Review
Biochemistry & Molecular Biology
Eiji Ishii, Yoko Eguchi
Summary: Two-component signal transduction systems are widely conserved in bacteria, serving as candidates for novel drug targets due to their involvement in controlling pathogen physiology. The diverse mechanisms of signal perception and response by HKs have been recently clarified, shedding light on their molecular mechanisms.
Article
Biochemistry & Molecular Biology
Blair Tupta, Eric Stuehr, Mamta P. Sumi, Elizabeth A. Sweeny, Brandon Smith, Dennis J. Stuehr, Arnab Ghosh
Summary: This study reveals the important role of GAPDH in the maturation of myoglobin and hemoglobins by regulating the formation of sGC alpha1 beta1 heterodimer, iron provision, and the expression of GAPDH. These findings provide insights into the mechanisms of heme-maturation in globins.
Article
Multidisciplinary Sciences
Iain C. Clark, Bruk Mensa, Christopher J. Ochs, Nathan W. Schmidt, Marco Mravic, Francisco J. Quintana, William F. DeGrado, Adam R. Abate
Summary: Using a hybrid valve- and droplet-based microfluidic system, a combinatorial DNA library encoding an engineered histidine kinase based on bacterial CpxA was successfully constructed. Surprising results were found, such as the different effects on catalytic activity caused by the combinations of the S helix and TM domain. It was concluded that the intervening HAMP domain passively transmits signals and shapes the signaling response depending on subtle changes in neighboring domains, leading to a richness in functional outputs as HKs vary in response to changing evolutionary pressures.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
Jie Tang, Dan Yao, Huizhen Zhou, Mingcheng Wang, Maurycy Daroch
Summary: This study investigated the structure and architecture of two-component systems (TCSs) in 17 thermophilic cyanobacteria and revealed their complex and diverse nature. The results showed a unique composition of TCS genes in these cyanobacteria, which were possibly associated with various functions. Horizontal gene transfer and gene duplication events might have played a role in the evolutionary history of TCS genes in certain genera. These findings highlight the potential of thermophilic cyanobacteria genomes for adapting to environmental fluctuations.
Article
Microbiology
Lingyuan Kong, Mingyang Su, Jiayan Sang, Shanshan Huang, Min Wang, Yongfei Cai, Mingquan Xie, Jun Wu, Shida Wang, Simon J. Foster, Jiaqin Zhang, Aidong Han
Summary: In Streptococcus mutans, the histidine kinase Walk's long C-terminal tail is crucial for its interaction with the response regulator WaIR, and plays a key role in signal transduction, transcriptional regulation, and biofilm formation.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Benjamin X. Wang, Kyle C. Cady, Gerardo C. Oyarce, Katharina Ribbeck, Michael T. Laub
Summary: Pseudomonas aeruginosa harbors over 60 two-component signaling systems that play a role in pathogenesis, with individual genes controlling multiple virulence traits. Deletion strains lacking histidine kinases were used to confirm functions and uncover new roles in controlling virulence-associated traits, providing insight into the functions of these signaling proteins and offering a resource for future studies.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Adeline Espinasse, Manibarsha Goswami, Junshu Yang, Onanong Vorasin, Yinduo Ji, Erin E. Carlson
Summary: The emergence of drug-resistant bacteria has led to the need for novel approaches and targets to combat this challenge. Bacterial two-component systems (TCSs) are important in bacterial adaptive responses and are linked to antibiotic resistance and virulence. A study developed maleimide-based compounds and evaluated them against a model histidine kinase, resulting in the identification of a molecule that decreased the lesion size caused by methicillin-resistant S. aureus skin infection by 65% in a murine model.
