Article
Biochemical Research Methods
Wen-Ching Lin, Hao-Cheng Tang, Han Ying Wang, Chia-Yi Kao, You-Chiun Chang, Athena Hsu Li, Shi-Bing Yang, Kurt Yun Mou
Summary: This study introduces a unique mutagenesis method called the reverse Kunkel method, which combines the advantages of user-defined mutagenesis and random mutagenesis. By coupling with phage display and yeast display selections, the method successfully generates improved antibodies with enhanced affinity and immunostaining performance.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Chemistry, Multidisciplinary
Yajie Wang, Pu Xue, Mingfeng Cao, Tianhao Yu, Stephan T. Lane, Huimin Zhao
Summary: Directed evolution aims to accelerate the natural evolution process of biological molecules and systems through gene diversification and library screening, serving as a powerful tool for engineering improved functions in proteins, metabolic pathways, and whole genomes. Common strategies include gene diversification, screening/selection methods, and continuous evolution, with applications in nucleic acids, proteins, pathways, genetic circuits, viruses, and cells. Challenges and future perspectives in directed evolution are also discussed.
Review
Biotechnology & Applied Microbiology
Zarina Iqbal, Saima Sadaf
Summary: Generating functional protein variants with novel or improved characteristics can be achieved through rational design and directed evolution. In laboratory evolution, new tools and methods are needed to create genetic diversity and identify variants with desired traits. Building large libraries of target molecules and protocols to alter their properties has been a challenge in directed evolution experiments.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Monica Castro-Cruz, Frederique Lembo, Jean-Paul Borg, Gilles Trave, Renaud Vincentelli, Pascale Zimmermann
Summary: PSD95-disc large-zonula occludens (PDZ) domains are globular modules that bind to carboxy-terminal sequences of membrane-associated proteins and influence their trafficking and signaling. PDZome 2.0 is a library for Yeast two-hybrid, consisting of 305 individual clones, that outperforms the previous resource in identifying PDZ interactions. Its boundaries were designed based on available PDZ structures, and it has been shown to effectively interact with the E6 oncoprotein from HPV16.
Article
Biochemical Research Methods
Veronica Saez-Jimenez, Simone Scrima, Matteo Lambrughi, Elena Papaleo, Valeria Mapelli, Martin K. M. Engqvist, Lisbeth Olsson
Summary: Pathway engineering is commonly used to improve the production of metabolites, but low catalytic activity can create bottlenecks in specific reaction steps. This study successfully obtained mutant variants of (R)-2-hydroxyglutarate dehydrogenase with a 100-fold higher catalytic efficiency, paving the way for the bio-based production of adipic acid. Rational analysis revealed that mutation A206V played a key role in the improved activity.
ACS SYNTHETIC BIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Haoran Yu, Shuang Ma, Yiwen Li, Paul A. Dalby
Summary: Directed evolution is a powerful strategy to engineer protein properties, and hot spot prediction is crucial for producing smart libraries. Selection of hot spots based on sequence and structure allows for efficient generation of proteins with desired properties.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Chemistry, Inorganic & Nuclear
Ting-ting Zhang, Xing Liu, Jian Zhou, Jiang-tao Liu
Summary: Two novel organic-inorganic hybrid iodoplumbates were synthesized under hydrothermal conditions, featuring a unique pentanuclear cluster and unprecedented 2-D polyiodoplumbate layer. Both compounds exhibit potential semiconductor properties with narrow absorption edges, and one of them also shows photocurrent response and photoluminescent properties.
INORGANIC CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Wenliang Hao, Wenjing Cui, Feiya Suo, Laichuang Han, Zhongyi Cheng, Zhemin Zhou
Summary: In this study, a genomic diversification platform was constructed using CRISPR-ABE8e-CDA-nCas9 technology to rapidly evolve bacterial chassis. The platform allows for adjustable conversion efficiency and editable window, enabling editing of any pre-defined genomic loci and generating a diverse repertoire of genomic sequence mutants.
