Article
Biochemistry & Molecular Biology
Min Gyu Jeong, Kai Zhou, Soyeon Park, HyeongJeon An, Yonghoon Kwon, Yeonho Chang, Do-Hyeon Kim, Sung Ho Ryu
Summary: A new method for analyzing protein interactions in the outer membrane of living cells has been developed, which could provide critical information to understand how cancer cells develop resistance to targeted drug therapies. By investigating weak protein-protein interactions, researchers found that the cancer-linked protein EGFR tends to bind with a range of other proteins, depending on the type of cancer cell studied, potentially contributing to drug resistance.
EXPERIMENTAL AND MOLECULAR MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Akanksha Srivastava, Arvind Kumar, Subhankar Biswas, Rajender Kumar, Vaibhav Srivastava, Hema Rajaram, Yogesh Mishra
Summary: This study revealed the role of a global regulator, LexA, in modulating the gamma-radiation stress response of the cyanobacterium Anabaena. Proteome analysis of Anabaena strains subjected to gamma-radiation showed differential accumulation of 41 proteins, corresponding to 29 distinct proteins, with LexA regulating 27 of the corresponding genes. The regulated genes were mainly involved in photosynthesis, carbon assimilation, and oxidative stress alleviation. The study also found that LexA influenced photosynthesis and thylakoid membrane proteome even under normal growth conditions, indicating its role in stress response management.
Article
Infectious Diseases
Yuanyuan Li, Lei Fu, Weiyan Zhang, Xi Chen, Yu Lu
Summary: This study revealed that the Rv1453 protein of Mycobacterium tuberculosis affects its susceptibility to clofazimine by regulating the transcription level of qor, shedding new light on the mechanism of clofazimine resistance.
INFECTION AND DRUG RESISTANCE
(2021)
Article
Biology
Roger S. Zou, Yang Liu, Taekjip Ha
Summary: CRISPR-Cas9 has revolutionized biomedical research and medicine with its convenient and targeted manipulation of DNA. The recently developed vfCRISPR system provides time- and spatially-resolved control over Cas9 activity, enabling comprehensive studies of DNA damage and repair. Understanding the fundamental principles of Cas9 binding and cleavage behavior is essential for widespread use of these systems, and can be achieved through in vitro assays like cleavage and electrophoretic mobility shift assays (EMSA).
Article
Biochemistry & Molecular Biology
Meenakshi, Sonar Shubham Balbhim, Shilpa Sarkar, Madavan K. Vasudevan, Sudip K. Ghosh
Summary: Studies have revealed that EhHbox and EiHbox1 are highly upregulated proteins during encystation process. They belong to the TALE homeobox protein family and are localized in the nucleus. They regulate the differentiation of the parasite by controlling key encystation-induced genes.
MOLECULAR MICROBIOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Laureen Christin Arndt, Susanne Heine, Lino Wendt, Emilia Wegele, Jan Titus Schomerus, Jutta Schulze, Reinhard Hehl
Summary: This study analyzed the genomic distribution and function of WT-boxes, revealing their enrichment in promoter regions and their role as novel WRKY binding sites required for basal and MAMP-induced gene expression.
Article
Physics, Multidisciplinary
Yeonghoon Kim, Ludvig Lizana, Jae-Hyung Jeon
Summary: The 3D folding and macromolecular size of chromosomes determine their transport characteristics. The fractal globule-like chromosome structure accelerates macromolecular diffusion and target search.
PHYSICAL REVIEW LETTERS
(2022)
Article
Chemistry, Medicinal
Reem K. Fathalla, Matthias Engel, Christian Ducho
Summary: 8-Anilinonaphthalene-1-sulfonic acid (ANS) is a fluorescent probe commonly used to detect conformational changes in proteins. This study discovered that ANS can inhibit the activity of various isoforms of MurA and identified a more potent ANS analog. These findings highlight the potential of targeting the ANS binding pocket for the development of antibiotics.
ARCHIV DER PHARMAZIE
(2023)
Article
Plant Sciences
Konstantin Kanofsky, Jendrik Rusche, Lea Eilert, Fabian Machens, Reinhard Hehl
Summary: The study reveals that WRKY50 in A. thaliana requires specific WT-boxes for activation and binding at target gene promoters, demonstrating high flexibility of WRKY50 binding site recognition beyond the classic W-box TTGACC/T.