Article
Microbiology
Yahui Feng, Shaodong Bian, Zhiping Pang, Yiyang Wen, Richard Calderone, Dongmei Li, Dongmei Shi
Summary: This study revealed the crucial roles of the S_Tkc and GAF domains of Candida albicans CHK1 in hyphal invasion and mucosal tissue damage. These domains are likely responsible for initiating cell growth and hyphal formation during the lag phase, maintaining the infectivity of C. albicans in vivo.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Bruk Mensa, Nicholas F. Polizzi, Kathleen S. Molnar, Andrew M. Natale, Thomas Lemmin, William F. DeGrado
Summary: In this study, the interaction between the sensor domain and cytoplasmic kinase domain of the E. coli two-component histidine kinase PhoQ was investigated, revealing a three-domain model to explain signal transduction mechanisms. The data suggests that signals transmit via interdomain allostery rather than propagation of a single concerted conformational change, explaining the diversity of signaling structural transitions observed in individual HK domains.
Article
Microbiology
Benjamin Vega-Baray, Clelia Domenzain, Sebastian Poggio, Georges Dreyfus, Laura Camarena
Summary: The study found that a protein called Osp inhibits the kinase activity of CckA in Rhodobacter sphaeroides by interacting with the transmitter domain of CckA, forming a negative feedback loop.
Article
Chemistry, Medicinal
Zhong Chen, Kun Song, Yongpeng Shang, Yanpeng Xiong, Zhihui Lyu, Junwen Chen, Jinxin Zheng, Peiyu Li, Yang Wu, Chenjian Gu, Youhua Xie, Qiwen Deng, Zhijian Yu, Jian Zhang, Di Qu
Summary: This study identified novel candidate molecules targeting histidine kinase YycG against Enterococcus faecalis through high-throughput virtual screening. Among the selected molecules, compound-16 and compound-62 were verified as potential YycG inhibitors. Compound-16 inhibited planktonic cells of E. faecalis, while compound-62 primarily inhibited biofilm formation.
JOURNAL OF MEDICINAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Hualiang Pi, Andy Weiss, Clare L. Laut, Caroline M. Grunenwald, Hannah K. Lin, Xinjie Yi, Devin L. Stauff, Eric P. Skaar
Summary: HitRS is a two-component system that responds to cell envelope damage in the human pathogen Bacillus anthracis. KrrA, an RNA-binding protein, regulates HitRS function by modulating the stability of the hitRS mRNA. KrrA also binds to over 70 RNAs and affects the expression of over 150 genes involved in multiple processes.
NATURE COMMUNICATIONS
(2022)
Article
Microbiology
Uchenna Watson Waturuocha, M. S. Krishna, Vandana Malhotra, Narendra M. Dixit, Deepak Kumar Saini
Summary: This study investigates the impact of a specific polymorphism in PhoR of Mycobacterium tuberculosis, revealing that the mutation causes a survival disadvantage in host cells, explaining the low prevalence of the SNP in clinical strains. It highlights the importance of considering such SNPs in testing therapeutic and co-therapeutic methods to combat tuberculosis.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Elina Multamaki, Andres Garcia de Fuentes, Oleksii Sieryi, Alexander Bykov, Uwe Gerken, Americo Tavares Ranzani, Juergen Koehler, Igor Meglinski, Andreas Moeglich, Heikki Takala
Summary: In optogenetics, BphP photoreceptors control cellular processes by sensing red and farred light and regulating downstream gene expression. By reprogramming bacterial gene expression from blue-light to red-light control, pREDusk and pREDawn systems enable high spatial resolution and tissue penetration, providing red-light-regulated expression for diverse use cases in bacteria.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Anna Cociurovscaia, Grzegorz Bujacz, Agnieszka J. Pietrzyk-Brzezinska
Summary: CusS is a component of the Escherichia coli signal transduction system, involved in responding to excessive copper ions in the cell periplasm. Understanding bacterial copper sensing mechanisms is important for reducing copper resistance and developing copper-based materials with bactericidal properties.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Terezia Koval'ova, Tomas Koval, Jan Stransky, Petr Kolenko, Jarmila Duskova, Leona Svecova, Patricie Vodickova, Vojtech Spiwok, Eva Benesova, Petra Lipovova, Jan Dohnalek
Summary: Fucosylated compounds are important in biological processes and have potential applications in medicine and biotechnology. This study investigates the structure and function of a glycoside hydrolase member from the GH151 family, revealing its unique oligomerization, active site properties, and substrate selectivity. The findings provide valuable insights into the mechanism of GH151 α-L-fucosidases and their potential applications.
