Bacterial RNA synthesis: back to the limelight.

Abstract

Bacterial RNA synthesis: back to the limelight Bacteria have been a mainstay of molecular biology, shaping our understanding of the fundamental principles of gene expression control for over half a century. The elegant simplicity of bacterial systems led to many textbook models. Early studies of transcription in bacteria and phages provided a foundation for analysis of more complex eukaryotic systems, and bacterial research started falling out of fashion, with its subjects increasingly seen as over-studied and far removed from modern public-health concerns. While bacterial systems are indeed simpler – from smaller, more information-packed genomes to fewer subunits in RNA polymerase (RNAP) – part of the simplicity in our explanatory models is due to experimental choices made by those who developed them. Limited by the tools and methods of earlier decades, researchers relied on elementary and direct approaches that nevertheless provided an evergreen source of insights that were generalized across the bacterial kingdom and beyond. However, bacteria live in complex environments and exchange not only metabolites but also genetic information. Studies of bacteria in exotic niches and extensive communities, from soils to shales to the human gut, prompted the development of new experimental and computational approaches, revealing that bacteria are very diverse, and many “bacterial” stereotypes do not apply to them all. In this Special Focus issue, we present a collection of reviews that reflect the rapidly changing field of bacterial transcription, highlighting the dawning realization that every aspect – the players, their parts, and their purpose in life and evolution – is more complex than we ever imagined. Key enzymes of the Central Dogma, RNAP and ribosome, are viewed as highly conserved machines. Yet, Miller et al. show that even the best-studied model bacteria, such as Bacillus subtilis and Escherichia coli, have notably diverse RNAPs [1]. Although biochemical and genetic data suggested that they used distinct strategies to regulate RNA synthesis, it took high-resolution cryo-EM structures to make it clear that even their enzymes are different, with two additional auxiliary subunits in B. subtilis “core” RNAP, ε and δ, thought to contribute to the transcription complex stability and disassembly, respectively [1]. Each RNAP has to adapt to the unique needs of its cell, and acquiring additional modules, either as large domain insertions in E. coli or as dissociable subunits, appears to be a common strategy; e.g., bacterial-type chloroplast RNAP apparently needs ten essential subunits to transcribe a ~150-kb genome. New approaches, such as cryo-electron tomography, can capture transcription complexes in their native environments and will no doubt show that bacteria use astonishingly diverse RNAPs and accessory factors. Coupling of transcription and translation is an accepted paradigm in prokaryotes that lack physical barriers between the two machineries. A model in which RNAP and ribosome are linked by NusG, the only universally conserved transcription factor, supported the ubiquity of the coupling mechanism. However, recent structural and biochemical data, summarized by Webster and Weixlbaumer [2], challenge this view. Coupling can be achieved by different protein bridges; alternatively, simply by synchronizing the rates of transcription and translation, RNAP and ribosome can stay in close proximity, protecting the nascent RNA. While this coupling underpins mRNA quality control in E. coli, it appears totally absent in B. subtilis, where RNAP outruns the ribosome. The discovery that bacteria must completely rewire their regulatory logic when coupling is absent provided researchers with an opportunity to explore its role in diverse phyla by simply examining the architecture of their operons for regulatory signals they may contain. The result suggests that many bacteria do not couple their RNA and protein syntheses, a topic for future studies. While making the RNA, RNAP also directs its folding. Co-transcriptional folding of the nascent RNA is broadly accepted, and many reports have been published illustrating its importance for proper folding of riboswitches, ribozymes, and TRANSCRIPTION 2021, VOL. 12, NO. 4, 89–91 https://doi.org/10.1080/21541264.2021.2001236