Article
Cell Biology
Hee-Sook Kim
Summary: In Trypanosoma brucei, genes are arranged in polycistronic transcription units, with transcription termination sites being crucial for controlling mRNA production. Three chromatin factors, H3v, H4v, and base J, contribute to the regulation of transcription termination sites in a coordinated manner, with H4v playing a major role in this process.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Cell Biology
Eliane Tihon, Karinna Rubio-Pena, Annick Dujeancourt-Henry, Aline Crouzols, Brice Rotureau, Lucy Glover
Summary: The life cycle of Trypanosoma brucei alternates between the tsetse fly vector and the mammalian host, and the infectivity to the host depends on the expression of metacyclic variant surface glycoprotein genes. This study reveals the role of VEX1 in the metacyclic differentiation process and its impact on the infectivity of T. brucei to mammalian hosts.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Microbiology
Emilia Jane McLaughlin, Karinna Rubio-Pena, Annick Dujeancourt-Henry, Lucy Glover
Summary: This study aimed to disrupt monoallelic VSG expression and found that the DNA sequence of the ectopic VSG is lost in a transcription-dependent manner following DSB-triggered VSG switching. The loss of the ectopic VSG does not disrupt the number or variety of templates used for BES DSB repair, revealing strict mechanisms within the cell to reinforce monoallelic expression during antigenic variation.
Review
Parasitology
Joana R. C. Faria
Summary: African trypanosomes are early divergent protozoan parasites responsible for high mortality and morbidity as well as a great economic burden among the world's poorest populations. Understanding the mechanisms underpinning antigen as well as general gene expression control is crucial for designing effective control strategies against these organisms. Recent technological developments have advanced our understanding of nuclear organization and gene expression control in trypanosomes, opening novel research avenues.
Article
Biochemistry & Molecular Biology
Isabella E. Maudlin, Steve Kelly, Angela Schwede, Mark Carrington
Summary: The bloodstream form of Trypanosoma brucei relies on antigenic variation of a cell surface coat composed of variant surface glycoprotein (VSG) for survival in mammalian hosts, with the integrity of the VSG coat being crucial for its persistence. Investigation into the regulation of VSG mRNA levels revealed that the copy number varies with the identity of the VSG and that a pathway detects synthesis of non-functional VSG protein, leading to an increase in VSG mRNA levels.
MOLECULAR AND BIOCHEMICAL PARASITOLOGY
(2021)
Article
Biology
Desislava P. Staneva, Stefan Bresson, Tatsiana Auchynnikava, Christos Spanos, Juri Rappsilber, A. Arockia Jeyaprakash, David Tollervey, Keith R. Matthews, Robin C. Allshire
Summary: This study reveals the unique gene expression regulation mechanism in kinetoplastids, a highly divergent lineage of eukaryotes. The researchers identified a complex called SPARC, which consists of SET27 and CRD1, among other components, that is involved in establishing accurate promoter position and directionality.
Review
Microbiology
Bibo Li, Yanxiang Zhao
Summary: Trypanosoma brucei regularly switches its major surface antigen to evade host immune response, with telomere and subtelomere structure integrity being crucial for its survival and pathogenesis. Telomere proteins TRF and RAP1, with unique nucleic acid binding activities, play key roles in VSG expression and switching. Targeting TbTRF and TbRAP1's nucleic acid binding activities may serve as a potential therapeutic strategy against T. brucei.
Article
Parasitology
Sara Silva Pereira, Kawira Mathenge, Daniel Masiga, Andrew Jackson
Summary: This study conducted transcriptome analysis of trypanosome parasites from naturally infected tsetse flies and found a phylotype 8 variant surface glycoprotein (VSG) gene to be constitutively expressed in metacyclic- and bloodstream-form parasites.
