合成生物学論文メモ (May 2022)
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。
30報
Synthetic Biology
Transcription/Translation Control
遺伝子回路、転写翻訳制御など- Modulating gene regulation function by chemically controlled transcription factor clustering
- Authors: Wu, Jiegen; Chen, Baoqiang; Liu, Yadi; Ma, Liang; Huang, Wen; Lin, Yihan
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30397-2
- Institution: Peking University, China
相分離によるタンパク質の隔離効果も組み合わせられると面白そう。
- DeepTESR: A Deep Learning Framework to Predict the Degree of Translational Elongation Short Ramp for Gene Expression Control
- Authors: Kim, Dong Jae; Kim, Jiwoo; Lee, Dong Hyun; Lee, Jongwuk; Woo, Han Min
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00202
- Institution: Sungkyunkwan University, Republic of Korea
GFPとRFPの違いで0.6程度の相関だと、他のコドン組成の影響もかなり大きそう。
- LOICA: Integrating Models with Data for Genetic Network Design Automation
- Authors: Vidal, Gonzalo; Vidal-C{\'e}spedes, Carlos; Rudge, Timothy J
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.1c00603
- Institution: Pontificia Universidad Católica de Chile, Chile
試してみたい。
- Engineering of a TrpR-Based Biosensor for Altered Dynamic Range and Ligand Preference
- Authors: Gong, Xinyu; Zhang, Ruihua; Wang, Jian; Yan, Yajun
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00134
- Institution: The University of Georgia, USA
- Complex dynamics in a synchronized cell-free genetic clock
- Authors: Aufinger, Lukas; Brenner, Johann; Simmel, Friedrich C
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30478-2
- Institution: Technical University Munich, Germany
RNA Synthetic Biology
アプタマー、リボザイムなど- SHAPE-enabled fragment-based ligand discovery for RNA
- Authors: Zeller, Meredith J; Favorov, Oleg; Li, Kelin; Nuthanakanti, Ashok; Hussein, Dina; Michaud, Aur{\'e}liane; Lafontaine, Daniel A; Busan, Steven; Serganov, Alexander; Aub{\'e}, Jeffrey; Weeks, Kevin M
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2122660119
- Institution: University of North Carolina, USA
SHAPEを使ったスクリーニングも、その後のリガンドデザインも面白かった。
Cell-free / Reconstruction
無細胞系、再構成など- Hyperaccurate Ribosomes for Improved Genetic Code Reprogramming
- Authors: Shakya, Bipasana; Joyner, Olivia G; Hartman, Matthew C T
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00150
- Institution: Virginia Commonwealth University, USA
細胞内でどの位差が出るのか気になる。
- Parainfluenza Fusion Peptide Promotes Membrane Fusion by Assembling into Oligomeric Porelike Structures
- Authors: Val{\'e}rio, Mariana; Mendon{\c c}a, Diogo A; Morais, Jo{\~a}o; Buga, Carolina C; Cruz, Carlos H; Castanho, Miguel A R B; Melo, Manuel N; Soares, Cl{\'a}udio M; Veiga, Ana Salom{\'e}; Lousa, Diana
- Journal: ACS chemical biology
- Year: 2022
- DOI: 10.1021/acschembio.2c00208
- Institution: Universidade Nova de Lisboa, Portugal
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- Signal transduction in light-oxygen-voltage receptors lacking the active-site glutamine
- Authors: Dietler, Julia; Gelfert, Renate; Kaiser, Jennifer; Borin, Veniamin; Renzl, Christian; Pilsl, Sebastian; Ranzani, Am{\'e}rico Tavares; Garc{\'\i}a de Fuentes, Andr{\'e}s; Gleichmann, Tobias; Diensthuber, Ralph P; Weyand, Michael; Mayer, G{\u}nter; Schapiro, Igor; M{\o}glich, Andreas
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30252-4
- Institution: University of Bayreuth, Germany
Fig2bが綺麗で面白い。実はちゃんと検証されていない活性グループがLOVドメイン以外にもありそう。
- Synthetic biology and bioelectrochemical tools for electrogenetic system engineering
- Authors: Lawrence, Joshua M; Yin, Yutong; Bombelli, Paolo; Scarampi, Alberto; Storch, Marko; Wey, Laura T; Climent-Catala, Alicia; {PixCell iGEM Team}; Baldwin, Geoff S; O'Hare, Danny; Howe, Christopher J; Zhang, Jenny Z; Ouldridge, Thomas E; Ledesma-Amaro, Rodrigo
- Journal: Science advances
- Year: 2022
