Article
Ecology
Soo Bin Kim, Eun Sun Lyou, Min Sung Kim, Tae Kwon Lee
Summary: This study investigates the morphological and molecular phenotypic changes in resuscitated bacteria using electron microscopy, flow cytometry, Raman spectroscopy, and RNA sequencing. The findings show that within 12 hours of resuscitation, the morphological, physiological, and molecular phenotypes of the bacteria recover to a similar extent as active cells. The study also reveals that the recovery rate and phenotypic properties of the resuscitated cells vary depending on the type and concentration of carbon sources.
Article
Microbiology
Neha Dhasmana, Nishant Kumar, Aakriti Gangwal, Chetkar Chandra Keshavam, Lalit K. Singh, Nitika Sangwan, Payal Nashier, Sagarika Biswas, Andrei P. Pomerantsev, Stephen H. Leppla, Yogendra Singh, Meetu Gupta
Summary: The study identifies a serine/threonine protein kinase, PrkC, in Bacillus anthracis, which plays a role in regulating the chaining phenotype of the bacteria. PrkC disruption leads to shorter bacterial chains and upregulation of proteins associated with dechaining. This disruption also affects bacterial growth, cell wall thickness, and septum formation.
JOURNAL OF BACTERIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Robert J. Trachman, Luiz F. M. Passalacqua, Adrian R. Ferre-D'Amare
Summary: Unlike most riboswitches, the bacterial yjdF riboswitch can bind to diverse azaaromatic compounds and activate translation by adopting a tRNA-like fold. Ligands that stabilize the tRNA-like fold of the yjdF riboswitch in its native mRNA context can outcompete the attenuated state and activate translation. This study demonstrates the ability of tRNA to function as a small-molecule responsive cis regulatory element.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Review
Chemistry, Multidisciplinary
Sujeet Kumar, Aurelio Mollo, Daniel Kahne, Natividad Ruiz
Summary: This review summarizes recent major discoveries in peptidoglycan (PG) biogenesis, with a focus on the translocation of Lipid II and the SEDs glycosyltransferases. These findings may lead to the development of new antibiotics to combat bacterial resistance.
Article
Biochemistry & Molecular Biology
Takanori Yokoo, Aki Tanabe, Yoko Yoshida, Jose M. M. Caaveiro, Makoto Nakakido, Yoichiro Ikeda, Yoshihiro Fujimura, Masaneori Matsumoto, Kevin Entzminger, Toshiaki Maruyama, C. J. Okumura, Masaomi Nangaku, Kouhei Tsumoto
Summary: Atypical hemolytic uremic syndrome (aHUS) is a disease associated with dysregulation of the immune complement system. Mutations and the presence of anti-CFH autoantibodies (AAbs) are known to cause CFH dysfunction. This study revealed the mechanism of recognition of CFH by anti-CFH AAbs and VHH4 using biophysical data and X-ray crystallography.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Fisheries
Chen Feng, Yiyang Tang, Xiaofeng Liu, Zejun Zhou
Summary: CMPK2 in fish, represented by 3nCmpk2, plays a role in host innate immunity and serves a protective role in antimicrobial responses during bacterial infection.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2021)
Article
Microbiology
Katarzyna Parys, Nicholas R. Colaianni, Ho-Seok Lee, Ulrich Hohmann, Natalie Edelbacher, Alen Trgovcevic, Zuzana Blahovska, Duhwa Lee, Alexander Mechtler, Zsuzsanna Muhari-Portik, Mathias Madalinski, Niklas Schandry, Isaac Rodriguez-Arevalo, Claude Becker, Elisabeth Sonnleitner, Arthur Korte, Udo Blasi, Niko Geldner, Michael Hothorn, Corbin D. Jones, Jeffery L. Dangl, Youssef Belkhadir
Summary: The study explores how microbial genes encoding MAMPs drive microbe elimination by activating immune responses in the presence of a host, and how the functionality of these genes is balanced against their immunogenicity. Decoding the immunogenic and motility profiles of a flagellin epitope in plants, the research identifies synthetic mutational tracks that undermine the detection activities of a plant flagellin receptor, leading to the discovery of antagonist or weaker agonist activities in the epitopes. This study also finds signatures of these mutational tracks in natural Pseudomonads.
