Article
Biochemistry & Molecular Biology
Lydia Herzel, Julian A. Stanley, Chun-Chen Yao, Gene-Wei Li
Summary: Bacterial mRNAs have short life cycles with rapid transcription, translation, and degradation processes. The diversity of mRNA molecules at different life-cycle stages impacts their functionality. This study quantitatively maps the 3' status of cellular RNAs in Escherichia coli and reveals that a large fraction of molecules are fragments of full-length mRNAs, with decay intermediates being prevalent. These intermediates are underrepresented in the pool of ribosome-associated transcripts, which may distort analyses of full-length functional mRNAs.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Tinashe P. Maviza, Anastasiia S. Zarechenskaia, Nadezhda R. Burmistrova, Andrey S. Tchoub, Olga A. Dontsova, Petr V. Sergiev, Ilya A. Osterman
Summary: Bacterial species have evolved to protect themselves by using antibiotics and toxins to fight off rival species. A recent study found that a specific toxin called colicin E3 ribotoxin can damage the translational apparatus of bacteria, but competing bacteria may have evolved counter-conflict mechanisms to prevent their demise. The study also showed that the RtcB2-PrfH module can confer resistance to colicin E3 toxicity in E. coli cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biotechnology & Applied Microbiology
Thomas Perli, Daan N. A. van der Vorm, Mats Wassink, Marcel van den Broek, Jack T. Pronk, Jean-Marc Daran
Summary: This study identified and expressed Moco biosynthesis genes in a non-conventional yeast for broadening the biocatalytic repertoire of industrial yeast. Engineered S. cerevisiae strain successfully utilized nitrate as nitrogen source for growth, showing competitiveness in co-culture with spoilage yeast.
METABOLIC ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Gillian Rexroad, John Paul Donohue, Laura Lancaster, Harry F. Noller
Summary: This study investigates the impact of GTP hydrolysis inhibition on the structural dynamics of the ribosome using ensemble FRET. The results show that blocking GTP hydrolysis slows both forward and reverse head rotation, and abolishes reverse head rotation. The study also reveals that the FRET pair used to monitor head rotation mainly reports on intersubunit rotation, and the signal from mRNA quenching correlates closely with reverse intersubunit rotation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Multidisciplinary
Yang Jiang, Syam Sundar Neti, Ian Sitarik, Priya Pradhan, Philip To, Yingzi Xia, Stephen D. Fried, Squire J. Booker, Edward P. O'Brien
Summary: Changes in codon translation rates induced by synonymous mutations cause shifts in folding pathways and result in long-lived states with reduced catalytic activity.
Article
Biotechnology & Applied Microbiology
Tingting Chen, Xiaonan Wang, Lei Zhuang, Alan Shao, Yinghua Lu, Haoran Zhang
Summary: This study developed an efficient microbial biosynthesis system for converting renewable carbon substrates to indigo using metabolic engineering strategies. By optimizing carbon sources and utilizing biosensor-assisted cell selection circuit, the indigo production was significantly improved. Additionally, the global transcription machinery engineering (gTME) approach was employed to enhance the indigo production through a high-performance co-culture variant.
MICROBIAL CELL FACTORIES
(2021)
Article
Multidisciplinary Sciences
Yan Zhang, Nikolay A. Aleksashin, Dorota Klepacki, Caleb Anderson, Nora Vazquez-Laslop, Carol A. Gross, Alexander S. Mankin
Summary: Kasugamycin (KSG) is a small ribosomal subunit-targeting antibiotic that interferes with translation in different stages. It inhibits protein synthesis by blocking the binding of canonical messenger RNA (mRNA) and initiator transfer RNA (tRNA) to the small ribosomal subunit. Even after the formation of the 70S initiation complex, KSG can still interfere with translation to a certain extent. However, it does not completely abolish translation and allows for the expression of certain proteins. The effectiveness of KSG depends on the nature of the mRNA residue preceding the start codon and is attenuated by translational coupling.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Swati Gaikwad, Fardin Ghobakhlou, David J. Young, Jyothsna Visweswaraiah, Hongen Zhang, Alan G. Hinnebusch
Summary: The formation of the 43S preinitiation complex is a critical step in translation in eukaryotes. Studies show that when there is a limitation in 43S PIC assembly, strong mRNAs outcompete weak mRNAs during translation, leading to a reprograming in translational efficiencies.
