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Two bacterial #Riboswitch classes sense #lithium ions, activating expression of pumps that eject this toxic ion. Our paper in Scientific Reports reveals how these small #ncRNA domains fold, activate genes (see photo), and sometimes mutate to sense #sodium ions. nature.com/articles/s4159…

Another update on the mysterious OLE #ncRNA from bacteria. In Journal of Biological Chemistry we report a third essential protein partner called OapC, which alters RNA folding to form a k-turn. We still think OLE is a #ribozyme relic from the #RNAWorld. pubmed.ncbi.nlm.nih.gov/36336078/

#Yale undergrad Matt Midy (center) representing the Breaker lab at #ABRCMS2022 by winning a poster award on his work to create synthetic #Riboswitch RNAs for #Quinine and #Caffeine. Paper under review. Grad School admission committees: watch for his application next year! ABRCMS

X-ray model of an NAD+-II #riboswitch by the Micura and Ren labs in Nucleic Acids Res reveals how #ncRNA senses the redox state of a ubiquitous enzyme cofactor. The #aptamer stacks G6 and G42 on the plus-charged nicotinamide ring (cation-pi interaction), and rejects NAD's puckered ring.

In Nucleic Acids Res, with postdoc Michael Mohsen, undergrad Matt Midy, and grad student Aparaajita Balaji, Ph.D., we exploit the guanine-I #riboswitch architecture to engineer genetic switches for #quinine and #caffeine. Next challenge: switches for gene therapy applications. doi.org/10.1093/nar/gk…

Variant #ppGpp #riboswitch class RNAs found by Jonathan Jagodnik, Rick Gourse and colleagues UW–Madison to have tuned their specificities to favor ppGpp, #pppGpp, and maybe other biomolecules. Findings showcase RNA functional diversity. Jonathan Jagodnik pubmed.ncbi.nlm.nih.gov/36617997/

Bacteria’s Brain? The mysterious OLE #ncRNA appears to be bacteria’s functional equivalent of eukaryotic #mTOR. The #OLERNA component of the #bTOR (bacterial Tasks OLE Regulates) complex looks like an #RNAWorld relic. Mol Micro Editors doi.org/10.1111/mmi.15…

A variant of #guanine #riboswitch RNAs has adapted to sense the modified base 8-oxoguanine (8-OxoG). Oxidizing agents that damage DNA, such as hydrogen peroxide, activate gene expression via this #ncRNA device. PNASNews pnas.org/doi/10.1073/pn…

The discovery of a #riboswitch class for 8-OxoG expands the diversity of #purine bases sensed by #aptamer RNAs. The image depicts sites of purine modification (colored boxes) relevant to the riboswitch classes whose names are in bold. PNASNews #RNAWorld pnas.org/doi/10.1073/pn…

Yale MB&B is seeking a Lecturer to contribute to our educational mission. Please consider joining our scientific community and using your skills for teaching biochemistry. You will work with fantastic colleagues and enthusiastic students! Yale MB&B apply.interfolio.com/114946

Large, conserved #noncoding RNAs in bacteria with major biochemical functions are rare. Here is #raiA RNA, which has the highest % of strictly conserved nts of any #ncRNA known, and a complex structure. This must be a #ribozyme. See article at tinyurl.com/2h7heypd. PNASNews

The bacterial OLE #noncoding RNA is needed for cells to grow on most carbon/energy sources (except glucose or citrate) and to secrete proteins. This find suggests OLE (#ribozyme?) is part of a major regulatory apparatus of many Gram+ species. PNAS Nexus tinyurl.com/5bf45s2h

X-ray structure of the azaaromatic #riboswitch in Cell Discovery by Joe Piccirilli and colleagues The University of Chicago reveals how a #ncRNA forms a pocket that broadly binds planar, hydrophobic ligands. A parallel-eye stereoview shows plenty of base-ligand stacking. nature.com/articles/s4142…

1000s of ligand-binding #riboswitch classes likely remain hidden in bacterial transcripts. In Nucleic Acids Res, we report many new candidate #ncRNA classes (including the opuB riboswitch candidate shown below) discovered by careful bioinfo analysis of 50 genomes. tinyurl.com/yj2n47sj

Here is a recent posting for a Lecturer position with the Department of Molecular Biophysics and Biochemistry (MB&B) at #Yale University. Please consider joining our research and educational community Yale MB&B and contributing to these important missions! apply.interfolio.com/145019

OLE #noncoding RNA always partners with OapA protein (unknown function). Chrishan Fernando used a computational approach to find that OapA anticorrelates with MpfA - a proven metal ion transporter. See Chrishan Fernando for his posts on this odd #ncRNA story. tinyurl.com/yt48x8pr

#ncRNA molecules are stranger than you think. We propose that OLE RNA is bacteria's functional mimic of #mTOR. The Das lab at Stanford proposes OLE RNA penetrates cell membranes! They also find that RNAs we called ROOL and GOLLD form 8-membered nanocages. biorxiv.org/content/10.110…

In the new year, I will try to post the most exciting Breaker Lab science content on my #Bluesky account at... @ronbreaker.bsky.social More interesting #riboswitch finds and other nucleic acid oddities are likely to come!

My Yale team has exciting RNA research advances related to neurological disorders, with relevance to #bipolar, #autism, #Parkinson’s, and more. Seeking private or commercial funding for our next steps. Possible partners DM Ronald Breaker or contact [email protected] for info.

Computational Biophysics and Biochemistry: Faculty Position Opening in the Department of Biophysics and Biochemistry at Yale.