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1. A concept for international societally relevant microbiology education and microbiology knowledge promulgation in society

Author

Timmis, Kenneth N. [0000-0002-0066-4670], Hallsworth, John E. [0000-0001-6797-9362], McGenity, Terry J. [0000-0002-1497-8822], Armstrong, Rachel [0000-0002-3516-6815], Colom, María Francisca [0000-0002-8672-5429], Karahan, Z. Ceren [0000-0001-7727-3363], Chavarría, Max [0000-0001-5901-3576], Bernal, Patricia [0000-0002-6228-0496], Boyd, Eric S. [0000-0003-4436-5856], Ramos, Juan L. [0000-0002-8731-7435], Kaltenpoth, Martin [0000-0001-9450-0345], Pruzzo, Carla [0000-0002-1280-4677], Clarke, Gerard [0000-0001-9771-3979], López-García, Purificación [0000-0002-0927-0651], Yakimov, Michail M. [0000-0003-1418-363X], Perlmutter, Jessamyn [0000-0002-9789-4674], Greening, Chris [0000-0001-7616-0594], Eloe-Fadrosh, Emiley [0000-0002-8162-1276], Verstraete, Willy [0000-0002-3140-3713], Nunes, Olga [0000-0003-4742-2537], Kotsyurbenko, Oleg R. [0000-0002-4748-3017], Nikel, Pablo I. [0000-0002-9313-7481], Scavone, Paola [0000-0002-8840-3757], Häggblom, Max M. [0000-0001-6307-7863], Lavigne, Rob [0000-0001-7377-1314], Le Roux, Frédérique [0000-0002-9112-6199], Timmis, James Kenneth [0000-0002-7773-0859], Parro, Victor [0000-0003-3738-0724], Michán, Carmen [0000-0003-2921-0987], García, José Luis [0000-0002-9238-2485], Casadevall, A. [0000-0002-9402-9167], Payne, Shelley M. [0000-0003-3112-4340], Frey, Joachim [0000-0001-9133-0280], Koren, Omry [0000-0002-7738-1337], Prosser, James I. [0000-0003-1757-5102], Lal, Rup [0000-0001-8364-8547], Anand, S. [0000-0001-7852-3512], Sood, U [0000-0002-0886-0107], Offre, Pierre [0000-0002-3660-2164], Bryce, Casey C. [0000-0002-1132-5201], Mswaka, Allen Y. [0000-0003-4868-1530], Jores, Jörg [0000-0003-3790-5746], Kaçar, Betül [0000-0002-0482-2357], Blank, Lars M. [0000-0003-0961-4976], Pope, Phillip B. [0000-0002-2067-4059], Banciu, Horia L. [0000-0002-6563-3226], Armitage, Judith [0000-0003-4983-9731], Lee, Sang Yup [0000-0003-0599-3091], Wang, Feng-Ping [0000-0002-0376-6947], Makhalanyane, Thulani P. [0000-0002-8173-1678], Gilbert, Jack A. [0000-0001-7920-7001], Wood, Thomas K. [0000-0002-6258-529X], Vasiljevic, Branka [0000-0002-2315-3590], Soberón, Mario [0000-0002-1593-9227], Udaondo, Zulema [0000-0003-3445-6842], Rojo, Fernando [0000-0003-1848-7745], Giraud, Tatiana [0000-0002-2685-6478], Ropars, Jeanne [0000-0002-3740-9673], Ezeji, T. C. [0000-0002-8384-895X], Müller, Volker [0000-0001-7955-5508], Averhoff, Beate [0000-0003-1460-3649], Sessitsch, Angela [0000-0003-0137-930X], Partida-Martinez, Laila Pamela [0000-0001-8037-2856], Huang, Wei [0000-0003-1302-6528], Molin, Søren [0000-0002-7973-2639], Junier, Pilar [0000-0002-8618-3340], Amils, Ricardo [0000-0002-7560-1033], Wu, Xiao-Lei [0000-0002-9897-6903], Ron, Eliora [0000-0003-2615-8685], Erten, Hüseyin [0000-0003-1537-2416], De Martinis, E.C.P. [0000-0002-6089-6238], Rapoport, Alexander [0000-0002-6185-0039], Öpik, Maarja [0000-0001-8025-7460], Pokatong, W. Donald R. [0009-0009-6692-9879], Stairs, Courtney W. [0000-0001-6650-0970], Amoozegar, Mohammad Ali [0000-0002-9638-0532], Gil-Serna, Jessica [0000-0002-2113-1830], Timmis, Kenneth N., Hallsworth, John E., McGenity, Terry J., Armstrong, Rachel, Colom, María Francisca, Karahan, Z. Ceren, Chavarría, Max, Bernal, Patricia, Boyd, Eric S., Ramos, Juan L., Kaltenpoth, Martin, Pruzzo, Carla, Clarke, Gerard, López-García, Purificación, Yakimov, Michail M., Perlmutter, Jessamyn, Greening, Chris, Eloe-Fadrosh, Emiley, Verstraete, Willy, Nunes, Olga, Kotsyurbenko, Oleg R., Nikel, Pablo I., Scavone, Paola, Häggblom, Max M., Lavigne, Rob, Le Roux, Frédérique, Timmis, James Kenneth, Parro, Victor, Michán, Carmen, García, José Luis, Casadevall, A., Payne, Shelley M., Frey, Joachim, Koren, Omry, Prosser, James I., Lal, Rup, Anand, S., Sood, U, Offre, Pierre, Bryce, Casey C., Mswaka, Allen Y., Jores, Jörg, Kaçar, Betül, Blank, Lars M., Pope, Phillip B., Banciu, Horia L., Armitage, Judith, Lee, Sang Yup, Wang, Feng-Ping, Makhalanyane, Thulani P., Gilbert, Jack A., Wood, Thomas K., Vasiljevic, Branka, Soberón, Mario, Udaondo, Zulema, Rojo, Fernando, Giraud, Tatiana, Ropars, Jeanne, Ezeji, T. C., Müller, Volker, Averhoff, Beate, Sessitsch, Angela, Huang, Wei, Molin, Søren, Junier, Pilar, Amils, Ricardo, Wu, Xiao-Lei, Ron, Eliora, Erten, Hüseyin, De Martinis, E.C.P., Rapoport, Alexander, Öpik, Maarja, Pokatong, W. Donald R., Stairs, Courtney W., Amoozegar, Mohammad Ali, Gil-Serna, Jessica, Timmis, Kenneth N. [0000-0002-0066-4670], Hallsworth, John E. [0000-0001-6797-9362], McGenity, Terry J. [0000-0002-1497-8822], Armstrong, Rachel [0000-0002-3516-6815], Colom, María Francisca [0000-0002-8672-5429], Karahan, Z. Ceren [0000-0001-7727-3363], Chavarría, Max [0000-0001-5901-3576], Bernal, Patricia [0000-0002-6228-0496], Boyd, Eric S. [0000-0003-4436-5856], Ramos, Juan L. [0000-0002-8731-7435], Kaltenpoth, Martin [0000-0001-9450-0345], Pruzzo, Carla [0000-0002-1280-4677], Clarke, Gerard [0000-0001-9771-3979], López-García, Purificación [0000-0002-0927-0651], Yakimov, Michail M. [0000-0003-1418-363X], Perlmutter, Jessamyn [0000-0002-9789-4674], Greening, Chris [0000-0001-7616-0594], Eloe-Fadrosh, Emiley [0000-0002-8162-1276], Verstraete, Willy [0000-0002-3140-3713], Nunes, Olga [0000-0003-4742-2537], Kotsyurbenko, Oleg R. [0000-0002-4748-3017], Nikel, Pablo I. [0000-0002-9313-7481], Scavone, Paola [0000-0002-8840-3757], Häggblom, Max M. [0000-0001-6307-7863], Lavigne, Rob [0000-0001-7377-1314], Le Roux, Frédérique [0000-0002-9112-6199], Timmis, James Kenneth [0000-0002-7773-0859], Parro, Victor [0000-0003-3738-0724], Michán, Carmen [0000-0003-2921-0987], García, José Luis [0000-0002-9238-2485], Casadevall, A. [0000-0002-9402-9167], Payne, Shelley M. [0000-0003-3112-4340], Frey, Joachim [0000-0001-9133-0280], Koren, Omry [0000-0002-7738-1337], Prosser, James