合成生物学論文メモ (Sep 2020)
読み流した論文のメモ。黒色はメモ、緑色は感想、赤色は特に面白いと思ったもの。
29報
Synthetic Biology
Transcription/Translation Control
遺伝子回路、転写翻訳制御など- Pyruvate-responsive genetic circuits for dynamic control of central metabolism
- Authors: X. Xu, X. Li, Y. Liu, Y. Zhu, J. Li, G. Du, J. Chen, R. Ledesma-Amaro & L. Liu
- Journal: Nature Chemical Biology
- Year: 2020
- DOI: 10.1038/s41589-020-0637-3
- Institution: Jiangnan University, China
RNAiのモデリングまでがっつり加えてある。
- Rational programming of history-dependent logic in cellular populations
- Authors: A. Zúñiga, S. Guiziou, P. Mayonove, Z.B. Meriem, M. Camacho, V. Moreau, L. Ciandrini, P. Hersen & J. Bonnet
- Journal: Nature Communications
- Year: 2020
- DOI: 10.1038/s41467-020-18455-z
- Institution: University of Montpellier, France
- Engineered systems of inducible anti-repressors for the next generation of biological programming
- Authors: T.M. Groseclose, R.E. Rondon, Z.D. Herde, C.A. Aldrete & C.J. Wilson
- Journal: Nature Communications
- Year: 2020
- DOI: 10.1038/s41467-020-18302-1
- Institution: Georgia Institute of Technology, USA
基質結合コアとDNA結合部位のモジュール性の高いTF(バクテリアのTCSなど)で広く応用出来そう。
- Characterization and mitigation of gene expression burden in mammalian cells
- Authors: T. Frei, F. Cella, F. Tedeschi, J. Gutiérrez, G.-B. Stan, M. Khammash & V. Siciliano
- Journal: Nature Communications
- Year: 2020
- DOI: 10.1038/s41467-020-18392-x
- Institution: ETH Zürich, Switzerland
一つ一つのステップが非常に丁寧で良い。
- Two Completely Orthogonal Quorum Sensing Systems with Self-Produced Autoinducers Enable Automatic Delayed Cascade Control
- Authors: W. Jiang, X. He, Y. Luo, Y. Mu, F. Gu, Q. Liang & Q. Qi
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00370
- Institution: Shandong University, China
- Engineering and application of a biosensor with focused ligand specificity
- Authors: D.D. Corte, H.L. van Beek, F. Syberg, M. Schallmey, F. Tobola, K.U. Cormann, C. Schlicker, P.T. Baumann, K. Krumbach, S. Sokolowsky, C.J. Morris, A. Grünberger, E. Hofmann, G.F. Schröder & J. Marienhagen
- Journal: Nature Communications
- Year: 2020
- DOI: 10.1038/s41467-020-18400-0
- Institution: Forschungszentrum Jülich, Germany
RNA Synthetic Biology
アプタマー、リボザイムなど- Switching the activity of Taq polymerase using clamp-like triplex aptamer structure
- Authors: Y. Hu, Z. Wang, Z. Chen & L. Pan
- Journal: Nucleic Acids Research
- Year: 2020
- DOI: 10.1093/nar/gkaa581
- Institution: Huazhong University of Science and Technology, China
ssDNAの論理式的なものを組み込めば制限酵素を使わなくてもON/OFF出来そう(?)
- Optoribogenetic control of regulatory RNA molecules
- Authors: S. Pilsl, C. Morgan, M. Choukeife, A. Möglich & G. Mayer
- Journal: Nature Communications
- Year: 2020
- DOI: 10.1038/s41467-020-18673-5
- Institution: University of Bonn, Germany
PAL自体も同二研究室から去年出ていたらしく、分野の広がる感じがして面白かった。
Optogenetics
光駆動型ツール、蛍光イメージング、光受容体など、その他〇〇genetics系- Optogenetic control of the lac operon for bacterial chemical and protein production
- Authors: M.A. Lalwani, S.S. Ip, C. Carrasco-López, C. Day, H. Kawabe & J.L. Avalos
- Journal: Nature Chemical Biology
- Year: 2020
- DOI: 10.1038/s41589-020-0639-1
- Institution: Princeton University, USA
暗条件でONになるようにしている辺り、YF1-FixJの光感度が高さが問題っぽい。
- CL6mN: Rationally Designed Optogenetic Photoswitches with Tunable Dissociation Dynamics
- Authors: A Mukherjee, C Sudrik, Y Hu, M Arha, M Stathos, J Baek, DV Schaffer & RS Kane
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00362
- Institution: Georgia Institute of Technology, USA
Wntシグナル伝達の相手との不活性な弱い相互作用がクラスターを長持ちさせているという感じか?
