Article
Multidisciplinary Sciences
Tamara Hoffmann, Devid Mrusek, Patricia Bedrunka, Fabiana Burchert, Christopher-Nils Mais, Daniel B. Kearns, Florian Altegoer, Erhard Bremer, Gert Bange
Summary: Biofilm formation in Bacillus subtilis requires the expression of matrix production genes, which are upregulated by the transcriptional activator RemA. The study revealed that RemA forms octameric rings with the potential to form a 16-meric superstructure, and it can wrap DNA through a LytTR-related domain.
NATURE COMMUNICATIONS
(2021)
Article
Food Science & Technology
Felix Kofi Agbeko Kuebutornye, Yishan Lu, Zhiwen Wang, Jan Mraz
Summary: This study proves the probiotic traits of Bacillus velezensis TPS3N, Bacillus subtilis TPS4, and Bacillus amyloliquefaciens TPS17, which were isolated from the gut of Nile tilapia, through genomic analysis. Gene clusters responsible for acid and bile tolerance, adhesion, and colonization of the host's gut were identified. Gene markers for bacteriocins and secondary metabolites were also found, suggesting their potential use as alternatives to traditional antibiotics. In addition, the isolates were shown to enhance the host's immunity, aid in digesting complex feed ingredients, and possess genes for synthesizing vitamins and amino acids. This study provides valuable insights into these isolates and opens avenues for genetic manipulations to enhance their characteristics.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2022)
Article
Chemistry, Analytical
Mei-yan Wu, Wen-wei Li, Graham Christie, Peter Setlow, Yong-qing Li
Summary: Using Raman tweezers and live-cell phase-contrast microscopy, this study characterized the lysis process of individual Bacillus subtilis cells carrying PBSX prophage during spores' germination, outgrowth, and vegetative growth. The findings showed that nucleic acid intensities in induced cultures decreased rapidly after prophage induction, with a delay before cell burst, and the latent time and burst time varied in cell populations under different culture conditions.
ANALYTICAL CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Ramamoorthy Sathishkumar, Ramachandran Kannan, Sekar Jinendiran, Natesan Sivakumar, Gopal Selvakumar, Rajaram Shyamkumar
Summary: In this study, the production of exopolysaccharide (EPS) by a potential endosymbiotic bacterium associated with sponge was optimized using response surface methodology. The purified EPS exhibited strong antioxidant activity and moderate anticoagulant efficacy, with the potential applications in food and pharmaceutical industries highlighted for the future.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Pamela Sweeney, Ashleigh Galliford, Abhishek Kumar, Dinesh Raju, Naveen B. Krishna, Emmajay Sutherland, Caitlin J. Leo, Gemma Fisher, Roopa Lalitha, Likith Muthuraj, Gladstone Sigamani, Verena Oehler, Silvia Synowsky, Sally L. Shirran, Tracey M. Gloster, Clarissa M. Czekster, Pravin Kumar, Rafael G. da Silva
Summary: This study characterizes the structure and function of Staphylococcus aureus TrmK, an enzyme essential for bacterial survival and a potential antibiotic target. The researchers used various experimental methods to investigate the binding of SAM and SAH to SaTrmK, and found that SAM binding affects the motion of the C-terminal domain, which may have implications for tRNA recruitment. They also discovered that adenine at position 22 is crucial for activity and identified a potential inhibitor for TrmK. These findings provide insights for future drug discovery efforts.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Food Science & Technology
Angela Maria Catania, Tiziana Civera, Pierluigi Aldo Di Ciccio, Maria Ausilia Grassi, Patrizia Morra, Alessandra Dalmasso
Summary: Processed cheeses from an Italian dairy plant were found to contain Bacillus strains in the initial production hours. Genetic analysis revealed different sequence types for Bacillus cereus strains and identification of a new sequence type for Bacillus subtilis strains. All isolates showed biofilm-forming ability, suggesting the presence of a recurring Bacillus population.
Article
Genetics & Heredity
Akiko Soma, Atsushi Kubota, Daisuke Tomoe, Yoshiho Ikeuchi, Fujio Kawamura, Hijiri Arimoto, Yuh Shiwa, Yu Kanesaki, Hideaki Nanamiya, Hirofumi Yoshikawa, Tsutomu Suzuki, Yasuhiko Sekine, Christos K. Kontos
Summary: Post-transcriptional modifications of tRNA are crucial. The yaaJ gene in Bacillus subtilis encodes a tRNA-specific adenosine deaminase, which is non-essential for viability. The results suggest that tRNA(Arg) has the intrinsic ability to recognize all four CGN codons, and inosine modification is beneficial for translational fidelity and proper growth-phase control.
