scholarly journals Diverse Eukaryotic CGG-Binding Proteins Produced by Independent Domestications of hAT Transposons

2021 ◽  
Author(s):  
Isaac Yellan ◽  
Ally W H Yang ◽  
Timothy R Hughes
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Sequence Specificity ◽  
Binding Motifs ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Dna Binding Motifs ◽  
Wide Range ◽  
Human Transcription Factor ◽  
Hat Transposons

Abstract The human transcription factor (TF) CGGBP1 (CGG-binding protein) is conserved only in amniotes and is believed to derive from the zf-BED and Hermes transposase DNA-binding domains (DBDs) of a hAT DNA transposon. Here, we show that sequence-specific DNA-binding proteins with this bipartite domain structure have resulted from dozens of independent hAT domestications in different eukaryotic lineages. CGGBPs display a wide range of sequence specificity, usually including preferences for CGG or CGC trinucleotides, whereas some bind AT-rich motifs. The CGGBPs are almost entirely nonsyntenic, and their protein sequences, DNA-binding motifs, and patterns of presence or absence in genomes are uncharacteristic of ancestry via speciation. At least eight CGGBPs in the coelacanth Latimeria chalumnae bind distinct motifs, and the expression of the corresponding genes varies considerably across tissues, suggesting tissue-restricted function.

scholarly journals The bldC Developmental Locus of Streptomyces coelicolor Encodes a Member of a Family of Small DNA-Binding Proteins Related to the DNA-Binding Domains of the MerR Family

2005 ◽  
Vol 187 (2) ◽  
pp. 716-728 ◽  
Author(s):  
Alison C. Hunt ◽  
Luis Servín-González ◽  
Gabriella H. Kelemen ◽  
Mark J. Buttner
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Antibiotic Production ◽  
Streptomyces Coelicolor ◽  
Aerial Mycelium ◽  
Dna Binding Proteins ◽  
S1 Nuclease ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Wide Range

ABSTRACT The bldC locus, required for formation of aerial hyphae in Streptomyces coelicolor, was localized by map-based cloning to the overlap between cosmids D17 and D25 of a minimal ordered library. Subcloning and sequencing showed that bldC encodes a member of a previously unrecognized family of small (58- to 78-residue) DNA-binding proteins, related to the DNA-binding domains of the MerR family of transcriptional activators. BldC family members are found in a wide range of gram-positive and gram-negative bacteria. Constructed ΔbldC mutants were defective in differentiation and antibiotic production. They failed to form an aerial mycelium on minimal medium and showed severe delays in aerial mycelium formation on rich medium. In addition, they failed to produce the polyketide antibiotic actinorhodin, and bldC was shown to be required for normal and sustained transcription of the pathway-specific activator gene actII-orf4. Although ΔbldC mutants produced the tripyrrole antibiotic undecylprodigiosin, transcripts of the pathway-specific activator gene (redD) were reduced to almost undetectable levels after 48 h in the bldC mutant, in contrast to the bldC + parent strain in which redD transcription continued during aerial mycelium formation and sporulation. This suggests that bldC may be required for maintenance of redD transcription during differentiation. bldC is expressed from a single promoter. S1 nuclease protection assays and immunoblotting showed that bldC is constitutively expressed and that transcription of bldC does not depend on any of the other known bld genes. The bldC18 mutation that originally defined the locus causes a Y49C substitution that results in instability of the protein.

scholarly journals SelexGLM differentiates androgen and glucocorticoid receptor DNA-binding preference over an extended binding site

2017 ◽  
Author(s):  
Liyang Zhang ◽  
Gabriella D. Martini ◽  
H. Tomas Rube ◽  
Judith F. Kribelbauer ◽  
Chaitanya Rastogi ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Site ◽  
Target Genes ◽  
Isothermal Calorimetry ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Relative Preference ◽  
Wide Range ◽  
Two Factors ◽  
Prostate Cancers

