Article
Computer Science, Artificial Intelligence
Mateo Torres, Haixuan Yang, Alfonso E. Romero, Alberto Paccanaro
Summary: S2F is a network propagation approach for functional annotation of newly sequenced organisms, transferring functionally relevant data from model organisms to newly sequenced ones for improved predictions. The method shows significant improvement in bacterial genomes and demonstrates that diffusion process is an effective way to enhance predictive accuracy.
NATURE MACHINE INTELLIGENCE
(2021)
Review
Genetics & Heredity
Madhura Kulkarni, J. Marie Hardwick
Summary: Programmed cell death is widely studied in animals, particularly in the context of cancer, degenerative disorders, and development. However, recent research has revealed similar mechanisms in bacteria and fungi, suggesting that self-induced cell death pathways also exist in microorganisms. While over 20 death pathways have been characterized in mammals, more than 100 mechanisms have been identified in bacteria and fungi. Unfortunately, little is known about cell death in human pathogenic microbes, despite their major public health impacts.
ANNUAL REVIEW OF GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Assaf Gal
Summary: The article discusses the dense ion pools in unicellular organisms and proposes three types of intracellular ion pools. Advanced techniques have led to the discovery of many labile pools in various organisms, raising new questions about their potential roles in the formation of stable mineralized structures.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Juan Guiza, Francisco Solis, Bernardita Valenzuela, Duxan Arancibia, Pedro Zamorano, Jorge Gonzalez, Jonathan Saavedra, Alan Neely, Magdiel Salgado, Agustin D. Martinez, Juan C. Saez, Jose L. Vega
Summary: Cells of vertebrate and invertebrate organisms communicate through membrane channels specialized in cell-cell communication, which are absent in unicellular organisms. This study discovered a family of large-pore channel proteins called unnexins in kinetoplastids, which share similarities with innexin and pannexin proteins. Specifically, the unnexin1 protein (Unx1) forms membrane channels that allow the influx of Ca2+. Low extracellular Ca2+/Mg2+ levels or extracellular alkalinization increase Unx1 channel activity, while mechanical stretching does not have this effect. Unx1 also plays a role in cell invasion and can be a potential target for developing drugs to treat Trypanosoma cruzi infections.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Youri Timsit, Magali Lescot, Martha Valiadi, Fabrice Not
Summary: Bioluminescence, catalyzed by luciferases, has evolved in various taxa and is prevalent in marine environments. It triggers behavioral responses in animals with nervous systems capable of processing light stimuli, while its function in unicellular organisms remains unclear, potentially evolving for perception by visual animals. Studies show that both bacteria and protists have photoreceptors capable of perceiving and integrating light stimuli, leading to responses ranging from phototaxis to complex behaviors. The interplay between light-emission and reception in unicellular organisms like bacteria and dinoflagellates could play multiple roles in communication and complex behavior.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Physics, Multidisciplinary
Mohammad Razavi, Seyed Majid Saberi Fathi, Jack Adam Tuszynski
Summary: This study presents a new approach to investigate the relationship between protein synthesis and cell size, and proposes a framework to estimate the optimal cell size based on entropy reduction calculations.
Review
Chemistry, Multidisciplinary
Lennart Doerr, Jana Kohl, Michael Schweikert, Marie-Louise Lemloh
Summary: Nature's diversity provides promising solutions for bioinspired functional materials and systems. Single-celled organisms, like ciliates, exhibit unique material properties and design at the nano- and micro-scales. This review highlights the background and recent progress in understanding and utilizing the characteristics of ciliates for novel applications in sustainable materials and development processes.
ADVANCED FUNCTIONAL MATERIALS
(2023)
Article
Microbiology
Jose Carrasco-Pujante, Carlos Bringas, Iker Malaina, Maria Fedetz, Luis Martinez, Gorka Perez-Yarza, Maria Dolores Boyano, Mariia Berdieva, Andrew Goodkov, Jose Lopez, Shira Knafo, Ildefonso M. De la Fuente
Summary: The study reveals that single-celled organisms from different species can modify their systemic response to specific stimuli through associative conditioning, exhibiting similar strong and stable characteristics in their new behaviors. These features, including directional persistence and trajectory straightness, may be crucial factors in enhancing cellular adaptability.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Dandan Zhang, Qi Wu, Guangbo Qu, Jianbo Shi, Guibin Jiang
Summary: This review summarizes the single-cell analysis methods for the quantitative determination of metal nanoparticles in aquatic organisms. The paper emphasizes the importance of quantitative analysis of intracellular metal nanoparticles for understanding the interaction between metal nanoparticles and aquatic organisms and evaluating potential risks. It also highlights the limitation of traditional methods in neglecting the heterogeneity of individual cells, which may result in the loss of significant information.