Article
Biochemistry & Molecular Biology
Abeera Shaeer, Mehwish Aslam, Naeem Rashid
Summary: In this study, a putative manganese-catalase gene Cat(Bsu) from Bacillus subtilis R5 was cloned and expressed in Escherichia coli, and its biochemical characteristics were described. Cat(Bsu) exhibited highest activity at pH 8.0 and 55 degrees C, with a half-life of 2 hours at 80 degrees C.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Microbiology
Patrick Fasshauer, Tobias Busche, Joern Kalinowski, Ulrike Maeder, Anja Poehlein, Rolf Daniel, Joerg Stuelke
Summary: Many bacteria encode cold shock proteins, which play important roles in bacterial growth and gene expression. In Bacillus subtilis, CspB and CspD are the most abundant cold shock proteins, and their simultaneous loss results in severe growth defects and loss of genetic competence. Overexpression of CspC can compensate for the lack of CspB and CspD. Transcription analysis shows that the absence of CspB and CspD affects the expression of about 20% of all genes and may be involved in the control of transcription termination.
Article
Biochemistry & Molecular Biology
Michael A. DiCandia, Adrianne N. Edwards, Joshua B. Jones, Grace L. Swaim, Brooke D. Mills, Shonna M. McBride
Summary: The study reveals that Spo0A in Clostridioides difficile interacts with similar proteins as in Bacillus, despite the absence of corresponding proteins in the C. difficile genome. Mutation analysis shows that several conserved residues in Spo0A affect the sporulation ability of C. difficile. Furthermore, the phosphorylation site of Spo0A and its impact on activity are determined.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Mengyao Hao, Aimin Huang, Bingjie Li, Yu Xin, Liang Zhang, ZhengHua Gu, Haiyan Sun, Youran Li, Guiyang Shi
Summary: In this study, a laccase-like gene from Thermomicrobium roseum DSM 5159 (TrLac-like) was expressed in Bacillus subtilis WB600. TrLac-like showed optimal temperature and pH of 50 degrees C and 6.0, respectively. Amino acid substitutions within 5 angstrom of the inosine ligand were simulated to improve catalytic efficiency.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Daniel Schindler, Roy S. K. Walker, Shuangying Jiang, Aaron N. Brooks, Yun Wang, Carolin A. Muller, Charlotte Cockram, Yisha Luo, Alicia Garcia, Daniel Schraivogel, Julien Mozziconacci, Noah Pena, Mahdi Assari, Maria del Carmen Sanchez Olmos, Yu Zhao, Alba Ballerini, Benjamin A. Blount, Jitong Cai, Lois Ogunlana, Wei Liu, Katarina Jonsson, Dariusz Abramczyk, Eva Garcia-Ruiz, Tomasz W. Turowski, Reem Swidah, Tom Ellis, Tao Pan, Francisco Antequera, Yue Shen, Conrad A. Nieduszynski, Romain Koszul, Junbiao Dai, Lars M. Steinmetz, Jef D. Boeke, Yizhi Cai
Summary: This study reports the design, construction, and characterization of a tRNA neochromosome, which functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. The tRNA neochromosome houses all relocated nuclear tRNA genes and exhibits a potent selective force. Its construction demonstrates the tractability of the yeast model and provides opportunities to test hypotheses surrounding non-coding RNAs.
Article
Food Science & Technology
Wenqiang Shen, Yaojun Liu, Xinyue Zhang, Xiong Zhang, Xiaoping Rong, Lihong Zhao, Cheng Ji, Yuanpei Lei, Fengjuan Li, Jing Chen, Qiugang Ma
Summary: In this study, the potential ameliorative effects of probiotic Bacillus subtilis and biodegradable Bacillus subtilis on ZEN toxicosis in gilts were compared. The results showed that the biodegradable Bacillus subtilis had significant protective effects on growth performance, immune function, hormone secretion, and ZEN elimination in gilts compared to the probiotic Bacillus subtilis.