PARASITES & VECTORS
(2022)
Article
Parasitology
Kennedy W. Mwangi, Rosaline W. Macharia, Joel L. Bargul
Summary: The study constructed a gene co-expression network of insect-stage trypanosomes using RNA-Seq data and identified enriched modules for genes that play key roles in the parasite's development in the tsetse fly. Additionally, potential 3' UTR regulatory elements for genes in the same module were predicted using the FIRE tool. This network provides a valuable resource for identifying candidate genes for functional studies and understanding the molecular mechanisms underlying important biological processes during the parasite's development in the tsetse fly, which could lead to the identification of potential molecular targets for disease control.
PARASITES & VECTORS
(2021)
Article
Multidisciplinary Sciences
Sabine Bachmaier, Giacomo Giacomelli, Estefania Calvo-Alvarez, Larissa Rezende Vieira, Jan Van Den Abbeele, Aris Aristodemou, Esben Lorentzen, Matthew Gould, Ana Brennand, Jean-Wiliam Dupuy, Ignasi Forne, Axel Imhof, Marc Bramkamp, Didier Salmon, Brice Rotureau, Michael Boshart
Summary: Researchers have discovered that social motility and cAMP signaling are linked to migration of trypanosomes in the salivary glands of tsetse flies. Trypanosomes can sense environmental signals and coordinate their movement by interacting with adenylate cyclases and other proteins. These findings provide insights into the mechanisms of trypanosome migration and transmission in tsetse flies.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Arpita Saha, Amit Kumar Gaurav, Unnati M. Pandya, Marjia Afrin, Ranjodh Sandhu, Vishal Nanavaty, Brittny Schnur, Bibo Li
Summary: In this study, several unique features of TERRA and telomere biology in Trypanosoma brucei were identified. It was found that TERRA foci number is cell cycle-regulated and influenced by TbTRF. TbTRF binds TERRA through its C-terminal Myb domain in a sequence-specific manner, suppressing TERRA levels without affecting its half-life, and depletion of TbTRF leads to increased telomeric R-loop and telomere DNA damage.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Microbiology
Sun Hee Lee, Kyoung-Dong Kim, Miyeon Cho, Sora Huh, Seong Ho An, Donghyun Seo, Kyuhyun Kang, Minhee Lee, Hideki Tanizawa, Inuk Jung, Hyosun Cho, Hyojeung Kang
Summary: A CCCTC-binding factor binding site (S13 locus) on the BamHI A right transcript miRNA promoter was identified, and its functional roles in EBV BART miRNA expression and lytic reactivation were investigated. The S13 locus forms a cluster of DNA loops with other genomic loci to coordinate the EBV life cycle. CTCF binding to the S13 locus is suggested to play a role in the regulation of EBV-related cancer pathogenesis.
Article
Microbiology
Julia Phenn, Jan Pane-Farre, Nikolai Meukow, Annelie Klein, Anne Troitzsch, Patrick Tan, Stephan Fuchs, Gabriel E. Wagner, Sabine Lichtenegger, Ivo Steinmetz, Christian Kohler
Summary: The RegAB redox sensing two-component signal transduction system is essential for anaerobic growth and full virulence of B. pseudomallei, playing a central role in anaerobic metabolism and the coordination of the response to hypoxic conditions. Further investigations into the regulators NarL and FNR provide insight into the complex regulatory network of anaerobic gene expression in this pathogen, which could be relevant for a broad range of bacteria.
Article
Multidisciplinary Sciences
Ya-Qin Wang, Dong-Hong Wu, Denghui Wei, Jia-Yi Shen, Zi-Wei Huang, Xiao-Yu Liang, William C. S. Cho, Jun Ma, Jiawei Lv, Yu-Pei Chen
Summary: By investigating transcription factor-target interactions, researchers identified TEA domain transcription factor 4 (TEAD4) as a master regulator in high-risk nasopharyngeal carcinoma (NPC). TEAD4 promotes NPC progression by inducing migration, invasion, and cisplatin resistance through its autopalmitoylation. This study also reveals that TEAD4's transcriptional activity is independent of its canonical coactivators YAP/ TAZ and serves as an independent predictor of prognosis and treatment response in NPC.