I. [0000-0003-1757-5102], Lal, Rup [0000-0001-8364-8547], Anand, S. [0000-0001-7852-3512], Sood, U [0000-0002-0886-0107], Offre, Pierre [0000-0002-3660-2164], Bryce, Casey C. [0000-0002-1132-5201], Mswaka, Allen Y. [0000-0003-4868-1530], Jores, Jörg [0000-0003-3790-5746], Kaçar, Betül [0000-0002-0482-2357], Blank, Lars M. [0000-0003-0961-4976], Pope, Phillip B. [0000-0002-2067-4059], Banciu, Horia L. [0000-0002-6563-3226], Armitage, Judith [0000-0003-4983-9731], Lee, Sang Yup [0000-0003-0599-3091], Wang, Feng-Ping [0000-0002-0376-6947], Makhalanyane, Thulani P. [0000-0002-8173-1678], Gilbert, Jack A. [0000-0001-7920-7001], Wood, Thomas K. [0000-0002-6258-529X], Vasiljevic, Branka [0000-0002-2315-3590], Soberón, Mario [0000-0002-1593-9227], Udaondo, Zulema [0000-0003-3445-6842], Rojo, Fernando [0000-0003-1848-7745], Giraud, Tatiana [0000-0002-2685-6478], Ropars, Jeanne [0000-0002-3740-9673], Ezeji, T. C. [0000-0002-8384-895X], Müller, Volker [0000-0001-7955-5508], Averhoff, Beate [0000-0003-1460-3649], Sessitsch, Angela [0000-0003-0137-930X], Partida-Martinez, Laila Pamela [0000-0001-8037-2856], Huang, Wei [0000-0003-1302-6528], Molin, Søren [0000-0002-7973-2639], Junier, Pilar [0000-0002-8618-3340], Amils, Ricardo [0000-0002-7560-1033], Wu, Xiao-Lei [0000-0002-9897-6903], Ron, Eliora [0000-0003-2615-8685], Erten, Hüseyin [0000-0003-1537-2416], De Martinis, E.C.P. [0000-0002-6089-6238], Rapoport, Alexander [0000-0002-6185-0039], Öpik, Maarja [0000-0001-8025-7460], Pokatong, W. Donald R. [0009-0009-6692-9879], Stairs, Courtney W. [0000-0001-6650-0970], Amoozegar, Mohammad Ali [0000-0002-9638-0532], Gil-Serna, Jessica [0000-0002-2113-1830], Timmis, Kenneth N., Hallsworth, John E., McGenity, Terry J., Armstrong, Rachel, Colom, María Francisca, Karahan, Z. Ceren, Chavarría, Max, Bernal, Patricia, Boyd, Eric S., Ramos, Juan L., Kaltenpoth, Martin, Pruzzo, Carla, Clarke, Gerard, López-García, Purificación, Yakimov, Michail M., Perlmutter, Jessamyn, Greening, Chris, Eloe-Fadrosh, Emiley, Verstraete, Willy, Nunes, Olga, Kotsyurbenko, Oleg R., Nikel, Pablo I., Scavone, Paola, Häggblom, Max M., Lavigne, Rob, Le Roux, Frédérique, Timmis, James Kenneth, Parro, Victor, Michán, Carmen, García, José Luis, Casadevall, A., Payne, Shelley M., Frey, Joachim, Koren, Omry, Prosser, James I., Lal, Rup, Anand, S., Sood, U, Offre, Pierre, Bryce, Casey C., Mswaka, Allen Y., Jores, Jörg, Kaçar, Betül, Blank, Lars M., Pope, Phillip B., Banciu, Horia L., Armitage, Judith, Lee, Sang Yup, Wang, Feng-Ping, Makhalanyane, Thulani P., Gilbert, Jack A., Wood, Thomas K., Vasiljevic, Branka, Soberón, Mario, Udaondo, Zulema, Rojo, Fernando, Giraud, Tatiana, Ropars, Jeanne, Ezeji, T. C., Müller, Volker, Averhoff, Beate, Sessitsch, Angela, Huang, Wei, Molin, Søren, Junier, Pilar, Amils, Ricardo, Wu, Xiao-Lei, Ron, Eliora, Erten, Hüseyin, De Martinis, E.C.P., Rapoport, Alexander, Öpik, Maarja, Pokatong, W. Donald R., Stairs, Courtney W., Amoozegar, Mohammad Ali, and Gil-Serna, Jessica

