Ronald Breaker

#Guanidine was known since the 1870s to affect muscle function. Vertebrates have guanidine-sensing #riboswitch RNAs linked to genes relevant to muscle disorders, including some for Ca2+ signaling and others relevant to #ataxia symptoms. @NatureComms nature.com/articles/s4146…

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

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 @RonBreaker or contact ronald.breaker@yale.edu for info.

@Szokoli_Deni Thanks for this message - and it is great to see a structure for this remarkable RNA. Still, no idea of its biological role. I've tried to secure funding for mass production of circRNAs using CP group II ribozymes, but sadly these proposals were rejected.

@RonBreaker The CP group II introns — another one of the ncRNAs discovered in your lab recently had its structure determined, as well. It's been a while since we last heard about them, do you have any thoughts on their function? Are you still working on them? doi.org/10.21203/rs.3.…

#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!

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 @thechrishan for his posts on this odd #ncRNA story. tinyurl.com/yt48x8pr

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 @YaleMBB and contributing to these important missions! apply.interfolio.com/145019

1000s of ligand-binding #riboswitch classes likely remain hidden in bacterial transcripts. In @NAR_Open, 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

X-ray structure of the azaaromatic #riboswitch in @CellDiscovery by Joe Piccirilli and colleagues @UChicago reveals how a #ncRNA forms a pocket that broadly binds planar, hydrophobic ligands. A parallel-eye stereoview shows plenty of base-ligand stacking. #Sec1" target="_blank" rel="nofollow noopener">nature.com/articles/s4142…

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. @PNASNexus tinyurl.com/5bf45s2h

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

@PhoebeARice Hello Phoebe! Our Biochem Lab course is the main duty for this job, but Lecturers often contribute to other courses that they design or that otherwise match their teaching skills/interests. Key Biochem major/non-major lecture courses are taught by ladder faculty - including me!

I'm sure this is a good opportunity - but it is sad when key Ugrad courses are not taught by experts with long-term job security. I look back on my own undergrad days when a biochemistry course for non-majors, taught by 2 national academy members, changed my life.

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! @YaleMBB apply.interfolio.com/114946

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…

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…

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. @MolMicroEditors doi.org/10.1111/mmi.15…

@zakir_tnimov Most #riboswitch RNAs likely are of ancient origin, although small and simple classes could be evolutionary reinventions of #RNAWorld structures. Gazing at their 3D strucures is like looking back in time to observe what life once looked like - well before proteins emerged.

Is there a reason why many riboswitches are activated by rnucleotides or derivatives, is it chemistry or it is an echo from the past? This morning brought me the paper from @RonBreaker discussing what #ribozymes activities gone extinct pubs.acs.org/doi/abs/10.102…

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

In @NAR_Open, with postdoc @mgmo7sen, undergrad Matt Midy, and grad student @Aparaajita_B, 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…