Article
Biochemistry & Molecular Biology
Paul Campitelli, Liskin Swint-Kruse, S. Banu Ozkan
Summary: Substitutions at nonconserved protein positions can have noncanonical and long-distance effects on protein function, potentially resulting from changes in the internal protein communication network and structural flexibility. Substitutions were found to have long-range effects on flexibilities and dynamic coupling of DNA-binding positions, with the degree of flexibility change correlating with experimentally measured changes in DNA binding. This study proposes that long-range and noncanonical substitution outcomes arise from rewiring long-range communication among functionally important positions.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Biochemical Research Methods
Michael A. Skinnider, Charley Cai, R. Greg Stacey, Leonard J. Foster
Summary: PrInCE is an R/Bioconductor package that uses machine-learning to infer protein-protein interaction networks from CF-MS data, with improvements in runtime and memory requirements and new features such as tests for co-eluting protein complexes and differential network analysis. Extensively documented and fully compatible with Bioconductor classes, PrInCE can seamlessly fit into existing proteomics workflows.
Article
Multidisciplinary Sciences
Mayank N. K. Choudhary, Kara Quaid, Xiaoyun Xing, Heather Schmidt, Ting Wang
Summary: Transposable elements (TEs), previously considered as junk DNA, contribute to species-specific 3D-genome structure by providing binding sites for CTCF protein. These elements play a role in gene regulation during mammalian evolution.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Ishita Mukherjee, Saikat Chakrabarti
Summary: Proteins involved in evolutionary interactions tend to co-evolve, with compensatory changes occurring to maintain interactions; however, certain residue pair alterations can be detrimental. The Co-Var method identifies crucial residues for functional protein interactions, with predictions suggesting their physiological relevance in maintaining interactions, as shown in cancer metastasis studies.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biotechnology & Applied Microbiology
Huilong Chen, Yingchao Zhang, Shuyan Feng
Summary: In this study, the evolutionary mechanisms of the TLP gene family in grasses were investigated. The results showed that whole-genome duplication, dispersed duplication, and transposed duplication all played roles in the evolution of this gene family. The size of the TLP gene family exhibited a pattern of progressive reduction, and its evolution was influenced by duplication, purifying selection, and base mutations.
Article
Multidisciplinary Sciences
Dia A. Ghose, Kaitlyn E. Przydzial, Emily M. Mahoney, Amy E. Keating, Michael T. Laub
Summary: The evolution of novel functions in biology relies on gene duplication and divergence, creating large paralogous protein families. However, the specificity of these paralogs to their interaction partners can be sensitive to mutation. Through deep mutational scanning, it was demonstrated that a family of bacterial signaling proteins exhibits marginal specificity, with individual substitutions leading to substantial cross-talk between pathways. These findings suggest that the evolution of bacterial signaling proteins is constrained by sequence space crowding, and that evolution selects for good enough rather than optimized phenotypes in paralogs.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Mathematics, Applied
Anuran Pal, Supratim Sengupta
Summary: We analyze a cooperative decision-making model based on individual aspiration levels in the framework of a public goods game. Sensitivity to payoff differences and dynamic aspiration levels affects individual satisfaction and subsequent behavior. The efficiency of aspiration level updates determines the collective outcome of strategy changes. Our work shows that even a small fraction of nodes restructuring their connections can promote cooperation across a wide range of learning efficiencies.
Article
Cell Biology
Joo Yeon Seok, Yong Hee Han, Jae-Seong Yang, Jina Yang, Hyun Gyu Lim, Seong Gyeong Kim, Sang Woo Seo, Gyoo Yeol Jung
Summary: Proper carbon flux distribution between cell growth and production of a target compound is crucial for biochemical production. Using a synthetic biosensor, cells were evolved under selective conditions towards optimal resource allocation. Mutations in conserved regions of transcriptional regulation proteins rewired central carbon flux, enhancing target compound yield and reducing accumulation of byproducts. This study provides insight into adaptive laboratory evolution using synthetic biosensors for metabolic pathway optimization.