- DOI: 10.1126/sciadv.abm5091
- Institution: University of Cambridge, UK
生体に内在性の溶質で出来るともっと面白くなりそう。
Protein Engineering
タンパク質工学- Functional Nanopore Screen: A Versatile High-Throughput Assay to Study and Engineer Protein Nanopores in Escherichia coli
- Authors: Weber, Wadim; Roeder, Markus; Probanowski, Tobias; Yang, Jie; Abujubara, Helal; Koeppl, Heinz; Tietze, Alesia; Stein, Viktor
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.1c00635
- Institution: TU Darmstadt, Germany
スクリーニングから工学までの流れが良かった、面白い。
- Deep mutational scanning of essential bacterial proteins can guide antibiotic development
- Authors: Dewachter, Liselot; Brooks, Aaron N; Noon, Katherine; Krishnamurthy, Nandini; Versees, Wim; Vranken, Wim; Michiels, Jan
- Journal: bioRxiv
- Year: 2022
- DOI: 10.1101/2022.05.23.493065
- Institution: KU Leuven, Belgium
結果はそれ程振るわなかった感じがあるが、面白い試み。
CRISPR/Cas
クリスパー系- Engineered Cas12i2 is a versatile high-efficiency platform for therapeutic genome editing
- Authors: McGaw, Colin; Garrity, Anthony J; Munoz, Gabrielle Z; Haswell, Jeffrey R; Sengupta, Sejuti; Keston-Smith, Elise; Hunnewell, Pratyusha; Ornstein, Alexa; Bose, Mishti; Wessells, Quinton; Jakimo, Noah; Yan, Paul; Zhang, Huaibin; Alfonse, Lauren E; Ziblat, Roy; Carte, Jason M; Lu, Wei-Cheng; Cerchione, Derek; Hilbert, Brendan; Sothiselvam, Shanmugapriya; Yan, Winston X; Cheng, David R; Scott, David A; DiTommaso, Tia; Chong, Shaorong
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30465-7
- Institution: Arbor Biotechnologies, USA
gRNAの設計難易度がどれくらい変わるのかが気になった。
- Structural basis for RNA-guided DNA cleavage by IscB-$\omega$RNA and mechanistic comparison with Cas9
- Authors: Schuler, Gabriel; Hu, Chunyi; Ke, Ailong
- Journal: Science
- Year: 2022
- DOI: 10.1126/science.abq7220
- Institution: Cornell University, USA
Cas9がトランスポゾン由来だとは知らなかった。
- Multiagent Screening Improves Directed Enzyme Evolution by Identifying Epistatic Mutations
- Authors: Yang, Tian; Ye, Zhixia; Lynch, Michael D
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00136
- Institution: Duke University, USA
やりようによっては酵素以外にも適用出来そうな面白いアイデア。配列の潜在空間を数理的に探索する場合との比較も気になる。
Alternative Hosts / Strain Engineering
宿主や系統株の開発- CRISPR-Cas Assisted Shotgun Mutagenesis Method for Evolutionary Genome Engineering
- Authors: Zhao, Ming; Gao, Miaomiao; Xiong, Liangbin; Liu, Yongjun; Tao, Xinyi; Gao, Bei; Liu, Min; Wang, Feng-Qing; Wei, Dong-Zhi
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00112
- Institution: East China University of Science and Technology, Chinaa
進化後のシーケンシングコストが大変そうだが、面白かった。
- An in vivo gene amplification system for high level expression in Saccharomyces cerevisiae
- Authors: Peng, Bingyin; Esquirol, Lygie; Lu, Zeyu; Shen, Qianyi; Cheah, Li Chen; Howard, Christopher B; Scott, Colin; Trau, Matt; Dumsday, Geoff; Vickers, Claudia E
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30529-8
- Institution: The University of Queensland, Australia
アイデアが面白かった、発展性もありそう。
Miscellany
その他Computational Biology / Bioinformatics
- iFeatureOmega: an integrative platform for engineering, visualization and analysis of features from molecular sequences, structural and ligand data sets
- Authors: Chen, Zhen; Liu, Xuhan; Zhao, Pei; Li, Chen; Wang, Yanan; Li, Fuyi; Akutsu, Tatsuya; Bain, Chris; Gasser, Robin B; Li, Junzhou; Yang, Zuoren; Gao, Xin; Kurgan, Lukasz; Song, Jiangning
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac351
- Institution: Henan Agricultural University, China
深層学習をかけられない小規模データで特徴抽出するのに助かる。
- Prediction of protein-protein interaction using graph neural networks
- Authors: Jha, Kanchan; Saha, Sriparna; Singh, Hiteshi
- Journal: Scientific reports
- Year: 2022
- DOI: 10.1038/s41598-022-12201-9
- Institution: Indian Institute of Technology, India
ProtBERTより他のモデルの方が良いかもしれないが、配列長の制約?
