Article
Multidisciplinary Sciences
Dmitry Leshchiner, Federico Rosconi, Bharathi Sundaresh, Emily Rudmann, Luisa Maria Nieto Ramirez, Andrew T. Nishimoto, Stephen J. Wood, Bimal Jana, Noemi Bujan, Kaicheng Li, Jianmin Gao, Matthew Frank, Stephanie M. Reeve, Richard E. Lee, Charles O. Rock, Jason W. Rosch, Tim van Opijnen
Summary: Understanding how bacteria evade antibiotics and develop resistance is crucial for the development of novel therapeutics and diagnostics. In this study, the authors conducted a comprehensive genetic analysis of how the human pathogen Streptococcus pneumoniae responds to different antibiotics. They identified genes and cellular processes that contribute to altered drug susceptibility and demonstrated their potential as therapeutic targets.
NATURE COMMUNICATIONS
(2022)
Article
Cell Biology
Kin Ki Jim, Rieza Aprianto, Rutger Koning, Arnau Domenech, Jun Kurushima, Diederik van de Beek, Christina M. J. E. Vandenbroucke-Grauls, Wilbert Bitter, Jan-Willem Veening
Summary: This study investigates the specific transcriptional responses of pneumolysin and identifies key pathways involved in early pneumococcal meningitis using an in vivo dual RNA sequencing approach. The study provides new insights into the interactions between the host and pathogen during the early phase of central nervous system infection.
Article
Immunology
Rui Ding, Yan Zhang, Xiangzhu Xu, Yunfeng Hou, Jing Nie, Xuming Deng, Jiazhang Qiu, Qianghua Lv
Summary: This study analyzed the inhibitory effect of the natural compound hederagenin on Streptococcus pneumoniae and found that it has great potential as a treatment strategy for pneumococcal diseases.
MICROBES AND INFECTION
(2022)
Article
Multidisciplinary Sciences
Shifu Aggarwal, Elaine Huang, Hackwon Do, Nishanth Makthal, Yanyan Li, Eric Bapteste, Philippe Lopez, Charles Bernard, Muthiah Kumaraswami
Summary: This study discovers the existence of short peptide LCP in various bacteria and validates its role as intercellular signals regulating gene expression. This finding may uncover new signaling mechanisms and play a significant role in coordinating diverse bacterial traits.
NATURE COMMUNICATIONS
(2023)
Editorial Material
Biochemistry & Molecular Biology
Vikrant Minhas, James C. Paton, Claudia Trappetti, Claudia Trappetti
Summary: This study highlights the importance of carbohydrate utilization systems in pneumococcal disease and provides insight into the mechanisms by which this pathogen causes a spectrum of diseases.
TRENDS IN MICROBIOLOGY
(2021)
Review
Immunology
Mary E. Marquart
Summary: Bacterial proteases and peptidases play essential roles in cell physiology and stability, with the proteases in Streptococcus pneumoniae serving dual functions as self-protein processors and virulence factors targeting host proteins during movement to various sites in the body.
Article
Immunology
Moe Takemura, Masaya Yamaguchi, Momoko Kobayashi, Tomoko Sumitomo, Yujiro Hirose, Daisuke Okuzaki, Masayuki Ono, Daisuke Motooka, Kana Goto, Masanobu Nakata, Narikazu Uzawa, Shigetada Kawabata
Summary: The gene bgaA in Streptococcus pneumoniae has been identified as a multifunctional virulence factor that affects glycan metabolism, bacterial adherence, and resistance to neutrophil-mediated killing. Deletion of bgaA reduces bacterial association with human cells and enhances neutrophil-mediated killing in human blood. In a mouse sepsis model, the absence of bgaA leads to increased host immune response, suppressed tissue damage, and blood coagulation. Therefore, BgaA could be a potential target for drug design and vaccine development against pneumococcal infection.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Review
Immunology
Murtadha Q. Ali, Thomas P. Kohler, Lukas Schulig, Gerhard Burchhardt, Sven Hammerschmidt
Summary: The pathogen Streptococcus pneumoniae expresses multiple extracellular serine proteases that play crucial roles in pathogenesis, interacting with host proteins and showing immunogenicity.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Food Science & Technology
Jasmin Bazant, Benjamin Ott, Martina Hudel, Torsten Hain, Rudolf Lucas, Mobarak Abu Mraheil
Summary: H2O2 negatively affects the activity and release of PLY. Decreased H2O2 production leads to a decline in PLY release, possibly due to the upregulation of certain genes.