Abstract

The biosphere of planet Earth is a microbial world: a vast reactor of countless microbially driven chemical transformations and energy transfers that push and pull many planetary geochemical processes, including the cycling of the elements of life, mitigate or amplify climate change (e.g., Nature Reviews Microbiology, 2019, 17, 569) and impact the well-being and activities of all organisms, including humans. Microbes are both our ancestors and creators of the planetary chemistry that allowed us to evolve (e.g., Life's engines: How microbes made earth habitable, 2023). To understand how the biosphere functions, how humans can influence its development and live more sustainably with the other organisms sharing it, we need to understand the microbes. In a recent editorial (Environmental Microbiology, 2019, 21, 1513), we advocated for improved microbiology literacy in society. Our concept of microbiology literacy is not based on knowledge of the academic subject of microbiology, with its multitude of component topics, plus the growing number of additional topics from other disciplines that become vitally important elements of current microbiology. Rather it is focused on microbial activities that impact us–individuals/communities/nations/the human world–and the biosphere and that are key to reaching informed decisions on a multitude of issues that regularly confront us, ranging from personal issues to crises of global importance. In other words, it is knowledge and understanding essential for adulthood and the transition to it, knowledge and understanding that must be acquired early in life in school. The 2019 Editorial marked the launch of the International Microbiology Literacy Initiative, the IMiLI.

Published
2024

2. Scientists’ warning to humanity: microorganisms and climate change

Author

Cavicchioli, Ricardo, Ripple, William J, Timmis, Kenneth N, Azam, Farooq, Bakken, Lars R, Baylis, Matthew, Behrenfeld, Michael J, Boetius, Antje, Boyd, Philip W, Classen, Aimée T, Crowther, Thomas W, Danovaro, Roberto, Foreman, Christine M, Huisman, Jef, Hutchins, David A, Jansson, Janet K, Karl, David M, Koskella, Britt, Mark Welch, David B, Martiny, Jennifer BH, Moran, Mary Ann, Orphan, Victoria J, Reay, David S, Remais, Justin V, Rich, Virginia I, Singh, Brajesh K, Stein, Lisa Y, Stewart, Frank J, Sullivan, Matthew B, van Oppen, Madeleine JH, Weaver, Scott C, Webb, Eric A, and Webster, Nicole S

Subjects
Microbiology, Biological Sciences, Climate Action, Climate Change, Ecosystem, Greenhouse Gases, Human Activities, Humans, Microbial Viability, Medical Microbiology
Abstract

In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial 'unseen majority'. We must learn not just how microorganisms affect climate change (including production and consumption of greenhouse gases) but also how they will be affected by climate change and other human activities. This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.