- PepNN: a deep attention model for the identification of peptide binding sites
- Authors: Abdin, Osama; Nim, Satra; Wen, Han; Kim, Philip M
- Journal: Communications Biology
- Year: 2022
- DOI: 10.1038/s42003-022-03445-2
- Institution: University of Toronto, Canada
Alphafoldとの比較を色々しないとで大変そう。
Machine Learning
機械学習を使ったバイオインフォ系のタスク- A systematic evaluation of data processing and problem formulation of CRISPR off-target site prediction
- Authors: Yaish, Ofir; Asif, Maor; Orenstein, Yaron
- Journal: Briefings in bioinformatics
- Year: 2022
- DOI: 10.1093/bib/bbac157
- Institution: Ben-Gurion University of the Negev, Israel
- ToxinPred2: an improved method for predicting toxicity of proteins
- Authors: Sharma, Neelam; Naorem, Leimarembi Devi; Jain, Shipra; Raghava, Gajendra P S
- Journal: Briefings in bioinformatics
- Year: 2022
- DOI: 10.1093/bib/bbac174
- Institution: Indraprastha Institute of Information Technology, Indis
マニアックな予測タスク、嫌いじゃない
- Prediction of protein--ligand binding affinity from sequencing data with interpretable machine learning
- Authors: Rube, H Tomas; Rastogi, Chaitanya; Feng, Siqian; Kribelbauer, Judith F; Li, Allyson; Becerra, Basheer; Melo, Lucas A N; Do, Bach Viet; Li, Xiaoting; Adam, Hammaad H; Shah, Neel H; Mann, Richard S; Bussemaker, Harmen J
- Journal: Nature biotechnology
- Year: 2022
- DOI: 10.1038/s41587-022-01307-0
- Institution: University of California, Merced, USA
泥臭いデータ処理を物凄い数やっていて尊敬する。
Bioinformatics in general
バイオインフォマティクス一般- DDGun: an untrained predictor of protein stability changes upon amino acid variants
- Authors: Montanucci, Ludovica; Capriotti, Emidio; Birolo, Giovanni; Benevenuta, Silvia; Pancotti, Corrado; Lal, Dennis; Fariselli, Piero
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac325
- Institution: Lerner Research Institute, USA
重みの定数は訓練していないと主張しているが、既知データセットとの相関度合いを参考にしたらしい。それはもう訓練してるし、素直にフィッティングした方が良くない?
- Automated Leak Analysis of Nucleic Acid Circuits
- Authors: Zarubiieva, Iuliia; Spaccasassi, Carlo; Kulkarni, Vishwesh; Phillips, Andrew
- Journal: ACS synthetic biology
- Year: 2022
- DOI: 10.1021/acssynbio.2c00084
- Institution: University of Warwick, UK
Biology in general
- The cyclic octapeptide antibiotic argyrin B inhibits translation by trapping EF-G on the ribosome during translocation
- Authors: Wieland, Maximiliane; Holm, Mikael; Rundlet, Emily J; Morici, Martino; Koller, Timm O; Maviza, Tinashe P; Pogorevc, Domen; Osterman, Ilya A; M{\u}ller, Rolf; Blanchard, Scott C; Wilson, Daniel N
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2114214119
- Institution: University of Hamburg, Germany
- Cellular perception of growth rate and the mechanistic origin of bacterial growth law
- Authors: Wu, Chenhao; Balakrishnan, Rohan; Braniff, Nathan; Mori, Matteo; Manzanarez, Gabriel; Zhang, Zhongge; Hwa, Terence
- Journal: Proceedings of the National Academy of Sciences of the United States of America
- Year: 2022
- DOI: 10.1073/pnas.2201585119
- Institution: UCSD, USA
- In vitro reconstitution of Escherichia coli divisome activation
- Authors: Radler, Philipp; Baranova, Natalia; Caldas, Paulo; Sommer, Christoph; L{\'o}pez-Pelegr{\'\i}n, Mar; Michalik, David; Loose, Martin
- Journal: Nature communications
- Year: 2022
- DOI: 10.1038/s41467-022-30301-y
- Institution: IST Austria, Austria
- Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome
- Authors: Herzel, Lydia; Stanley, Julian A; Yao, Chun-Chen; Li, Gene-Wei
- Journal: Nucleic acids research
- Year: 2022
- DOI: 10.1093/nar/gkac295
- Institution: MIT, USA
分解中のRNAに生物学的な役割があると面白そうなくらいの割合。
- Live-Cell Fluorescence Lifetime Multiplexing Using Synthetic Fluorescent Probes
- Authors: Frei, Michelle S; Koch, Birgit; Hiblot, Julien; Johnsson, Kai
- Journal: ACS chemical biology
- Year: 2022
- DOI: 10.1021/acschembio.2c00041
- Institution: Max Planck Institute, Germany
パラメータ次第では蛍光タンパクにも応用できるかも。持続時間をターゲットにした蛍光タンパクデザインも出来るかもしれない。