Article
Biochemistry & Molecular Biology
Eric A. Hunt, Esta Tamanaha, Kevin Bonanno, Eric J. Cantor, Nathan A. Tanner
Summary: Research on the Argonaute protein from Thermus thermophilus has revealed specific preferences for guide sequences, which can be used to enhance guide design for molecular applications. Notable preferences include a strong cleavage enhancement from a first position dT independent of target sequence, a significant decrease in activity with dA at position 12, and an impact of GC dinucleotides at positions 10 and 11. This approach could potentially be extended to characterize other variants and improve their utility in biology and genome editing applications.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Jiani Xing, Lixia Ma, Xinzhen Cheng, Jinrong Ma, Ruyu Wang, Kun Xu, Joe S. Mymryk, Zhiying Zhang
Summary: The study successfully expressed Thermus thermophilus pAgo and established a screening system for isolating loss-of-function mutants. By utilizing the property of pAgo inducing loss of its expression plasmid, the mechanisms by which TtAgo functions as a defense against foreign DNA invasion were revealed.
Article
Biochemistry & Molecular Biology
Sergey A. Siletsky, Tewfik Soulimane, Ilya Belevich, Robert B. Gennis, Marten Wikstrom
Summary: This study investigated the effect of T315V substitution in the K channel of B-type cytochrome ba(3) oxidase on proton pumping, suggesting that the mutated enzyme does not pump protons during a single turnover. The K channel of B-type oxidases is essential for the electrogenic transfer of both pumped and substrate protons during the oxidative half-reaction of the catalytic cycle, unlike the A family oxidases.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Biochemistry & Molecular Biology
Yuvaraj Iyyappan, Vaigundan Dhayabaran, Mohanapriya Elayappan, Santosh Kumar Chaudhary, Chandrasekaran Palaniappan, Sekar Kanagaraj
Summary: Thermus thermophilus is a thermophilic organism that thrives at a temperature of 65 degrees C. The genome of T. thermophilus consists of 2218 genes, with 66% (1482 genes) being annotated and 34% (736 genes) assigned as hypothetical proteins. Experimental results show that the hypothetical protein TTHA1873 acts as a nuclease, cutting both methylated and non-methylated DNA in the presence of divalent metal ions and relaxing plasmid DNA in the presence of ATP. Chelation of metal ions with EDTA inhibits its activity. These findings suggest that TTHA1873 is a CRISPR-associated protein with non-specific DNase activity and ATP-dependent DNA-relaxing activity.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Deniz Yaman, Beate Averhoff
Summary: The study reveals the significance of PilW in stable assembly of PilQ complexes and highlights the crucial role of a central disordered region in PilW dynamics.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Biochemistry & Molecular Biology
Yang-Xue Dai, Wei-Fei Chen, Na-Nv Liu, Fang-Yuan Teng, Hai-Lei Guo, Xi-Miao Hou, Shuo-Xing Dou, Stephane Rety, Xu-Guang Xi
Summary: The study reveals the crystal structures of ToPif1 and its mechanism of forming a stable dimer when binding to single-stranded DNA. Moreover, it is found that dimerization of ToPif1 has an inhibitory effect on its helicase activity.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Xueqin Zhang, Georgina H. Joyce, Andy O. Leu, Jing Zhao, Hesamoddin Rabiee, Bernardino Virdis, Gene W. Tyson, Zhiguo Yuan, Simon J. Mcilroy, Shihu Hu
Summary: Anaerobic methanotrophic archaea (ANME) use multi-heme c-type cytochromes (MHCs) to mediate the reduction of metals and electrodes. Experimental evidence supports the involvement of these cytochromes in extracellular electron transfer (EET) from ANME to different electron sinks.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Huihui Wan, Xiaoying Ouyang, Ting Yang, Tianyun Ye, Minfei Jin, Jing Huang
Summary: In this study, the 4GT gene was cloned and expressed, and its catalytic function and expression conditions were investigated. High yield of recombinant 4GT enzyme was obtained through optimization of fermentation process. This study provides valuable references for the characterization and expression of food-grade enzymes.
CURRENT MICROBIOLOGY
(2022)
Article
Chemistry, Inorganic & Nuclear
Jitumani Rajbongshi, Diganta Kumar Das, Shyamalava Mazumdar
Summary: A detailed study on the pH-induced conformational changes at the Cu2S2 coordination site of the CuA centre of cytochrome oxidase from Thermus thermophilus was conducted to investigate the effect of these changes on the redox potential and electron transfer kinetics of the metal centre. It was found that the metal centre undergoes an equilibrium conformational transition involving three different forms, which exhibit different redox potentials. These findings provide insights into understanding the electron transfer processes in the enzyme.
