Carbon extension in peptidylnucleoside biosynthesis by radical SAM enzymes

September 19th, 2016 by Edward A Lilla

Nature Chemical Biology 12, 905 (2016). doi:10.1038/nchembio.2187

Authors: Edward A Lilla & Kenichi Yokoyama

Nikkomycins and polyoxins are antifungal peptidylnucleoside antibiotics active against human and plant pathogens. Here we report that during peptidylnucleoside biosynthesis in Streptomyces cacaoi and S. tendae, the C5′ extension of the nucleoside essential for downstream structural diversification is catalyzed by a conserved radical S-adenosyl-L-methionine (SAM) enzyme, PolH or NikJ. This is distinct from the nucleophilic mechanism reported for antibacterial nucleosides and represents a new mechanism of nucleoside natural product biosynthesis.

  • Posted in Nat Chem Biol, Publications
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Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast

September 19th, 2016 by Mette L Skjoedt

Nature Chemical Biology 12, 951 (2016). doi:10.1038/nchembio.2177

Authors: Mette L Skjoedt, Tim Snoek, Kanchana R Kildegaard, Dushica Arsovska, Michael Eichenberger, Tobias J Goedecke, Arun S Rajkumar, Jie Zhang, Mette Kristensen, Beata J Lehka, Solvej Siedler, Irina Borodina, Michael K Jensen & Jay D Keasling

  • Posted in Nat Chem Biol, Publications
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Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder

September 19th, 2016 by Yangyang Bian

Nature Chemical Biology 12, 959 (2016). doi:10.1038/nchembio.2178

Authors: Yangyang Bian, Lei Li, Mingming Dong, Xuguang Liu, Tomonori Kaneko, Kai Cheng, Huadong Liu, Courtney Voss, Xuan Cao, Yan Wang, David Litchfield, Mingliang Ye, Shawn S-C Li & Hanfa Zou

  • Posted in Nat Chem Biol, Publications
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Fourteen Ways to Reroute Cooperative Communication in the Lactose Repressor: Engineering Regulatory Proteins with Alternate Repressive Functions

September 14th, 2016 by David H. Richards, Sarai Meyer and Corey J. Wilson

TOC Graphic

ACS Synthetic Biology
DOI: 10.1021/acssynbio.6b00048
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The Influenza M2 Ectodomain Regulates the Conformational Equilibria of the Transmembrane Proton Channel: Insights from Solid-State Nuclear Magnetic Resonance

September 12th, 2016 by Byungsu Kwon and Mei Hong

TOC Graphic

Biochemistry
DOI: 10.1021/acs.biochem.6b00727

The role of protein dynamics in the evolution of new enzyme function

September 12th, 2016 by Eleanor Campbell

Nature Chemical Biology 12, 944 (2016). doi:10.1038/nchembio.2175

Authors: Eleanor Campbell, Miriam Kaltenbach, Galen J Correy, Paul D Carr, Benjamin T Porebski, Emma K Livingstone, Livnat Afriat-Jurnou, Ashley M Buckle, Martin Weik, Florian Hollfelder, Nobuhiko Tokuriki & Colin J Jackson

A chemical-inducible CRISPR–Cas9 system for rapid control of genome editing

September 12th, 2016 by Kaiwen Ivy Liu

Nature Chemical Biology 12, 980 (2016). doi:10.1038/nchembio.2179

Authors: Kaiwen Ivy Liu, Muhammad Nadzim Bin Ramli, Cheok Wei Ariel Woo, Yuanming Wang, Tianyun Zhao, Xiujun Zhang, Guo Rong Daniel Yim, Bao Yi Chong, Ali Gowher, Mervyn Zi Hao Chua, Jonathan Jung, Jia Hui Jane Lee & Meng How Tan

  • Posted in Nat Chem Biol, Publications
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Lactate metabolism is associated with mammalian mitochondria

September 12th, 2016 by Ying-Jr Chen

Nature Chemical Biology 12, 937 (2016). doi:10.1038/nchembio.2172

Authors: Ying-Jr Chen, Nathaniel G Mahieu, Xiaojing Huang, Manmilan Singh, Peter A Crawford, Stephen L Johnson, Richard W Gross, Jacob Schaefer & Gary J Patti

How the glycosyltransferase OGT catalyzes amide bond cleavage

September 12th, 2016 by John Janetzko

Nature Chemical Biology 12, 899 (2016). doi:10.1038/nchembio.2173

Authors: John Janetzko, Sunia A Trauger, Michael B Lazarus & Suzanne Walker

The essential human enzyme O-linked β-N-acetylglucosamine transferase (OGT), known for modulating the functions of nuclear and cytoplasmic proteins through serine and threonine glycosylation, was unexpectedly implicated in the proteolytic maturation of the cell cycle regulator host cell factor-1 (HCF-1). Here we show that HCF-1 cleavage occurs via glycosylation of a glutamate side chain followed by on-enzyme formation of an internal pyroglutamate, which undergoes spontaneous backbone hydrolysis.

N6-methyladenosine seqencing highlights the involvement of mRNA methylation in oocyte meiotic maturation and embryo development by regulating translation in Xenopus laevis [Developmental Biology]

September 9th, 2016 by Qi, S.-T., Ma, J.-Y., Wang, Z.-B., Guo, L., Hou, Y., Sun, Q.-Y.

During the oogenesis of Xenopus laevis, oocytes accumulate maternal materials for early embryo development. As the transcription activity of oocyte is silenced at the fully-grown stage and the global genome is reactivated only by the mid-blastula embryo stage, the translation of maternal mRNAs accumulated during oocyte growth should be accurately regulated. Previous evidence has illustrated that the poly(A) tail length and RNA binding elements mediate RNA translation regulation in oocyte. Recently, RNA methylation is found to exist in various systems. In the present study, we sequenced the N6-methyladenosine (m6A) modified mRNAs in fully-grown germinal vesicle (GV) stage and metaphase II (MII) stage oocytes. As a result, we identified 4207 mRNAs with m6A peaks in the GV stage or MII stage oocytes. When we integrated the mRNA methylation data with transcriptome and proteome data, we found that the highly methylated mRNAs showed significantly lower protein levels than those of the hypomethylated mRNAs, although the RNA levels showed no significant difference. We also found that the hypomethylated mRNAs were mainly enriched in the cell cycle and translation pathways, whereas the highly methylated mRNAs were mainly associated with the protein phosphorylation. Our results suggest that the oocyte mRNA methylation can regulate the cellular translation and cell division during oocyte meiotic maturation and early embryo development.
  • Posted in Journal of Biological Chemistry, Publications
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