Article
Genetics & Heredity
Raul O. Cosentino, Benedikt G. Brink, T. Nicolai Siegel
Summary: This study presents an allele-specific genome assembly of the diploid parasite Trypanosoma brucei, revealing allelic variants affecting gene expression and resolving artefacts as well as recombination events. Phasing haplotypes allows for lineage tracing and the absence of a nonsense-mediated decay mechanism in trypanosomes is identified through transcriptome and translatome data analysis.
NAR GENOMICS AND BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Sophie Ridewood, Cher-Pheng Ooi, Belinda Hall, Anna Trenaman, Nadina Vasileva Wand, Georgios Sioutas, Iris Scherwitzl, Gloria Rudenko
MOLECULAR MICROBIOLOGY
(2017)
Article
Infectious Diseases
Louise E. Kerry, Elaine E. Pegg, Donald P. Cameron, James Budzak, Gretchen Poortinga, Katherine M. Hannan, Ross D. Hannan, Gloria Rudenko
PLOS NEGLECTED TROPICAL DISEASES
(2017)
Article
Multidisciplinary Sciences
Jacob Beal, Traci Haddock-Angelli, Geoff Baldwin, Markus Gershater, Ari Dwijayanti, Marko Storch, Kim de Mora, Meagan Lizarazo, Randy Rettberg
Article
Cell Biology
Cher-Pheng Ooi, Terry K. Smith, Eva Gluenz, Nadina Vasileva Wand, Sue Vaughan, Gloria Rudenko
Article
Multidisciplinary Sciences
James Budzak, Louise E. Kerry, Aris Aristodemou, Belinda S. Hall, Kathrin Witmer, Manish Kushwaha, Carys Davies, Megan L. Povelones, Jacquelyn R. McDonald, Aakash Sur, Peter J. Myler, Gloria Rudenko
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2019)
Article
Multidisciplinary Sciences
Amir Pandi, Mathilde Koch, Peter L. Voyvodic, Paul Soudier, Jerome Bonnet, Manish Kushwaha, Jean-Loup Faulon
NATURE COMMUNICATIONS
(2019)
Article
Genetics & Heredity
Roberto Galizi, John N. Duncan, William Rostain, Charlotte M. Quinn, Marko Storch, Manish Kushwaha, Alfonso Jaramillo
Article
Multidisciplinary Sciences
Jacob Beal, Geoff S. Baldwin, Natalie G. Farny, Markus Gershater, Traci Haddock-Angelli, Russell Buckley-Taylor, Ari Dwijayanti, Daisuke Kiga, Meagan Lizarazo, John Marken, Kim de Mora, Randy Rettberg, Vishal Sanchania, Vinoo Selvarajah, Abigail Sison, Marko Storch, Christopher T. Workman
Summary: The research found that fluorescence measurements from engineered constructs are highly reproducible, but there is a critical need for quality controlled fluorescent calibrants for plate readers to improve reproducibility.
Article
Computer Science, Theory & Methods
Da-Jung Cho, Matthias Fugger, Corbin Hopper, Manish Kushwaha, Thomas Nowak, Quentin Soubeyran
Summary: Computing via synthetically engineered bacteria has numerous applications in bio-production, bio-sensing, and medicine. Distributed approaches with communication among bacteria have gained interest due to the lack of robustness and resource limitation inside single cells. This paper presents fast protocols for solving the majority consensus problem and computing the Nand of two inputs with high probability, as well as extends the protocols to biologically relevant settings.