Editorial Material
Biochemistry & Molecular Biology
Bing Wang, Irina Artsimovitch
Summary: Bacillus subtilis utilizes uncoupled transcription and translation strategies to meet its unique regulatory needs, showing that bacteria employ diverse gene expression strategies.
TRENDS IN MICROBIOLOGY
(2021)
Article
Environmental Sciences
Huichun Xiang, Yanhui He, Xiaobo Wang, Jianwen Wang, Tao Li, Shuangxi Zhu, Ziyan Zhang, Xiaolin Xu, Zhansheng Wu
Summary: Using rhizobacteria as biological fertilizer is expanding in agriculture as substitutes for chemical fertilizers. Bacillus subtilis SL-44 can produce beneficial secondary metabolites and secrete antifungal substances, effectively controlling plant diseases. Genome-wide analysis of SL-44 revealed potential to produce bioantagonistic natural products and growth-promoting metabolites, which may facilitate further research into effective therapies for harmful diseases.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Multidisciplinary Sciences
Brian P. Anton, Alexey Fomenkov, Victoria Wu, Richard J. Roberts
Summary: The MFRE-Seq method provides a straightforward and cost-effective approach for determining prokaryotic 5-methylcytosine methylation motifs by excising and isolating fully methylated fragments using MspJI-Family Restriction Enzymes. This method is compatible with Illumina and Ion Torrent sequencing platforms, and requires only a digestion step and simple column purification before standard library preparation procedures. MFRE-Seq has been successfully applied to bacterial and archaeal genomic DNA preparations to confirm known motifs and identify new ones, making it a valuable complement to existing methodologies for studying prokaryotic methylomes and characterizing methyltransferases.
Article
Biochemistry & Molecular Biology
Chloe Baum, Yu-Cheng Lin, Alexey Fomenkov, Brian P. Anton, Lixin Chen, Bo Yan, Thomas C. Evans, Richard J. Roberts, Andrew C. Tolonen, Laurence Ettwiller
Summary: DNA methylation, found in both eukaryotes and prokaryotes, is a widespread mechanism used to regulate gene expression and confer viral resistance. The RIMS-seq method allows for simultaneous sequencing of bacterial genomes and determination of m5C methylase specificities, supporting routine study of m5C methylation.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Elena V. Liyaskina, Nadezhda A. Rakova, Alevtina A. Kitykina, Valentina V. Rusyaeva, Philip V. Toukach, Alexey Fomenkov, Saulius Vainauskas, Richard J. Roberts, Victor V. Revin
Summary: Paenibacillus spp. exopolysaccharides (EPSs) are gaining interest as biomaterials, with P. polymyxa 2020 strain isolated from wasp honeycombs and producing a high quantity of EPS. The genome and methylome analysis, as well as bioinformatics, revealed a levan synthetic operon in the strain. The levan polymer produced showed low toxicity and high biocompatibility, making it a potential source for industrial production of EPSs and biomaterials.
Article
Biochemistry & Molecular Biology
Mariana Estevez, Satenik Valesyan, Manasses Jora, Patrick A. Limbach, Balasubrahmanyam Addepalli
Summary: Oxidative stress can damage RNA through oxidation of nucleotides, but the presence of ribonucleoprotein complexes can reduce the extent of damage. Position-specific modifications and protein associations can alter the susceptibility of RNA to oxidative damage.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Sameer Dixit, Alan C. Kessler, Jeremy Henderson, Xiaobei Pan, Ruoxia Zhao, Gabriel Silveira D'Almeida, Sneha Kulkarni, Mary Anne T. Rubio, Eva Hegedusova, Robert L. Ross, Patrick A. Limbach, Brian D. Green, Zdenek Paris, Juan D. Alfonzo
Summary: Research shows that the levels of tRNA Q in Trypanosoma brucei dynamically change in response to variations in amino acid concentrations, particularly tyrosine. These changes have negligible effects on global translation or growth rate, but can impact codon choice in tRNA(Tyr).
