Article
Multidisciplinary Sciences
Martin Klapper, Alexander Huebner, Anan Ibrahim, Ina Wasmuth, Maxime Borry, Veit G. Haensch, Shuaibing Zhang, Walid K. Al-Jammal, Harikumar Suma, James A. Fellows Yates, Jasmin Frangenberg, Irina M. Velsko, Somak Chowdhury, Rosa Herbst, Evgeni Bratovanov, Hans-Martin Dahse, Therese Horch, Christian Hertweck, Manuel Ramon Gonzalez Morales, Lawrence Guy Straus, Ivan Vilotijevic, Christina Warinner, Pierre Stallforth
Summary: Major advances in ancient DNA research have allowed access to paleogenomic diversity, however, the functions and capabilities of this genetic material remain largely unknown. In this study, dental calculus samples from ancient humans were examined, leading to the discovery of a biosynthetic gene cluster that produces previously unknown metabolites called paleofurans. This demonstrates the possibility of obtaining natural products from ancient organisms and opens up new opportunities for exploration in this field.
Review
Biochemistry & Molecular Biology
Iveta Fizikova, Jozef Dragasek, Peter Racay
Summary: The complexity of the brain can lead to the development of serious neuropsychiatric disorders, such as schizophrenia. The etiopathogenesis of schizophrenia involves multiple mechanisms, highlighting its complexity and providing a new perspective for studying this disorder. This review focuses on the contribution of mitochondria, particularly oxidative damage, ROS, and energy metabolism. It also discusses the role of redox imbalance and lactate in oxidative stress, lipid peroxidation, and cognitive functions in schizophrenia.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Editorial Material
Microbiology
Anja Spang
Summary: The origin of complex cellular life is a puzzling topic in evolutionary research, with wide variations in perspectives depending on world views and contexts. This article shares a biological perspective on the origin of eukaryotic cells, specifically focusing on the question of whether an archaeon was the ancestor of eukaryotes.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Andreia Faria-Pereira, Vanessa A. Morais
Summary: The brain is one of the most energy-consuming organs in the body, and synaptic transmission is a major contributor to this energy consumption. The brain primarily uses glucose for energy, which is metabolized through glycolysis and/or mitochondrial oxidative phosphorylation. This review examines the balance between glycolysis and oxidative phosphorylation in meeting synaptic energy demands. Dysregulation of synaptic bioenergetics is increasingly associated with neurodegenerative disorders.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Clinical Neurology
Lais Cunha, Mayara Paschalidis, Mariana Moyses-Oliveira, Bruna Pereira Marquezini, Tais Bassani Deconto, Pedro Guerreiro, Anna Kloster, Amanda Cristina Mosini, Luana Nayara Gallego Adami, Monica L. Andersen, Sergio Tufik
Summary: This study investigates the shared molecular mechanisms between insomnia and CREBBP loss-of-function. The researchers find that there are overlapping genes between these two conditions, and these genes may impact insomnia-related biological pathways through the modulation of energy metabolism.
Review
Biochemistry & Molecular Biology
Anna Atlante, Daniela Valenti
Summary: Mitochondria have evolved from ancient bacteria to become crucial organelles within eukaryotic cells, playing a central role in energy metabolism and inheriting genetic material from the maternal line. In recent years, mitochondria have been recognized as more than just powerhouses, with roles in biosynthesis, signaling, and influencing cell behavior. This review focuses on overlooked aspects of mitochondrial biology, such as their metabolism, energy efficiency, and specific functions related to cell and tissue specialization. Additionally, the involvement of mitochondria in certain diseases will be discussed.
CURRENT ISSUES IN MOLECULAR BIOLOGY
(2023)
Review
Endocrinology & Metabolism
Alberto Zullo, Rosa Guida, Rosaria Sciarrillo, Francesco P. Mancini
Summary: Cardiovascular disease (CVD) remains the leading cause of death globally. Oxidative stress, a common trait of several CVD manifestations, can be regulated by sirtuins.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Review
Cell Biology
Pengcheng Zhang, Daniels Konja, Yiwei Zhang, Yu Wang
Summary: MAM serves as a crucial hub for integrating cellular and organelle homeostasis, facilitating adaptation of energy metabolism. Abnormalities in MAM can lead to impaired insulin sensitivity and metabolic diseases.
