three domains in this protein: a putative DNA-binding domain containing a zinc finger motif, a region more involved in the repression activity located around the RNase-like sequence, and a large activation domain.

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.

Dissection of the bifunctional ARGRII protein involved in the regulation of arginine anabolic and catabolic pathways

1991 ◽  
Vol 11 (4) ◽  
pp. 2169-2179
Author(s):  
H F Qui ◽  
E Dubois ◽  
F Messenguy
Keyword(s):  
Dna Binding ◽  
Zinc Finger ◽  
Regulatory Protein ◽  
Protein A ◽  
Regulatory Proteins ◽  
Dna Binding Domain ◽  
Zinc Finger Motif ◽  
Activation Domain ◽  
Catabolic Pathways ◽  
Lexa Protein

ARGRII is a regulatory protein which regulates the arginine anabolic and catabolic pathways in combination with ARGRI and ARGRIII. We have investigated, by deletion analysis and fusion to LexA protein, the different domains of ARGRII protein. In contrast to other yeast regulatory proteins, 92% of ARGRII is necessary for its anabolic repression function and 80% is necessary for its catabolic activator function. We can define three domains in this protein: a putative DNA-binding domain containing a zinc finger motif, a region more involved in the repression activity located around the RNase-like sequence, and a large activation domain.

scholarly journals Characterization of the Neisseria gonorrhoeae Iron and Fur Regulatory Network

2016 ◽  
Vol 198 (16) ◽  
pp. 2180-2191 ◽  
Author(s):  
Chunxiao Yu ◽  
Ryan McClure ◽  
Kathleen Nudel ◽  
Nadine Daou ◽  
Caroline Attardo Genco
Keyword(s):  
Dna Binding ◽  
Neisseria Gonorrhoeae ◽  
Promoter Region ◽  
Dna Binding Protein ◽  
Dna Binding Proteins ◽  
Host Cells ◽  
Regulatory Proteins ◽  
Wild Type ◽  
Content Type ◽  
Large Repertoire

ABSTRACTTheNeisseria gonorrhoeaeferricuptakeregulator (Fur) protein controls expression of iron homeostasis genes in response to intracellular iron levels. In this study, using transcriptome sequencing (RNA-seq) analysis of anN. gonorrhoeaefurstrain, we defined the gonococcal Fur and iron regulons and characterized Fur-controlled expression of an ArsR-like DNA binding protein. We observed that 158 genes (8% of the genome) showed differential expression in response to iron in anN. gonorrhoeaewild-type orfurstrain, while 54 genes exhibited differential expression in response to Fur. The Fur regulon was extended to additional regulators, including NrrF and 13 other small RNAs (sRNAs), and two transcriptional factors. One transcriptional factor, coding for an ArsR-like regulator (ArsR), exhibited increased expression under iron-replete conditions in the wild-type strain but showed decreased expression across iron conditions in thefurstrain, an effect that was reversed in afur-complemented strain. Fur was shown to bind to the promoter region of thearsRgene downstream of a predicted σ70promoter region. Electrophoretic mobility shift assay (EMSA) analysis confirmed binding of the ArsR protein to thenorBpromoter region, and sequence analysis identified two additional putative targets, NGO1411 and NGO1646. A gonococcalarsRstrain demonstrated decreased survival in human endocervical epithelial cells compared to that of the wild-type andarsR-complemented strains, suggesting that the ArsR regulon includes genes required for survival in host cells. Collectively, these results demonstrate that theN. gonorrhoeaeFur functions as a global regulatory protein to repress or activate expression of a large repertoire of genes, including additional transcriptional regulatory proteins.IMPORTANCEGene regulation in bacteria in response to environmental stimuli, including iron, is of paramount importance to both bacterial replication and, in the case of pathogenic bacteria, successful infection. Bacterial DNA binding proteins are a common mechanism utilized by pathogens to control gene expression under various environmental conditions. Here, we show that the DNA binding protein Fur, expressed by the human pathogenNeisseria gonorrhoeae, controls the expression of a large repertoire of genes and extends this regulon by controlling expression of additional DNA binding proteins. One of these proteins, an ArsR-like regulator, was required forN. gonorrhoeaesurvival within host cells. These results show that the Fur regulon extends to additional regulatory proteins, which together contribute to gonococcal mechanisms of pathogenesis.

scholarly journals DNA binding is not sufficient for nuclear localization of regulatory proteins in Saccharomyces cerevisiae.