Review
Biotechnology & Applied Microbiology
Jan Dohnalek, Tereza Skalova
Summary: The C-type lectin-like fold (CTL fold) is a versatile structural motif found in many proteins, and its interactions play significant roles in various biological processes. Understanding the rules governing these interactions can aid in the development of new protein binders for biomedical and biotechnological applications.
BIOTECHNOLOGY ADVANCES
(2022)
Article
Anesthesiology
Stefan Hofer, Jan Blaha, Peter W. Collins, Anne-Sophie Ducloy-Bouthors, Emilia Guasch, Francesco Labate, Filipa Lanca, Lill Trine Nyflot, Kostja Steiner, Marc van de Velde
Summary: Postpartum haemorrhage is the leading cause of pregnancy-related deaths globally and requires timely obstetric measures and coagulopathy treatment. However, there is a lack of consensus in current guidelines and the need for a multidisciplinary approach and standardized algorithms to improve clinical outcomes. Organisational considerations are also crucial in managing PPH.
EUROPEAN JOURNAL OF ANAESTHESIOLOGY
(2023)
Article
Multidisciplinary Sciences
Jan Blaha, Tereza Skalova, Barbora Kalouskova, Ondrej Skorepa, Denis Cmunt, Valeria Grobarova, Samuel Pazicky, Edita Polachova, Celeste Abreu, Jan Stransky, Tomas Koval, Jarmila Duskova, Yuguang Zhao, Karl Harlos, Jindrich Hasek, Jan Dohnalek, Ondrej Vanek
Summary: In this study, the authors established a comprehensive model of NKR-P1-LLT1 interaction, revealing that NKR-P1 forms homodimers on the cell surface and bridges two LLT1 molecules in two modes. Through experimental observations, they demonstrated that only the ligation of both LLT1 binding interfaces leads to effective NKR-P1 inhibitory signaling.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Kristyna Adamkova, Tomas Koval, Lars H. Ostergaard, Jarmila Duskova, Martin Maly, Leona Svecova, Tereza Skalova, Petr Kolenko, Jan Dohnalek
Summary: The handheld bio-detection device being developed by Manitech Technologies can detect and diagnose a variety of diseases. This mini device provides real-time data through simple blood sample analysis, helping doctors and patients better understand their physical condition.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Physical
Jakub Vavra, Artur Sergunin, Alzbeta Farna, Tomas Ovad, Toru Shimizu, Marketa Martinkova
Summary: The heme-regulated eIF2 alpha kinase, also known as HRI, detects misfolded proteins and induces cytoprotective response to stress mainly caused by heme-shortage. In this study, the effects of four substrates (ATP, CTP, GTP, and UTP) on HRI kinase activity were evaluated, and a detailed kinetics study of the HRI G202S mutant, associated with cancer development, was performed for the first time. The results showed that GTP had a lower kcat value compared to ATP, but significantly higher than CTP and UTP. Additionally, the kcat value of GTP for G202S was higher than that for wild-type.
Article
Biochemistry & Molecular Biology
Blanka Hustakova, Maria Trundova, Kristyna Adamkova, Tomas Koval, Jarmila Duskova, Jan Dohnalek
Summary: A recombinant form of S1-P1 nuclease, called SmNuc1, from opportunistic pathogen Stenotrophomonas maltophilia, acts predominantly as an RNase with high activity in a wide range of temperatures and pH. SmNuc1 exhibits superior catalytic rates compared to S1 nuclease from Aspergillus oryzae and other similar nucleases on all types of substrates. Additionally, SmNuc1 degrades the bacterial second messenger molecule c-di-GMP, which may have implications for the pathogenicity of S. maltophilia.