Article
Biochemical Research Methods
Artyom A. Egorov, Gemma C. Atkinson
Summary: This article presents a tool for annotating conserved uORFs, which can predict functional ORFs in the upstream sequences of a user-defined protein or a set of protein homologs. It generates publication-quality figures with multiple sequence alignments, sequence logos, and locus annotation of the predicted conserved uORFs in graphical vector format.
Article
Multidisciplinary Sciences
Yuzuru Itoh, Anas Khawaja, Ivan Laptev, Miriam Cipullo, Ilian Atanassov, Petr Sergiev, Joanna Rorbach, Alexey Amunts
Summary: This study reveals the sequential assembly mechanism of the small mitoribosomal subunit (SSU) using cryo-electron microscopy. The results demonstrate the role of auxiliary factors in promoting rRNA maturation and conformational changes, leading to the formation of the catalytic human mitoribosome.
Article
Biotechnology & Applied Microbiology
Lukas R. Dahlin, Michael T. Guarnieri
Summary: Microalgae, specifically the Picochlorum genus, offer a potential solution for combating climate change by capturing and reducing CO2 to sustainable fuels and chemicals. In this study, the researchers aimed to expand the genetic toolbox available for the Picochlorum genus by heterologously expressing the phosphite dehydrogenase gene. The results showed that the transgenic algae were able to utilize phosphite as a sole phosphorus source and exhibited comparable growth and composition to conventionally grown algae. This research presents new possibilities for genetic engineering and crop protection strategies.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Multidisciplinary Sciences
Zachary D. Aron, Atousa Mehrani, Eric D. Hoffer, Kristie L. Connolly, Pooja Srinivas, Matthew C. Torhan, John N. Alumasa, Mynthia Cabrera, Divya Hosangadi, Jay S. Barbor, Steven C. Cardinale, Steven M. Kwasny, Lucas R. Morin, Michelle M. Butler, Timothy J. Opperman, Terry L. Bowlin, Ann Jerse, Scott M. Stagg, Christine M. Dunham, Kenneth C. Keiler
Summary: Bacterial ribosome rescue pathways are potential antibiotic targets that selectively inhibit the main ribosome rescue pathway trans-translation. Optimization of pharmacokinetic and antibiotic properties of acylaminooxadiazoles produced MBX-4132, effective in clearing multi-drug resistant Neisseria gonorrhoeae infection in mice. Structural analyses reveal a new mechanism for specific inhibition of trans-translation and a novel conformation within the bacterial ribosome critical for ribosome rescue pathways.
NATURE COMMUNICATIONS
(2021)
Article
Plant Sciences
Carla Navarro-Quiles, Eduardo Mateo-Bonmati, Hector Candela, Pedro Robles, Antonio Martinez-Laborda, Yolanda Fernandez, Jan Simura, Karin Ljung, Vicente Rubio, Maria Rosa Ponce, Jose Luis Micol
Summary: ABCE proteins play a conserved role in translation in plants, dissociating cytoplasmic ribosomes and contributing to ribosome recycling. In Arabidopsis, the ABCE2 protein is important for general growth and vascular development, likely through indirect effects on auxin metabolism.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Chemistry, Physical
Haruhiko Teramoto, Tetsu Shimizu, Masako Suda, Masayuki Inui
Summary: This study explored the genetic engineering of Escherichia coli for hydrogen production. The introduction of exogenous hydrogenase and inactivation of endogenous hydrogenases resulted in both hydrogen production and uptake. Disabling the pathways for ethanol, lactate, and succinate production significantly increased hydrogen production. Unexpectedly, high expression of exogenous hydrogenase completely repressed hydrogen production, and the introduction of heterologous enzyme repressed the endogenous hydrogen production ability.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2022)
Article
Microbiology
Huong Le Nguyen, Marie-Pierre Duviau, Sandrine Laguerre, Sebastien Nouaille, Muriel Cocaign-Bousquet, Laurence Girbal
Summary: Translational regulation was investigated at the genome-scale in Escherichia coli cells. The study found that translation is positively controlled by transcript availability, and mRNA concentration has a positive effect on translation regulation. Multiple linear regression was used to identify key intrinsic factors involved in the genome-wide regulation of ribosome occupancy and ribosome density.