- Optogenetic Control of Heterologous Metabolism in E. coli
- Authors: AR Raghavan, K Salim & VG Yadav
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.9b00454
- Institution: The University of British Columbia, Canada
Protein Engineering
タンパク質工学- Conditional Recruitment to a DNA-Bound CRISPR−Cas Complex Using a Colocalization-Dependent Protein Switch
- Authors: R.L. Kirkpatrick, K. Lewis, R.A. Langan, M.J. Lajoie, S.E. Boyken, M. Eakman, D. Baker & J.G. Zalatan
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00012
- Institution: University of Washington, USA
このスピードで実用化してるのえぐい。
CRISPR/Cas
クリスパー系- Enhancement of target specificity of CRISPR–Cas12a by using a chimeric DNA–RNA guide
- Authors: H. Kim, W. Lee, Y. Oh, S.-H. Kang, J.K. Hur, H. Lee, W. Song, K.-S. Lim, Y.-H. Park, B.-S. Song, Y.B. Jin, B.-H. Jun, C. Jung, D.-S. Lee, S.-U. Kim, & S.H. Lee
- Journal: Nucleic Acids Research
- Year: 2020
- DOI: 10.1093/nar/gkaa605
- Institution: KRIBB, Korea
ターゲット配列の一塩基をRNAからDNAに変えるだけで特異性が4倍近くなっているサンプルもあり、DNAへの置換も考慮するとデザイン空間がかなり広がる。
- A Single Cas9-VPR Nuclease for Simultaneous Gene Activation, Repression, and Editing in Saccharomyces cerevisiae
- Authors: C. Dong, L. Jiang, S. Xu, L. Huang, J. Cai, J. Lian & Z. Xu
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00218
- Institution: Zhejiang University, China
Metabolic/Signal Pathway Engineering
シグナル経路、代謝経路、酵素工学など- Constructing Microbial Hosts for the Production of Benzoheterocyclic Derivatives
- Authors: X.-L. Bu, B.-B. He, J.-Y. Weng, C.-C. Jiang, Y.-L. Zhao, S.-M. Li, J. Xu & M.-J. Xu
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.9b00405
- Institution: Shanghai Jiao Tong University, China
- Recruiting a Phosphite Dehydrogenase/Formamidase-Driven Antimicrobial Contamination System in Bacillus subtilis for Nonsterilized Fermentation of Acetoin
- Authors: Z.-W. Guo, X.-Y. Ou, S. Liang, H.-F. Gao, L.-Y. Zhang, M.-H. Zong & W.-Y. Lou
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00312
- Institution: South China University of Technology, China
- Development of a Biosensor for Crotonobetaine-CoA Ligase Screening Based on the Elucidation of Escherichia coli Carnitine Metabolism
- Authors: P. Kugler, D. Fröhlich & V.F. Wendisch
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00234
- Institution: Bielefeld University, Germany
- Combining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism
- Authors: J. Zhang, S.D. Petersen, T. Radivojevic, A. Ramirez, A. Pérez-Manríquez, E. Abeliuk, B.J. Sánchez, Z. Costello, Y. Chen, M.J. Fero, H.G. Martin, J. Nielsen, J.D. Keasling & M.K. Jensen
- Journal: Nature Communications
- Year: 2020
- DOI: 10.1038/s41467-020-17910-1
- Institution: Technical University of Denmark, Denmark
学習させたMLのパラメータで別の代謝経路が作られればブレイクスルーになりそうだけど、代謝経路レベルの複雑度になると一つの代謝産物へのfittingは特異的過ぎる気もする。
Cell-free / Reconstruction
無細胞系、再構成など- Synthesis and Characterization of Heterodimers and Fluorescent Nisin Species by Incorporation of Methionine Analogues and Subsequent Click Chemistry
- Authors: J. Deng, J.H. Viel, J. Chen & O.P. Kuipers