Published
2019

3. Viable cyanobacteria in the deep continental subsurface

Author

Puente-Sánchez, Fernando, Arce-Rodríguez, Alejandro, Oggerin, Monike, García-Villadangos, Miriam, Moreno-Paz, Mercedes, Blanco, Yolanda, Rodríguez, Nuria, Bird, Laurence, Lincoln, Sara A., Tornos, Fernando, Prieto-Ballesteros, Olga, Freeman, Katherine H., Pieper, Dietmar H., Timmis, Kenneth N., Amils, Ricardo, and Parro, Víctor

Published
2018

5. The Enigma of Prokaryotic Life in Deep Hypersaline Anoxic Basins

Author

Bolhuis, Henk, Borin, Sara, Daffonchio, Daniele, Corselli, Cesare, Giuliano, Laura, D'Auria, Giuseppe, de Lange, Gert J., Huebner, Andreas, Varnavas, Sotirios P., Thomson, John, Tamburini, Christian, Marty, Danielle, McGenity, Terry J., Timmis, Kenneth N., and Party, BioDeep Scientific

Published
2005

7. The importance of naturally attenuated SARS-CoV-2in the fight against COVID-19

Author

Armengaud, Jean [0000-0003-1589-445X], Thuret, Jean-Yves [0000-0001-5385-7620], Anken, Eelco van [0000-0001-9529-2701], Acosta-Alvear, Diego [0000-0002-1139-8486], Aragón, Tomás [0000-0002-1700-2729], Arias, Carolina [0000-0002-4445-0826], Blondel, Marc [0000-0003-4897-2995], Braakman, Ineke [0000-0003-1592-4364], Collet, Jean-François [0000-0001-8069-7036], Courcol, René [0000-0003-2324-5687], Danchin, Antoine [0000-0002-6350-5001], Deleuze, Jean-François [0000-0002-5358-4463], Lavigne, Jean-Philippe [0000-0002-9484-0304], Lucas, Sophie [0000-0003-1287-7996], Michiels, Thomas [0000-0001-9615-8053], Moore, Edward R.B. [0000-0001-7693-924X], Nixon-Abell, Jonathon [0000-0003-4169-0012], Rosselló-Mora, Ramón [0000-0001-8253-3107], Shi, Zheng-Li [0000-0001-8089-163X], Siccardi, Antonio G. [0000-0002-1654-5545], Sitia, Roberto [0000-0001-7086-4152], Tillett, Daniel [0000-0003-1061-0489], Timmis, Kenneth N. [0000-0002-0066-4670], Toledano, Michel B. [0000-0002-3079-1179], Sluijs, Peter van der [0000-0002-4485-3342], Vicenzi, Elisa [0000-0003-0051-3968], Armengaud, Jean, Delaunay, Agnes, Thuret, Jean-Yves, Anken, Eelco van, Acosta-Alvear, Diego, Aragón, Tomás, Arias, Carolina, Blondel, Marc, Braakman, Ineke, Collet, Jean-François, Courcol, René, Danchin, Antoine, Deleuze, Jean-François, Lavigne, Jean-Philippe, Lucas, Sophie, Michiels, Thomas, Moore, Edward R.B., Nixon-Abell, Jonathon, Rosselló-Mora, Ramón, Shi, Zheng-Li, Siccardi, Antonio G., Sitia, Roberto, Tillett, Daniel, Timmis, Kenneth N., Toledano, Michel B., Sluijs, Peter van der, Vicenzi, Elisa, Armengaud, Jean [0000-0003-1589-445X], Thuret, Jean-Yves [0000-0001-5385-7620], Anken, Eelco van [0000-0001-9529-2701], Acosta-Alvear, Diego [0000-0002-1139-8486], Aragón, Tomás [0000-0002-1700-2729], Arias, Carolina [0000-0002-4445-0826], Blondel, Marc [0000-0003-4897-2995], Braakman, Ineke [0000-0003-1592-4364], Collet, Jean-François [0000-0001-8069-7036], Courcol, René [0000-0003-2324-5687], Danchin, Antoine [0000-0002-6350-5001], Deleuze, Jean-François [0000-0002-5358-4463], Lavigne, Jean-Philippe [0000-0002-9484-0304], Lucas, Sophie [0000-0003-1287-7996], Michiels, Thomas [0000-0001-9615-8053], Moore, Edward R.B. [0000-0001-7693-924X], Nixon-Abell, Jonathon [0000-0003-4169-0012], Rosselló-Mora, Ramón [0000-0001-8253-3107], Shi, Zheng-Li [0000-0001-8089-163X], Siccardi, Antonio G. [0000-0002-1654-5545], Sitia, Roberto [0000-0001-7086-4152], Tillett, Daniel [0000-0003-1061-0489], Timmis, Kenneth N. [0000-0002-0066-4670], Toledano, Michel B. [0000-0002-3079-1179], Sluijs, Peter van der [0000-0002-4485-3342], Vicenzi, Elisa [0000-0003-0051-3968], Armengaud, Jean, Delaunay, Agnes, Thuret, Jean-Yves, Anken, Eelco van, Acosta-Alvear, Diego, Aragón, Tomás, Arias, Carolina, Blondel, Marc, Braakman, Ineke, Collet, Jean-François, Courcol, René, Danchin, Antoine, Deleuze, Jean-François, Lavigne, Jean-Philippe, Lucas, Sophie, Michiels, Thomas, Moore, Edward R.B., Nixon-Abell, Jonathon, Rosselló-Mora, Ramón, Shi, Zheng-Li, Siccardi, Antonio G., Sitia, Roberto, Tillett, Daniel, Timmis, Kenneth N., Toledano, Michel B., Sluijs, Peter van der, and Vicenzi, Elisa