Article
Fisheries
Zhongzhuan Yin, Man Li, Yan Cai, Lin Qi, Chunhong Yuan, Yuanyong Tian
Summary: Postharvest dry storage of scallops at 4 degrees C was simulated, and the energy metabolism related to glycolysis, tricarboxylic acid cycle, and oxidative phosphorylation pathways was analyzed. The early stage of dry storage showed inhibition of glycolysis and a low level of the tricarboxylic acid cycle, while the middle and late stages exhibited altered metabolic pathways and changes in the NADH level. Long-term dry storage had a lasting and irreversible impact on mitochondrial energy metabolism. The dynamics of mitochondrial metabolism were found to be sensitive to dry exposure during postharvest operations.
Review
Cell Biology
Donald Bajia, Emanuela Bottani, Katarzyna Derwich
Summary: Noonan syndrome and Noonan syndrome with multiple lentigines are genetic disorders that contribute to human diseases in the RASopathy family. Understanding the role of mutated genes and mitochondrial metabolism is crucial for therapeutic strategies.
Article
Biochemistry & Molecular Biology
Qingbin Cui, Wenwen Ding, Panpan Liu, Bingling Luo, Jing Yang, Wenhua Lu, Yumin Hu, Peng Huang, Shijun Wen
Summary: This study demonstrates that enhancing the mitochondria-targeting capacity of gold compounds can enhance their efficacy in eradicating cancer cells. Bi-gold compounds showed better suppression of cancer cell proliferation compared to mono-gold compounds, and the most potent compound, BGC2a, inhibited the antioxidant enzyme TrxR and increased cellular ROS. BGC2a accumulated within mitochondria, leading to mitochondrial dysfunction and inhibition of tumor growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Seung-Bin Na, Bong-Jong Seo, Tae-Kyung Hong, Seung-Yeon Oh, Yean-Ju Hong, Jae-Hoon Song, Sang-Jun Uhm, Kwonho Hong, Jeong-Tae Do
Summary: This study investigated the impact of knocking out the key regulator of mitochondrial fission, the Dnm1l gene, on neural stem cells (NSCs). The results suggest that Dnm1l deficiency leads to impaired self-renewal ability and accelerated cellular aging in NSCs, possibly due to mitochondrial morphological and functional changes as well as increased inflammation and cellular stress response.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Environmental Sciences
Chaoshuai Liang, Qiuyao Jiang, Zhenzhen Liu, Jian Yang, Jie Zhang, Shuping Zhang, Wei Xin
Summary: Metallic nanomaterials (MNMs) are widely used in medicine due to their various properties, but their toxicological behavior and interactions with cellular mechanisms are not fully understood. This study investigated the effects of four types of MNMs on mitochondrial function and structure. The results showed that MNMs significantly inhibited mitochondrial function and cell energy metabolism, and damaged the mitochondrial structure. The activity of mitochondrial electron transport chains is critical for assessing MNM-induced mitochondrial dysfunction and cytotoxicity.
Article
Biochemistry & Molecular Biology
Natalya Venediktova, Ilya Solomadin, Anna Nikiforova, Konstantin N. Belosludtsev, Galina Mironova
Summary: This study investigates the effect of uridine on the functions of liver mitochondria in rats with experimentally induced hyperthyroidism. Uridine injection normalized the body weight and improved the parameters of oxidative phosphorylation and the activity of some complexes of the electron transport chain in the liver mitochondria of hyperthyroid rats. Uridine also affected mitochondrial biogenesis by regulating the expression of genes responsible for mitophagy and oxidative phosphorylation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Medicine, General & Internal
Ying Li, Mark Hepokoski, Wanjun Gu, Tatum Simonson, Prabhleen Singh
Summary: Acute kidney injury (AKI) significantly impacts critically ill patients and is an independent risk factor for the development of chronic kidney disease. Research indicates a prominent role of mitochondrial dysfunction and altered tubular metabolism in the pathogenesis of AKI, highlighting the importance of understanding these mechanisms for the development of novel therapies.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Biotechnology & Applied Microbiology
Ramona Marasco, Jean-Baptiste Ramond, Marc W. W. Van Goethem, Federico Rossi, Daniele Daffonchio
Summary: Our planet is facing massive ecosystem collapses and arid regions are experiencing various environmental and climatic challenges, leading to aridification and desertification. Preserving and restoring soil health in these areas is crucial to mitigate climate change's impact. Microorganisms and their functional properties and networks play a key role in fighting desertification. Relying on native dryland microorganisms and microbial communities as well as dryland plants and their associated microbiota is a practical approach to conserve and restore soil health and biodiversity.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Microbiology
Anastasia Tsiola, Evangelia Krasakopoulou, Daniele Daffonchio, Constantin Frangoulis, Tatiana M. Tsagaraki, Stilianos Fodelianakis, Paraskevi Pitta
Summary: Human-induced climate change, with increased atmospheric CO2 concentration and sea-surface temperature, has poorly understood synergistic effects on bacterial communities in vulnerable oligotrophic marine ecosystems. In an experiment simulating future changes in surface waters of the eastern Mediterranean, we observed taxonomic differences in bacterial communities, driven by the combined effects of time and treatment. The acidification had a persistent impact on community composition, while warming benefited certain bacterial clades immediately.