Article
Infectious Diseases
Shihui Peng, Hongyu Ren, Jianping Deng, Na Zhao, Yinan Li, Ming Li, Qiwu Yuan, Zhengdong Zhang, Longze Luo, Linzi Zeng, Bin Wang, Nianli Zou, Changguo Gu, Xin Huang, Zheng Liao, Shenen Chen, Haiying Chen, Qun Li, Tian Qin
Summary: This study compared the serotypes, virulence genes, and antibiotic susceptibility of S. pneumoniae from healthy individuals and CAP patients, finding significant differences between the two groups. The high coverage rate of PCV13 and prevalence of MDR in Sichuan, China suggest the need for expanded immunization with PCV13 and rational antibiotic use, with long-term surveillance to assess vaccine effectiveness. The findings may provide guidance for developing new pneumococcal vaccines.
BMC INFECTIOUS DISEASES
(2021)
Article
Microbiology
Linlin Cao, Nan Li, Yingshan Dong, Xiao-Yan Yang, Jiajia Liu, Qing-Yu He, Ruiguang Ge, Xuesong Sun
Summary: The SPD_0090 gene in Streptococcus pneumoniae plays an important role in bacterial growth, invasion, adhesion, and regulation of virulence.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Hannes Eichner, Jens Karlsson, Edmund Loh
Summary: Pathogenic bacteria have evolved to regulate gene expression through RNA, and understanding the function of regulatory RNAs in disease could provide valuable insights into their pathogenicity.
TRENDS IN MICROBIOLOGY
(2022)
Article
Microbiology
Rebecca A. Keogh, Brady L. Spencer, Hailee M. Sorensen, Rachel L. Zapf, Paul Briaud, Abigail E. Bonsall, Kelly S. Doran, Ronan K. Carroll
Summary: Advancements in sequencing technologies have allowed researchers to identify a large number of putative sRNAs in the human pathogen group B Streptococcus, more than previously mentioned in transcriptomic analyses. Through analyzing sRNA expression, a specific sRNA was found to be upregulated during vaginal colonization, and overexpression of this sRNA increased bacterial invasion into host epithelial cells.
Article
Immunology
Lei Xu, Juan Fang, Deyuan Ou, Jingwen Xu, Xuming Deng, Gefu Chi, Haihua Feng, Jianfeng Wang
Summary: Co-infections with Streptococcus pneumoniae pose a significant threat to the diagnosis, therapy, and prognosis of COVID-19. In this study, kaempferol, a natural flavonoid, was identified as a potential drug candidate for infection therapeutics by targeting bacterial virulence factors. It showed promising anti-infection properties by inhibiting the activity of pneumolysin and sortase A, and exhibited notable treatment benefits in vivo.
MICROBES AND INFECTION
(2023)
Article
Immunology
Naoko Fuji, Michael E. Pichichero, Ravinder Kaur
Summary: Among Rochester NY children, an increase in nasopharyngeal colonization by non-vaccine pneumococcal serotypes 35B and 15A was observed during 2010-2015 after the introduction of PCV13. While 35B strains colonized the nasopharynx without causing acute otitis media (AOM), serotype 15A strains displayed virulence by causing AOM. Differences in the regulation of various virulence genes and host immune response were observed between the two serotypes, with IL23 proinflammatory response significantly higher in children colonized by 35B strains compared to 15A during asymptomatic colonization.
