Article
Biochemistry & Molecular Biology
Pallabi Basu, Shoshy Altuvia
Summary: RelA protein binds RNAs carrying the GGAG sequence to inhibit translation of specific mRNAs while also facilitating regulation of target genes by sRNA partners lacking GGAG. However, binding of mRNAs carrying GGAG at position -7 relative to the AUG by RelA protein renders sRNA-mRNA basepairing regulation ineffective.
MOLECULAR MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Laricca Y. London, Joseph Aubee, Jalisa Nurse, Karl M. Thompson
Summary: The study identified RyhB and FnrS as small RNA regulators that activate the expression of RseA from the RseA(P3) transcript, overcoming redundancy in sigma(E)-dependent stress response in E. coli and related bacteria.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Biotechnology & Applied Microbiology
Chiara Guidi, Lien De Wannemaeker, Jasmine De Baets, Wouter Demeester, Jo Maertens, Brecht De Paepe, Marjan De Mey
Summary: A dynamically regulated feedback circuit was developed to improve cell growth and production by downregulating the expression of membrane proteins. This strategy was effective in countering membrane stress and showed potential for addressing metabolic burden in general.
MICROBIAL CELL FACTORIES
(2022)
Article
Cell Biology
Jinjin Xu, Lingjia Kong, Blayne A. Oliver, Bihua Li, Elizabeth A. Creasey, Gaelen Guzman, Monica Schenone, Kimberly L. Carey, Steven A. Carr, Daniel B. Graham, Jacques Deguine, Ramnik J. Xavier
Summary: This study investigates the impact of autophagic modulation on inflammatory conditions. The authors show that increased autophagy suppresses cytokine production during macrophage activation syndrome and Escherichia coli infection. Additionally, loss of functional autophagy enhances innate immunity in these contexts. Through transcriptomics and proteomics analysis, glutamine/glutathione metabolism and the RNF128/TBK1 axis are identified as independent regulators of inflammation. Overall, this work highlights the potential of increased autophagy as an approach to reduce inflammation and defines mechanistic cascades involved in this control.
Article
Biochemistry & Molecular Biology
Heladia Salgado, Socorro Gama-Castro, Paloma Lara, Citlalli Mejia-Almonte, Gabriel Alarcon-Carranza, Andres G. Lopez-Almazo, Felipe Betancourt-Figueroa, Pablo Pena-Loredo, Shirley Alquicira-Hernandez, Daniela Ledezma-Tejeida, Lizeth Arizmendi-Zagal, Francisco Mendez-Hernandez, Ana K. Diaz-Gomez, Elizabeth Ochoa-Praxedis, Luis J. Muniz-Rascado, Jair S. Garcia-Sotelo, Fanny A. Flores-Gallegos, Laura Gomez, Cesar Bonavides-Martinez, Victor M. del Moral-Chavez, Alfredo J. Hernandez-Alvarez, Alberto Santos-Zavaleta, Salvador Capella-Gutierrez, Josep Lluis Gelpi, Julio Collado-Vides
Summary: RegulonDB is a database that contains comprehensive knowledge on the regulation of transcription initiation of Escherichia coli K-12. The latest version, 12.0, offers improved data storage, retrieval, and accessibility, as well as intuitive graphical tools for data interpretation.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Microbiology
Rocio Fernandez-Fernandez, Sara B. Hernandez, Elena Puerta-Fernandez, Maria A. Sanchez-Romero, Veronica Urdaneta, Josep Casadesus
Summary: Genes ygfE and yiiU in Salmonella enterica serovar Typhimurium encode proteins homologous to E. coli cell division factors ZapA and ZapB. Mutants lacking ZapA and ZapB in S. enterica are sensitive to bile. In the presence of sublethal concentration of sodium deoxycholate, the stability of zapB mRNA increases, possibly due to involvement of regulatory mRNA MicA and Lon protease in degradation of ZapB protein. This mechanism may counter bile damage and maintain functional ZapB protein levels for Z-ring assembly.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biochemical Research Methods
Mattia Furlan, Stefano de Pretis, Mattia Pelizzola
Summary: Despite RNA abundance being commonly assumed as a proxy for transcriptional activity, it is now possible to calculate how synthesis, processing, and degradation rates collectively determine the abundance of each gene's RNA. Different transcriptional outputs can correspond to different combinations of kinetic rates, indicating the existence of markedly different modes of gene expression regulation and their profound effects on gene self-expression regulation.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Heung Jin Jeon, Yonho Lee, Monford Paul N. Abishek, Xun Wang, Dhruba K. Chattoraj, Heon M. Lim
Summary: Small RNA plays a crucial role in regulating gene expression in all forms of life, particularly in bacteria where it can lead to transcription termination and mRNA degradation through base-pairing with mRNA. This study demonstrates that both transcription termination and transcript cleavage can occur on the same sRNA-mRNA pair, generating new stable mRNA species with functional significance. The choice between these mechanisms is determined by the location of base pairing on the mRNA, offering a novel mode of action for sRNAs in bacterial gene regulation.