CELL HOST & MICROBE
(2021)
Article
Biology
Bence Hajdusits, Marcin J. Suskiewicz, Nikolas Hundt, Anton Meinhart, Robert Kurzbauer, Julia Leodolter, Philipp Kukura, Tim Clausen
Summary: The McsB protein in Gram-positive bacteria plays a central role in protein quality control by targeting aberrant proteins for degradation. Structural data reveal a self-compartmentalized kinase, with closed octamers preferentially labeling unfolded proteins during stress conditions. The interconversion of open and closed oligomers represents a distinct regulatory mechanism for the McsB kinase to adapt its enzyme function according to the needs of the bacterial cell in surviving stress situations.
Review
Microbiology
Erwin C. Stuffle, Mark S. Johnson, Kylie J. Watts
Summary: PAS domains are versatile domains found in proteins across different kingdoms, with a conserved cleft for cofactor or ligand binding. Recent years have seen a significant increase in identified PAS domains and corresponding structures, leading to a better understanding of PAS signaling mechanisms. New bacterial PAS ligands have been discovered, expanding the list of bacterial PAS functions beyond signal sensing to include modulation, transduction, dimerization, protein interaction, and cellular localization.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Plant Sciences
Xiang-Yu Cao, Qian Zhao, Ya-Na Sun, Ming-Xiang Yu, Fang Liu, Zhe Zhang, Zhen-Hua Jia, Shui-Shan Song
Summary: Our study found that C10-HSL triggered a rapid increase in cytosolic free calcium and ROS levels, activated MPK6, and induced NO production in Arabidopsis roots. Inhibitors of calcium channels alleviated the inhibitory effects of C10-HSL on primary root growth. ROS and NO were found to be involved in the inhibition of primary root growth by C10-HSL. Activation of MPK6 was necessary for C10-HSL to inhibit primary root growth.
Article
Biology
Matej Horvath, Olivia Petrvalska, Petr Herman, Veronika Obsilova, Tomas Obsil
Summary: The study structurally and biochemically characterized the full-length human DAPK2:14-3-3 complex, investigating the effects of binding to DAPK2 on its dimerization, activation by dephosphorylation of Ser318, and Ca2+/calmodulin binding. The results provide mechanistic insights into 14-3-3-mediated DAPK2 inhibition and highlight the potential of the DAPK2:14-3-3 complex as a target for anti-inflammatory therapies.
COMMUNICATIONS BIOLOGY
(2021)
Article
Food Science & Technology
Ruoyu Wang, Pengsheng Dong, Yueyue Zhu, Mengchen Yan, Wei Liu, Yueji Zhao, Lei Huang, Demin Zhang, Haipeng Guo
Summary: The research found that natural fermentation of soybean meal can significantly increase the water-soluble protein content and digestive enzyme activities, while altering the bacterial community structure. Inoculation of Bacillus amyloliquefaciens ZB through bioaugmentation significantly enhanced WSP content and enzyme activities, reducing fermentation time.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Multidisciplinary Sciences
Prabha Singh, Krishan Kumar, Abhishek Kumar Jha, Pranjal Yadava, Madan Pal, Sujay Rakshit, Ishwar Singh
Summary: Maize is a heavy consumer of fertilizer nitrogen, resulting in high cultivation costs and potential environmental pollution. In this study, transcriptome analysis was conducted on leaf and root tissues of contrasting inbred lines to identify the differentially expressed genes under low-N stress. The results showed that key genes involved in N uptake, N assimilation and metabolism, redox homeostasis, and transcription factors were highly expressed in the tolerant genotype. This study highlights the importance of these genes in low-N stress adaptation in maize and their potential value in further research on N metabolism and the development of N-deficiency tolerant maize cultivars.
SCIENTIFIC REPORTS
(2022)
Article
Cell Biology
Yan Lu, Qi Shan, Mei Ling, Xi-An Ni, Su-Su Mao, Bin Yu, Qian-Qian Cao
Summary: Peripheral nerve injury repair requires cooperation between axon regeneration and Wallerian degeneration. This study identified differentially expressed gene modules in proximal and distal sciatic nerve segments from rats with sciatic nerve injury using weighted gene co-expression network analysis. The results showed that genes in the proximal modules promoted nerve regeneration, while genes in the distal modules promoted neurodegeneration. Further experiments identified Kif22 as a key hub gene involved in Schwann cell proliferation and migration.