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Michel Fasnacht, Stefano Gallo, Puneet Sharma, Maximilian Himmelstoss, Patrick A. Limbach, Jessica Willi, Norbert Polacek
Summary: Post-transcriptional modifications of ribosomal RNAs, such as the ho(5)C2501 modification, play a crucial role in regulating protein biosynthesis in bacteria. Studies show that high levels of ho(5)C2501 reduce protein biosynthesis in E. coli but are beneficial for the bacteria in adapting to oxidative stress, especially in the presence of hydrogen peroxide. This unique modification provides functional insights into ribosome functions and bacterial growth under oxidative stress.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Melissa Kelley, Melissa Uhran, Cassandra Herbert, George Yoshida, Emmarie R. Watts, Patrick A. Limbach, Joshua B. Benoit
Summary: The modification of tRNA in mosquitoes, especially in females, may play a critical role in reproduction and could be a potential target for controlling fertility.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Melissa Kelley, Mellie June Paulines, George Yoshida, Ryan Myers, Manasses Jora, Joel P. Levoy, Balasubrahmanyam Addepalli, Joshua B. Benoit, Patrick A. Limbach
Summary: This study focuses on the modifications and stability of tRNAs in the fungus C. neoformans, which is known for its ability to withstand oxidative conditions. The results show that the modifications and transcripts of tRNAs are minimally affected regardless of environmental conditions. The study also proposes a theoretical explanation for the rapid adaptation of C. neoformans to oxidative environments.
Article
Multidisciplinary Sciences
Luigi D'Ascenzo, Anna M. Popova, Scott Abernathy, Kai Sheng, Patrick A. Limbach, James R. Williamson
Summary: This article introduces an automated software tool, Pytheas, for the analysis of modified RNA using mass spectrometry. Pytheas features flexible handling of isotope labeling and RNA modifications, with statistical validation of false discovery rate using sequence decoys. It is a valuable tool for bottom-up mass spectrometry characterization of diverse RNA sequences, with applications in the biology of stable RNAs, as well as quality control of RNA therapeutics and mRNA vaccines.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Julie Zaworski, Oyut Dagva, Julius Brandt, Chloe Baum, Laurence Ettwiller, Alexey Fomenkov, Elisabeth A. Raleigh
Summary: Understanding the mechanisms that control horizontal gene transfer in prokaryotes is an important problem in biology. One major factor that limits DNA entry is the restriction-modification (RM) process, which depends on the DNA modification pattern at specific sites. Recent research has identified a novel system called BREX, which employs DNA modification for host protection but does not involve nuclease action on unmodified phage DNA. This study focuses on the stySA RM locus in Salmonella enterica sv Typhimurium and demonstrates that it is a variant of the BREX system. The findings provide insights into the function and mechanism of the BREX system.
Article
Biochemistry & Molecular Biology
Priti Thakur, Jowad Atway, Patrick A. Limbach, Balasubrahmanyam Addepalli
Summary: Knowledge of the cleavage specificity of ribonucleases is critical for their application in RNA modification mapping or RNA-protein binding studies. In this study, the cleavage specificity and efficiency of ribonuclease MC1 and cusativin were investigated using a customized RNA sequence. The results showed that both enzymes exhibited different preferences for dinucleotide combinations, and the observed substrate specificity was supported by molecular docking analysis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Analytical
Manasses Jora, Daniel Corcoran, Gwenn G. Parungao, Peter A. Lobue, Luiz F. L. Oliveira, George Stan, Balasubrahmanyam Addepalli, Patrick A. Limbach
Summary: This study demonstrates the capability of using higher-energy collisional dissociation (HCD) spectra in combination with spectral matching for the semi-automated characterization of ribonucleosides. Analysis of tRNA hydrolysates using systematic spectral matching has provided evidence for the existence of novel ribonucleoside modifications. This approach has the potential to simplify the characterization of unknown modified ribonucleosides and accelerate discoveries in the epitranscriptome.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis
Summary: REBASE is a comprehensive database of information about restriction-modification (RM) system components, providing details on recognition and cleavage sites for restriction enzymes and DNA methyltransferases, their commercial availability, sensitivity to methylation, crystal and sequence data. The database is regularly updated and can be accessed through a website and FTP.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Brian P. Anton, Richard J. Roberts
Summary: Compared with bacteria, less is known about the restriction-modification systems of archaea. Through a survey of the restriction enzyme database, we discovered similarities between the RM systems of archaea and bacteria, including shared genetic pool and horizontal gene transfer. We also identified persistent DNA methyltransferases in archaeal taxa.
Meeting Abstract
Zoology
M. Kelley, M. Uhran, C. Herbert, G. Yoshida, P. A. Limbach, J. B. Benoit
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2023)