Review
Cell Biology
Qiuqin Ma, Shihui Long, Zhending Gan, Gianluca Tettamanti, Kang Li, Ling Tian
Summary: Autophagy, a widely conserved process in eukaryotes, is regulated by nutrient deprivation, energy stress, and other unfavorable conditions through multiple pathways. It is primarily governed at the RNA and protein levels in a synergistic manner.
Article
Multidisciplinary Sciences
Puhua Niu, Maria J. Soto, Byung-Jun Yoon, Edward R. Dougherty, Francis J. Alexander, Ian Blaby, Xiaoning Qian
Summary: Extensive research has been done on predictive modeling of genome-scale metabolic reaction networks. Living systems involve complex stochastic processes, and for more accurate predictions, both metabolic reactions and genetic regulatory relationships should be modeled. TRIMER is a new modeling and simulation pipeline that integrates transcription regulation with metabolic regulation, demonstrating applicability to both simulated and experimental data.
Review
Microbiology
Sarah Smallets, Melissa M. Kendall
Summary: Enteric pathogens utilize environmental signals to navigate and precisely control virulence gene expression through post-transcriptional and post-translational gene regulation. Recent studies highlight the initiation of regulatory circuits by physiologically relevant signals and their impact on attaching and effacing pathogens.
CURRENT OPINION IN MICROBIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Hui Han, Kaijie Zhang, Guoxiong Li, Ying Yu, Shuqi Shi, Caice Liang, Huanqing Niu, Wei Zhuang, Dong Liu, Pengpeng Yang, Tianpeng Chen, Wenjun Sun, Yong Chen
Summary: This study enhances biofilm formation in E. coli and increases L-threonine production by regulating key genes involved in the quorum sensing system. It demonstrates significant improvements in biofilm formation, curli expression, fermentation period, and production efficiency through immobilized continuous fermentation.
FERMENTATION-BASEL
(2023)
Article
Biochemistry & Molecular Biology
Paul Bolay, Luisa Hemm, Francisco J. Florencio, Wolfgang R. Hess, M. Isabel Muro-Pastor, Stephan Klaehn
Summary: This study reveals the mechanism by which cyanobacteria regulate metabolic pathways through the interaction of small protein inhibitors and sRNAs, further highlighting the importance of cyanobacteria in regulating metabolic flexibility in response to nitrogen fluctuations.
Article
Biochemistry & Molecular Biology
Bijoy K. Mohanty, Sidney R. Kushner
Summary: Ribonuclease P (RNase P) plays essential roles in tRNA maturation in all organisms, and in Escherichia coli, it affects the abundances of approximately 46% of expressed transcripts, particularly by modulating the generation of pre-tRNAs from polycistronic tRNA transcripts. The inactivation of RNase P leads to changes in transcript abundances and half-lives, with effects on genes in cysteine regulons, toxin-antitoxin modules, and sigma S-controlled genes. Interestingly, Poly(A) polymerase (PAP I) also plays a role in modulating transcript abundances affected by RNase P, suggesting distinct substrate specificities among RNase P, RNase E, and RNase III mutants.