ABSTRACTThe DNA-binding interfaces of the androgen (AR) and glucocorticoid (GR) receptors are virtually identical, yet these transcription factors share only about a third of their genomic binding sites and regulate similarly distinct sets of target genes. To address this paradox, we determined the intrinsic specificities of the AR and GR DNA binding domains using a refined version of SELEX-seq. We developed an algorithm, SelexGLM, that quantifies binding specificity over a large (31 bp) binding-site by iteratively fitting a feature-based generalized linear model to SELEX probe counts. This analysis revealed that the DNA binding preferences of AR and GR homodimers differ significantly, both within and outside the 15bp core binding site. The relative preference between the two factors can be tuned over a wide range by changing the DNA sequence, with AR more sensitive to sequence changes than GR. The specificity of AR extends to the regions flanking the core 15bp site, where isothermal calorimetry measurements reveal that affinity is augmented by enthalpy-driven readout of poly-A sequences associated with narrowed minor groove width. We conclude that the increased specificity of AR is correlated with more enthalpy-driven binding than GR. The binding models help explain differences in AR and GR genomic binding, and provide a biophysical rationale for how promiscuous binding by GR allows functional substitution for AR in some castration-resistant prostate cancers.

scholarly journals Structural variation affecting DNA backbone interactions underlies adaptation of B3 DNA binding domains to constraints imposed by protein architecture

2020 ◽  
Author(s):  
Haiyan Jia ◽  
Masaharu Suzuki ◽  
Donald R. McCarty
Keyword(s):  
Dna Binding ◽  
Electrostatic Interactions ◽  
Structural Variation ◽  
General Mechanism ◽  
Sequence Specificity ◽  
In Planta ◽  
Dna Binding Domains ◽  
Cis Element ◽  
Binding Domains ◽  
Dna Backbone

ABSTRACTFunctional diversification of transcription factor families through variation in modular domain architectures has played a central role in the independent evolution of gene regulatory networks underlying complex development in plants and animals. Here we show that architecture has in turn constrained evolution of B3 DNA binding domains in the B3 network regulating embryo formation in plants. B3 domains of ABI3, FUS3, LEC2 and VAL1 proteins recognize the same cis-element. ABI3 and VAL1 have complex architectures that physically integrate cis-element recognition with other signals, whereas LEC2 and FUS3 have reduced architectures conducive to their roles as pioneer activators. Qualitatively different activities of LEC2 and ABI3 B3 domains measured in vivo and in vitro are attributed in part to clade-specific substitutions in three amino acids that interact with the DNA backbone. Activities of FUS3 and VAL1 B3 domains show a similar correlation with architectural complexity. Domain-swap analyses in planta show that in a complex architecture setting the attenuated activities of ABI3 and VAL1 B3 domains are required for proper integration of ciselement recognition with hormone signalling. These results highlight modes of structural variation affecting non-specific, electrostatic interactions with the DNA backbone as a general mechanism allowing adaptation of DNA binding affinity to architectural constraints while preserving DNA sequence specificity.

scholarly journals Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Kamesh Narasimhan ◽  
Samuel A Lambert ◽  
Ally WH Yang ◽  
Jeremy Riddell ◽  
Sanie Mnaimneh ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Dna Binding ◽  
Regulatory Elements ◽  
Nuclear Hormone Receptor ◽  
Binding Motifs ◽  
T Box ◽  
C Elegans ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Protein Binding Microarray

Caenorhabditis elegans is a powerful model for studying gene regulation, as it has a compact genome and a wealth of genomic tools. However, identification of regulatory elements has been limited, as DNA-binding motifs are known for only 71 of the estimated 763 sequence-specific transcription factors (TFs). To address this problem, we performed protein binding microarray experiments on representatives of canonical TF families in C. elegans, obtaining motifs for 129 TFs. Additionally, we predict motifs for many TFs that have DNA-binding domains similar to those already characterized, increasing coverage of binding specificities to 292 C. elegans TFs (∼40%). These data highlight the diversification of binding motifs for the nuclear hormone receptor and C2H2 zinc finger families and reveal unexpected diversity of motifs for T-box and DM families. Motif enrichment in promoters of functionally related genes is consistent with known biology and also identifies putative regulatory roles for unstudied TFs.