INORGANICA CHIMICA ACTA
(2022)
Article
Chemistry, Physical
Malaisamy Veerapandian, Nagarajan Hemavathy, Alagesan Karthika, Jayaraman Manikandan, Umashankar Vetrivel, Jeyaraman Jeyakanthan
Summary: This study investigates the conformational stability and flexibility of SpeB enzyme and its interactions with substrate. The research finds that neutral pH 7 and alkaline pH 11 are the optimal conditions for stable binding between SpeB and substrate.
MOLECULAR SIMULATION
(2024)
Article
Biochemistry & Molecular Biology
Wilfred R. Hagen, Ricardo O. Louro
Summary: Distances between Fe ions in multiheme cytochromes are short, allowing for intramolecular dipole-dipole interactions. Previous analysis of cytochrome EPR data has ignored this interaction. In this study, a low-frequency broadband EPR spectrometer was used to investigate the dipolar interaction in two cytochromes and identify limitations in analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Engineering, Electrical & Electronic
Josue Castaneda Cisneros, Sami Yangui, Saul E. Pomares Hernandez, Khalil Drira
Summary: This survey focuses on multi-domain orchestration works from an algorithmic perspective, classifying and evaluating algorithms by considering cooperative and competitive approaches. A taxonomy is proposed to classify works based on different life cycle tasks of network services and evaluate them according to defined key requirements, providing an overview of the current state of multi-domain orchestration algorithms. Future research directions are also identified based on the current perspective.
IEEE COMMUNICATIONS MAGAZINE
(2022)
Article
Biotechnology & Applied Microbiology
Gota Kawai, Gen-ichi Sampei, Makoto Nishiyama, Yoshitaka Bessho
Summary: This article summarizes the small non-coding RNAs and functional RNA elements found in Thermus thermophilus, along with their annotations. Additionally, a set of conserved sequences found in T. thermophilus HB27 is also described.
JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Maya Nakatani, Shun-ya Nakahara, Kenji Fukui, Momoka Urano, Yuki Fujii, Takeshi Murakawa, Seiki Baba, Takashi Kumasaka, Hiroki Okanishi, Yoshikatsu Kanai, Takato Yano, Ryoji Masui
Summary: This study determined the crystal structure of the N-terminal domain of FakA bound to ADP and constructed a model of the complex of T. thermophilus FakB and the N-terminal domain of FakA. The results provide insights into the composite active site of the Fatty acid kinase complex.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Plant Sciences
Wen Li, Peng Li, Xiaofan Zhou, Junjian Situ, Yiming Lin, Jiahui Qiu, Yuling Yuan, Pinggen Xi, Zide Jiang, Guanghui Kong
Summary: This study identified a gene encoding a Cyt-b(5) domain protein in the plant pathogenic oomycete Peronophythora litchii, highlighting its crucial role in development, stress response, and pathogenicity. Knockout mutants of PlCB5L1 showed reduced growth rate, altered stress tolerance, and impaired pathogenicity, demonstrating the significance of Cyt-b(5) domain proteins in plant pathogenic oomycetes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Giacomo Parisi, Linda Celeste Montemiglio, Alessandro Giuffre, Alberto Macone, Antonella Scaglione, Gabriele Cerutti, Cecile Exertier, Carmelinda Savino, Beatrice Vallone
Article
Biochemistry & Molecular Biology
Vitaliy B. Borisov, Sergey A. Siletsky, Alessandro Paiardini, David Hoogewijs, Elena Forte, Alessandro Giuffre, Robert K. Poole
Summary: Cytochrome bd is an important ubiquinol:oxygen oxidoreductase found in many prokaryotic respiratory chains, playing a crucial role in generating a proton motive force for ATP production by reducing molecular oxygen to water. Recent advancements have shed light on its structure, biochemistry, and roles in protecting bacteria against various stressors. Future research should focus on utilizing its unique properties for developing novel antibacterial agents.
ANTIOXIDANTS & REDOX SIGNALING
(2021)
Article
Biochemistry & Molecular Biology
Elena Forte, Sergey A. Siletsky, Vitaliy B. Borisov
Summary: The interaction between Escherichia coli's redox enzymes, cytochrome bo(3) and cytochrome bd-I, with ammonium sulfate/ammonia at different pH levels was studied. It was found that while cytochrome bo(3) was inhibited by the ligand at pH 8.3, cytochrome bd-I's activity increased with increasing ligand concentration. The effector molecule in both cases appeared to be NH3 rather than NH4+.
