
@article {166864,
	title = {Early Evolution of the Prokaryotic Transcription Factor Repertoire},
	journal = {Genome Biology and Evolution},
	volume = {18},
	year = {2026},
	month = {06},
	pages = {evag141},
	abstract = {<p>Transcription initiation is regulated by transcription factors (TFs). Though TFs determine phenotype, they are nonessential for minimal cellular life. Given this and the idea that it is a certain level of organism {\textquotedblleft}complexity{\textquotedblright} that calls for transcription regulation, we traced the evolution of TF repertoire on a bacterio-archaeal phylogeny using a dataset of \~{}500,000 TFs. The most ancestral prokaryotes probably encoded multiple TFs. These, based on functions of extant relatives, possibly regulated sugar-fermentation metabolism, sensed overall metabolic state and redox, responded to DNA damage or bound metals; many of which are consistent with some reconstructions of ancestral gene pools and physiologies. The number of TFs and their superfamily-level diversity, through evolutionary history, are similar to those in extant bacteria. These suggest pre-LUCA diversification of TF families. Emergence of new TFs along the phylogeny shows innovation early in prokaryote evolution, in contrast to eukaryotes, in which many TF families emerged in bursts at multicellular lineages. Gains of TFs late in prokaryotic evolution appear to be products of horizontal acquisition of proteins discovered earlier along some other lineage. We speculate on the difference between the evolutionary trajectory of prokaryotic and eukaryotic TF repertoire and how this might be explained by how complexity is envisioned in these two different kingdoms.</p>
},
	keywords = {evolution; prokaryote; regulatory network; transcription factor},
	issn = {1759-6653},
	doi = {10.1093/gbe/evag141},
	url = {https://doi.org/10.1093/gbe/evag141},
	author = {Singh, Inder Raj and Dubey, Akshara and Seshasayee, Aswin Sai Narain}
}
@article {73644,
	title = {Laboratory Evolution Experiments Help Identify a Predominant Region of Constitutive Stable DNA Replication Initiation.},
	journal = {mSphere},
	volume = {5},
	year = {2020},
	month = {2020 Feb 26},
	abstract = {<p>The bacterium can initiate replication in the absence of the replication initiator protein DnaA and/or the canonical origin of replication in a background. This phenomenon, which can be primed by R-loops, is called constitutive stable DNA replication (cSDR). Whether DNA replication during cSDR initiates in a stochastic manner through the length of the chromosome or at specific sites and how can find adaptations to loss of fitness caused by cSDR remain inadequately answered. We use laboratory evolution experiments of strains followed by deep sequencing to show that DNA replication preferentially initiates within a broad region located \~{}0.4 to 0.7 Mb clockwise of This region includes many bisulfite-sensitive sites, which have been previously defined as R-loop-forming regions, and includes a site containing sequence motifs that favor R-loop formation. Initiation from this region would result in head-on replication-transcription conflicts at rRNA loci. Inversions of these rRNA loci, which can partly resolve these conflicts, help the bacterium suppress the fitness defects of cSDR. These inversions partially restore the gene expression changes brought about by cSDR. The inversion, however, increases the possibility of conflicts at essential mRNA genes, which would utilize only a minuscule fraction of RNA polymerase molecules, most of which transcribe rRNA genes. Whether subsequent adaptive strategies would attempt to resolve these conflicts remains an open question. The bacterium can replicate its DNA even in the absence of the molecules that are required for canonical replication initiation. This often requires the formation of RNA-DNA hybrid structures and is referred to as constitutive stable DNA replication (cSDR). Where on the chromosome does cSDR initiate? We answer this question using laboratory evolution experiments and genomics and show that selection favors cSDR initiation predominantly at a region \~{}0.6 Mb clockwise of Initiation from this site will result in more head-on collisions of DNA polymerase with RNA polymerase operating on rRNA loci. The bacterium adapts to this problem by inverting a region of the genome including several rRNA loci such that head-on collisions between the two polymerases are minimized. Understanding such evolutionary strategies in the context of cSDR can provide insights into the potential causes of resistance to antibiotics that target initiation of DNA replication.</p>
},
	issn = {2379-5042},
	doi = {10.1128/mSphere.00939-19},
	author = {Veetil, Reshma T and Malhotra, Nitish and Dubey, Akshara and Seshasayee, Aswin Sai Narain}
}
