Article
Chemistry, Multidisciplinary
Songya Zhang, Jing Zhu, Shuai Fan, Wenhao Xie, Zhaoyong Yang, Tong Si
Summary: Directed evolution is a powerful method for engineering enzymes through iterative creation and screening of variant libraries. This study presents an automated workflow for directed evolution of new enzymatic activities using high-throughput library creation and label-free mass spectrometry screening. The approach was demonstrated by engineering a cyclodipeptide synthase to generate therapeutic compounds. The results show that this robotic, label-free mass spectrometry screening approach could be generally applicable to engineering enzymes with new activities in a high-throughput manner.
Article
Biochemistry & Molecular Biology
Marta Cela, Anne Theobald-Dietrich, Joelle Rudinger-Thirion, Philippe Wolff, Renaud Geslain, Magali Frugier
Summary: The membrane protein tRip mediates the import of host tRNAs into the parasite, binding to a subset of human tRNAs with varying affinities. It is revealed that tRip does not bind specific tRNAs solely based on their primary sequence, suggesting post-transcriptional modifications play a role in modulating the host/parasite molecular complex formation. The study discusses the potential use of efficient tRip ligands for translating the parasite's genetic information.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Can Wang, Nathalie Ulryck, Lydia Herzel, Nicolas Pythoud, Nicole Kleiber, Vincent Guerineau, Vincent Jactel, Chloe Moritz, Markus T. Bohnsack, Christine Carapito, David Touboul, Katherine E. Bohnsack, Marc Graille
Summary: Modified nucleotides in non-coding RNAs play an important role in gene expression regulation. In this study, TRMT11, THUMPD3, and THUMPD2 were identified as direct partners of TRMT112, and their functions in tRNA and U6-snRNA modification were elucidated. TRMT11 and THUMPD3 methylate specific positions in tRNAs, while THUMPD2 is involved in the last 'orphan' modification in U6-snRNA. These findings demonstrate the importance of TRMT112 and its interacting partners in mRNA maturation and translation, as well as pre-mRNA splicing.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Qiufen He, Xiao He, Yun Xiao, Qiong Zhao, Zhenzhen Ye, Limei Cui, Ye Chen, Min-Xin Guan
Summary: The study showed significant tissue-specific differences in mammalian mitochondrial tRNA expression, correlating with mtDNA contents but not with 2-thiouridylation levels of specific tRNAs. Aminoacylation levels of mt-tRNAs varied among tissues, with a negative correlation observed between levels and mitochondrial tRNA synthetases expression. Differential levels of OXPHOS subunits encoded by mtDNA or nuclear genes may reflect functional emphasis for mitochondria in each tissue.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Raquel Garcia-Vilchez, Ana M. Anazco-Guenkova, Judith Lopez, Sabine Dietmann, Mercedes Tome, Sonia Jimeno, Mikel Azkargorta, Felix Elortza, Laura Barcena, Monika Gonzalez-Lopez, Ana M. Aransay, Manuel A. Sanchez-Martin, Pablo Huertas, Raul V. Duran, Sandra Blanco
Summary: Tumour progression and therapy tolerance depend largely on the plasticity of cancer cells. A study has found that N7-guanosine methylation (m7G) of tRNAs, regulated by METTL1, plays a crucial role in cancer cell survival under stress conditions. Loss of tRNA m7G methylation activates stress response pathways and sensitises cancer cells to stress, while reducing METTL1 expression inhibits tumour growth and increases cytotoxic stress in vivo. Targeting METTL1 could potentially enhance the sensitivity of cancer cells to chemotherapy.
