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Architecture Mapping of the Inner Mitochondrial Membrane Proteome by Chemical Tools in Live Cells
Lee, Song-Yi,Kang, Myeong-Gyun,Shin, Sanghee,Kwak, Chulhwan,Kwon, Taejoon,Seo, Jeong Kon,Kim, Jong-Seo,Rhee, Hyun-Woo American Chemical Society 2017 JOURNAL OF THE AMERICAN CHEMICAL SOCIETY - Vol.139 No.10
<P>The inner mitochondria membrane (IMM) proteome plays a central role in maintaining mitochondria' physiology and cellular metabolism. Various important biochemical reactions such as oxidative phosphorylation, metabolite production, and mitochondrial biogenesis are conducted by the IMM proteome, and mitochondria-targeted therapeutics have been developed for IMM proteins, which is deeply related for various human metabolic diseases including cancer and neurodegenerative diseases. However, the membrane topology of the IMM proteome remains largely unclear because of the lack of methods to evaluate it in live cells in a high-throughput manner. In this article, we reveal the in vivo topological direction of 135 IMM proteins, using an in situ-generated radical probe with genetically targeted peroxidase (APEX). Owing to the short lifetime of phenoxyl radicals generated in situ by submitochondrial targeted APEX and the impermeability of the IMM to small molecules, the solvent-exposed tyrosine residues of both the matrix and intermembrane space (IMS) sides of IMM proteins were exclusively labeled with the radical probe in live cells by Matrix-APEX and IMS-APEX, respectively and identified by mass spectrometry. From this analysis, we confirmed 58 IMM protein topologies and we could determine the topological direction of 77 IMM proteins whose topology at the IMM has not been fully characterized. We also found several 1MM proteins (e.g., LETM1 and OXA1) whose topological information should be revised on the basis of our results. Overall, our identification of structural information on the mitochondria' inner-membrane proteome can provide valuable insights for the architecture and connectome of the IMM proteome in live cells.</P>
PKR Senses Nuclear and Mitochondrial Signals by Interacting with Endogenous Double-Stranded RNAs
Kim, Yoosik,Park, Joha,Kim, Sujin,Kim, MinA,Kang, Myeong-Gyun,Kwak, Chulhwan,Kang, Minjeong,Kim, Baekgyu,Rhee, Hyun-Woo,Kim, V. Narry Elsevier 2018 Molecular cell Vol.71 No.6
<P><B>Summary</B></P> <P>Protein kinase RNA-activated (PKR) induces immune response by sensing viral double-stranded RNAs (dsRNAs). However, growing evidence suggests that PKR can also be activated by endogenously expressed dsRNAs. Here, we capture these dsRNAs by formaldehyde-mediated crosslinking and immunoprecipitation sequencing and find that various noncoding RNAs interact with PKR. Surprisingly, the majority of the PKR-interacting RNA repertoire is occupied by mitochondrial RNAs (mtRNAs). MtRNAs can form intermolecular dsRNAs owing to bidirectional transcription of the mitochondrial genome and regulate PKR and eIF2α phosphorylation to control cell signaling and translation. Moreover, PKR activation by mtRNAs is counteracted by PKR phosphatases, disruption of which causes apoptosis from PKR overactivation even in uninfected cells. Our work unveils dynamic regulation of PKR even without infection and establishes PKR as a sensor for nuclear and mitochondrial signaling cues in regulating cellular metabolism.</P> <P><B>Highlights</B></P> <P> <UL> <LI> fCLIP-seq reveals PKR-interacting endogenously expressed dsRNAs </LI> <LI> PKR binds to various noncoding RNAs such as retrotransposons and satellite RNAs </LI> <LI> MtRNAs can form intermolecular dsRNAs and strongly interact with PKR </LI> <LI> MtRNAs can regulate PKR phosphorylation and signaling, especially under stress </LI> </UL> </P> <P><B>Graphical Abstract</B></P> <P>[DISPLAY OMISSION]</P>
Ju Hun LEE,Do Yoon LEE,Hyeong Ryeol KIM,Kyung Rae KIM,Eun Jeong KIM,Chulhwan PARK,Hah Young YOO,Ho Seok KWAK,Seung Wook KIM,Ja Hyun LEE 한국생물공학회 2021 한국생물공학회 학술대회 Vol.2021 No.10
In this study, extracted sugars of microalgae, which cause algal blooms and crude glycerol, which is a biodiesel industry by-product, were used simultaneously to produce 2,3-BDO. The 2,3-BDO production using only extracted algal sugars was about 4.8 g/L at 18 h, and the production of 2,3-BDO using both extracted algal sugar and crude glycerol was about 7 g/L at 18 h. It was confirmed that the main culture with crude glycerol was increased 1.5-fold compared to the case of using only extracted algal sugars. In addition, four components of the main medium (ammonium sulfate, casein hydrolysate, yeast extract and crude glycerol) were statistically optimized and the concentrations of the medium were 12 g/L, 16 g/L, 12 g/L and 13 g/L, respectively. In addition, the final 2,3-BDO production was about 11g/L, which 1.6-fold higher than before optimization process. As a result, it has been confirmed that 2,3-BDO production is possible through the simultaneous use of algal sugars and crude glycerol, which can greatly contribute to the development of zero-waste processes.