PLANT CELL REPORTS
(2021)
Article
Reproductive Biology
Jaime Gosalvez, Javier Bartolome-Nebreda, Eva Tvrda, Carmen Lopez-Fernandez, Jose Luis Fernandez, Stephen Johnston
Summary: The study aimed to investigate the relationship between DNase activity associated with bacterial contamination of incubated bovine frozen-thawed spermatozoa and elevated sperm DNA fragmentation. The experiments showed that incubation of plasmid with the supernatant of infected bovine semen straws resulted in clear evidence of DNase activity compared to non-infected supernatant. The presence of bacteria in semen straws led to an exponential increase in bacterial growth and sperm DNA fragmentation, highlighting the importance of hygiene practices during semen processing.
Article
Biochemistry & Molecular Biology
Weiqi Xie, Qin Xia, Ling Chen, Guangming Xiong, Yuwei Gao, Yuanhua Yu, Xiuxia He
Summary: The second tetR gene acts as a negative regulator in the expression of 3,17 beta-HSD, and the mutant strain of C. testosteroni with the second tetR gene knocked-out exhibits slightly higher expression of 3,17 beta-HSD compared to the wild type under testosterone induction, suggesting potential application in bioremediation of steroids contaminated environment.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Timothy C. Saylor, Christina R. Savage, Andrew C. Krusenstjerna, Nerina Jusufovic, Wolfram R. Zueckert, Catherine A. Brissette, Md Motaleb, Paula J. Schlax, Brian Stevenson
Summary: The Borrelia burgdorferi SpoVG protein exhibits different affinities for various RNAs, ssDNAs, and dsDNAs. Mutagenesis studies suggest that the formation of SpoVG-nucleic acid complexes is not solely dependent on sequence or structure. The substitution of uracil with thymine in ssDNAs does not affect protein-nucleic acid complex formation.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Chemistry, Organic
Guralamatta Siddappa Ravi Kumara, Young Jun Seo
Summary: This paper reports the synthesis of two deoxyuridine derivatives functioning as molecular rotors, and demonstrates the utility of this probing system in sensing gene regulation arising from interactions between G-quadruplex and nucleolin.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Josiah L. Teague, John K. Barrows, Cynthia A. Baafi, Michael W. Van Dyke
Summary: Transcription regulatory proteins, also known as transcription factors, act as molecular switches modulating gene expression at the transcription initiation stage. This study applied a reverse-genetic methodology to analyze the DNA-binding consensus sequence of TTHA1359 and identified regulatory binding sites within the T. thermophilus HB8 genome.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Rosario Sanchez, Irene Gonzalez-Thuillier, Monica Venegas-Caleron, Rafael Garces, Joaquin J. Salas, Enrique Martinez-Force
Summary: This study identified the WRI1 gene in sunflower and characterized its role in regulating plastidial fatty acid synthesis. Sunflower WRI1 acts as a co-regulator for multiple genes involved in oleic acid synthesis.
Article
Microbiology
Ana M. Oliveira Paiva, Annemieke H. Friggen, Roxanne Douwes, Bert Wittekoek, Wiep Klaas Smits
Summary: This study characterized commonly used fluorescent systems in Clostridioides difficile cells and compared their applicability as transcriptional or translational reporters in microscopy. The results showed that SNAP(Cd) is the most suitable candidate for live-cell imaging in C. difficile to date.
ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY
(2022)
Review
Microbiology
Wiep Klaas Smits, Anna Maria Roseboom, Jeroen Corver
Summary: Plasmids are common in the enteropathogen Clostridioides difficile and may encode functions relevant to pathogenesis, such as antimicrobial resistance and toxin production.