Article
Biochemistry & Molecular Biology
Jakub Vavra, Artur Sergunin, Petr Pompach, Dariya Savchenko, Jakub Hranicek, Ivana Sloufova, Toru Shimizu, Marketa Martinkova
Summary: The interaction between p53 and heme was thoroughly investigated in this study, focusing on the oxidation, spin, coordination, and ligand state of heme iron. The results showed that p53 oligomeric state and zinc binding ability remained unchanged upon heme binding. The conformational dynamics of p53 were significantly affected by heme, leading to increased flexibility and reduced affinity to a specific DNA sequence. The inhibitory effect of heme on DNA binding was found to be partially reversible. Potential heme binding sites in p53 were discussed in relation to the observed conformational changes and perturbed DNA binding ability.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2023)
Article
Biochemical Research Methods
Jakub Svoboda, Daniel Berdar, Petr Kolenko, Jiri Cerny, Zora NovaKova, Jiri Pavlicek, Bohdan Schneider
Summary: Nine new crystal structures of CG-rich DNA 18-mers related to bacterial repetitive extragenic palindromes are reported. Mutations of the central XZ dinucleotide in the 18-mers showed complex behavior in solution, but the successfully crystallized 18-mers were all A-form duplexes. The refinement protocol used the geometries of dinucleotide conformer classes as restraints and can be adapted to other low-resolution data.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Petr Kolenko, Pavel Mikulecky, Phuong Ngoc Pham, Martin Maly, Bohdan Schneider
Summary: Binder H33 is a small protein binder that specifically binds to human interleukin 10 and was engineered using ribosome display. The crystals of binder H33 show severe diffraction anisotropy. To correct for this, a set of data files with different local signal-to-noise ratios was prepared. By using paired refinement, the optimal anisotropic high-resolution diffraction limit of the data was determined to be 3.13-2.47 angstrom. The structure of binder H33 belongs to the top 2% crystal structures with the highest solvent content in the Protein Data Bank.
JOURNAL OF APPLIED CRYSTALLOGRAPHY
(2023)
Article
Biochemical Research Methods
Martin Maly, Petr Kolenko, Jan Stransky, Leona Svecova, Jarmila Duskova, Tomas Koval', Tereza Skalova, Maria Trundova, Kristyna Adamkova, Jiri Cerny, Paulina Bozikova, Jan Dohnalek
Summary: The resistance of Stenotrophomonas maltophilia to tetracycline antibiotics is mainly due to multidrug efflux pumps and ribosomal protection enzymes. However, some strains of this Gram-negative bacterium also possess a FAD-dependent monooxygenase (SmTetX), similar to tetracycline destructases. SmTetX was produced and studied, showing its ability to modify oxytetracycline. It shares a fold with TetX from Bacteroides thetaiotaomicron but has a unique aromatic region in its active site, and docking studies confirmed tetracycline and its analogues as preferred binders.
ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS
(2023)
Article
Immunology
Klaudia Meskova, Katarina Martonova, Patricia Hrasnova, Kristina Sinska, Michaela Skrabanova, Lubica Fialova, Stefana Njemoga, Ondrej Cehlar, Olga Parmar, Petr Kolenko, Vladimir Pevala, Rostislav Skrabana
Summary: Laboratory production of recombinant mammalian proteins, particularly antibodies, can be achieved using transient gene expression in suspension-adapted Chinese Hamster Ovary (CHO) cell lines. This method allows for secretion of antibodies into the media and can be glycosylated. However, protein production in CHO cells can be costly and variable. Optimization can be done in aspects such as gene delivery, cultivation process, and expression plasmid design. In this study, a TGE platform for medium-scale production of antibodies and other proteins in CHO cells was proposed, using a new expression vector and recyclable labware to reduce production cost. The platform's potential was demonstrated through the production and crystallization of antibody Fabs and their complexes.