Abstract

The current SARS‐CoV‐2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID‐19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS‐CoV‐2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS‐CoV‐2 would offer significant relief, although vaccine developers have warned that design, testing and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (i), but the earliest vaccines were based on the live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS‐CoV‐2 will mutate and may naturally attenuate over time (ii). What makes the current pandemic unique is that, thanks to state‐of‐the‐art nucleic acid sequencing technologies, we can follow in detail how SARS‐CoV‐2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS‐CoV‐2 variants across the globe should be of key interest in our fight against the pandemic.

Published
2020

9. The importance of naturally attenuated SARS‐CoV ‐2 in the fight against COVID ‐19

Author

Armengaud, Jean, Delaunay‐Moisan, Agnès, Thuret, Jean‐Yves, Anken, Eelco, Acosta‐Alvear, Diego, Aragón, Tomás, Arias, Carolina, Blondel, Marc, Braakman, Ineke, Collet, Jean‐François, Courcol, René, Danchin, Antoine, Deleuze, Jean‐François, Lavigne, Jean‐Philippe, Lucas, Sophie, Michiels, Thomas, Moore, Edward R. B., Nixon‐Abell, Jonathon, Rossello‐Mora, Ramon, Shi, Zheng‐Li, Siccardi, Antonio G., Sitia, Roberto, Tillett, Daniel, Timmis, Kenneth N., Toledano, Michel B., Sluijs, Peter, Vicenzi, Elisa, Médicaments et Technologies pour la Santé (MTS), Université Paris-Saclay-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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Stress Oxydatif et Cancer (SOC), Département Biologie Cellulaire (BioCell), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Sénescence et stabilité génomique (SEN), Département Biologie des Génomes (DBG), San Raffaele Scientific Institute, Vita-Salute San Raffaele University and Center for Translational Genomics and Bioinformatics, University of California [Santa Barbara] (UC Santa Barbara), University of California (UC), Universidad Pública de Navarra [Espagne] = Public University of Navarra (UPNA), Génétique, génomique fonctionnelle et biotechnologies (UMR 1078) (GGB), EFS-Université de Brest (UBO)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO), Université de Bretagne Occidentale - UFR Médecine et Sciences de la Santé (UBO UFR MSS), Utrecht University [Utrecht], Université Catholique de Louvain = Catholic University of Louvain (UCL), Walloon Excellence in Life sciences and BIOtechnology [Liège] (WELBIO), Institut Cochin (IC UM3 (UMR 8104 / U1016)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Centre National de Recherche en Génomique Humaine (CNRGH), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut de Biologie François JACOB (JACOB), 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), Virulence bactérienne et maladies infectieuses (VBMI), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), University of Gothenburg (GU), Sahlgrenska University Hospital [Gothenburg], University of Cambridge [UK] (CAM), Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de