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1. Complete biosynthesis of the potent vaccine adjuvant QS-21

Author

Martin, Laetitia BB, Kikuchi, Shingo, Rejzek, Martin, Owen, Charlotte, Reed, James, Orme, Anastasia, Misra, Rajesh C, El-Demerdash, Amr, Hill, Lionel, Hodgson, Hannah, Liu, Yuzhong, Keasling, Jay D, Field, Robert A, Truman, Andrew W, and Osbourn, Anne

Subjects
Biochemistry and Cell Biology, Medicinal and Biomolecular Chemistry, Chemical Sciences, Biological Sciences, Infectious Diseases, Rare Diseases, Immunization, Vaccine Related, Prevention, Infection, Good Health and Well Being, Humans, Adjuvants, Vaccine, Saponins, Adjuvants, Immunologic, Triterpenes, Adjuvants, Immunologic, Vaccine, Biochemistry & Molecular Biology, Biochemistry and cell biology, Medicinal and biomolecular chemistry
Abstract

QS-21 is a potent vaccine adjuvant currently sourced by extraction from the Chilean soapbark tree. It is a key component of human vaccines for shingles, malaria, coronavirus disease 2019 and others under development. The structure of QS-21 consists of a glycosylated triterpene scaffold coupled to a complex glycosylated 18-carbon acyl chain that is critical for immunostimulant activity. We previously identified the early pathway steps needed to make the triterpene glycoside scaffold; however, the biosynthetic route to the acyl chain, which is needed for stimulation of T cell proliferation, was unknown. Here, we report the biogenic origin of the acyl chain, characterize the series of enzymes required for its synthesis and addition and reconstitute the entire 20-step pathway in tobacco, thereby demonstrating the production of QS-21 in a heterologous expression system. This advance opens up unprecedented opportunities for bioengineering of vaccine adjuvants, investigating structure-activity relationships and understanding the mechanisms by which these compounds promote the human immune response.

Published
2024

2. Editorial : A new chapter for Cell Stress and Chaperones

Author

Bourboulia, Dimitra, Blair, Laura J., Clark, Melody S., Edkins, Adrienne L., Hightower, Lawrence E., Mollapour, Mehdi, Prahlad, Veena, Repasky, Elizabeth A., Truebano, Manuela, Truman, Andrew W., Truttmann, Matthias C., van Oosten-Hawle, Patricija, and Woodford, Mark R.

Published
2024

3. Second international symposium on the chaperone code, 2023

Author

Buchner, Johannes, Alasady, Milad J., Backe, Sarah J., Blagg, Brian S.J., Carpenter, Richard L., Colombo, Giorgio, Gelis, Ioannis, Gewirth, Daniel T., Gierasch, Lila M., Houry, Walid A., Johnson, Jill L., Kang, Byoung Heon, Kao, Aimee W., LaPointe, Paul, Mattoo, Seema, McClellan, Amie J., Neckers, Leonard M., Prodromou, Chrisostomos, Rasola, Andrea, Sager, Rebecca A., Theodoraki, Maria A., Truman, Andrew W., Truttman, Matthias C., Zachara, Natasha E., Bourboulia, Dimitra, Mollapour, Mehdi, and Woodford, Mark R.

Published
2024

5. Second Virtual International Symposium on Cellular and Organismal Stress Responses, September 8–9, 2022

Author

van Oosten-Hawle, Patricija, Backe, Sarah J., Ben-Zvi, Anat, Bourboulia, Dimitra, Brancaccio, Mara, Brodsky, Jeff, Clark, Melody, Colombo, Giorgio, Cox, Marc B., De Los Rios, Paolo, Echtenkamp, Frank, Edkins, Adrienne, Freeman, Brian, Goloubinoff, Pierre, Houry, Walid, Johnson, Jill, LaPointe, Paul, Li, Wei, Mezger, Valerie, Neckers, Len, Nillegoda, Nadinath B., Prahlad, Veena, Reitzel, Adam, Scherz-Shouval, Ruth, Sistonen, Lea, Tsai, Francis T. F., Woodford, Mark R., Mollapour, Mehdi, and Truman, Andrew W.

