@book {155537, title = {Bacterial Genomes Trees and Networks}, series = {Bacterial Genomes Trees and Networks}, volume = {1}, year = {2025}, pages = {254}, publisher = {Open Book Publishers}, organization = {Open Book Publishers}, abstract = {
Microbes form the {\textquotedblleft}unseen majority{\textquotedblright} of life on Earth, with bacteria at the forefront as both the architects of life{\textquoteright}s chemical foundations and agents of disease. But their story is far more complex. Bacteria thrive in diverse and extreme environments, driven by the dynamic evolution of their genomes. These tiny organisms wield an extraordinary ability to adapt, balancing genetic changes across generations with rapid physiological responses to environmental shifts.
In Bacterial Genomes, the evolutionary and regulatory processes that shape bacterial life are brought to life. This textbook offers a conceptual exploration of how bacterial genomes are organized, how they evolve, and how their genetic information is interpreted through intricate molecular networks. Drawing on both cutting-edge research and the historical milestones that shaped microbiology, it illuminates how bacteria navigate the intersection of genetic adaptation and ecological resilience.
Designed for college students, interdisciplinary researchers, and even the determined amateur, Aswin Seshasayee moves beyond technical jargon to provide a thought-provoking synthesis of bacterial evolution and adaptation. Unlike traditional genomics texts, this book blends historical insights with contemporary discoveries, offering a fresh perspective on the role of bacteria in shaping the living world.
}, isbn = {Paperback: 978-1-80511-495-6; Hardback: 978-1-80511-496-3; PDF 978-1-80511-497-0; HTML:978-1-80511-499-4; EPUB:978-1-80511-498-7}, doi = {https://doi.org/10.11647/OBP.0446}, url = {https://www.openbookpublishers.com/books/10.11647/OBP.0446}, author = {Aswin Sai Narain Seshasayee} } @article {153342, title = {Evolution of transcription factor-containing superfamilies in Eukaryotes.}, journal = {Journal of Molecular Biology}, year = {2025}, month = {2025 Jan 23}, pages = {168959}, abstract = {

Regulation of gene expression helps determine various phenotypes in most cellular life forms. It is orchestrated at different levels and at the point of transcription initiation by transcription factors (TFs). TFs bind to DNA through domains that are evolutionarily related, by shared membership of the same superfamilies (TF-SFs), to those found in other nucleic acid binding and protein-binding functions (nTFs for non-TFs). Here we ask how TF DNA binding sequence families in eukaryotes have evolved in relation to their nTF relatives. TF numbers scale by power law with the total number of protein-coding genes differently in different clades, with fungi usually showing sub-linear powers whereas chordates show super-linear scaling. The LECA probably encoded a complex regulatory machinery with both TFs and nTFs, but with an excess of nTFs when compared to the relative distribution of TFs and nTFs in extant organisms. Losses drive the evolution of TFs and nTFs, with the possible exception of TFs in animals for some tree topologies. TFs are highly dynamic in evolution, showing higher gain and loss rates than nTFs though both are conserved to similar extents. Gains of TFs and nTFs are driven by the appearance of a large number of new sequence clusters in a small number of nodes, which determine the presence of as many as a third of extant TFs and nTFs as well as the relative presence of TFs and nTFs. Whereas nodes showing explosion of TF numbers belong to multicellular clades, those for nTFs lie among the fungi and the protists.

}, keywords = {DNA-binding domains; Transcription Factor; Transcription Factor evolution.}, issn = {1089-8638}, doi = {10.1016/j.jmb.2025.168959}, author = {Akshara Dubey and Ganesh Muthu and Aswin Sai Narain Seshasayee} }