Article
Biochemistry & Molecular Biology
Karim Zuhra, Catarina S. Tome, Elena Forte, Joao B. Vicente, Alessandro Giuffre
Summary: Sulfane sulfur species, which include various biologically relevant compounds and proteins, play a significant role in cancer biology by modulating cell bioenergetics and contributing to metabolic reprogramming. They achieve this by binding to target proteins or sulfidating specific cysteine residues, thereby regulating cellular functions and exhibiting anti-tumoral properties.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2021)
Article
Biochemistry & Molecular Biology
Dalila G. F. Fernandes, Joao Nunes, Catarina S. Tome, Karim Zuhra, Joao M. F. Costa, Alexandra M. M. Antunes, Alessandro Giuffre, Joao B. Vicente
Summary: Gasotransmitters hydrogen sulfide, nitric oxide, and carbon monoxide play critical roles in human physiology by mediating signal transduction through interaction with protein targets. Research shows that S-nitrosation can inhibit hydrogen sulfide production through affecting various protein cysteine residues, highlighting a new mechanism of crosstalk between gasotransmitters.
Review
Biochemistry & Molecular Biology
Vitaliy B. Borisov, Sergey A. Siletsky, Martina R. Nastasi, Elena Forte
Summary: Reactive oxygen species (ROS) can damage various macromolecules and compromise cell viability, prompting bacteria to utilize different defense mechanisms, such as ROS scavenging enzymes. Additionally, some terminal oxidases in bacterial respiratory chains may also play a protective role against ROS, as suggested by recent findings.
Review
Biochemistry & Molecular Biology
Vitaliy B. Borisov, Elena Forte
Summary: Hydrogen sulfide (H2S) has biphasic effects on the bioenergetic molecular machines in mitochondria and bacteria, either enhancing or inhibiting cellular functions; H2S acts as a signaling molecule that plays critical roles in physiology and pathophysiology through its interactions with protein complexes and enzymes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Vitaliy B. Borisov, Elena Forte
Summary: This review summarizes recent studies on the molecular basis of the effects of nitric oxide and peroxynitrite on microbial respiration and energy conservation. The possible molecular mechanisms underlying bacteria's resistance to RNS, including unique respiratory oxygen reductases and cytochromes, are discussed. Although a complete picture of the impact of RNS on microbial bioenergetics is not yet available, the rapidly developing research in this area will help in developing new methods of treating infectious diseases.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Elisabetta Profumo, Elisa Maggi, Marzia Arese, Claudio Di Cristofano, Bruno Salvati, Luciano Saso, Rita Businaro, Brigitta Buttari
Summary: This study reveals that neuropeptide Y (NPY) can modulate the phenotype and functions of human macrophages, promoting their transition to a reparative phenotype that has therapeutic effects on atherosclerosis. NPY reduces lipid droplet accumulation and enhances autophagosome formation in macrophages. Additionally, NPY increases the activation of the antioxidant signaling pathway in macrophages, protecting cells from further damage in the inflammatory pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Somayyeh Ghareghomi, Mehran Habibi-Rezaei, Marzia Arese, Luciano Saso, Ali Akbar Moosavi-Movahedi
Summary: ROS play a crucial role in cellular processes, with Keap1-Nrf2 pathway acting as a master antioxidant mechanism. While activation of Nrf2 benefits cells in early stages by reducing ROS levels, hyperactivation can support the survival of healthy and cancer cells against oxidative stress and treatments. Understanding the dual role of Nrf2 in cancer cells can be important in cancer treatment strategies.
Review
Biochemistry & Molecular Biology
Cristobal avila, Jose Ignacio Vinay, Marzia Arese, Luciano Saso, Ramon Rodrigo
Summary: Infertility is a common condition that affects a significant percentage of couples worldwide, with male infertility being a prominent cause. Oxidative stress has been increasingly recognized as a key factor in male infertility, but effective antioxidant interventions have not yet been established.
Review
Neurosciences
Ilker Ates, Ayse Didem Yilmaz, Brigitta Buttari, Marzia Arese, Luciano Saso, Sibel Suzen
Summary: Autoimmune disease occurs when the immune system attacks healthy cells instead of protecting them, and inflammation and oxidative stress are key processes related to this. The transcription factor Nrf2 plays an important role in defense against oxidative stress and regulating anti-inflammatory activities. The Nrf2 signaling pathway is deregulated in various diseases, including autoimmune disorders.
Article
Biochemistry & Molecular Biology
Maria Chiara Magnifico, Marla Xhani, Benedetta Sprovera, Brigitta Buttari, Giorgia Abballe, Flaminia Desideri, Emiliano Panieri, Luciano Saso, Marzia Arese
Summary: The results of this study demonstrate that BPA and PFOA induce persistent alteration of cell redox homeostasis and mitochondrial dysfunction, with the major involvement of the NO signaling axis. Treatment with PFOA specifically activates nitrosative stress and increases the production of ROS, NOx, and 3-NT.
FRONTIERS IN BIOSCIENCE-LANDMARK
(2022)
Article
Biochemistry & Molecular Biology
Elena Forte, Alessandro Giuffre, Li-shar Huang, Edward A. Berry, Vitaliy B. Borisov
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)