Published
2023

12. Towards the sustainable discovery and development of new antibiotics

Author

Miethke, Marcus, Pieroni, Marco, Weber, Tilmann, Brönstrup, Mark, Hammann, Peter, Halby, Ludovic, Arimondo, Paola B., Glaser, Philippe, Aigle, Bertrand, Bode, Helge B., Moreira, Rui, Li, Yanyan, Luzhetskyy, Andriy, Medema, Marnix H., Pernodet, Jean-Luc, Stadler, Marc, Tormo, José Rubén, Genilloud, Olga, Truman, Andrew W., Weissman, Kira J., Takano, Eriko, Sabatini, Stefano, Stegmann, Evi, Brötz-Oesterhelt, Heike, Wohlleben, Wolfgang, Seemann, Myriam, Empting, Martin, Hirsch, Anna K. H., Loretz, Brigitta, Lehr, Claus-Michael, Titz, Alexander, Herrmann, Jennifer, Jaeger, Timo, Alt, Silke, Hesterkamp, Thomas, Winterhalter, Mathias, Schiefer, Andrea, Pfarr, Kenneth, Hoerauf, Achim, Graz, Heather, Graz, Michael, Lindvall, Mika, Ramurthy, Savithri, Karlén, Anders, van Dongen, Maarten, Petkovic, Hrvoje, Keller, Andreas, Peyrane, Frédéric, Donadio, Stefano, Fraisse, Laurent, Piddock, Laura J. V., Gilbert, Ian H., Moser, Heinz E., and Müller, Rolf

Published
2021
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21. Reproducible molecular networking of untargeted mass spectrometry data using GNPS

Author

Aron, Allegra T., Gentry, Emily C., McPhail, Kerry L., Nothias, Louis-Félix, Nothias-Esposito, Mélissa, Bouslimani, Amina, Petras, Daniel, Gauglitz, Julia M., Sikora, Nicole, Vargas, Fernando, van der Hooft, Justin J. J., Ernst, Madeleine, Kang, Kyo Bin, Aceves, Christine M., Caraballo-Rodríguez, Andrés Mauricio, Koester, Irina, Weldon, Kelly C., Bertrand, Samuel, Roullier, Catherine, Sun, Kunyang, Tehan, Richard M., Boya P., Cristopher A., Christian, Martin H., Gutiérrez, Marcelino, Ulloa, Aldo Moreno, Tejeda Mora, Javier Andres, Mojica-Flores, Randy, Lakey-Beitia, Johant, Vásquez-Chaves, Victor, Zhang, Yilue, Calderón, Angela I., Tayler, Nicole, Keyzers, Robert A., Tugizimana, Fidele, Ndlovu, Nombuso, Aksenov, Alexander A., Jarmusch, Alan K., Schmid, Robin, Truman, Andrew W., Bandeira, Nuno, Wang, Mingxun, and Dorrestein, Pieter C.

Published
2020
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33. The Hsp90 requirement in the Slt2p stress-activated MAP kinase activity of yeast

Author

Truman, Andrew William

Subjects
572.633
Abstract

The Hsp90 molecular chaperone function is essential and extremely well conserved in eukaryotic organisms, yet much of the mechanism of Hsp90 action remains a mystery. This investigation set out to identify a model client protein of Hsp90 in the yeast Saccharomyces cerevisiae that would be amenable to structural and genetic analysis. Initial studies were conducted on HSF (1-583) strain, which has a C-terminally truncated heat shock transcription factor resulting in low Hsp90 expression. This mutant displayed a swollen cell phenotype that could be suppressed with osmotic stabilisation, indicating that the mutant had defective maintenance of cell wall integrity under stress conditions. This was shown to be a result of an inability to activate Rim 1p, the transcription factor regulated by the cell integrity MAP kinase pathway. Expression of the T22I mutant form of the Hsp82 isoform of Hsp90 expressed as the sole Hsp90 of the cell was also shown to generate a cell integrity defect. Unlike with HSF (1-583), this is apparent at low as well as high temperatures of growth. An interaction between Hsp82 and the MAP kinase Slt2p, the activator of RIm 1p, was demonstrated by both protein binding and two hybrid studies. This interaction was shown to be reinforced under cell wall stressing conditions and dependent on the phosphorylation status of S1t2p. The final part of this investigation revealed that mammalian BMK1 (ERK5) MAP kinase can substantially provide Slt2p MAP kinase function in yeast. We demonstrated that this BMKl protein could associate with both isoforms of Hsp90 in yeast, Hsp82 and Hsc82. Overall, the data indicated the Slt2p MAP kinase is a client protein of Hsp82, providing the first evidence for an Hsp90 involvement in activity of a member of the MAP kinase family proteins.

Published
2005

34. Biosynthesis of peptide–nucleobase hybrids in ribosomal peptides

Author

Pei, Zeng-Fei, Vior, Natalia M., Zhu, Lingyang, Truman, Andrew W., and Nair, Satish K.

