Letter
Biochemistry & Molecular Biology
Roberto Del Amparo, Miguel Arenas
Summary: Selecting the best-fitting substitution model is recommended for accurately reconstructing ancestral sequences.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Multidisciplinary Sciences
Felix L. Wascher, Nancy Stralis-Pavese, J. Mitchell McGrath, Britta Schulz, Heinz Himmelbauer, Juliane C. Dohm
Summary: The phylogeny of wild and cultivated beets is clarified using genomic analysis and it is found that Greece is the domestication site of sugar beet. This study provides comprehensive insights into the evolutionary relationships of beets.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Gongwang Yu, Yao Liu, Zizhang Li, Shuyun Deng, Zhuoxing Wu, Xiaoyu Zhang, Wenbo Chen, Junnan Yang, Xiaoshu Chen, Jian-Rong Yang
Summary: The authors present eSPET-seq, a method to measure cotranscriptional RNA folding in eukaryotes. Further analysis reveals an antimutagenic effect of nascent RNA folding and contribution to the variability of local mutation rates across the yeast genome.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
John M. McBride, Jean-Pierre Eckmann, Tsvi Tlusty
Summary: In this study, a model combining chemistry, mechanics, and genetics is presented to explain how these factors interact in the evolution of protein-ligand interactions. The model demonstrates that precision is the key to achieving molecular discrimination, and harder discrimination tasks require more coaction of structure, forces, and movements. The model also suggests that increasing protein size enables the solution of more complicated tasks and makes proteins more evolvable and robust.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Nir Hecht, Caroline L. Monteil, Guy Perriere, Marina Vishkautzan, Eyal Gur
Summary: This study investigates the differences in functionality between two homologous bacterial enzymes, PafA and Dop, by analyzing their amino acid sequences and structural elements. Through reciprocal mutagenesis, researchers were able to alter the activity of the enzymes and identify key residues and structural components responsible for their unique functions. The study demonstrates the evolutionary pathways that led to the emergence of novel catalytic functions in these enzymes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Dan-dan Li, Jin-lan Wang, Ya Liu, Yue-zhong Li, Zheng Zhang
Summary: Glycoside hydrolases (GHs) have multiple evolutionary origins and are structurally derived from 27 homologous superfamilies and 16 folds, with a bias towards a few superfamilies and folds. Different superfamilies exhibit variations in enzyme function, with some showing extreme functional diversity that is highly correlated with sequence diversity. Convergent evolution is observed in over one-third of glycosidase activities, especially in the degradation functions of GHs on polysaccharides.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Jianfeng Sun, Dmitrij Frishman
Summary: The study introduces a novel deep-learning approach for predicting interaction sites in transmembrane proteins, which outperforms existing methods. Results also show that approximately 10-25% of amino acid sites are predicted to be involved in interactions in the main functional families of human transmembrane proteins.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Entomology
Qian Jia, Hui Zeng, Jinbing Zhang, Shangfang Gao, Nan Xiao, Jing Tang, Xiaolin Dong, Wei Xie
Summary: Insects can accurately respond to environmental chemical signals through chemosensory proteins (CSPs). The crystal structure of CSP8 protein from the tobacco cutworm was studied, providing insights into the molecular recognition mechanism of SlCSP8 and the CSP protein family. The research suggests that CSP8 is crucial for insects to identify certain compounds, which may have implications for future CSP-based drug design.
Article
Computer Science, Artificial Intelligence
Hongyang Li, Yuanfang Guan
Summary: The authors introduce Ocelot, a machine learning approach for inferring cell-type-specific epigenomic signals, to uncover molecular mechanisms and potential mechanisms of diseases. By dissecting the spatial contributions of six histone marks, the prevalent and asymmetric cross-prediction relationships among these marks are revealed, with high predictive performance achieved on future epigenomic data.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Biochemistry & Molecular Biology
Mahan Ghafari, Louis du Plessis, Jayna Raghwani, Samir Bhatt, Bo Xu, Oliver G. Pybus, Aris Katzourakis
Summary: High-throughput sequencing allows rapid genome sequencing during outbreaks, providing insight into pathogen evolution dynamics. Evolutionary analyses over short timescales are challenging due to the time-dependent nature of evolutionary rate estimates. The study on SARS-CoV-2 and pH1N1 influenza found that inferred evolutionary parameters decline over time, with growth rates and emergence dates stable after 4 months. Terminal branches exhibit elevated substitution rates, correlated with purifying selection generating time dependency in evolutionary parameters.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Shilpi Chaurasia, Julien Y. Dutheil
Summary: Compensatory substitutions occur when advantageous mutations restore fitness lost due to previous deleterious mutations. This study presents an atlas of intra-protein compensatory substitutions built using a phylogenetic approach and a dataset of 1,630 bacterial protein families. Through the analysis of evolutionary and structural properties, it is shown that compensatory mutations are rare but widespread in proteins. Coevolving residues are typically evolving slowly and located in the protein core, and they are more often in contact than expected by chance. The findings provide insights into the relationship between protein structure and fitness landscape.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Chemistry, Applied
Liping Guo, Wallace Yokoyama, Ling Chen, Fei Liu, Maoshen Chen, Fang Zhong
Summary: The objective of this research was to identify the structural and physicochemical factors of konjac glucomannan (KGM). The results indicated that hydration rate and viscosity development of KGM solutions were related to particle size and surface morphology, rather than molecular structure. Lower M/G ratios led to lower viscosity, while higher acetyl content exhibited higher viscosity.
FOOD HYDROCOLLOIDS
(2021)
Article
Multidisciplinary Sciences
Ting Zhou, Kun Ning, Zhenghai Mo, Fan Zhang, Yanwei Zhou, Xinran Chong, Donglin Zhang, Yousry A. El-Kassaby, Jian Bian, Hong Chen
Summary: By assembling and analyzing the chloroplast genome of Ilex dabieshanensis, potential genetic markers for distinguishing different species within the Ilex genus were identified, along with divergent regions compared to other traditional Ilex tea species.
Article
Biochemistry & Molecular Biology
Arindam De Tarafder, Narayan Prasad Parajuli, Soneya Majumdar, Betul Kacar, Suparna Sanyal
Summary: This study investigates the evolution of ribosome specificity in translation factors using elongation factor-Tu (EF-Tu) as a model system. The results show that while modern EF-Tus exhibit preference for their respective ribosomes, ancestral EF-Tus display similar specificity for diverse ribosomes. Additionally, the ribosome specificity of thermophilic EF-Tus remains unchanged despite an increase in catalytic activity with temperature.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Review
Immunology
Samer Halabi, Jim Kaufman
Summary: The functions and structures of MHC and MHC molecules have been extensively studied, and many findings are considered as established knowledge. However, there is significant variation of MHC and MHC molecules in non-mammalian vertebrates, particularly in domestic chickens. Studies on chicken class I and class II molecules have revealed unexpected structural features, which could contribute to a deeper understanding of how MHC molecules bind and present peptides to lymphocytes.
FRONTIERS IN IMMUNOLOGY
(2022)