1986 ◽  
Vol 6 (12) ◽  
pp. 4763-4766 ◽  
Author(s):  
P A Silver ◽  
R Brent ◽  
M Ptashne
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acids ◽  
Dna Binding ◽  
Gene Product ◽  
Nuclear Localization ◽  
Binding Protein ◽  
Chimeric Protein ◽  
Dna Binding Protein ◽  
Regulatory Proteins

We showed by immunofluorescence that the procaryotic DNA-binding protein LexA and a chimeric protein that contains the DNA-binding portion of LexA (amino acids 1 to 87) and a large portion (amino acids 74 to 881) of the Saccharomyces cerevisiae positive regulatory GAL4 protein (GAL4 gene product) are not preferentially localized in the nucleus in S. cerevisiae.

DNA binding is not sufficient for nuclear localization of regulatory proteins in Saccharomyces cerevisiae

1986 ◽  
Vol 6 (12) ◽  
pp. 4763-4766
Author(s):  
P A Silver ◽  
R Brent ◽  
M Ptashne
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acids ◽  
Dna Binding ◽  
Gene Product ◽  
Nuclear Localization ◽  
Binding Protein ◽  
Chimeric Protein ◽  
Dna Binding Protein ◽  
Regulatory Proteins

We showed by immunofluorescence that the procaryotic DNA-binding protein LexA and a chimeric protein that contains the DNA-binding portion of LexA (amino acids 1 to 87) and a large portion (amino acids 74 to 881) of the Saccharomyces cerevisiae positive regulatory GAL4 protein (GAL4 gene product) are not preferentially localized in the nucleus in S. cerevisiae.

Aberrant expression of TAR DNA binding protein-43 is associated with spermatogenic disorders in men

2016 ◽  
Vol 28 (6) ◽  
pp. 713 ◽  
Author(s):  
Divya Saro Varghese ◽  
Uma Chandran ◽  
Ambili Soumya ◽  
Sathy M. Pillai ◽  
Krishnapillai Jayakrishnan ◽  
...  
Keyword(s):  
Dna Binding ◽  
Germ Cells ◽  
Binding Protein ◽  
Dna Binding Protein ◽  
Loss Of Function ◽  
Male Factor ◽  
Aberrant Expression ◽  
Cis Acting ◽  
Potential Association ◽  
Polymerase Chain

Loss of function of TAR DNA-binding protein (TDP-43) has been implicated in neurodegenerative disorders in both humans and animal models. TDP-43 has also been shown to be cis-acting transcriptional repressor of the acrosome vesicle (Acrv) gene in mice. In the present study, we investigated the expression of the TDP-43 transcript (TARDBP) and protein in germ cells from 11 fertile and 98 subfertile men to verify its potential association with poor seminograms. The expression profile of TDP-43 was characterised in immature germ cells and spermatozoa from semen from fertile and subfertile men using reverse transcription–polymerase chain reaction, western blotting and immunofluorescence. Although germ cells from subfertile men tested negative for TARDBP, the full-length message of the same was detected in fertile men. TDP-43 was detected in spermatozoa from fertile men using western blot analysis and immunofluorescence. The expression of this protein was negligible in spermatozoa from men with primary spermatogenic dysfunction. We conclude that a deficiency in the TDP-43 expression is associated with defective spermatogenesis and male infertility. We propose that TDP-43 could be used as a marker of male factor infertility.

scholarly journals Collaborative Competition Mechanism for Gene Activation In Vivo

2003 ◽  
Vol 23 (5) ◽  
pp. 1623-1632 ◽  
Author(s):  
Joanna A. Miller ◽  
Jonathan Widom
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Regulatory Protein ◽  
Gene Activation ◽  
Dna Binding Proteins ◽  
Regulatory Proteins ◽  
Target Sites ◽  
Collaborative Competition

ABSTRACT The mechanism by which gene regulatory proteins gain access to their DNA target sites is not known. In vitro, binding is inherently cooperative between arbitrary DNA binding proteins whose target sites are located within the same nucleosome. We refer to such competition-based cooperativity as collaborative competition. Here we show that arbitrarily chosen foreign DNA binding proteins, LexA and Tet repressor, cooperate with an adjacently binding endogenous activator protein, Gcn4, to coactivate expression of chromosomal reporter genes in Saccharomyces cerevisiae. Coactivation requires that the cooperating target sites be within a nucleosome-length distance; it leads to increased occupancy by Gcn4 at its binding site; and it requires both Gcn5 and Swi/Snf which, at an endogenous Gcn4-dependent promoter, act subsequent to Gcn4 binding. These results imply that collaborative competition contributes to gene regulation in vivo. They further imply that, even in the presence of the cell's full wild-type complement of chromatin remodeling factors, competition of regulatory proteins with histone octamer for access to regulatory target sites remains a quantitative determinant of gene expression levels. We speculate that initial target site recognition and binding may occur via spontaneous nucleosomal site exposure, with remodeling factor action required downstream to lock in higher levels of regulatory protein occupancy.

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