Article
Biochemical Research Methods
Sai Hu, Zhihong Zhang, Huijun Xiong, Meiping Jiang, Yingchun Luo, Wei Yan, Bihai Zhao
Summary: In this paper, a tensor-based random walk model called RWRT is proposed for protein function prediction. The method outperforms state-of-the-art methods and improves function prediction performance by utilizing functional similarity information.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Kaitlyn Bacon, Abigail Blain, John Bowen, Matthew Burroughs, Nikki McArthur, Stefano Menegatti, Balaji M. Rao
Summary: The article introduces a qYY2H system for discovering specific protein-protein interactions and quantitatively estimating their binding affinities, achieved by expressing bait and prey proteins as yeast cell surface fusions in experiments. This system can identify protein interactions and evaluate their binding affinities.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Jiaqi Li, Guangbo Kang, Jiewen Wang, Haibin Yuan, Yili Wu, Shuxian Meng, Ping Wang, Miao Zhang, Yuli Wang, Yuanhang Feng, He Huang, Ario de Marco
Summary: Routinely screened antibody fragments often require further in vitro maturation for optimal biophysical properties. In vitro strategies can introduce random mutations into the sequences and select for improved ligands under more stringent conditions. Rational approaches aim to identify specific residues involved in biophysical mechanisms and evaluate mutations to improve characteristics. Understanding antigen-antibody interactions is crucial for reliable development, with deep learning methods promising for accelerating model building.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Chemistry, Multidisciplinary
Romany J. McLure, Sheena E. Radford, David J. Brockwell
Summary: Directed evolution is a powerful tool for engineering new functions in biomolecules and gaining insights into protein behavior. It accelerates the process of natural evolution through multiple rounds of gene diversification and selection.
TRENDS IN CHEMISTRY
(2022)
Article
Biology
Xiujuan Zhao, Yanping Zhang, Xiuquan Du
Summary: DFpin is a method for predicting protein-interacting nucleotides in RNA. It removes redundancy based on feature similarity and uses a deep forest model to extract key features, achieving an accuracy of 85.4%.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biochemical Research Methods
Michael Gossing, Angelo Limeta, Christos Skrekas, Mark Wigglesworth, Andrew Davis, Verena Siewers, Florian David
Summary: Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology allows for targeted mutagenesis with guide RNAs (gRNAs). This study investigates the effect of multiplexed expression of gRNAs surrounding a short stretch of DNA on reversion and mutation frequencies using the yEvolvR system. The results show that simultaneous expression of multiple gRNAs leads to higher reversion frequencies and a synergistic effect on mutation frequencies, especially in mutants with defective DNA mismatch repair systems. Additionally, a galactose-inducible yEvolvR system enables temporal control of mutagenesis.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Soroosh Pouyan, Milad Lagzian, Mohammad Hossein Sangtarash
Summary: This study characterized a new alpha-amylase from Bacillus cereus GL96 and used an in-silico approach to redesign the enzyme for improved thermal stability. The engineered enzyme showed higher stability and activity at elevated temperatures compared to the wild-type enzyme. Specifically, the D162K mutation resulted in the best performance, with increased optimum temperature and improved stability. This mutant enzyme holds promise for further investigation and industrial applications.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Yuping Tan, Xia Zhou, Yanqiu Gong, Kun Gou, Youfu Luo, Da Jia, Lunzhi Dai, Yinglan Zhao, Qingxiang Sun
Summary: The study identified a new PHGDH inhibitor, oridonin, and revealed the mechanism of its binding to PHGDH structure, providing new insights for the future design of PHGDH inhibitors.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biology
Sabrina Adam, Julia Bracker, Viviane Klingel, Bernd Osteresch, Nicole E. Radde, Jens Brockmeyer, Pavel Bashtrykov, Albert Jeltsch
Summary: This study reveals that the catalytic activities of TET1 and TET2 are influenced by the flanking sequences of DNA substrates, and this influence is related to 5mC and 5hmC. Furthermore, enhanced flanking sequence preferences and profound effects on the specificity of TET2 are observed at non-CpG sites. The flanking sequence preferences of TET are reflected in genome-wide and local patterns of 5hmC and DNA demethylation.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Alexandra Mack, Max Emperle, Philipp Schnee, Sabrina Adam, Juergen Pleiss, Pavel Bashtrykov, Albert Jeltsch
Summary: Somatic R882H DNMT3A mutations are common in AML, but their pathogenic mechanism is unclear. R882H mutations affect the sequence preferences of DNMT3A and have a dominant effect on its catalytic properties in samples containing WT and R882H subunits.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biology
Alexander Broehm, Tabea Schoch, Michael Dukatz, Nora Graf, Franziska Dorscht, Evelin Mantai, Sabrina Adam, Pavel Bashtrykov, Albert Jeltsch
Summary: DNMT3A efficiently methylates recombinant mononucleosome linker DNA, and H3K36me3 stimulates linker DNA methylation independent of its interaction with the PWWP domain.