CURRENT OPINION IN MICROBIOLOGY
(2022)
Article
Microbiology
A. Baktash, J. Corver, C. Harmanus, W. K. Smits, W. Fawley, M. H. Wilcox, N. Kumar, D. W. Eyre, A. Indra, A. Mellmann, E. J. Kuijper
Summary: Clostridioides difficile is the most common cause of antibiotic-associated gastrointestinal infections. Capillary electrophoresis-PCR ribotyping is the current gold standard for C. difficile typing, but lacks the ability to study transmission and outbreaks in detail. New molecular methods, such as core genome multilocus sequence typing (cgMLST), have the potential to provide better differentiation and standardized data exchange. However, adjusted cutoff thresholds and epidemiological data are necessary to recognize outbreaks of specific ribotypes.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Fatema-Zahra M. Rashid, Eike Mahlandt, Michiel van der Vaart, Daphne E. C. Boer, Monica Varela Alvarez, Bram Henneman, Daan J. W. Brocken, Patrick Voskamp, Anneloes J. Blok, Thomas S. Shimizu, Annemarie H. Meijer, Martijn S. Luijsterburg, Joachim Goedhart, Frederic G. E. Cremazy, Remus T. Dame
Summary: The interplay between three-dimensional chromosome organisation and genomic processes requires in vivo studies. However, the use of fluorescent organic dyes for chromosome labelling can cause structural changes in DNA, leading to interference with gene expression, genome replication, and cell cycle progression. Researchers have developed a minimally-perturbing, genetically encoded fluorescent DNA label that effectively labels chromosomes in eukaryotic cells and zebrafish embryos.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Wiep Klaas Smits, Yassene Mohammed, Arnoud H. de Ru, Valentina Cordo', Annemieke H. Friggen, Peter A. van Veelen, Paul J. Hensbergen
Summary: This paper presents a comprehensive analysis of protein phosphorylation in the Gram-positive enteropathogen Clostridioides difficile. The study explores the extent and nature of phosphorylation events in C. difficile and identifies target proteins and phosphorylation sites. The findings provide a foundation for further research on the role of phosphorylation in C. difficile physiology and pathogenesis.
Article
Biochemistry & Molecular Biology
Paul J. Hensbergen, Arnoud H. de Ru, Annemieke H. Friggen, Jeroen Corver, Wiep Klaas Smits, Peter A. van Veelen
Summary: In this study, we demonstrate that a commonly used enrichment strategy can reliably identify peptides carrying a type A glycan modification and discovered a rare modification structure. These findings can be used to advance the understanding of biosynthesis models for this modification.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
David Forrest, Emily A. Warman, Amanda M. Erkelens, Remus T. Dame, David C. Grainger
Summary: Bacteria employ silencing proteins to prevent improper transcription of horizontally acquired DNA, with differences in strategies between E. coli and Bacillus subtilis due to the specificities of the silencing protein and RNA polymerase in each organism.
NATURE COMMUNICATIONS
(2022)
Article
Infectious Diseases
Quinten R. Ducarmon, Tjomme van der Bruggen, Celine Harmanus, Ingrid M. J. G. Sanders, Laura G. M. Daenen, Ad C. Fluit, Rolf H. A. M. Vossen, Susan L. Kloet, Ed J. Kuijper, Wiep Klaas Smits
Summary: This study reports a patient case of pseudomembranous colitis caused by a rare polymerase chain reaction (PCR) ribotype (RT) 151 Clostridioides difficile strain that produces a single toxin. Genomic analysis revealed that the RT151 strain was unable to be identified using routine commercial tests. The study also provides conclusive evidence for the pathogenicity of C-II isolates of the cryptic clade and highlights the need for vigilance towards C. difficile infections caused by cryptic clade isolates.
CLINICAL MICROBIOLOGY AND INFECTION
(2023)
Article
Genetics & Heredity
Anna M. Roseboom, Quinten R. Ducarmon, Bastian V. H. Hornung, Celine Harmanus, Monique J. T. Crobach, Ed J. Kuijper, Rolf H. A. M. Vossen, Susan L. Kloet, Wiep Klaas Smits
Summary: A subset of clinical isolates of Clostridioides difficile contains plasmids that can carry virulence and antimicrobial resistance genes. However, C. difficile plasmids are poorly studied. Here, we provide the complete genome sequence of a clinical isolate carrying three high-copy number plasmids from different families, advancing our understanding of C. difficile plasmid biology.