CRITERIA FOR AN UPDATED CLASSIFICATION OF HUMAN TRANSCRIPTION FACTOR DNA-BINDING DOMAINS

2013 ◽  
Vol 11 (01) ◽  
pp. 1340007 ◽  
Author(s):  
EDGAR WINGENDER
Keyword(s):  
Dna Binding ◽  
Leucine Zipper ◽  
Regulatory Elements ◽  
Biological Species ◽  
Basic Leucine Zipper ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Comprehensive Classification ◽  
Human Transcription Factor

By binding to cis-regulatory elements in a sequence-specific manner, transcription factors regulate the activity of nearby genes. Here, we discuss the criteria for a comprehensive classification of human TFs based on their DNA-binding domains. In particular, classification of basic leucine zipper (bZIP) and zinc finger factors is exemplarily discussed. The resulting classification can be used as a template for TFs of other biological species.

scholarly journals xUBF, an RNA polymerase I transcription factor, binds crossover DNA with low sequence specificity.

1994 ◽  
Vol 14 (5) ◽  
pp. 2871-2882 ◽  
Author(s):  
C H Hu ◽  
B McStay ◽  
S W Jeong ◽  
R H Reeder
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Rna Polymerase ◽  
Rna Polymerase I ◽  
Intact Protein ◽  
Sequence Specificity ◽  
Binding Motifs ◽  
Double Helices ◽  
Dna Binding Motifs ◽  
Polymerase I

Xenopus UBF (xUBF) is a transcription factor for RNA polymerase I which contains multiple DNA-binding motifs. These include a short basic region adjacent to a dimer motif plus five high-mobility-group (HMG) boxes. All of these DNA-binding motifs exhibit low sequence specificity, whether assayed singly or together. In contrast, the HMG boxes recognize DNA structure that is formed when two double helices are crossed over each other. HMG box 1, in particular, requires association of two double helices before it will bind and, either by itself or in the context of the intact protein, will loop DNA and organize it into higher-order structures. We discuss how this mode of binding affects the function of xUBF as a transcription factor.

scholarly journals Characterization of the dead ringer gene identifies a novel, highly conserved family of sequence-specific DNA-binding proteins.

1996 ◽  
Vol 16 (3) ◽  
pp. 792-799 ◽  
Author(s):  
S L Gregory ◽  
R D Kortschak ◽  
B Kalionis ◽  
R Saint
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Binding Domain ◽  
Dna Binding Domain ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
The Dead

We reported the identification of a new family of DNA-binding proteins from our characterization of the dead ringer (dri) gene of Drosophila melanogaster. We show that dri encodes a nuclear protein that contains a sequence-specific DNA-binding domain that bears no similarity to known DNA-binding domains. A number of proteins were found to contain sequences homologous to this domain. Other proteins containing the conserved motif include yeast SWI1, two human retinoblastoma binding proteins, and other mammalian regulatory proteins. A mouse B-cell-specific regulator exhibits 75% identity with DRI over the 137-amino-acid DNA-binding domains of these proteins, indicating a high degree of conservation of this domain. Gel retardation and optimal binding site screens revealed that the in vitro sequence specificity of DRI is strikingly similar to that of many homeodomain proteins, although the sequence and predicted secondary structure do not resemble a homeodomain. The early general expression of dri and the similarity of DRI and homeodomain in vitro DNA-binding specificity compound the problem of understanding the in vivo specificity of action of these proteins. Maternally derived dri product is found throughout the embryo until germ band extension, when dri is expressed in a developmentally regulated set of tissues, including salivary gland ducts, parts of the gut, and a subset of neural cells. The discovery of this new, conserved DNA-binding domain offers an explanation for the regulatory activity of several important members of this class and predicts significant regulatory roles for the others.

Sign in / Sign up

Export Citation Format

Share Document