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

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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

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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

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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.
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Identification of the plant ribokinase and discovery of a role for Arabidopsis ribokinase in nucleoside metabolism [Plant Biology]

September 6th, 2016 by Riggs, J. W., Rockwell, N. C., Cavales, P. C., Callis, J.

Ribose can be used for energy or as a component of several important biomolecules but in order for it to be used in either capacity it must first be phosphorylated by ribokinase (RBSK). RBSK proteins are part of the phosphofructokinase-B (pfkB) family of carbohydrate kinases. Sequence comparisons of pfkB proteins from the model plant Arabidopsis thaliana with the human and E. coli RBSK identified a single candidate RBSK, At1g17160 (AtRBSK). AtRBSK is more similar to predicted RBSKs from other plant species and to known mammalian and prokaryotic RBSK than to all other PfkB proteins in Arabidopsis. AtRBSK contains a predicted chloroplast transit peptide, and we confirmed plastid localization using AtRBSK fused to YFP. Structure prediction software verified that the AtRBSK sequence mapped onto a known RBSK structure. Kinetic parameters of purified recombinant AtRBSK were determined to be Kmribose = 153 μM +/- 17 μM, KmATP = 45.9 μM +/- 5.6 μM, kcat = 2.0 s-1. Substrate inhibition was observed for AtRBSK (KiATP = 2.44 mM +/- 0.36 mM), as has been demonstrated for other RBSK proteins. Ribose accumulated in Arabidopsis plants lacking AtRBSK. Such plants grew normally unless media was supplemented with ribose, which led to chlorosis and growth inhibition. Ribose accumulated in plants lacking AtRBSK. Both chlorosis and ribose accumulation were abolished upon the introduction of a transgene expressing AtRBSK-MYC, demonstrating that the loss of protein is responsible for the ribose hypersensitivity. Ribose accumulation in plants lacking AtRBSK was reduced in plants also deficient in the nucleoside ribohydrolase NSH1, linking AtRBSK activity to nucleoside metabolism.

Structures of a Nonribosomal Peptide Synthetase Module Bound to MbtH-Like Proteins Support a Highly Dynamic Domain Architecture [Protein Structure and Folding]

September 5th, 2016 by Miller, B. R., Drake, E. J., Shi, C., Aldrich, C. C., Gulick, A. M.

Nonribosomal peptide synthetases (NRPSs) produce a wide variety of peptide natural products. During synthesis, the multidomain NRPSs act as an assembly line, passing the growing product from one module to the next. Each module generally consists of an integrated peptidyl carrier protein (PCP), an amino acid-loading adenylation domain, and a condensation domain that catalyzes peptide bond formation. Some adenylation domains interact with small partner proteins called MbtH-like proteins (MLPs) that enhance solubility or activity. A structure of an MLP bound to an adenylation domain has been previously reported using a truncated adenylation domain, precluding any insight that might derive from understanding the influence of the MLP on the intact adenylation domain or on the dynamics of the entire NRPS module. Here, we present the structures of the full length NRPS EntF bound to the MLPs from E. coli and Pseudomonas aeruginosa. These new structures, along with biochemical and bioinformatic support, further elaborate the residues that define the MLP-adenylation domain interface. Additionally the structures highlight the dynamic behavior of NRPS modules, including the module core formed by the adenylation and condensation domains as well as the orientation of the mobile thioesterase domain.
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