MEDICAL MICROBIOLOGY AND IMMUNOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Joao P. C. Pinto, Rutger Brouwer, Araz Zeyniyev, Oscar P. Kuipers, Jan Kok
Summary: This data set is a rich resource for microbiologists interested in common mechanisms of gene expression, regulation, and the physiology of L. lactis. It is also an opportunity for bioinformaticians to develop novel tools for in-depth analysis.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Plant Sciences
Ruben Cebrian, Qian Li, Pablo Penalver, Efres Belmonte-Reche, Maria Andres-Bilbao, Ricardo Lucas, Maria Violante de Paz, Oscar P. Kuipers, Juan Carlos Morales
Summary: Researchers have designed new antimicrobial compounds using resveratrol and found that they exhibit synergistic antibacterial activity when combined with traditional antibiotics. These derivatives show bactericidal activity against Gram-positive bacteria with a unique mechanism of action, and do not lead to cross-resistance with traditional antibiotics.
JOURNAL OF NATURAL PRODUCTS
(2022)
Article
Biochemistry & Molecular Biology
Anne de Jong, Oscar P. Kuipers, Jan Kok
Summary: Recent advances in high-throughput (meta-)transcriptomics and proteomics have made it necessary to develop easy and rapid methods for exploring the functional classification of genes and proteins. In this study, a comprehensive database containing multiple functional classifications of bacterial genomes was described. Additionally, a web server called FUNAGE-Pro was developed for fast functional analysis of prokaryote species or strains.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Jakob H. Viel, Oscar P. Kuipers
Summary: Mutational studies of the mersacidin leader-core interface were performed, revealing the crucial role of the GDMEAA sequence in both mersacidin modification and leader processing, enabling the wider application of mersacidin modifications in RiPP engineering.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
David M. Ekkers, Sergio Tusso, Stefany Moreno-Gamez, Marina C. Rillo, Oscar P. Kuipers, G. Sander van Doorn
Summary: Mitigating trade-offs between different resource-utilization functions is crucial for the ecological and evolutionary success of organisms. The underlying metabolic constraints have been difficult to understand due to their complex molecular basis. This study investigates how metabolic architecture induces resource-utilization constraints and how these constraints drive evolutionary specialization and diversification. By studying the bacterium Lactococcus cremoris, the researchers found that the evolution of different metabolic specialists can be influenced by the metabolic network structure and historical contingency. These findings contribute to a better understanding of the relationship between molecular constraints and phenotypic trade-offs, and shed light on the mechanisms underlying evolutionary specialization and diversification.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biotechnology & Applied Microbiology
Luiza P. Morawska, Ruud G. J. Detert Oude Weme, Elrike Frenzel, Maarten Dirkzwager, Tamara Hoffmann, Erhard Bremer, Oscar P. Kuipers
Summary: Bacillus subtilis adapts to osmotic stress by accumulating proline, and the activation of the proHJ promoter is a reliable indicator of its adaptation to stress. This study investigates the kinetics of proHJ promoter activation and early adaptation to mild osmotic upshift at the single-cell level, revealing heterogeneous proline biosynthesis gene expression.
MICROBIAL BIOTECHNOLOGY
(2022)
Article
Multidisciplinary Sciences
Luiza P. Morawska, Oscar P. Kuipers
Summary: The article discusses the physiological adaptation of bacteria to the viable but non-culturable (VBNC) state and the similarities in transcriptional response between VBNC cells and antibiotic-sensitive cells. The study also reveals the strong upregulation of genes involved in proline uptake and catabolism, suggesting a potential role of proline as a nutrient in VBNC cells.
SCIENTIFIC REPORTS
(2022)
Article
Biochemical Research Methods
Jakob H. Viel, Oscar P. Kuipers
Summary: The enzyme MrsM from the mersacidin gene cluster can be used in RiPP engineering to introduce the unique ring A of mersacidin into linear peptides, potentially creating new stabilized structures or small modules for chemical modification. Additionally, it was found that ring A can form in a core peptide as small as five amino acids, opening up new possibilities for utilizing this molecule in RiPP engineering.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ruben Cebrian, Ricardo Lucas, Maria Victoria Fernandez-Cantos, Koen Slot, Pablo Penalver, Marta Martinez-Garcia, Antonio Parraga-Leo, Maria Violante de Paz, Federico Garcia, Oscar P. P. Kuipers, Juan Carlos Morales
Summary: In this study, a family of aminoalkyl resveratrol derivatives with antibacterial activity inspired by cationic amphipathic antimicrobial peptides was discovered. These molecules showed good antimicrobial activity against anaerobic bacteria and exhibited synergistic effects with traditional antibiotics against Gram-negative pathogens. The mechanism of action was found to be at the membrane level and no cross-resistance was observed, although some cytotoxicity was detected.