Article
Biochemistry & Molecular Biology
Fatema-Zahra M. Rashid, Remus T. Dame
Summary: Nucleoid-associated proteins (NAPs) are bacterial architectural proteins and transcription factors that regulate gene expression in response to environmental signals. However, the coupling between their structural and regulatory functions in vivo is still uncertain. This study focuses on the NAP H-NS, proposing it as a sensor-effector protein that directly remodels chromatin to regulate gene expression. The findings suggest that the interplay between chromosome structure and gene expression may be an underappreciated concept in bacterial transcription regulation.
MOLECULAR MICROBIOLOGY
(2023)
Article
Medicine, Research & Experimental
Zhuang Li, Enchen Zhou, Cong Liu, Hope Wicks, Sena Yildiz, Farhana Razack, Zhixiong Ying, Sander Kooijman, Debby P. Y. Koonen, Marieke Heijink, Sarantos Kostidis, Martin Giera, Ingrid M. J. G. Sanders, Ed J. Kuijper, Wiep Klaas Smits, Ko Willems van Dijk, Patrick C. N. Rensen, Yanan Wang
Summary: This study found that short-chain fatty acids, including butyrate, do not have multiple metabolic benefits in individuals with metabolic syndrome. However, the underlying mechanisms are still unclear. The researchers used antibiotic-induced microbiota depletion and fecal microbiota transplantation (FMT) to investigate the role of gut microbiota in the metabolic benefits of dietary butyrate. They found that dietary butyrate reduced appetite and ameliorated high-fat diet-induced weight gain, and these effects were dependent on the presence of gut microbiota.
Article
Microbiology
Ishani Wickramage, Zhong Peng, Soumyadeep Chakraborty, Celine Harmanus, Ed J. Kuijper, Sally Alrabaa, Wiep Klaas Smits, Xingmin Sun
Summary: Clostridioides difficile has a complex relationship with antibiotics, as they can both increase the risk of infection and be the primary treatment for C. difficile infection (CDI). This study identified two clinical isolates of C. difficile with elevated resistance to vancomycin and rifaximin, as well as mutations related to resistance. The findings highlight the importance of surveillance in understanding antibiotic resistance and developing effective treatment strategies.
MICROBIOLOGY SPECTRUM
(2023)
Article
Infectious Diseases
Perezimor Etifa, Cesar Rodriguez, Celine Harmanus, Ingrid M. J. G. Sanders, Igor A. Sidorov, Olufunmilayo A. Mohammed, Emily Savage, Andrew R. Timms, Jane Freeman, Wiep Klaas Smits, Mark H. Wilcox, Simon D. Baines
Summary: This study evaluated the efficacy of metronidazole-resistant non-toxigenic Clostridioides difficile strains (NTCD-E4) in preventing C. difficile infection facilitated by various antimicrobials in an in vitro human gut model. The results showed that NTCD-E4 inhibited cytotoxin production and prevented infection by the pathogenic strain RT027.
Article
Immunology
Wiep Klaas Smits, Celine Harmanus, Ingrid M. J. G. Sanders, Lynn Bry, Grace A. Blackwell, Quinten R. Ducarmon, Eliane de Oliveira Ferreira, Ed J. Kuijper
Summary: The plasmid pCD-METRO is responsible for metronidazole resistance in different isolates of Clostridioides difficile. We found high sequence similarity among pCD-METRO plasmids from various sources and identified pCD-METRO and associated metronidazole-resistant isolates in clinical and veterinary reservoirs in the Americas. We suggest using PCR or genomic assays to detect pCD-METRO in metronidazole-resistant C. difficile.
EMERGING INFECTIOUS DISEASES
(2022)
Article
Biochemistry & Molecular Biology
Ankita Chadda, Alexander G. Kozlov, Binh Nguyen, Timothy M. Lohman, Eric A. Galburt
Summary: In this study, it was found that the DNA damage response in Mycobacterium tuberculosis differs from well-studied model bacteria. The DNA repair helicase UvrD1 in Mtb is activated through a redox-dependent process and is closely associated with the homo-dimeric Ku protein. Additionally, Ku protein is shown to stimulate the helicase activity of UvrD1.
JOURNAL OF MOLECULAR BIOLOGY
(2024)