Abstract

The main biopolymers in nature are oligonucleotides and polypeptides. However, naturally occurring peptide–nucleobase hybrids are rare. Here we report the characterization of the founding member of a class of peptide–nucleobase hybrid natural products with a pyrimidone motif from a widely distributed ribosomally synthesized and post-translationally modified (RiPP) biosynthetic pathway. This pathway features two steps where a heteromeric RRE–YcaO–dehydrogenase complex catalyzes the formation of a six-membered pyrimidone ring from an asparagine residue on the precursor peptide, and an acyl esterase selectively recognizes this moiety to cleave the C-terminal follower peptide. Mechanistic studies reveal that the pyrimidone formation occurs in a substrate-assisted catalysis manner, requiring a His residue in the precursor to activate asparagine for heterocyclization. Our study expands the chemotypes of RiPP natural products and the catalytic scope of YcaO enzymes. This discovery opens avenues to create artificial biohybrid molecules that resemble both peptide and nucleobase, a modality of growing interest.

Published
2024
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36. Second Virtual International Symposium on Cellular and Organismal Stress Responses, September 8–9, 2022 [Meeting Review]

Author

van Oosten-Hawle, Patricija, Backe, Sarah J., Ben-Zvi, Anat, Bourboulia, Dimitra, Brancaccio, Mara, Brodsky, Jeff, Clark, Melody, Colombo, Giorgio, Cox, Marc B., De Los Rios, Paolo, Echtenkamp, Frank, Edkins, Adrienne, Freeman, Brian, Goloubinoff, Pierre, Houry, Walid, Johnson, Jill, LaPointe, Paul, Li, Wei, Mezger, Valerie, Neckers, Len, Nillegoda, Nadinath B., Prahlad, Veena, Reitzel, Adam, Scherz-Shouval, Ruth, Sistonen, Lea, Tsai, Francis T. F., Woodford, Mark R., Mollapour, Mehdi, and Truman, Andrew W.

Abstract

The Second International Symposium on Cellular and Organismal Stress Responses took place virtually on September 8–9, 2022. This meeting was supported by the Cell Stress Society International (CSSI) and organized by Patricija Van Oosten-Hawle and Andrew Truman (University of North Carolina at Charlotte, USA) and Mehdi Mollapour (SUNY Upstate Medical University, USA). The goal of this symposium was to continue the theme from the initial meeting in 2020 by providing a platform for established researchers, new investigators, postdoctoral fellows, and students to present and exchange ideas on various topics on cellular stress and chaperones. We will summarize the highlights of the meeting here and recognize those that received recognition from the CSSI.

Published
2023
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44. Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition

Author

Pacheco-Moreno, Alba, primary, Stefanato, Francesca L, primary, Ford, Jonathan J, additional, Trippel, Christine, additional, Uszkoreit, Simon, additional, Ferrafiat, Laura, additional, Grenga, Lucia, additional, Dickens, Ruth, additional, Kelly, Nathan, additional, Kingdon, Alexander DH, additional, Ambrosetti, Liana, additional, Nepogodiev, Sergey A, additional, Findlay, Kim C, additional, Cheema, Jitender, additional, Trick, Martin, additional, Chandra, Govind, additional, Tomalin, Graham, additional, Malone, Jacob G, additional, and Truman, Andrew W, additional

Published
2021
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45. Author response: Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition

Author

Pacheco-Moreno, Alba, primary, Stefanato, Francesca L, primary, Ford, Jonathan J, additional, Trippel, Christine, additional, Uszkoreit, Simon, additional, Ferrafiat, Laura, additional, Grenga, Lucia, additional, Dickens, Ruth, additional, Kelly, Nathan, additional, Kingdon, Alexander DH, additional, Ambrosetti, Liana, additional, Nepogodiev, Sergey A, additional, Findlay, Kim C, additional, Cheema, Jitender, additional, Trick, Martin, additional, Chandra, Govind, additional, Tomalin, Graham, additional, Malone, Jacob G, additional, and Truman, Andrew W, additional

Published
2021
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46. Roadmap towards the sustainable discovery and development of new antibiotics

Author

Miethke, Marcus, Pieroni, Marco, Weber, Tilmann, Brönstrup, Mark, Hammann, Peter, Halby, Ludovic, Arimondo, Paola, GLASER, Philippe, Aigle, Bertrand, Bode, Helge, Moreira, Rui, Li, Yanyan, Luzhetskyy, Andriy, Medema, Marnix, Pernodet, Jean-Luc, Stadler, Marc, Tormo, José Rubén, Genilloud, Olga, Truman, Andrew, Weissman, Kira, Takano, Eriko, Sabatini, Stefano, Stegmann, Evi, Brötz-Oesterhelt, Heike, Wohlleben, Wolfgang, Seemann, Myriam, Empting, Martin, Hirsch, Anna, Loretz, Brigitta, Lehr, Claus-Michael, Titz, Alexander, Herrmann, Jennifer, Jaeger, Timo, Alt, Silke, Hesterkamp, Thomas, Winterhalter, Mathias, Schiefer, Andrea, Pfarr, Kenneth, Hoerauf, Achim, Graz, Heather, Graz, Michael, Lindvall, Mika, Ramurthy, Savithri, Karlén, Anders, van Dongen, Maarten, Petkovic, Hrvoje, Keller, Andreas, Peyrane, Frédéric, Donadio, Stefano, Fraisse, Laurent, Piddock, Laura, Gilbert, Ian, Moser, Heinz, Müller, Rolf, Molécules de Communication et Adaptation des Micro-organismes (MCAM), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)