Article
Chemistry, Multidisciplinary
Takayuki Katoh, Hiroaki Suga
Summary: In this study, we have successfully overcome the challenge of ribosomal elongation of aromatic cyclic beta(2,3)-amino acids and discovered potent binding peptides against human IFNGR1 and FXIIa. These peptides not only exhibit high inhibitory activity but also demonstrate high protease resistance in human serum.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Ha An Nguyen, Eric D. Hoffer, Crystal E. Fagan, Tatsuya Maehigashi, Christine M. Dunham
Summary: Rapid and accurate translation is crucial for producing functional proteins. The ribosome monitors the interaction between mRNA codons and tRNA anticodons to ensure fidelity in tRNA selection. The presence of a mismatched tRNA-mRNA pair in the ribosome triggers a reduction in fidelity, facilitating the recognition of sense codons and the degradation of aberrant peptides. Crystal structures of the ribosome reveal the mispositioning of mRNA nucleotides, potentially leading to premature termination.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Suki Albers, Bertrand Beckert, Marco C. Matthies, Chandra Sekhar Mandava, Raphael Schuster, Carolin Seuring, Maria Riedner, Suparna Sanyal, Andrew E. Torda, Daniel N. Wilson, Zoya Ignatova
Summary: The researchers designed novel tRNAs that decode UGA stop codons in E. coli efficiently by optimizing the tRNA structure to enhance suppression activity. The study determined the ribosome structure bound to the designed tRNA with a UGA stop codon, showing that the conformation of the stop codon is influenced by distinct A-site ligands.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Joshua D. Jones, Kathleen T. Grassmyer, Robert T. Kennedy, Kristin S. Koutmou, Todd D. Maloney
Summary: siRNA therapeutics provide a selective and powerful approach to reduce the expression of disease-causing genes. A bottom-up siRNA sequencing platform was developed using nuclease P1, which enables easier sequencing data analysis and provides full sequence coverage. This enzymatic digestion scheme shows high-quality and highly reproducible RNA sequencing, regardless of the siRNA modifications, making it suitable for existing sequence confirmation workflows.
ANALYTICAL CHEMISTRY
(2023)
Article
Biochemistry & Molecular Biology
Bruno Faivre, Murielle Lombard, Soufyan Fakroun, Chau-Duy-Tam Vo, Catherine Goyenvalle, Vincent Guerineau, Ludovic Pecqueur, Marc Fontecave, Valerie De Crecy-Lagard, Damien Bregeon, Djemel Hamdane
Summary: Dihydrouridine (D) is a conserved tRNA-modified base in all kingdoms of life, synthesized by conserved dihydrouridine synthases (Dus). Characterization of a unique DusB gene in Mollicutes revealed its ability to simultaneously modify U17 to D17 and synthesize D20/D20a, exhibiting unprecedented multisite specificity.
Article
Biochemistry & Molecular Biology
Yoshihiko Iwane, Hiroyuki Kimura, Takayuki Katoh, Hiroaki Suga
Summary: This study experimentally verified that the incorporation efficiency of N-methyl-amino acids ((Me)AAs) into peptide chains is lower due to insufficient affinity of (Me)AA-tRNAs to EF-Tu. By engineering the T-stem sequence of tRNA to adjust the affinity of (Me)AA-tRNAs to EF-Tu, the uniform affinity-tuning of individual pairs successfully enhanced the incorporation of (Me)AAs into peptide scaffolds.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Anna Fryszkowska, Chihui An, Oscar Alvizo, Goutami Banerjee, Keith A. Canada, Yang Cao, Duane DeMong, Paul N. Devine, Da Duan, David M. Elgart, Iman Farasat, Donald R. Gauthier, Erin N. Guidry, Xiujuan Jia, Jongrock Kong, Nikki Kruse, Katrina W. Lexa, Alexey A. Makarov, Benjamin F. Mann, Erika M. Milczek, Vesna Mitchell, Jovana Nazor, Claudia Neri, Robert K. Orr, Peter Orth, Eric M. Phillips, James N. Riggins, Wes A. Schafer, Steven M. Silverman, Christopher A. Strulson, Nandhitha Subramanian, Rama Voladri, Hao Yang, Jie Yang, Xiang Yi, Xiyun Zhang, Wendy Zhong
Summary: This article introduces a bioconjugation strategy for selectively modifying native peptides using high site selectivity conveyed by engineered enzymes. By modifying certain amino groups and cleavable phenylacetamide groups in insulin, homogeneous bioconjugates with improved yield and purity were synthesized.