Article
Multidisciplinary Sciences
Irene Garcia, Bessem Chouaia, Merce Llabres, Marta Simeoni
Summary: Metabolism is a complex network structure composed of interconnected chemical reactions. An abstract metabolic network, represented by metabolic pathways as nodes and shared compounds as edges, is a suitable model for large-scale comparison of organisms' metabolism. By using graph kernel methods, pairwise comparisons of abstract metabolic networks show that they can discriminate macro evolutionary events and capture key steps in metabolism evolution.
Article
Multidisciplinary Sciences
Ramona Marasco, Marco Fusi, Cristina Coscolin, Alan Barozzi, David Almendral, Rafael Bargiela, Christina Gohlke Nee Nutschel, Christopher Pfleger, Jonas Dittrich, Holger Gohlke, Ruth Matesanz, Sergio Sanchez-Carrillo, Francesca Mapelli, Tatyana N. Chernikova, Peter N. Golyshin, Manuel Ferrer, Daniele Daffonchio
Summary: Temperature has a significant impact on the adaptation and composition of microbiomes, and their enzymes play a crucial role in the thermal response. This study demonstrates that enzyme thermal properties not only explain microbial thermal plasticity but are also finely tuned by the thermal variability of the environment. The findings highlight the importance of temperature-driven enzyme selection in shaping microbiome thermal plasticity and emphasize the need to consider thermal variability in addition to mean annual temperature in understanding microbial community response to temperature.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Ramona Marasco, Gregoire Michoud, Fatmah O. Sefrji, Marco Fusi, Chakkiath P. Antony, Kholoud A. Seferji, Alan Barozzi, Giuseppe Merlino, Daniele Daffonchio
Summary: The Red Sea is a unique ocean due to its geological isolation, lack of freshwater inputs and specific internal water circulations. We hypothesize that the mangrove sediments in the Red Sea are hotspots/reservoirs of unexplored microbial diversity that have evolved to cope with extreme conditions. Our study revealed a vast diversity of taxonomically novel microbial hydrocarbon degraders within the Red Sea mangrove sediments.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Mauro Degli Esposti
Summary: The merger of an anaerobic archaeon and an aerobic bacterium resulted in the development of eukaryotic cells. Current models propose that the archaeon engulfed bacteria through external protrusions and then fused together to form the membrane organelles of eukaryotic cells, including mitochondria. However, new data suggests that inositol lipids, previously thought to have evolved in archaea, actually emerged in bacteria. This finding has implications for our understanding of how eukaryotic cells originated.
Article
Geosciences, Multidisciplinary
Folco Giomi, Alberto Barausse, Alexandra Steckbauer, Daniele Daffonchio, Carlos M. Duarte, Marco Fusi
Summary: The decline of dissolved oxygen in the oceans could have negative impacts on marine life and biogeochemical cycles. Current models that focus on large-scale mean values may lead to inaccurate predictions. Short-term and small-scale oxygen fluctuations strongly influence marine ecosystems, but they are often neglected in large-scale modelling. Understanding the dynamics of dissolved oxygen at small relevant scales is crucial for accurate projection of the impacts of ocean and coastal deoxygenation on marine biogeochemical processes and communities.
Article
Microbiology
Marco Fusi, David K. Ngugi, Ramona Marasco, Jenny Marie Booth, Massimiliano Cardinale, Luciano Sacchi, Emanuela Clementi, Xinyuan Yang, Elisa Garuglieri, Stilianos Fodelianakis, Gregoire Michoud, Daniele Daffonchio
Summary: The microbial composition on the gills of fiddler crabs may play a crucial role in their adaptation to dynamic intertidal ecosystems and the transition from water to air.
Article
Multidisciplinary Sciences
Gregoire Michoud, Tyler J. Kohler, Leila Ezzat, Hannes Peter, Juliet Kigongo Nattabi, Rosemary Nalwanga, Paraskevi Pramateftaki, Michail Styllas, Matteo Tolosano, Vincent De Staercke, Martina Schon, Ramona Marasco, Daniele Daffonchio, Massimo Bourquin, Susheel Bhanu Busi, Tom J. Battin
Summary: Due to climate change, the glaciers on Africa's 'Mountains of the Moon' in Rwenzori National Park, Uganda are expected to disappear within the next few decades. This will result in the disappearance of the glacier-fed streams and their resident microbial communities. A study on the benthic microbiome from the Mt. Stanley glacier-fed stream showed distinct differences from other glacier-fed streams, with the presence of novel taxa and different abundances of common groups. The primary producer community in this stream is rich, likely due to the greater environmental stability of the Afrotropics, and heterotrophic processes dominate the bacterial community.
