From Genomes to Function: Regulatory Networks and Evolution in Bacteria and Archaea

Bacteria and archaea display remarkable functional diversity across host-associated and environmental settings. Their capacity to grow, adapt, interact, and evolve is encoded in genome content and shaped by regulatory systems, metabolic pathways, mobile genetic elements, and evolutionary history. Advances in genome sequencing, comparative genomics, transcriptomics, proteomics, metabolomics, and computational biology now make it possible to investigate these relationships at increasing scale and resolution. However, a central challenge remains: translating genomic variation into a mechanistic understanding of microbial function.This Research Topic will bring together studies that examine how bacterial and archaeal genomes encode, regulate, and diversify biological functions. It will focus on genome-centred research that links genes, pathways, regulatory elements, and genome architecture to experimentally or computationally supported functional interpretation. Studies may investigate how genomic variation influences metabolism, stress responses, host association, environmental adaptation, interspecies interactions, or evolutionary innovation in bacteria and archaea.The Topic is particularly interested in the functional and evolutionary organisation of prokaryotic genomes. Relevant work may address regulatory networks, operons and regulons, transcription factors, sigma factors, two-component systems, non-coding RNAs, riboswitches, metabolic pathways, gene context, plasmids, bacteriophages, horizontal gene transfer, and pangenome variation. Studies may investigate the conservation, diversification, loss, acquisition, or rewiring of these genomic and regulatory features across species, strains, or populations.Multi-omics integration, systems modelling, artificial intelligence, and machine-learning approaches are welcome when they address a clearly defined bacterial or archaeal genomic question and lead to biological insight. Computational studies should go beyond general algorithm development and contribute directly to understanding prokaryotic function, regulation, or evolution.Genome-informed studies of microbial adaptation in environmental, host-associated, or applied contexts are also welcome where relevant. Studies centred primarily on descriptive community profiling, broad microbiome surveys, ecosystem-scale modelling, synthetic microbial consortia, or stand-alone computational tools fall outside the core scope unless they include a clear bacterial or archaeal genomic and functional anchor.Potential topics include, but are not limited to:• Functional annotation and experimental validation of bacterial and archaeal genes, pathways, and regulatory elements• Comparative genomics and molecular evolution of prokaryotic genomes• Genome architecture, gene context, operons, regulons, and transcriptional regulation• Regulatory and metabolic network organisation in bacteria and archaea• Genotype–phenotype relationships and the functional effects of genomic variation• Horizontal gene transfer, mobile genetic elements, plasmids, bacteriophages, and genome plasticity• Population genomics and pangenomics linked to prokaryotic adaptation or function• Genome-anchored integration of transcriptomic, proteomic, and metabolomic data• AI and machine learning for interpretable functional prediction in prokaryotic genomics• Genome-informed studies of microbial adaptation in environmental, host-associated, or applied settingsWe welcome Original Research, Methods, Reviews, Mini Reviews, Perspectives, and Data Reports addressing these aspects of bacterial and archaeal functional genomics, regulation, and evolution. Topic editors: Rosa-Maria Gutierrez-Rios, Irma Martínez-Flores Source: https://www.frontiersin.org/research-topics/85167/from-genomes-to-function-regulatory-networks-and-evolution-in-bacteria-and-archaea