NEURAL REGENERATION RESEARCH
(2022)
Article
Cell Biology
Taha Aghajanzadeh, Kiarash Tebbi, Mahmood Talkhabi
Summary: This study utilized a bioinformatics approach to investigate key genes and molecular mechanisms of hepatoblastoma (HB) pathogenesis, identifying 594 differentially expressed genes with 11 hub genes validated. The findings provide new insights for better prognosis and therapeutic strategies for HB.
JOURNAL OF CELL COMMUNICATION AND SIGNALING
(2021)
Review
Chemistry, Multidisciplinary
Flaviana Di Lorenzo, Katarzyna A. Duda, Rosa Lanzetta, Alba Silipo, Cristina De Castro, Antonio Molinaro
Summary: This review discusses the chemical structure, functions, and immunological outcomes of lipopolysaccharide (LPS). By providing key information, it enhances our understanding of LPS and offers innovative approaches to manipulate this controversial biomolecule.
Correction
Biochemistry & Molecular Biology
Giulia Vessella, Roberta Marchetti, Angela Del Prete, Serena Traboni, Alfonso Iadonisi, Chiara Schiraldi, Alba Silipo, Emiliano Bedini
Article
Biochemistry & Molecular Biology
Flavia Squeglia, Daniela Marasco, Alessia Ruggiero, Genni Testa, Luciana Esposito, Rita Berisio
Summary: This study explores the suitability of RipA, a key cell division protein of Mycobacterium tuberculosis, for whole cell biosensing of Gram-positive bacteria. The research findings show the potential of the engineered RipA molecule to be integrated in the development of early warning biosensors for Gram-positive contamination in clinical diagnosis or food-borne infections.
CURRENT MEDICINAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Flavia Squeglia, Maria Romano, Luciana Esposito, Giovanni Barra, Pietro Campiglia, Marina Sala, Maria Carmina Scala, Alessia Ruggiero, Rita Berisio
Summary: The study engineered stable S-plug molecules through a computational approach to potentially inhibit viral entry by interfering with the interaction between SARS-CoV-2 spike protein and ACE2. These molecules have high stability and affinity to the spike protein, providing a solid foundation for the development of therapeutic and diagnostic tools against ACE2-accessing coronaviruses.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Rita Berisio, Giovanni Barra, Maria Romano, Flavia Squeglia, Alessia Ruggiero
Summary: This article introduces a putative endo-beta-1,4-glucanase (DtCel5A) identified through bioinformatics, and investigates its structural and functional characteristics. It is found that DtCel5A shows remarkable thermal and chemical stability, and retains its activity on cellulose at high temperatures and elevated salt concentrations.
Article
Infectious Diseases
Antonella Migliaccio, Maria Stabile, Maria Bagattini, Maria Triassi, Rita Berisio, Eliana De Gregorio, Raffaele Zarrilli
Summary: Resveratrol can reverse tolerance and restore susceptibility to CHX and BZK in the majority of microorganisms causing HAI. The efflux pump inhibitor reduced the MIC and MBC of CHX and BZK in most strains, while resveratrol dose-dependently decreased the MIC and MBC of the biocides.
Article
Biophysics
I. S. Vaskan, A. T. Prikhodko, M. V. Petoukhov, E. V. Shtykova, N. V. Bovin, A. B. Tuzikov, V. A. Oleinikov, A. V. Zalygin
Summary: The detailed analysis of the surface structure of nanoparticles is essential for the rational design of drug delivery systems. However, characterizing the surface structure under physiological conditions is challenging. In this study, the combination of SAXS contrast variation and ab initio bead modeling was used to investigate nanoparticle surface structure. By gradually increasing the solvent electron density, the shell coating thickness and uniformity around the nanoparticle core were assessed.
COLLOIDS AND SURFACES B-BIOINTERFACES
(2023)
Review
Cell Biology
Maria Romano, Flavia Squeglia, Eliza Kramarska, Giovanni Barra, Han-Gyu Choi, Hwa-Jung Kim, Alessia Ruggiero, Rita Berisio
Summary: Tuberculosis remains the leading infectious bacterial cause of death worldwide. Developing a new vaccine with better coverage than the current BCG vaccine is vital to stop its spread. Structural Vaccinology and the development of vaccine adjuvants can enhance the immunostimulating effects of subunit vaccines, accelerating the development of a safer and more effective tuberculosis vaccine.