Article
Engineering, Environmental
Shizhen Wang, Chengwei Ma, An-Ping Zeng
Summary: This study investigates the co-evolved interaction network involved in the allosteric regulation of kinase by using aspartokinase III (AKIII) from E. coli as a model system. It identifies rearrangement of side-chain interactions upon inhibitor binding and studies dynamic conformational changes and energy transduction processes through steered molecular dynamics simulations. The co-evolved allo-network is verified through mutations of AKIII and modulation of allosteric regulation, demonstrating a strategy to quickly determine key residues involved in the energy transfer pathway.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Plant Sciences
Kuan-Ting Hsin, Tzu-Jing Yang, Yu-Hsuan Lee, Yi-Sheng Cheng
Summary: This study revealed the phylogeny of NLP genes in land plants and their potential role in the nitrate-signaling pathway. The duplication and divergence of NLP genes across different plant lineages highlighted the importance of NLP genes in the evolution of land plants. Analysis of the PB1 domain in Arabidopsis thaliana NLP7 provided insight into the molecular oligomerization and function of NLP proteins in mediating protein-protein interactions.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Jerome Teuliere, Charles Bernard, Hugo Bonnefous, Johannes Martens, Philippe Lopez, Eric Bapteste
Summary: Some viruses have been experimentally shown to accelerate human aging and cellular senescence. There is a hypothesis that aging in humans may also depend on virally encoded interactions, in addition to genetic factors. Through network-based analyses, it was found that many viruses interact with proteins associated with human aging. Influenza A virus (subtype H1N1) was identified as a major candidate for manipulating cellular senescence. The findings have implications for various fields including evolutionary biology, aging study, virology, medicine, and demography.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Alla Gagarinova, Ali Hosseinnia, Matineh Rahmatbakhsh, Zoe Istace, Sadhna Phanse, Mohamed Taha Moutaoufik, Mara Zilocchi, Qingzhou Zhang, Hiroyuki Aoki, Matthew Jessulat, Sunyoung Kim, Khaled A. Aly, Mohan Babu
Summary: By studying genetic interactions among all transcription factor genes in E. coli, this research reveals condition-dependent interactions and uncovers the roles of uncharacterized transcription factors.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Zhourun Wu, Qing Liao, Shixi Fan, Bin Liu
Summary: A novel computational method idenPC-CAP was developed to identify protein complexes from the RNA-protein heterogeneous interaction network, reducing the false positive proteins ratio and outperforming other state-of-the-art methods in this field as demonstrated by experimental results.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Max A. English, Miguel A. Alcantar, James J. Collins
Summary: In this study, a synthetic transposon platform is developed for continuous genome-wide mutagenesis and dynamic rewiring of gene networks in bacteria. The platform is used to investigate the impact of transposon functionalization on the evolution of Escherichia coli populations and to demonstrate the emergence of inducible multigenic phenotypes. A modular assembly pipeline is also developed for the functionalization of transposons with gene regulatory elements and DNA barcodes. This work establishes a valuable tool for optimizing bacterial strains and understanding the dynamics of gene networks.
MOLECULAR SYSTEMS BIOLOGY
(2023)
Article
Ecology
Amparo Lazaro, Carmelo Gomez-Martinez
Summary: This study demonstrates that the loss of natural habitats leads to an increase in seasonal interaction rewiring in plant-pollinator networks and has indirect effects on network structure. The presence of generalist species and the abundance of certain species also influence the rewiring probability.
FUNCTIONAL ECOLOGY
(2022)
Article
Ophthalmology
Rachel L. Gillespie, Jill Urquhart, Simon C. Lovell, Susmito Biswas, Neil R. A. Parry, Daniel F. Schorderet, I. Chris Lloyd, Jill Clayton-Smith, Graeme C. Black
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2015)
Article
Genetics & Heredity
Panagiotis I. Sergouniotis, Jill E. Urquhart, Simon G. Williams, Sanjeev S. Bhaskar, Graeme C. Black, Simon C. Lovell, David J. Whitby, William G. Newman, Jill Clayton-Smith
JOURNAL OF HUMAN GENETICS
(2015)
Article
Biochemistry & Molecular Biology
David Talavera, Simon C. Lovell, Simon Whelan
MOLECULAR BIOLOGY AND EVOLUTION
(2015)
Article
Virology
Abayomi S. Olabode, Xiaowei Jiang, David L. Robertson, Simon C. Lovell
Article
Evolutionary Biology
Ryan M. Ames, David Talavera, Simon G. Williams, David L. Robertson, Simon C. Lovell
BMC EVOLUTIONARY BIOLOGY
(2016)
Article
Computer Science, Artificial Intelligence
Mario Garza-Fabre, Shaun M. Kandathil, Julia Handl, Joshua Knowles, Simon C. Lovell
EVOLUTIONARY COMPUTATION
(2016)
Article
Genetics & Heredity
Panagiotis I. Sergouniotis, Stephanie J. Barton, Sarah Waller, Rahat Perveen, Jamie M. Ellingford, Christopher Campbell, Georgina Hall, Rachel L. Gillespie, Sanjeev S. Bhaskar, Simon C. Ramsden, Graeme C. Black, Simon C. Lovell
ORPHANET JOURNAL OF RARE DISEASES
(2016)
Article
Biochemistry & Molecular Biology
Shaun M. Kandathil, Julia Handl, Simon C. Lovell
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2016)
Article
Biology
Samina Naseeb, Ryan M. Ames, Daniela Delneri, Simon C. Lovell
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2017)
Article
Biochemical Research Methods
Ryan M. Ames, Simon C. Lovell
Letter
Biotechnology & Applied Microbiology
David Talavera, David L. Robertson, Simon C. Lovell
NATURE BIOTECHNOLOGY
(2013)
Article
Multidisciplinary Sciences
Sarah K. Hewitt, Ian J. Donaldson, Simon C. Lovell, Daniela Delneri
Article
Multidisciplinary Sciences
Ryan M. Ames, Daniel Money, Simon C. Lovell
Article
Multidisciplinary Sciences
Gennadiy Tenin, Christopher Clowes, Kathryn Wolton, Eliska Krejci, Jayne A. Wright, Simon C. Lovell, David Sedmera, Kathryn E. Hentges
Article
Virology
Jeongmin Woo, David L. Robertson, Simon C. Lovell