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Duan and Kaushik et al. reveal the structural basis of how Escherichia coli and Thermus thermophilus RNA polymerases initiate transcription from Np₄A alarmones producing Np₄-capped transcripts. The caps form various interactions with a polymerase during initial steps, influencing capping efficiency.

This paper reports the unusual structure of the metabolite-sensing domain of a flavin mononucleotide (FMN)-specific riboswitch bound to FMN, riboflavin and an antibiotic. The relatively open ligand-binding pocket suggests that antimicrobials based on FMN could be devised.

Here, using cryo-EM and biochemical methods, the authors demonstrate that second messenger (p)ppGpp regulates the bacterial RNA polymerase by binding to a site that is functionally relevant during transcriptional elongation but not initiation. Moreover, they demonstrate that binding to that site bears functional implications for nucleotide excision DNA repair and genome stability.

This study shows how Escherichia coli ApaH hydrolyzes enigmatic Np₄N alarmones and decaps Np₄-capped RNAs, thereby impacting their lifetimes. Key features enable ApaH to bind RNA substrates in two orientations, depending on the cap and the first RNA nucleotide.

The structure of the ribosomal protein S15 reveals a novel predominantly α-helical fold and allows for a prediction of the RNA binding surface and orientation within the assembled ribosome.

Adenosylcobalamin is a form of vitamin B₁₂ that serves as a coenzyme in different reactions and as a ligand for riboswitches to control bacterial gene expression. The crystal structure of a B₁₂ riboswitch from Symbiobacterium thermophilum bound to its ligand adenosylcobalamin is now presented, revealing the determinants for ligand recognition and gene expression control.

Structural analysis of PRPP and ppGpp riboswitches reveals that they employ a helical element to create a tunnel for the ligand, whose specificity is determined by the conserved nucleotides forming the tunnel and long-distance contacts.

Crystal structures of the ydaO riboswitch from two thermophilic bacteria reveal a square-shaped RNA architecture that is locked together by two c-di-AMP ligands that bind in pseudosymmetric binding pockets.

Purine base binding specificity in adenine and guanine riboswitches is governed primarily by specific base pairing interactions in the ligand-binding site. A series of 2′-deoxyguanosine riboswitch structures reveals remodeling of the ligand-binding site and remote regions of the structure to accommodate the sugar moiety of the nucleoside substrate.

Reliable quantification and tracing of RNA molecules remain challenging goals. A new fluorescent RNA tag, developed based on a natural adenine-sensing riboswitch and named Squash, offers superior imaging properties and accurate quantification in living cells.

Bacterial T-boxes are regulatory mRNA regions that control the transcription or translation of factors involved in amino acid supply. T-boxes act by directly binding to non-aminoacylated tRNA in response to amino acid starvation. Three studies now capture three-dimensional structures of tRNA–T-box complexes and reveal a set of RNA features that are required for the recognition of specific tRNAs and modulation of gene expression.

Recent findings suggest that RNA-based elements such as ribozymes and RNA sensors have a widespread role in gene expression regulation. Studies of these RNAs provide insights into mechanisms of gene expression control and the evolution of cellular functions from RNA-based origins.

G-quadruplexes form from G rich sequences and have previously been suggested to be involved in various aspects of mRNA metabolism. The structure of an RNA quadruplex-duplex junction in complex with an Arg-Gly-rich peptide from Fragile X mental retardation protein (FMRP) now reveals an unprecedented RNA scaffold and principles underlying its specific recognition.

Aromatic amines can form covalent DNA adducts, in which the damaged base can cause mutations in the vicinity of the lesion. A mechanism for such semi-targeted mutagenesis is now proposed, based on structural and functional data on Dpo4: the bulky lesion-bypass polymerase interaction leads to a conformation of Dpo4 that stabilizes misaligned intermediates.