scholarly journals Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254025
Author(s):  
Luis Martinez-Liu ◽  
Rafael Hernandez-Guerrero ◽  
Nancy Rivera-Gomez ◽  
Mario Alberto Martinez-Nuñez ◽  
Pedro Escobar-Turriza ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Regulatory Proteins ◽  
Regulatory Mechanisms ◽  
Global Level ◽  
Bacterial Genomes ◽  
Free Living ◽  
Significant Similarity ◽  
Bacterial Proteins ◽  
Basal Transcriptional Machinery

Archaea represent a diverse phylogenetic group that includes free-living, extremophile, mesophile, symbiont, and opportunistic organisms. These prokaryotic organisms share a high significant similarity with the basal transcriptional machinery of Eukarya, and they share regulatory mechanisms with Bacteria, such as operonic organization and DNA-binding transcription factors (TFs). In this work, we identified the repertoire of TFs in 415 archaeal genomes and compared them with their counterparts in bacterial genomes. The comparisons of TFs, at a global level and per family, allowed us to identify similarities and differences between the repertoires of regulatory proteins of bacteria and archaea. For example, 11 of 62 families are more highly abundant in archaea than bacteria, and 13 families are abundant in bacteria but not in archaea and 38 families have similar abundances in the two groups. In addition, we found that archaeal TFs have a lower isoelectric point than bacterial proteins, i.e., they contain more acidic amino acids, and are smaller than bacterial TFs. Our findings suggest a divergence occurred for the regulatory proteins, even though they are common to archaea and bacteria. We consider that this analysis contributes to the comprehension of the structure and functionality of regulatory proteins of archaeal organisms.

scholarly journals Bach proteins belong to a novel family of BTB-basic leucine zipper transcription factors that interact with MafK and regulate transcription through the NF-E2 site.

1996 ◽  
Vol 16 (11) ◽  
pp. 6083-6095 ◽  
Author(s):  
T Oyake ◽  
K Itoh ◽  
H Motohashi ◽  
N Hayashi ◽  
H Hoshino ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Leucine Zipper ◽  
Basic Leucine Zipper ◽  
Significant Similarity ◽  
Btb Domain ◽  
Binding Forms ◽  
Bzip Domain ◽  
Bzip Proteins

Members of the small Maf family (MafK, MafF, and MafG) are basic region leucine zipper (bZip) proteins that can function as transcriptional activators or repressors. The dimer compositions of their DNA binding forms determine whether the small Maf family proteins activate or repress transcription. Using a yeast two-hybrid screen with a GAL4-MafK fusion protein, we have identified two novel bZip transcription factors, Bach1 and Bach2, as heterodimerization partners of MafK. In addition to a Cap'n'collar-type bZip domain, these Bach proteins possess a BTB domain which is a protein interaction motif; Bach1 and Bach2 show significant similarity to each other in these regions but are otherwise divergent. Whereas expression of Bach1 appears ubiquitous, that of Bach2 is restricted to monocytes and neuronal cells. Bach proteins bind in vitro to NF-E2 binding sites, recognition elements for the hematopoietic transcription factor NF-E2, by forming heterodimers with MafK. Furthermore, a DNA binding complex that contained MafK as well as Bach2 or a protein related closely to Bach2 was found to be present in mouse brain cells. Bach1 and Bach2 function as transcription repressors in transfection assays using fibroblast cells, but they function as a transcriptional activator and repressor, respectively, in cultured erythroid cells. The results suggest that members of the Bach family play important roles in coordinating transcription activation and repression by MafK.

scholarly journals Complete Genomic Sequence of Bacteriophage B3, a Mu-Like Phage of Pseudomonas aeruginosa

2004 ◽  
Vol 186 (19) ◽  
pp. 6560-6574 ◽  
Author(s):  
Michael D. Braid ◽  
Jennifer L. Silhavy ◽  
Christopher L. Kitts ◽  
Raul J. Cano ◽  
Martha M. Howe
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Dna Sequence ◽  
Genomic Sequence ◽  
Open Reading Frames ◽  
Early Gene ◽  
Bacterial Genomes ◽  
Significant Similarity ◽  
Bacterial Proteins ◽  
Genetic Pool ◽  
Tail Proteins

ABSTRACT Bacteriophage B3 is a transposable phage of Pseudomonas aeruginosa. In this report, we present the complete DNA sequence and annotation of the B3 genome. DNA sequence analysis revealed that the B3 genome is 38,439 bp long with a G+C content of 63.3%. The genome contains 59 proposed open reading frames (ORFs) organized into at least three operons. Of these ORFs, the predicted proteins from 41 ORFs (68%) display significant similarity to other phage or bacterial proteins. Many of the predicted B3 proteins are homologous to those encoded by the early genes and head genes of Mu and Mu-like prophages found in sequenced bacterial genomes. Only two of the predicted B3 tail proteins are homologous to other well-characterized phage tail proteins; however, several Mu-like prophages and transposable phage D3112 encode approximately 10 highly similar proteins in their predicted tail gene regions. Comparison of the B3 genomic organization with that of Mu revealed evidence of multiple genetic rearrangements, the most notable being the inversion of the proposed B3 immunity/early gene region, the loss of Mu-like tail genes, and an extreme leftward shift of the B3 DNA modification gene cluster. These differences illustrate and support the widely held view that tailed phages are genetic mosaics arising by the exchange of functional modules within a diverse genetic pool.