MICROBIOLOGY SPECTRUM
(2022)
Article
Mycology
Niloofar Vaghefi, Julie R. Kikkert, Frank S. Hay, Gavriela D. Carver, Lori B. Koenick, Melvin D. Bolton, Linda E. Hanson, Gary A. Secor, Sarah J. Pethybridge
Article
Virology
J. Lucina Romero Romero, Gavriela Dena Carver, Patricio Arce Johnson, Keith L. Perry, Jeremy R. Thompson
ARCHIVES OF VIROLOGY
(2019)
Article
Ecology
Jia Zheng, Sinisa Bratulic, Heidi E. L. Lischer, Andreas Wagner
Summary: The study reveals that mistranslation can increase the accessibility of alternative evolutionary pathways and high fitness genotypes. Under high mistranslation rates, different evolving populations of TEM-1 can reach different high cefotaxime-resistance genotypes, leading to greater genotypic diversity among populations.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Sinisa Bratulic, Angelo Limeta, Francesca Maccari, Fabio Galeotti, Nicola Volpi, Max Levin, Jens Nielsen, Francesco Gatto
Summary: This study is the first large-scale determination of reference intervals for normal free GAGomes in plasma and urine, which is a critical resource for future physiology and biomarker research.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Fan Liu, Sinisa Bratulic, Alan Costello, Teemu P. Miettinen, Ahmed H. Badran
Summary: Ribosome kinetics are rate-limiting for protein synthesis. The authors evolved diverse 16S rRNAs to enhance protein synthesis rates and genetic code expansion efficiencies in vivo.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Erika A. DeBenedictis, Gavriela D. Carver, Christina Z. Chung, Dieter Soll, Ahmed H. Badran
Summary: The authors demonstrate the discovery and evolution of quadruplet-decoding tRNAs, enabling four independent decoding events in a single protein in living cells. By developing a new evolution strategy, they significantly improve the translation efficiency of quadruplet codons and showcase the multiplexed decoding of up to four unique quadruplet codons in a protein.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
K. Eerik Kaseniit, Noa Katz, Natalie S. Kolber, Connor C. Call, Diego L. Wengier, Will B. Cody, Elizabeth S. Sattely, Xiaojing J. Gao
Summary: This study presents a system for live RNA sensing in cells using endogenous ADAR enzymes. The system has the potential for studying and treating specific cell types/states, with high compatibility and performance.
NATURE BIOTECHNOLOGY
(2023)
Correction
Biotechnology & Applied Microbiology
K. Eerik Kaseniit, Noa Katz, Natalie S. Kolber, Connor C. Call, Diego L. Wengier, Will B. Cody, Elizabeth S. Sattely, Xiaojing J. Gao
NATURE BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Sinisa Bratulic, Angelo Limeta, Saeed Dabestani, Helgi Birgisson, Gunilla Enblad, Karin Stalberg, Goran Hesselager, Michael Haggman, Martin Hoglund, Oscar E. Simonson, Peter Stalberg, Henrik Lindman, Anna Bang-Rudenstam, Matias Ekstrand, Gunjan Kumar, Ilaria Cavarretta, Massimo Alfano, Francesco Pellegrino, Thomas Mandel-Clausen, Ali Salanti, Francesca Maccari, Fabio Galeotti, Nicola Volpi, Mads Daugaard, Mattias Belting, Sven Lundstam, Ulrika Stierner, Jan Nyman, Bengt Bergman, Per-Henrik Edqvist, Max Levin, Andrea Salonia, Henrik Kjolhede, Eric Jonasch, Jens Nielsen, Francesco Gatto
Summary: The study found that urine and plasma free glycosaminoglycan profiles (GAGomes) can serve as tumor metabolism biomarkers for early detection of multiple cancers. Machine learning models based on GAGomes can detect any cancer with high sensitivity and specificity. Undetected cancer patients had a significantly lower risk of death.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Biomedical
Sinisa Bratulic, Francesco Gatto, Jens Nielsen
Summary: Precision oncology aims to tailor clinical decisions to individual patients by accurately characterizing tumors using omics information. Liquid biopsies, as non-invasive alternatives to traditional tissue biopsies, can provide multiple layers of tumor-specific biological information, leading to discovery of new diagnostic markers with the help of statistical and machine learning approaches. This rapidly advancing field of cancer biomarker research faces both successes and challenges.
REGENERATIVE ENGINEERING AND TRANSLATIONAL MEDICINE
(2021)