MOLECULAR MICROBIOLOGY
(2022)
Article
Microbiology
Antonio Leal-Morales, Marta Pulido-Sanchez, Aroa Lopez-Sanchez, Fernando Govantes
Summary: This study elucidates the transcriptional organization and regulation of flagellar genes in the Pseudomonas putida genome. The synthesis of flagellar apparatus and chemotaxis machinery is regulated by a three-tier cascade, revealing the complexity and importance of the flagellar system in environmental pseudomonads.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Martin Ogonowski, Asa Motiei, Karolina Ininbergs, Eva Hell, Zandra Gerdes, Klas I. Udekwu, Zoltan Bacsik, Elena Gorokhova
ENVIRONMENTAL MICROBIOLOGY
(2018)
Article
Genetics & Heredity
Fitz Gerald S. Silao, Meliza Ward, Kicki Ryman, Axel Wallstroem, Bjorn Brindefalk, Klas Udekwu, Per O. Ljungdahl
Article
Nutrition & Dietetics
Joana Rossell, Bjorn Brindefalk, Juan Antonio Baena-Fustegueras, Julia Peinado-Onsurbe, Klas Udekwu
EUROPEAN JOURNAL OF NUTRITION
(2020)
Article
Multidisciplinary Sciences
Asa Motiei, Bjorn Brindefalk, Martin Ogonowski, Rehab El-Shehawy, Paulina Pastuszek, Karin Ek, Birgitta Liewenborg, Klas Udekwu, Elena Gorokhova
Article
Immunology
Nuno Rufino de Sousa, Niklas Sandstrom, Lei Shen, Kathleen Hakansson, Rafaella Vezozzo, Klas Udekwu, Julio Croda, Antonio Gigliotti Rothfuchs
Article
Microbiology
Jostein Gohli, Kari Oline Boifot, Line Victoria Moen, Paulina Pastuszek, Gunnar Skogan, Klas Udekwu, Marius Dybwad
Article
Biochemistry & Molecular Biology
Axel Furevi, Jonas Stahle, Claudio Muheim, Spyridon Gkotzis, Klas Udekwu, Daniel O. Daley, Goran Widmalm
CARBOHYDRATE RESEARCH
(2020)
Article
Environmental Sciences
Stefano Bonaglia, Elias Broman, Bjorn Brindefalk, Erika Hedlund, Tomas Hjorth, Carl Rolff, Francisco J. A. Nascimento, Klas Udekwu, Jonas S. Gunnarsson
Article
Biochemistry & Molecular Biology
David Danko, Daniela Bezdan, Evan E. Afshin, Sofia Ahsanuddin, Chandrima Bhattacharya, Daniel J. Butler, Kern Rei Chng, Daisy Donnellan, Jochen Hecht, Katelyn Jackson, Katerina Kuchin, Mikhail Karasikov, Abigail Lyons, Lauren Mak, Dmitry Meleshko, Harun Mustafa, Beth Mutai, Russell Y. Neches, Amanda Ng, Olga Nikolayeva, Tatyana Nikolayeva, Eileen Png, Krista A. Ryon, Jorge L. Sanchez, Heba Shaaban, Maria A. Sierra, Dominique Thomas, Ben Young, Omar O. Abudayyeh, Josue Alicea, Malay Bhattacharyya, Ran Blekhman, Eduardo Castro-Nallar, Ana M. Canas, Aspassia D. Chatziefthimiou, Robert W. Crawford, Francesca De Filippis, Youping Deng, Christelle Desnues, Emmanuel Dias-Neto, Marius Dybwad, Eran Elhaik, Danilo Ercolini, Alina Frolova, Dennis Gankin, Jonathan S. Gootenberg, Alexandra B. Graf, David C. Green, Iman Hajirasouliha, Jaden J. A. Hastings, Mark Hernandez, Gregorio Iraola, Soojin Jang, Andre Kahles, Frank J. Kelly, Kaymisha Knights, Nikos C. Kyrpides, Pawel P. Labaj, Patrick K. H. Lee, Marcus H. Y. Leung, Per O. Ljungdahl, Gabriella Mason-Buck, Ken McGrath, Cem Meydan, Emmanuel F. Mongodin, Milton Ozorio Moraes, Niranjan Nagarajan, Marina Nieto-Caballero, Houtan Noushmehr, Manuela Oliveira, Stephan Ossowski, Olayinka O. Osuolale, Orhan Ozcan, David Paez-Espino, Nicolas Rascovan, Hugues Richard, Gunnar Ratsch, Lynn M. Schriml, Torsten Semmler, Osman U. Sezerman, Leming Shi, Tieliu Shi, Rania Siam, Le Huu Song, Haruo Suzuki, Denise Syndercombe Court, Scott W. Tighe, Xinzhao Tong, Klas Udekwu, Juan A. Ugalde, Brandon Valentine, Dimitar Vassilev, Elena M. Vayndorf, Thirumalaisamy P. Velavan, Jun Wu, Maria M. Zambrano, Jifeng Zhu, Sibo Zhu, Christopher E. Mason
Summary: This study establishes a global metagenomic atlas of urban microbial ecosystems, revealing a vast number of unknown microbial species and genetic elements, highlighting the distribution of antibiotic resistance genes in cities, and indicating the influence of geographical and climatic characteristics on urban microbial composition.