scholarly journals A comprehensive manually-curated Compendium of Bovine Transcription Factors

2018 ◽  
Author(s):  
Marcela M de Souza ◽  
Juan M Vaquerizas ◽  
Adhemar Zerlotini ◽  
Ludwig Geistlinger ◽  
Benjamín Hernández-Rodríguez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Regulation Of Gene Expression ◽  
Regulatory Proteins ◽  
Regulatory Mechanisms ◽  
Domain Family ◽  
Specific Expression ◽  
Tissue Specific ◽  
Control Gene Expression ◽  
Specific Manner

ABSTRACTTranscription factors (TFs) are pivotal regulatory proteins that control gene expression in a context-dependent and tissue-specific manner. In contrast to human, where comprehensive curated TF collections exist, bovine TFs are only rudimentary recorded and characterized. In this article, we present a manually-curated compendium of 865 sequence-specific DNA-binding bovines TFs, which we analyzed for domain family distribution, evolutionary conservation, and tissue-specific expression. In addition, we provide a list of putative transcription cofactors derived from known interactions with the identified TFs. Since there is a general lack of knowledge concerning the regulation of gene expression in cattle, the curated list of TF should provide a basis for an improved comprehension of regulatory mechanisms that are specific to the species.

scholarly journals Transcription Factors Indirectly Regulate Genes through Nuclear Colocalization

Cells ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 754 ◽  
Author(s):  
Zhiming Dai
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Biological Process ◽  
Expression Profiles ◽  
Dna Interaction ◽  
Cellular Component ◽  
Regulatory Mechanisms ◽  
Nuclear Positioning ◽  
Conventional View

Various types of data, including genomic sequences, transcription factor (TF) knockout data, TF-DNA interaction and expression profiles, have been used to decipher TF regulatory mechanisms. However, most of the genes affected by knockout of a particular TF are not bound by that factor. Here, I showed that this interesting result can be partially explained by considering the nuclear positioning of TF knockout affected genes and TF bound genes. I found that a statistically significant number of TF knockout affected genes show nuclear colocalization with genes bound by the corresponding TF. Although these TF knockout affected genes are not directly bound by the corresponding TF; the TF tend to be in the same cellular component with the TFs that directly bind these genes. TF knockout affected genes show co-expression and tend to be involved in the same biological process with the spatially adjacent genes that are bound by the corresponding TF. These results demonstrate that TFs can regulate genes through nuclear colocalization without direct DNA binding, complementing the conventional view that TFs directly bind DNA to regulate genes. My findings will have implications in understanding TF regulatory mechanisms.

DNA-binding profiles of mammalian transcription factors

2012 ◽  
Vol 34 (8) ◽  
pp. 950-968
Author(s):  
Guang-Ming GU ◽  
Jin-Ke WANG
Keyword(s):  
Transcription Factors ◽  
Dna Binding

scholarly journals Mechanistic Heterogeneity in Site Recognition by the Structurally Homologous DNA-binding Domains of the ETS Family Transcription Factors Ets-1 and PU.1

2014 ◽  
Vol 289 (31) ◽  
pp. 21605-21616 ◽  
Author(s):  
Shuo Wang ◽  
Miles H. Linde ◽  
Manoj Munde ◽  
Victor D. Carvalho ◽  
W. David Wilson ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Dna Binding Domains ◽  
Binding Domains ◽  
Ets Family ◽  
Site Recognition

scholarly journals DNA-binding specificity of GATA family transcription factors.

1993 ◽  
Vol 13 (7) ◽  
pp. 3999-4010 ◽  
Author(s):  
M Merika ◽  
S H Orkin
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Mammalian Cells ◽  
Chimeric Protein ◽  
Binding Specificity ◽  
Mobility Shift ◽  
Binding Domains ◽  
Dna Binding Specificity ◽  
Mobility Shift Assay ◽  
Gata Family

GATA-binding proteins constitute a family of transcription factors that recognize a target site conforming to the consensus WGATAR (W = A or T and R = A or G). Here we have used the method of polymerase chain reaction-mediated random site selection to assess in an unbiased manner the DNA-binding specificity of GATA proteins. Contrary to our expectations, we show that GATA proteins bind a variety of motifs that deviate from the previously assigned consensus. Many of the nonconsensus sequences bind protein with high affinity, equivalent to that of conventional GATA motifs. By using the selected sequences as probes in the electrophoretic mobility shift assay, we demonstrate overlapping, but distinct, sequence preferences for GATA family members, specified by their respective DNA-binding domains. Furthermore, we provide additional evidence for interaction of amino and carboxy fingers of GATA-1 in defining its binding site. By performing cotransfection experiments, we also show that transactivation parallels DNA binding. A chimeric protein containing the finger domain of areA and the activation domains of GATA-1 is capable of activating transcription in mammalian cells through GATA motifs. Our findings suggest a mechanism by which GATA proteins might selectively regulate gene expression in cells in which they are coexpressed.

scholarly journals Studies on DNA-binding selectivity of WRKY transcription factors lend structural clues into WRKY-domain function

2008 ◽  
Vol 68 (1-2) ◽  
pp. 81-92 ◽  
Author(s):  
Ingo Ciolkowski ◽  
Dierk Wanke ◽  
Rainer P. Birkenbihl ◽  
Imre E. Somssich
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Wrky Domain ◽  
Wrky Transcription Factors ◽  
Binding Selectivity
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