COMMUNICATIONS BIOLOGY
(2022)
Editorial Material
Biology
Arunkumar Dhayalan, Albert Jeltsch
Article
Biochemistry & Molecular Biology
Alexander Broehm, Tabea Schoch, David Gruenberger, Mina S. Khella, Maren Kirstin Schuhmacher, Sara Weirich, Albert Jeltsch
Summary: The H3.3 G34W mutation is commonly found in giant cell tumor of bone (GCTB) patients and is associated with reduced SETD2 activity and global reduction in DNA methylation. Our study reveals that the G34W mutation enhances the activity of NSD1 methyltransferase, but has mild effects on NSD2. We discuss the potential downstream effects of the G34W-induced hyperactivity of NSD1 on DNA methylation, histone modifications, and splicing.
Review
Biochemistry & Molecular Biology
Yuying Li, Xinmin Yang, Linrui Peng, Qing Xia, Yuwei Zhang, Wei Huang, Tingting Liu, Da Jia
Summary: This study comprehensively summarizes the phenotypes, mechanisms, and treatment options of human diseases caused by BSCL2 gene mutations, as well as relevant findings in animal studies. Restoring adipose tissue function and targeting seipin-related pathways are effective strategies for CGL2 treatment and also have potential therapeutic value in other diseases.
Article
Chemistry, Multidisciplinary
Philipp Schnee, Michel Choudalakis, Sara Weirich, Mina S. Khella, Henrique Carvalho, Juergen Pleiss, Albert Jeltsch
Summary: This study investigates the mechanisms responsible for the increased activity of SETD2 towards ssK36 peptide. Molecular dynamics simulations and biochemical experiments reveal that ssK36 adopts a hairpin conformation in solution and unfolds during the association process with SETD2. Introducing a stable hairpin conformation increases the methylation of H3K36 peptide by SETD2.
COMMUNICATIONS CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Stefan Kunert, Max Emperle, Sabrina Adam, Julia Bracker, Jens Bracker, Arumugam Rajavelu, Albert Jeltsch
Summary: The DNMT3A DNA methyltransferase is frequently mutated in cancers, especially in AML. The R736H mutation in the FF-interface of the enzyme leads to a moderate reduction in catalytic activity but no changes in CpG specificity or sub-nuclear localization. DNMT3L strongly stimulates the activity of R736H, and mixed interfaces involving R736H also enhance the activity.
Article
Biochemistry & Molecular Biology
Dimitri Graf, Laura Laistner, Viviane Klingel, Nicole E. Radde, Sara Weirich, Albert Jeltsch
Summary: A DNA methylation-based epigenetic memory system was developed to detect environmental signals and trigger phenotypic switches in bacteria. The system's reversible reset was achieved by adding ZnSO4, and the long-term stability of the ON-state was studied, showing a gradual loss of signal over time.
Article
Biology
Julian Broche, Anja R. R. Koehler, Fiona Kuehnel, Bernd Osteresch, Thyagarajan T. T. Chandrasekaran, Sabrina Adam, Jens Brockmeyer, Albert Jeltsch
Summary: Although cytosine-C5 methylation of DNA is essential in higher eukaryotes, the presence and importance of 6-methyladenine (m6dA) in human cells are controversial. We introduced m6dA in human cells and observed reductions in cell viability, particularly after global GANTC methylation. Genes directly regulated by m6dA in a GANTC context showed changes in H3K27me3 and JUN family transcription factor binding, indicating an inhibitory effect on the PRC2 complex and reduced recruitment of JUN transcription factors. Our study demonstrates the physiological effects of m6dA introduction in human DNA and identifies target genes and molecular pathways that affect gene expression and cell phenotypes.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Sabrina Adam, Viviane Klingel, Nicole E. Radde, Pavel Bashtrykov, Albert Jeltsch
Summary: The specificity of DNMT1 for hemimethylated DNA is strongly influenced by the flanking sequence, with an average specificity of 80-fold. This preference is enhanced on long hemimethylated DNA substrates. The presence of a single methyl group in the DNA changes the conformation of the DNMT1-DNA complex, leading to an active conformation by steric repulsion. Passive DNA demethylation by 5hmC generation is not efficient in many flanking contexts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Genetics & Heredity
Nivethika Rajaram, Alexandra G. Kouroukli, Susanne Bens, Pavel Bashtrykov, Albert Jeltsch
Summary: Specific allele-specific targeted DNA methylation was achieved at multiple gene loci using epigenome editing, which can be potentially applied in the treatment of diseases caused by dominant mutations with minimal side effects.
EPIGENETICS & CHROMATIN
(2023)
Editorial Material
Multidisciplinary Sciences
Sara Weirich, Albert Jeltsch
Summary: Protein lysine methylation is important but lacks suitable mimetics for experimental characterization. This limits biochemical and cellular studies. We summarize the challenges and propose alternative approaches.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)