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY
(2023)
Article
Biotechnology & Applied Microbiology
Luiza P. Morawska, Oscar P. Kuipers
Summary: Bacillus subtilis, a soil-dwelling bacterium, can interact with various other microorganisms. A study found that it can transfer plasmids to lactic acid bacteria, without involving conjugation or activating the competent state. The study also discovered non-conjugative cell-to-cell plasmid transfer in non-competent strains of Lactococcus lactis sp. cremoris. This suggests that cell-to-cell transformation is a common form of horizontal gene transfer and could be used as an alternative tool for natural strain improvement.
MICROBIAL BIOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Silja Mordhorst, Fleur Ruijne, Anna L. Vagstad, Oscar P. Kuipers, Joern Piel
Summary: Peptide natural products are valuable structures for drug design and engineering. This review focuses on comparing structural features between nonribosomal and ribosomally synthesised and posttranslationally modified peptides, and highlights synthetic biology strategies for emulating nonribosomal peptides using ribosomal pathways.
RSC CHEMICAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Fangfang Liu, Auke J. van Heel, Oscar P. Kuipers
Summary: In this study, the leader and terminal residue requirements for the biosynthesis of circularin A were investigated through systematic mutational analyses. The results showed that a leader with only one Met residue is sufficient for producing mature circularin A. Short-sidechain hydrophobic residues at positions Val1 and Ala2 of the N-terminus and an aromatic residue at the C-terminal Tyr69 position are required for the formation of active peptide derivatives. The requirements for the residue at position Ala68 are more relaxed. Overall, this study provides new insights into the biosynthesis of circular bacteriocins and their potential applications in modified peptide engineering.
ACS SYNTHETIC BIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Roderick Corstiaan Abraham Versloot, Patricia Arias-Orozco, Matthijs Jonathan Tadema, Florian Leonardus Rudolfus Lucas, Xinghong Zhao, Siewert J. J. Marrink, Oscar Paul Kuipers, Giovanni Maglia
Summary: Mass spectrometry cannot distinguish between molecules with the same mass-to-charge ratio, but nanopore technology can differentiate diastereomeric and enantiomeric differences in peptides that cannot be observed by conventional MS analysis. The resolution in nanopore analysis is likely due to multiple chiral interactions during peptide transport across the nanopore, similar to chiral chromatography. Nanopore technology also offers possibilities for the rapid and cost-effective analysis of peptides, including those that cannot be easily differentiated by mass spectrometry.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Review
Microbiology
Yuxin Fu, Yanli Xu, Fleur Ruijne, Oscar P. Kuipers
Summary: Potent non-ribosomal antimicrobial peptides can be mimicked by combining posttranslational modifications of gene-encoded lanthipeptides, allowing screening of mutant libraries. Synthetic biology provides new avenues in peptide engineering to produce new-to-nature peptides with enhanced bioactivities. The modularity of lanthipeptides enables their engineering and screening in a high-throughput manner, making them promising tools for the production and screening of novel peptides, including mimics of potent non-ribosomally produced antimicrobial peptides.
FEMS MICROBIOLOGY REVIEWS
(2023)
Article
Microbiology
Longcheng Guo, Joseph Wambui, Chenhui Wang, Francis Muchaamba, Maria Victoria Fernandez-Cantos, Jaap Broos, Taurai Tasara, Oscar P. Kuipers, Roger Stephan
Summary: Cesin, a novel variant of nisin, efficiently kills bacteria by inhibiting cell wall synthesis without pore formation. It demonstrates a broad and potent antimicrobial profile, attributed to lipid II binding and electrostatic interactions with teichoic acids. The stability tests show that cesin is highly stable under different environmental conditions.
MICROBIOLOGY SPECTRUM
(2023)