Dissecting the protein architecture of DNA-binding transcription factors in bacteria and archaea

Abstract

Gene regulation at the transcriptional level is a central process in all organisms where DNA-binding transcription factors play a fundamental role. This class of proteins binds specifically at DNA sequences, activating or repressing gene expression as a function of the cell's metabolic status, operator context and ligand-binding status, among other factors, through the DNA-binding domain (DBD). In addition, TFs may contain partner domains (PaDos), which are involved in ligand binding and protein-protein interactions. In this work, we systematically evaluated the distribution, abundance and domain organization of DNA-binding TFs in 799 non-redundant bacterial and archaeal genomes. We found that the distributions of the DBDs and their corresponding PaDos correlated with the size of the genome. We also identified specific combinations between the DBDs and their corresponding PaDos. Within each class of DBDs there are differences in the actual angle formed at the dimerization interface, responding to the presence/absence of ligands and/or crystallization conditions, setting the orientation of the resulting helices and wings facing the DNA. Our results highlight the importance of PaDos as central elements that enhance the diversity of regulatory functions in all bacterial and archaeal organisms, and our results also demonstrate the role of PaDos in sensing diverse signal compounds. The highly specific interactions between DBDs and PaDos observed in this work, together with our structural analysis highlighting the difficulty in predicting both inter-domain geometry and quaternary structure, suggest that these systems appeared once and evolved with diverse duplication events in all the analysed organisms.

Evaluation of the Abundance of DNA-Binding Transcription Factors in Prokaryotes

“…In contrast, 56.3% of the collection do not exhibit a clear correlation with the genome size, suggesting that a large proportion of families have independent evolutionary events associated with their increasing, such as duplications or gene losses, opening questions to be further explored, such as how many families in a genome are product of lateral gene transfer or what occurs with the regulated genes or how many families with a similar distribution pattern across Bacteria and Archaea, are product coevolution processes. In addition, we found a specific association between the DNA-binding domains and their associated companion domains, as it has previously described [3], suggesting that the scaffold to protein-protein interactions could be conserved among members of the same family contacts, as occurs in the Crp family and that their association in diverse bacterial and archaeal genomes could increase the ability of the organisms to recognize and respond to diverse environmental stimuli [30]. This result opens the opportunity to predict and modify the probable ligands to understand the diversity of signals that modulate the activity of transcription factors, as it has been identified for E. coli [31].…”

“…activating or repressing gene expression. In general, TFs are two-domain proteins, with a DNA-binding domain (DBD) in either the amino or carboxy terminus, which is involved in specific contacts with the regulatory region of the corresponding cognate genes, and an additional domain associated with diverse functions such as ligand binding or protein-protein interactions [3,4]. To date, diverse studies have shown that some TF families are common to bacteria and archaea, suggesting that the mechanisms affecting gene expression could be similar in the cellular domains of both of these groups of prokaryotes [5,6].…”

Conserved principles of transcriptional networks controlling metabolic flexibility in archaea

“…Homology has been observed between bacterial and archaeal TFs that activate or repress genes in response to environmental stimuli [27,28]. In archaea, these regulatory TFs differ from the general transcription factors (GTFs [29]) required for the initiation of basal transcription, such as TATA-binding protein (TBP) and RNA polymerase, which resemble those of eukaryotes.…”

“…Archaeal regulatory TFs are enriched for DNA-binding domains that strongly resemble those of bacteria, such as helix-turn-helix domains [28,33]. As in bacteria, the majority of archaeal TFs consist of a DNA-binding domain and a partner domain [27,28]. Nearly 50% of known bacterial partner domains bind to a small molecule, also called an inducer or ligand, that affect DNA-binding affinity [34,35].…”

“…Nearly 50% of known bacterial partner domains bind to a small molecule, also called an inducer or ligand, that affect DNA-binding affinity [34,35]. Recent predictions based on phylogenetic analysis of genome sequences estimate that archaeal TFs share these attributes [27]. To date, ∼40% of TFs studied experimentally in archaea bind a ligand to govern DNA binding [5]; however, this is likely an underestimate given that the specific ligands for some TFs have been predicted but not yet been experimentally characterized [5,[36][37][38][39].…”