Article
Chemistry, Multidisciplinary
Ryan P. Sweeney, Phillip M. Danby, Andreas Geissner, Ryan Karimi, Jesper Brask, Stephen G. Withers
Summary: Efforts have been made to find better amylase mutants through high-throughput screening, aided by the development of efficient active site titration reagents for quantitation of active mutants in crude cell lysates. The designed reagent incorporates a highly reactive fluorogenic leaving group onto unsaturated cyclitol ethers, providing a convenient titrant for alpha-amylases down to low nanomolar levels.
Article
Chemistry, Multidisciplinary
Emmajay Sutherland, Christopher John Harding, Clarissa Melo Czekster
Summary: Cyclodipeptide synthases (CDPSs) generate a wide range of cyclic dipeptides using aminoacylated tRNAs as substrates. However, the substrate selection mechanism is not yet known. Here, the authors investigate the substrate promiscuity of two histidine-incorporating CDPSs to generate an extensive library of products which complement the chemical realm of histidine-containing cyclic dipeptides.
COMMUNICATIONS CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Sasilada Sirirungruang, Omer Ad, Thomas M. Privalsky, Swetha Ramesh, Joel L. Sax, Hongjun Done, Edward E. K. Baidoo, Bashar Amer, Chaitan Khosla, Michelle C. Y. Chang
Summary: A method to selectively incorporate fluorine into complex structures has been developed, which allows for the production of regioselectively fluorinated full-length polyketides. This approach combines the attributes of synthetic and natural molecules, offering potential for the identification and development of bioactive fluorinated small molecules.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ewelina M. Malecka, Joanna Strozecka, Daria Sobanska, Mikolaj Olejniczak
Article
Biochemistry & Molecular Biology
Agata Groszewska, Zuzanna Wroblewska, Mikolaj Olejniczak
ACTA BIOCHIMICA POLONICA
(2016)
Review
Biochemistry & Molecular Biology
Zuzanna Wroblewska, Mikolaj Olejniczak
ACTA BIOCHIMICA POLONICA
(2016)
Article
Biochemistry & Molecular Biology
Zuzanna Wroblewska, Mikolaj Olejniczak
Review
Biochemistry & Molecular Biology
Mikolaj Olejniczak, Gisela Storz
MOLECULAR MICROBIOLOGY
(2017)
Article
Biochemistry & Molecular Biology
Mikolaj Olejniczak
Article
Biochemistry & Molecular Biology
Sarah Ledoux, Mikolaj Olejniczak, Olke C. Uhlenbeck
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2009)
Article
Biochemistry & Molecular Biology
Joanna Kwiatkowska, Zuzanna Wroblewska, Kenneth A. Johnson, Mikolaj Olejniczak
Article
Biochemistry & Molecular Biology
Ewa M. Stein, Joanna Kwiatkowska, Maciej M. Basczok, Chandra M. Gravel, Katherine E. Berry, Mikolaj Olejniczak
NUCLEIC ACIDS RESEARCH
(2020)
Review
Biochemistry & Molecular Biology
Mikolaj Olejniczak, Xiaofang Jiang, Maciej M. Basczok, Gisela Storz
Summary: In many bacteria, the stability and function of sRNAs are dependent on RNA chaperone proteins like Hfq or ProQ/FinO-domain proteins. However, some bacteria lack these chaperone proteins, leading to the investigation of KH domain proteins like KhpA and KhpB as potential sRNA chaperones. Therefore, these KH domain proteins may serve as sRNA chaperones in certain bacteria.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sapna G. Thoduka, Paul A. Zaleski, Zofia Dabrowska, Marcin Rownicki, Joanna Strozecka, Anna Gorska, Mikolaj Olejniczak, Joanna Trylska
Article
Biochemistry & Molecular Biology
Mikolaj Olejniczak, Olke C. Uhlenbeck
Article
Biochemistry & Molecular Biology
RP Fahlman, M Olejniczak, OC Uhlenbeck
JOURNAL OF MOLECULAR BIOLOGY
(2006)
Article
Biochemistry & Molecular Biology
M Olejniczak, T Dale, RP Fahlman, OC Uhlenbeck
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2005)