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00308
- Institution: University of Groningen, Netherlands
メチオニン誘導体を利用させる手法に感心。
- Cell-free biogenesis of bacterial division proto-rings that can constrict liposomes
- Authors: E. Godino, J.N. López, I. Zarguit, A. Doerr, M. Jimenez, G. Rivas & C. Danelon
- Journal: Communications Biology
- Year: 2020
- DOI: 10.1038/s42003-020-01258-9
- Institution: Delft University of Technology, Netherlands
Alternative Hosts / Strain Engineering
宿主や系統株の開発- Chemical Controllable Gene Drive in Drosophila
- Authors: D. Chae, J. Lee, N. Lee, K. Park, S.J. Moon & H.H. Kim
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00117
- Institution: Yonsei University College ofMedicine, Korea
実用的には食害の対象になっている作物に自然に含まれている化学因子が必要となってくる
- Identifying Improved Sites for Heterologous Gene Integration Using ATAC-seq
- Authors: J.R. Brady, M.C. Tan, C.A. Whittaker, N.A. Colant, N.C. Dalvie, K.R. Love & J.C. Love
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00299
- Institution: MIT, USA
企業等でニッチな生物種を扱う必要のある場面での研究可能性を拡げる。
- Naked Bacterium: Emerging Properties of a Surfome-Streamlined Pseudomonas putida Strain
- Authors: E Martínez-García, S Fraile, DR Espeso, D Vecchietti, G Bertoni & V de Lorenzo
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00272
- Institution: Centro Nacional de Biotecnología, Spain
物理的な特徴を変化させるユニークな研究。物理的な効果の他に、代謝やシグナル伝達にどのような変化が起こるのかも気になるところ。
Computational Biology
- Genetic Circuit Dynamics: Hazard and Glitch Analysis
- Authors: P. Fontanarrosa, H. Doosthosseini, A.E. Borujeni, Y. Dorfan, C.A. Voigt & C. Myers
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00055
- Institution: University of Utah, USA
Bioinformatics
- Capturing Multicellular System Designs Using Synthetic Biology Open Language (SBOL)
- Authors: B. Brown, B. Bartley, J. Beal, J.E. Bird, Á. Goñi-Moreno, J.A. McLaughlin, G. Mısırlı, N. Roehner, D.J. Skelton, C.L. Poh, I.D. Ofiteru, K. James & A. Wipat
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00176
- Institution: Newcastle University, UK
Biology in general
- FlopR: An Open Source Software Package for Calibration and Normalization of Plate Reader and Flow Cytometry
- Authors: A.J.H. Fedorec, C.M. Robinson, K.Y. Wen & C.P. Barnes
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00296
- Institution: University of College London, UK
- Rapid Fabrication of Protein Microarrays via Autogeneration and on-Chip Purification of Biotinylated Probes
- Authors: B-W Li, Y Zhang, Y-C Wang, Y Xue & X-Y Nie
- Journal: ACS Synthetic Biology
- Year: 2020
- DOI: 10.1021/acssynbio.0c00343
- Institution: Chinese Academy of Sciences, China
- A possible universal role for mRNA secondary structure in bacterial translation revealed using a synthetic operon
- Authors: Y. Chemla, M. Peeri, M.L. Heltberg, J. Eichler, M.H. Jensen, T. Tuller & L. Alfonta
- Journal: Nature Communications
- Year: 2020
- DOI: 10.1038/s41467-020-18577-4
- Institution: Ben-Gurion University of the Negev, Israel
構成的なアプローチで発見をしていくのがとても面白い。結果も面白いので追加検証に期待。