Article
Biochemistry & Molecular Biology
Annamaria Sandomenico, Alessia Ruggiero, Emanuela Iaccarino, Angela Oliver, Flavia Squeglia, Miguel Moreira, Luciana Esposito, Menotti Ruvo, Rita Berisio
Summary: CD59 is an abundant protein in humans that protects cells from damage by inhibiting the complement system. It inhibits the assembly of the Membrane Attack Complex (MAC) and is incorporated by pathogenic viruses like HIV-1 to escape complement-mediated virolysis. CD59 is also overexpressed in cancer cells to resist complement attack. In this study, bioinformatics and computational tools were used to identify CD59 interactions and design paratope-mimicking peptides that target CD59.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Eliza Kramarska, Flavio De Maio, Giovanni Delogu, Rita Berisio
Summary: This study used AlphaFold2.0 computations to model the polymorphic forms of the PE_PGRS33 protein. Through sequence distribution, phylogenetic and antigenic prediction analyses, the structural impact of the observed mutations was predicted. The results correlated well with the observed frequency and phenotypic features, and protein variants associated with bacterial evolution were identified.
Article
Biology
Giovanni Smaldone, Giovanni Pecoraro, Katia Pane, Monica Franzese, Alessia Ruggiero, Luigi Vitagliano, Marco Salvatore
Summary: The KCTD protein family has been traditionally recognized as playing important roles in neurological physiopathology, but recent studies have shown their involvement in various biological processes, including cancers. This study focused on KCTD1 and its role in colorectal cancer. Knocking down KCTD1 in SW480 cells led to significant effects on their motility and stemness, indicating an oncosuppressor role for this protein. Similar effects were also observed with KCTD12 misregulation. These results expand the understanding of KCTD1's involvement in different physiological and pathological processes and suggest analogous activities among KCTD protein family members.
Article
Chemistry, Multidisciplinary
Flaviana Di Lorenzo, Simone Nicolardi, Roberta Marchetti, Adele Vanacore, Noemi Gallucci, Katarzyna Duda, Ferran Nieto Fabregat, Ha Ngoc Anh Nguyen, Djamel Gully, James Saenz, Eric Giraud, Luigi Paduano, Antonio Molinaro, Gerardino D'Errico, Alba Silipo
Summary: The ability of Methylobacterium extorquens to grow on methanol as the sole carbon and energy source is influenced by the composition and function of the lipopolysaccharide (LPS) in the outer membrane. The LPS of M. extorquens is unique, with non-phosphorylated and heavily O-methylated core oligosaccharides, and a distinctive lipid A structure. These chemical features impact the resistance of the membrane to methanol, regulating membrane ordering and dynamics.
Article
Chemistry, Multidisciplinary
Antonio De Nicola, Costanza Montis, Greta Donati, Antonio Molinaro, Alba Silipo, Arianna Balestri, Debora Berti, Flaviana Di Lorenzo, You-Liang Zhu, Giuseppe Milano
Summary: By combining simulations and experiments, the complex supramolecular structures of lipopolysaccharides (LPS) and lipid A at low hydration levels were revealed, uncovering the presence of a nano-compartmentalized phase composed of liposomes of variable size and shape, which can be utilized in synthetic biological applications.
Article
Biochemistry & Molecular Biology
Alexander L. L. Ksenofontov, Maxim V. V. Petoukhov, Vladimir V. V. Matveev, Natalia V. V. Fedorova, Pavel I. I. Semenyuk, Alexander M. M. Arutyunyan, Tatiana I. I. Manukhova, Ekaterina A. A. Evtushenko, Nikolai A. A. Nikitin, Olga K. V. Karpova, Eleonora V. V. Shtykova
Summary: The amino acid sequences of the coat proteins (CPs) of PVX and AltMV share about 40% identity. The N-terminal domains of these proteins differ in sequence and the presence of an N-terminal fragment in PVX CP. The N-terminal domain of PVX CP contributes to the higher thermal stability and ordered structure of PVX virions compared to AltMV.
BIOCHEMISTRY-MOSCOW
(2023)