Thomas A. Steitz

Poly(A) and RNA: More ways to interact: One of the most conserved RNA modifications across organisms is the addition of a polyadenosine, or poly(A), tail to the 3′ end of RNA molecules. Cis-acting RNA stabilization elements, such as the triplex-forming element for nuclear expression (ENE), retard RNA decay, thereby controlling the maturation and abundance of cellular transcripts. Torabi et al. determined the high-resolution crystal structure of a double ENE complexed with 28-mer poly(A) to reveal new modes of the RNA-RNA interaction, including a pocket motif that protects the extreme 3′ end of the poly(A) tail. Discovery of such interactions opens new venues to better understanding poly(A) tail function in RNA biology. Science , this issue p. eabe6523

Rapid generation of drug-resistant mutations in HIV-1 reverse transcriptase (RT), a prime target for anti-HIV therapy, poses a major impediment to effective anti-HIV treatment. Our previous efforts have led to the development of two novel non-nucleoside reverse transcriptase inhibitors (NNRTIs) with piperidine-substituted thiophene[3,2-d]pyrimidine scaffolds, compounds K-5a2 and 25a, which demonstrate highly potent anti-HIV-1 activities and improved resistance profiles compared with etravirine and rilpivirine, respectively. Here, we have determined the crystal structures of HIV-1 wild-type (WT) RT and seven RT variants bearing prevalent drug-resistant mutations in complex with K-5a2 or 25a at ~2 Å resolution. These high-resolution structures illustrate the molecular details of the extensive hydrophobic interactions and the network of main chain hydrogen bonds formed between the NNRTIs and the RT inhibitor-binding pocket, and provide valuable insights into the favorable structural features that can be employed for designing NNRTIs that are broadly active against drug-resistant HIV-1 variants.

Genetic information is translated into proteins by the ribosome. Structural studies of the ribosome and of its complexes with factors and inhibitors have provided invaluable information on the mechanism of protein synthesis. Ribosome inhibitors are among the most successful antimicrobial drugs and constitute more than half of all medicines used to treat infections. However, bacterial infections are becoming increasingly difficult to treat because the microbes have developed resistance to the most effective antibiotics, creating a major public health care threat. This has spurred a renewed interest in structure-function studies of protein synthesis inhibitors, and in few cases, compounds have been developed into potent therapeutic agents against drug-resistant pathogens. In this review, we describe the modes of action of many ribosome-targeting antibiotics, highlight the major resistance mechanisms developed by pathogenic bacteria, and discuss recent advances in structure-assisted design of new molecules.

Structural basis for transcription activation: Bacteria can initiate transcription through two independent classes of recruitment mechanisms. Liu et al. determined the cryo-electron microscopy structure of an intact class I transcription activation complex. The positions and orientations of all the components and the detailed protein-protein and protein-nucleic acid interactions reveal how an activator interacts with the promoter DNA and recruits RNA polymerase through the class I mechanism. Together with a recently reported class II transcription activation complex, the findings complete our structural understanding of bacterial transcription activation. Science , this issue p. 947

Significance: Based on the “RNA world” theory, ribozymes likely carried out biochemical reactions long before organisms evolved to use protein enzymes as biocatalysts. The continued discovery of new structures for small self-cleaving ribozymes has shed light on conserved mechanisms in evolution, such as acid–base catalysis for self-cleavage reaction. Here, we present the crystal structure of a newly discovered class of self-cleaving ribozymes called Pistol and how it likely uses the phosphoester transfer mechanism for self-cleavage. The results presented here suggest that Pistol uses an evolutionarily conserved cleavage mechanism that is like other self-cleaving ribozymes, such as Twister, Hammerhead, Hairpin, and Hepatitis Delta Virus ribozymes.

NusG is an essential transcription factor that plays multiple key regulatory roles in transcription elongation, termination and coupling translation and transcription. The core role of NusG is to enhance transcription elongation and RNA polymerase processivity. Here, we present the structure of Escherichia coli RNA polymerase complexed with NusG. The structure shows that the NusG N-terminal domain (NGN) binds at the central cleft of RNA polymerase surrounded by the β' clamp helices, the β protrusion, and the β lobe domains to close the promoter DNA binding channel and constrain the β' clamp domain, but with an orientation that is different from the one observed in the archaeal β' clamp-Spt4/5 complex. The structure also allows us to construct a reliable model of the complete NusG-associated transcription elongation complex, suggesting that the NGN domain binds at the upstream fork junction of the transcription elongation complex, similar to σ2 in the transcription initiation complex, to stabilize the junction, and therefore enhances transcription processivity.