ROYAL SOCIETY OPEN SCIENCE
(2023)
Article
Multidisciplinary Sciences
Otto Geiger, Alejandro Sanchez-Flores, Jonathan Padilla-Gomez, Mauro Degli Esposti
Summary: We breathe by using oxygen consumed by mitochondria in our cells to extract energy. Mitochondria, which derive from aerobic bacteria, play crucial roles in oxidative phosphorylation and other metabolic pathways in eukaryotic cells. The exact bacterial origin of mitochondria and their relationship to the aerobic metabolism of our cells is still controversial despite the abundance of genomic data. In this study, we employ various approaches to identify the most likely bacteria that are the living relatives of the ancestral bacteria from which mitochondria originated. These bacteria inhabit marine environments and possess a high frequency of aerobic traits as well as genes for the metabolism of essential lipids found in eukaryotic membranes, such as sphingolipids and cardiolipin.
Article
Limnology
Erik S. Yando, Scott F. Jones, W. Ryan James, Denise D. Colombano, Diana I. Montemayor, Stefanie Nolte, Jacqueline L. Raw, Shelby L. Ziegler, Luzhen Chen, Daniele Daffonchio, Marco Fusi, Kerrylee Rogers, Liudmila Sergienko
Summary: Salt marshes are important linkages between terrestrial and marine ecosystems, but the lack of a unifying conceptual framework has affected effective comparisons across different salt marshes. To address this issue, an integrative salt marsh conceptual framework has been developed, providing guidance on applying it to different locations. This framework allows for appropriate comparison by accounting for unique spatial settings in each salt marsh, and it is expected to enhance our understanding of salt marsh function.
LIMNOLOGY AND OCEANOGRAPHY LETTERS
(2023)
Article
Environmental Sciences
Sreejith Kottuparambil, Ananya Ashok, Alan Barozzi, Gregoire Michoud, Chunzhi Cai, Daniele Daffonchio, Carlos M. Duarte, Susana Agusti
Summary: Understanding the immediate impacts of oil spills is crucial for predicting their long-term consequences on the marine environment. This study investigated the early signals of crude oil in seawater and plankton after a major oil spill in the Red Sea. The findings revealed significant incorporation of oil carbon into the dissolved organic carbon pool, alterations in UV absorption, elevated oil fluorescence emissions, changes in the carbon isotope composition of the seawater, enrichment of specific bacterial genera, and the presence of oil pollutants in zooplankton tissues. These early signs highlight the importance of predicting the long-term impacts of marine oil spills.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Erica M. Prosdocimi, Stefania Arioli, Francesca Mapelli, Zahraa Zeaiter, Marco Fusi, Daniele Daffonchio, Sara Borin, Elena Crotti
Summary: This study investigates the induction and resuscitation of viable but non-culturable (VBNC) state in four Vibrio strains in cold seawater, as well as their response to hydrogen peroxide-induced oxidative stress. The results show that VBNC state leads to phenotypic changes in the cells, causing a loss of ability to grow on solid media, which can be partially or fully reverted upon resuscitation. Low concentrations of hydrogen peroxide can prevent cell resuscitation, while prolonged exposure to hydrogen peroxide, even at concentrations lower than inhibitory levels for log-phase growth, permanently damages VBNC cells.
ANNALS OF MICROBIOLOGY
(2023)
Article
Microbiology
Mauro Degli Esposti, Gabriela Guerrero, Marco A. Rogel, Francisco Issotta, Camila Rojas-Villalobos, Raquel Quatrini, Esperanza Martinez-Romero
Summary: This study presents a comprehensive phylogenomic analysis of Acetobacteraceae, a group of alphaproteobacteria with economic importance. The results suggest that the ancestor of Acetobacteraceae was likely photosynthetic and evolved to acetous physiology via a progressive transition. The study also reveals the presence of vestigial signs of photosynthetic metabolism and the derivation of dominant terminal oxidase in acetous bacteria. Furthermore, the bioenergetic traits and alternative pathways for electron transfer functions are analyzed. Based on the analysis, the order Acetobacterales needs to be emended to include three families.
MICROBIOLOGY SPECTRUM
(2023)