DISTRIBUTED COMPUTING
(2022)
Article
Biochemical Research Methods
Angelo Cardoso Batista, Antoine Levrier, Paul Soudier, Peter L. Voyvodic, Tatjana Achmedov, Tristan Reif-Trauttmansdor, Angelique DeVisch, Martin Cohen-Gonsaud, Jean-Loup Faulon, Chase L. Beisel, Jerome Bonnet, Manish Kushwaha
Summary: This study presents a simple, efficient, and cost-effective solution for using linear DNA templates in cell-free systems by deleting the exonuclease gene cluster from Escherichia coli. The research highlights the importance of tailoring buffer composition for the optimal experimental setup, and suggests that similar strategies can be applied to other species in cell-free synthetic biology.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Paul Soudier, Daniel Rodriguez Pinzon, Tristan Reif-Trauttmansdorff, Hassan Hijazi, Maeva Cherriere, Catia Goncalves Pereira, Doriane Blaise, Maxime Pispisa, Angelyne Saint-Julien, William Hamlet, Melissa Nguevo, Eva Gomes, Sophia Belkhelfa, Anna Niarakis, Manish Kushwaha, Ioana Grigoras
Summary: Nucleic acid sensing is a challenging area of application for different biological sub-domains, and nucleic acid biosensing technologies show promise as innovative detection methods. These technologies can overcome the limitations of PCR techniques and sequencing methods in terms of speed, cost, complexity, and specificity.
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Paul Soudier, Ana Zuniga, Thomas Duigou, Peter L. Voyvodic, Kenza Bazi-Kabbaj, Manish Kushwaha, Julie A. Vendrell, Jerome Solassol, Jerome Bonnet, Jean-Loup Faulon
Summary: This study reports the engineering of PeroxiHUB, a sensing platform centered around H2O2, that supports cell-free detection of different metabolites. The PeroxiHUB platform utilizes enzymatic transducers to convert metabolites of interest into H2O2, allowing for rapid reprogramming of sensor specificity. This platform has the potential to detect a wide range of metabolites in a modular and scalable fashion.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Mahnaz Sabeti Azad, Angelo Cardoso Batista, Jean-Loup Faulon, Chase L. Beisel, Jerome Bonnet, Manish Kushwaha
Summary: Cell-free protein synthesis (CFPS) using linear DNA templates has the potential to improve the efficiency and reduce the time required for CFPS. However, linear DNA templates are susceptible to degradation by exonucleases present in cell extracts. This article presents an alternative strategy for using linear DNA templates in CFPS by using exonuclease-deficient knockout cells, eliminating the need for extra modifications. The method described in this article achieves protein expression levels comparable to plasmid DNA in CFPS.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2022)
Article
Multidisciplinary Sciences
Joan Herisson, Thomas Duigou, Melchior du Lac, Kenza Bazi-Kabbaj, Mahnaz Sabeti Azad, Gizem Buldum, Olivier Telle, Yorgo El Moubayed, Pablo Carbonell, Neil Swainston, Valentin Zulkower, Manish Kushwaha, Geoff S. Baldwin, Jean-Loup Faulon
Summary: Introduced the Galaxy-SynBioCAD portal, a toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The portal provides tools and workflows to facilitate the design and engineering process of metabolic pathways, from strain and target selection to DNA part design and plasmid assembly.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Amir Pandi, David Adam, Amir Zare, Van Tuan Trinh, Stefan L. Schaefer, Marie Burt, Bjorn Klabunde, Elizaveta Bobkova, Manish Kushwaha, Yeganeh Foroughijabbari, Peter Braun, Christoph Spahn, Christian Preusser, Elke Pogge von Strandmann, Helge B. Bode, Heiner von Buttlar, Wilhelm Bertrams, Anna Lena Jung, Frank Abendroth, Bernd Schmeck, Gerhard Hummer, Olalla Vazquez, Tobias J. Erb
Summary: This study demonstrates the potential of using deep learning and cell-free protein synthesis for the rapid and cost-effective production and testing of bioactive peptides. Through computational methods and experimental validation, the authors identified 30 functional peptides, including six with broad-spectrum activity against drug-resistant pathogens.
NATURE COMMUNICATIONS
(2023)