PROGRESS IN CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Luciana Esposito, Nicole Balasco, Luigi Vitagliano
Summary: Oligomerization plays an important role in conferring certain properties to proteins. This study utilized the machine-learning algorithms implemented in AlphaFold to predict the structural states of functional oligomers in the KCTD protein family. The findings identified reliable three-dimensional models for several pentameric states that were previously uncharacterized from a structural point of view. The study provides a comprehensive view of KCTD protein oligomerization and offers insights into key biological processes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Luciana Esposito, Nicole Balasco, Giovanni Smaldone, Rita Berisio, Alessia Ruggiero, Luigi Vitagliano
Summary: One of the key features of KCTD proteins is their involvement in various physiological and pathological processes. Despite the lack of structural data, the use of predicted three-dimensional models by AlphaFold has enabled researchers to gain insights into the relationships within the KCTD family. A novel pseudo-phylogenetic tree based on a common structurally similar domain in the C-terminal region has revealed previously undetected similarities among the KCTD proteins, providing a solid foundation for understanding their diverse functions.
Article
Multidisciplinary Sciences
Eloy Vallina Estrada, Mikael Oliveberg
Summary: The hypervariable residues on protein surfaces play a critical role in cellular interactions and are not as random as previously thought. The electrostatics inside cells carefully orchestrate these interactions to optimize protein diffusion, interactivity, and partner search. Protein surface-charge density is the most influential factor, with different optimal values in different organisms. The study shows that global proteome properties, such as net-charge density, can not only distinguish organisms but also provide information about functional adaptation at the species level.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Computer Science, Artificial Intelligence
Marcelo B. A. Veras, Bishnu Sarker, Sabeur Aridhi, Joao P. P. Gomes, Jose A. F. Macedo, Engelbert Mephu Nguifo, Marie-Dominique Devignes, Malika Smail-Tabbone
Summary: Automatic protein function annotation is crucial for disease understanding and drug design. Similarity functions play an important role in protein function prediction, but there is a lack of specifically designed similarity functions for protein function annotation. This study analyzes the best similarity functions for the task and proposes a new one.
KNOWLEDGE-BASED SYSTEMS
(2022)
Article
Biochemistry & Molecular Biology
Aliaa A. Alamoudi
Summary: Disruption of circadian clock may lead cancer cells to reprogram their metabolism. In unicellular organisms, activation of oxidative pentose phosphate pathway and production of NADPH are crucial for night survival. The circadian clock controls sugar metabolism, shifting between anabolic proliferation and homeostatic survival modes.
Article
Nanoscience & Nanotechnology
Shengliang Wang, Haixu Chen, Zhijun Xu, Xiaoliang Wang, Zhengyu Tao, Lei Wang, Xiaoman Liu, Xin Huang
Summary: Cell surface engineering is an effective strategy to improve cell tolerance and impart various properties. However, research on collective functionality is limited. In this study, a single cell was encapsulated with TiO2 nanoparticles and conductive polymer PPy. The engineered cells exhibited collective behaviors under different conditions, including swarming negative phototaxis migration. This technique has potential in cell therapy and biosensors.
ACS APPLIED NANO MATERIALS
(2023)
Article
Multidisciplinary Sciences
Reut Ben-Menachem, Katherine Wang, Orly Marcu, Zhang Yu, Teck Kwang Lim, Qingsong Lin, Ora Schueler-Furman, Ophry Pines
SCIENTIFIC REPORTS
(2018)
Article
Cell Biology
Anais Brasseur, Shima Bayat, Xiu Ling Chua, Yu Zhang, Qing Zhou, Boon Chuan Low, Cynthia Y. He
JOURNAL OF CELL SCIENCE
(2014)
Article
Biochemistry & Molecular Biology
Suqing Wang, Dharanidharan Ramamurthy, Jasper Tan, Jingyan Liu, Joyce Yip, Andrea Chua, Zhang Yu, Teck Kwang Lim, Qingsong Lin, Ophry Pines, Norbert Lehming
JOURNAL OF MOLECULAR BIOLOGY
(2020)
Article
Multidisciplinary Sciences
Joyce Yip, Suqing Wang, Jasper Tan, Teck Kwang Lim, Qingsong Lin, Zhang Yu, Ofri Karmon, Ophry Pines, Norbert Lehming
Summary: The Krebs cycle enzyme fumarase is involved in DNA damage response by protecting the desulfurase Nfs1p in mitochondria from modification and inactivation. Overexpression of Nfs1p can enhance DNA repair enzyme activity and compensate for the lack of fumarase.
Article
Cell Biology
Yu Zhang, Ofri Karmon, Koyeli Das, Reuven Wiener, Norbert Lehming, Ophry Pines
Summary: Ubiquitination is a critical post-translational modification in cells, involved in regulating cellular processes. The study shows that ubiquitination occurs in yeast mitochondria, independent of proteasome activity, and is regulated by E2 Rad6.
Article
Cell Biology
Maayan Mark, Ofir Klein, Yu Zhang, Koyeli Das, Adi Elbaz, Reut Noa Hazan, Michal Lichtenstein, Norbert Lehming, Maya Schuldiner, Ophry Pines
Summary: Dual localization refers to proteins being localized to multiple compartments within a cell. In this study, the authors identified 280 new protein candidates that have an eclipsed distribution to mitochondria, meaning their main activity is outside mitochondria but they are also present at low levels within mitochondria. The researchers focused on a particular protein family, Triose-phosphate DeHydrogenases, and showed that their eclipsed distribution in mitochondria is important for mitochondrial activity. This work provides insights into the deliberate eclipsed localization, targeting, and function of proteins in mitochondria, and expands our understanding of mitochondrial function in health and disease.
