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Creators/Authors contains: "Yu, Huan"

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  1. Abstract In Escherichia coli, RNase E is the key enzyme for RNA processing and mRNA degradation. Despite the conserved function across bacteria, the domain composition of RNase E varies significantly among species, possibly affecting the enzyme’s subcellular localization, mobility, and function. In this work, we used super-resolution microscopy to find that 93% of RNase E is localized to the membrane in E. coli and exhibits slow diffusion comparable to polysomes diffusing in the cytoplasm. By replacing the native amphipathic membrane targeting sequence (MTS) with a transmembrane motif, we discovered that the MTS results in slower diffusion and stronger membrane binding than a transmembrane motif. Additionally, the evolutionarily divergent C-terminal domain (CTD) was shown to grant slow diffusion of RNase E but to weaken its membrane binding. By analyzing how membrane localization and diffusion of RNase E affect mRNA degradation rates in vivo, we provide new insights into RNase E’s role in the spatiotemporal organization of RNA processes in bacterial cells. 
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    Free, publicly-accessible full text available January 29, 2026
  2. Abstract In eukaryotic cells, transcription, translation, and mRNA degradation occur in distinct subcellular regions. How these mRNA processes are organized in bacteria, without employing membrane-bound compartments, remains unclear. Here, we present generalizable principles underlying coordination between these processes in bacteria. InEscherichia coli, we found that co-transcriptional degradation is rare for mRNAs except for those encoding inner membrane proteins, due to membrane localization of the main ribonuclease, RNase E. We further found, by varying ribosome binding sequences, that translation affects mRNA stability not because ribosomes protect mRNA from degradation, but because low translation leads to premature transcription termination in the absence of transcription-translation coupling. Extending our analyses toBacillus subtilisandCaulobacter crescentus, we established subcellular localization of RNase E (or its homolog) and premature transcription termination in the absence of transcription-translation coupling as key determinants that explain differences in transcriptional and translational coupling to mRNA degradation across genes and species. 
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  3. Abstract. New particle formation (NPF) consists of two steps: nucleation andsubsequent growth. At present, chemical and physical mechanisms that governthese two processes are not well understood. Here, we report initial resultsobtained from the TANGENT (Tandem Aerosol Nucleation and Growth EnvironmentTube) experiments. The TANGENT apparatus enables us to study these twoprocesses independently. The present study focuses on the effects oftemperature on sulfuric acid nucleation and further growth. Our results showthat lower temperatures enhance both the nucleation and growth rate.However, under temperatures below 268 K the effects of temperature on thenucleation rate become less significant and the nucleation rate becomes lessdependent on relative humidity, indicating that particle formation in the conditions of ourflow tube takes place via barrierless nucleation at lower temperatures. Wealso examined the growth of newly formed particles under differingtemperature conditions for nucleation and further growth. Our results showthat newly nucleated clusters formed at low temperatures can indeed surviveevaporation and grow in a warmer environment in the presence of SO2 andozone and potentially other contaminant vapors. These results implythat some heterogeneous reactions involving nanoparticles affect nucleationand growth of newly formed particles. 
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  4. Abstract New particle formation (NPF) represents the first step in the complex processes leading to formation of cloud condensation nuclei. Newly formed nanoparticles affect human health, air quality, weather, and climate. This review provides a brief history, synthesizes recent significant progresses, and outlines the challenges and future directions for research relevant to NPF. New developments include the emergence of state‐of‐the‐art instruments that measure prenucleation clusters and newly nucleated nanoparticles down to about 1 nm; systematic laboratory studies of multicomponent nucleation systems, including collaborative experiments conducted in the Cosmics Leaving Outdoor Droplets chamber at CERN; observations of NPF in different types of forests, extremely polluted urban locations, coastal sites, polar regions, and high‐elevation sites; and improved nucleation theories and parameterizations to account for NPF in atmospheric models. The challenges include the lack of understanding of the fundamental chemical mechanisms responsible for aerosol nucleation and growth under diverse environments, the effects of SO2and NOxon NPF, and the contribution of anthropogenic organic compounds to NPF. It is also critical to develop instruments that can detect chemical composition of particles from 3 to 20 nm and improve parameterizations to represent NPF over a wide range of atmospheric conditions of chemical precursor, temperature, and humidity. 
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