Article
Microbiology
M. H. Y. Leung, X. Tong, K. O. Boifot, D. Bezdan, D. J. Butler, D. C. Danko, J. Gohli, D. C. Green, M. T. Hernandez, F. J. Kelly, S. Levy, G. Mason-Buck, M. Nieto-Caballero, D. Syndercombe-Court, K. Udekwu, B. G. Young, C. E. Mason, M. Dybwad, P. K. H. Lee
Summary: The study found that city was the main factor influencing differences in the public transit air microbiome, with diverse taxa driving geography-specific functional potentials. Bacterial strains in different cities showed variations in genes related to resistance and other functions. Human skin, soil, and wastewater were identified as major presumptive sources of resistome in the public transit air, with a significant presence of resistance genes co-located with mobile genetic elements like plasmids. Geographical specificity played a key role in shaping the public transit air microbiome, highlighting the need for global efforts to better understand this built environment.
Article
Genetics & Heredity
Gabriela E. de Albuquerque, Bruno S. Moda, Marianna S. Serpa, Gabriela P. Branco, Alexandre Defelicibus, Isabella K. T. M. Takenaka, Maria G. de Amorim, Elizabeth C. Miola, Valquiria C. A. Martins, Katia L. Torres, Stephania M. Bezerra, Laura C. L. Claro, Adriane G. Pelosof, Claudia Z. Sztokfisz, Lais L. S. Abrantes, Felipe J. F. Coimbra, Luiz P. Kowalski, Fabio A. Alves, Stenio C. Zequi, Klas I. Udekwu, Israel T. Silva, Diana N. Nunes, Thais F. Bartelli, Emmanuel Dias-Neto
Summary: This study presents a targeted qPCR approach to determine the absolute and relative abundance of bacteria and fungi in different human tissue types. The results show that fungi are more abundant in stool and skin samples, while bacteria are more prevalent in stool, skin, oral swabs, saliva, and gastric fluids.
Article
Construction & Building Technology
Nuno Rufino de Sousa, Laura Steponaviciute, Lucille Margerie, Karolina Nissen, Midori Kjellin, Bjorn Reinius, Erik Salaneck, Klas Udekwu, Antonio Gigliotti Rothfuchs
Summary: This study detected aerosol transmission of SARS-CoV-2 in rooms occupied by COVID-19 patients in a hospital in Sweden and found infectious SARS-CoV-2 particles in the air. This suggests the need for revising existing infection control frameworks to include airborne transmission.
Letter
Construction & Building Technology
Nuno Rufino de Sousa, Laura Steponaviciute, Lucille Margerie, Karolina Nissen, Midori Kjellin, Bjorn Reinius, Erik Salaneck, Klas I. Udekwu, Antonio Gigliotti Rothfuchs
Article
Biochemistry & Molecular Biology
Axel Furevi, Klas Udekwu, Goran Widmalm
Summary: This study elucidates the structure of the O-antigen polysaccharide from Enteropathogenic Escherichia coli O125ac:H6 through NMR experiments and sugar analysis, confirming a branched pentasaccharide structure for the repeating unit. Additionally, by utilizing the CASPER program, the O-antigen structure of O125ab, composed of hexasaccharide repeating units, was established in a semi-automated manner. The close similarity between the O-antigen structures supports the presence of two subgroups within the E. coli O125 serogroup.
Article
Public, Environmental & Occupational Health
Jaime R. Cabrera-Pardo, Rolf Lood, Klas Udekwu, Gerardo Gonzalez-Rocha, Jose M. Munita, Josef D. Jarhult, Andres Opazo-Capurro