Subjects
[CHIM]Chemical Sciences, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2021

47. New developments in RiPP discovery, enzymology and engineering

Author

Montalbán-López, Manuel, Scott, Thomas, Ramesh, Sangeetha, Rahman, Imran, van Heel, Auke, Viel, Jakob, Bandarian, Vahe, Dittmann, Elke, Genilloud, Olga, Goto, Yuki, Grande Burgos, María José, Hill, Colin, Kim, Seokhee, Koehnke, Jesko, Latham, John, Link, A James, Martínez, Beatriz, Nair, Satish, Nicolet, Yvain, Rebuffat, Sylvie, Sahl, Hans-Georg, Sareen, Dipti, Schmidt, Eric, Schmitt, Lutz, Severinov, Konstantin, Süssmuth, Roderich, Truman, Andrew, Wang, Huan, Weng, Jing-Ke, van Wezel, Gilles, Zhang, Qi, Zhong, Jin, Piel, Jörn, Mitchell, Douglas, Kuipers, Oscar, van der Donk, Wilfred, Link, A. James, Institut de biologie structurale (IBS - UMR 5075), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)

Subjects
Engineering, Protein Sorting Signals, 010402 general chemistry, Hydroxylation, Protein Engineering, 01 natural sciences, Biochemistry, Methylation, Article, 03 medical and health sciences, Drug Discovery, Phosphorylation, 030304 developmental biology, 0303 health sciences, Biological Products, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], business.industry, Extramural, Organic Chemistry, Computational Biology, Data science, 0104 chemical sciences, Enzymes, Genome mining, business, Large group, Peptides, Protein Processing, Post-Translational, Ribosomes
Abstract

International audience; Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.

Published
2021

50. The C-terminal domain of Hsp70 is responsible for paralog-specific regulation of ribonucleotide reductase.

Author

Knighton, Laura E., Nitika, Omkar, Siddhi, and Truman, Andrew W.

Subjects
RIBONUCLEOSIDE diphosphate reductase, MOLECULAR chaperones, PROTEIN conformation, DNA replication, PROTEIN folding, HEAT shock proteins, BUDS
Abstract

The Hsp70 family of molecular chaperones is well-conserved and expressed in all organisms. In budding yeast, cells express four highly similar cytosolic Hsp70s Ssa1, 2, 3 and 4 which arose from gene duplication. Ssa1 and 2 are constitutively expressed while Ssa3 and 4 are induced upon heat shock. Recent evidence suggests that despite their amino acid similarity, these Ssas have unique roles in the cell. Here we examine the relative importance of Ssa1-4 in the regulation of the enzyme ribonucleotide reductase (RNR). We demonstrate that cells expressing either Ssa3 or Ssa4 as their sole Ssa are compromised for their resistance to DNA damaging agents and activation of DNA damage response (DDR)-regulated transcription. In addition, we show that the steady state levels and stability of RNR small subunits Rnr2 and Rnr4 are reduced in Ssa3 or Ssa4-expressing cells, a result of decreased Ssa-RNR interaction. Interaction between the Hsp70 co-chaperone Ydj1 and RNR is correspondingly decreased in cells only expressing Ssa3 and 4. Through studies of Ssa2/4 domain swap chimeras, we determined that the C-terminal domain of Ssas are the source of this functional specificity. Taking together, our work suggests a distinct role for Ssa paralogs in regulating DNA replication mediated by C-terminus sequence variation. Author summary: Cells require molecular chaperones to fold proteins into their active conformation. A major mystery however is why cells express so many highly-related and apparently redundant Hsp70 paralogs. We examined the role of four Hsp70 paralogs in budding yeast (Ssa1, 2, 3 and 4) on the activity of the ribonucleotide reductase (RNR complex). Importantly, we demonstrate there is selectivity of RNR subunits for Ssa1 and Ssa2 subunits, which is dictated by the co-chaperone Ydj1. Taken together, our work provides new insight into the functional specificity of Hsp70 paralogs using a native client protein. [ABSTRACT FROM AUTHOR]

Published
2022
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