Dynamic refolding of IFN-γ mRNA enables it to function as PKR activator and translation template
Nature Chemical Biology. doi:10.1038/nchembio.234
Authors: Smadar Cohen-Chalamish, Anat Hasson, Dahlia Weinberg, Lise Sarah Namer, Yona Banai, Farhat Osman & Raymond Kaempfer
LC/MS analysis of cellular RNA reveals NAD-linked RNA
Nature Chemical Biology. doi:10.1038/nchembio.235
Authors: Y Grace Chen, Walter E Kowtoniuk, Isha Agarwal, Yinghua Shen & David R Liu
We developed a general method to detect cellular small molecule–RNA conjugates that does not rely on the reactivity of the small molecule. This technique revealed NAD-linked RNA in Escherichia coli and Streptomyces venezuelae. Subsequent characterization showed that NAD is a 5′ modification of RNA, cannot be installed in vitro through aberrant transcriptional initiation, is only found among smaller cellular RNAs and is present at a surprisingly high abundance of ∼3,000 copies per cell.
Coupling DNA unwinding activity with primer synthesis in the bacteriophage T4 primosome
Nature Chemical Biology. doi:10.1038/nchembio.236
Authors: Maria Manosas, Michelle M Spiering, Zhihao Zhuang, Stephen J Benkovic & Vincent Croquette
The Vibrio cholerae quorum-sensing autoinducer CAI-1: analysis of the biosynthetic enzyme CqsA
Nature Chemical Biology. doi:10.1038/nchembio.237
Authors: Robert C Kelly, Megan E Bolitho, Douglas A Higgins, Wenyun Lu, Wai-Leung Ng, Philip D Jeffrey, Joshua D Rabinowitz, Martin F Semmelhack, Frederick M Hughson & Bonnie L Bassler
Small-molecule inhibitors target Escherichia coli amyloid biogenesis and biofilm formation
Nature Chemical Biology. doi:10.1038/nchembio.242
Authors: Lynette Cegelski, Jerome S Pinkner, Neal D Hammer, Corinne K Cusumano, Chia S Hung, Erik Chorell, Veronica Åberg, Jennifer N Walker, Patrick C Seed, Fredrik Almqvist, Matthew R Chapman & Scott J Hultgren
Moonlighting proteins Hal3 and Vhs3 form a heteromeric PPCDC with Ykl088w in yeast CoA biosynthesis
Nature Chemical Biology. doi:10.1038/nchembio.243
Authors: Amparo Ruiz, Asier González, Ivan Muñoz, Raquel Serrano, J Albert Abrie, Erick Strauss & Joaquín Ariño
Spatiotemporal modulation of biodiversity in a synthetic chemical-mediated ecosystem
Nature Chemical Biology. doi:10.1038/nchembio.244
Authors: Hao Song, Stephen Payne, Meagan Gray & Lingchong You
A synergistic small-molecule combination directly eradicates diverse prion strain structures
Nature Chemical Biology. doi:10.1038/nchembio.246
Authors: Blake E Roberts, Martin L Duennwald, Huan Wang, Chan Chung, Nicholas P Lopreiato, Elizabeth A Sweeny, M Noelle Knight & James Shorter
Translating metabolic exchange with imaging mass spectrometry
Nature Chemical Biology. doi:10.1038/nchembio.252
Authors: Yu-Liang Yang, Yuquan Xu, Paul Straight & Pieter C Dorrestein
Metabolic exchange between an organism and the environment, including interactions with neighboring organisms, is important for processes of organismal development. Here we develop and use thin-layer agar natural product MALDI-TOF imaging mass spectrometry of intact bacterial colonies grown on top of the MALDI target plate to study an interaction between two species of bacteria and provide direct evidence that Bacillus subtilis silences the defensive arsenal of Streptomyces coelicolor.
Natural amino acids do not require their native tRNAs for efficient selection by the ribosome
Nature Chemical Biology. doi:10.1038/nchembio.255
Authors: Philip R Effraim, Jiangning Wang, Michael T Englander, Josh Avins, Thomas S Leyh, Ruben L Gonzalez & Virginia W Cornish
An artificial di-iron oxo-protein with phenol oxidase activity
Nature Chemical Biology. doi:10.1038/nchembio.257
Authors: Marina Faiella, Concetta Andreozzi, Rafael Torres Martin de Rosales, Vincenzo Pavone, Ornella Maglio, Flavia Nastri, William F DeGrado & Angela Lombardi
Here we report the de novo design and NMR structure of a four-helical bundle di-iron protein with phenol oxidase activity. The introduction of the cofactor-binding and phenol-binding sites required the incorporation of residues that were detrimental to the free energy of folding of the protein. Sufficient stability was, however, obtained by optimizing the sequence of a loop distant from the active site.
Diverse backbone-cyclized peptides via codon reprogramming
Nature Chemical Biology. doi:10.1038/nchembio.259
Authors: Takashi Kawakami, Atsushi Ohta, Masaki Ohuchi, Hiroshi Ashigai, Hiroshi Murakami & Hiroaki Suga
We report a methodology for the ribosomal synthesis of backbone-cyclized peptides involving genetic code reprogramming to introduce one or more nonproteinogenic amino acids. Expression of linear peptides bearing a cysteine-proline dipeptide sequence followed by glycolic acid results in self-rearrangement to a C-terminal diketopiperadine-thioester, which non-enzymatically generates a cyclized peptide. We demonstrate the ribosomal synthesis of several naturally occurring backbone-cyclized peptides and a library based on a bicyclic scaffold, and we identify bioactive sequences by screening and deconvolution.