las Islas Baleares (UIB), Wuhan Institute of Virology [Wuhan, China], Chinese Academy of Sciences [Wuhan Branch], Technische Universität Braunschweig = Technical University of Braunschweig [Braunschweig], ANR-17-CE18-0023,Phylopeptidomics,Identification rapide de bactéries pathogènes et résistances aux antibiotiques(2017), Armengaud, Jean [0000-0003-1589-445X], Thuret, Jean-Yves [0000-0001-5385-7620], Anken, Eelco van [0000-0001-9529-2701], Acosta-Alvear, Diego [0000-0002-1139-8486], Aragón, Tomás [0000-0002-1700-2729], Arias, Carolina [0000-0002-4445-0826], Blondel, Marc [0000-0003-4897-2995], Braakman, Ineke [0000-0003-1592-4364], Collet, Jean-François [0000-0001-8069-7036], Courcol, René [0000-0003-2324-5687], Danchin, Antoine [0000-0002-6350-5001], Deleuze, Jean-François [0000-0002-5358-4463], Lavigne, Jean-Philippe [0000-0002-9484-0304], Lucas, Sophie [0000-0003-1287-7996], Michiels, Thomas [0000-0001-9615-8053], Moore, Edward R.B. [0000-0001-7693-924X], Nixon-Abell, Jonathon [0000-0003-4169-0012], Rosselló-Mora, Ramón [0000-0001-8253-3107], Shi, Zheng-Li [0000-0001-8089-163X], Siccardi, Antonio G. [0000-0002-1654-5545], Sitia, Roberto [0000-0001-7086-4152], Tillett, Daniel [0000-0003-1061-0489], Timmis, Kenneth N. [0000-0002-0066-4670], Toledano, Michel B. [0000-0002-3079-1179], Sluijs, Peter van der [0000-0002-4485-3342], Vicenzi, Elisa [0000-0003-0051-3968], University of California [Santa Barbara] (UCSB), University of California, Institut Brestois Santé Agro Matière (IBSAM), Université de Brest (UBO)-Université de Brest (UBO)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Technical University Braunschweig, Armengaud, Jean, Thuret, Jean-Yves, Anken, Eelco van, Acosta-Alvear, Diego, Aragón, Tomás, Arias, Carolina, Blondel, Marc, Braakman, Ineke, Collet, Jean-François, Courcol, René, Danchin, Antoine, Deleuze, Jean-François, Lavigne, Jean-Philippe, Lucas, Sophie, Michiels, Thomas, Moore, Edward R.B., Nixon-Abell, Jonathon, Rosselló-Mora, Ramón, Shi, Zheng-Li, Siccardi, Antonio G., Sitia, Roberto, Tillett, Daniel, Timmis, Kenneth N., Toledano, Michel B., Sluijs, Peter van der, Vicenzi, Elisa, Armengaud, J., Delaunay-Moisan, A., Thuret, J. -Y., van Anken, E., Acosta-Alvear, D., Aragon, T., Arias, C., Blondel, M., Braakman, I., Collet, J. -F., Courcol, R., Danchin, A., Deleuze, J. -F., Lavigne, J. -P., Lucas, S., Michiels, T., Moore, E. R. B., Nixon-Abell, J., Rossello-Mora, R., Shi, Z., Siccardi, A. G., Sitia, R., Tillett, D., Timmis, K. N., Toledano, M. B., van der Sluijs, P., Vicenzi, E., and UCL - SSS/DDUV - Institut de Duve

Subjects
Opinion, viruses, Pneumonia, Viral, Gene Expression, Microbiology, Disease Outbreaks, Evolution, Molecular, Betacoronavirus, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Animals, Humans, Health emergency, Selection, Genetic, Pandemics, Ecology, Evolution, Behavior and Systematics, [SDV.MHEP.ME]Life Sciences [q-bio]/Human health and pathology/Emerging diseases, Virulence, SARS-CoV-2, fungi, COVID-19, SARS Virus, Adaptation, Physiological, Severe acute respiratory syndrome-related coronavirus, Host-Pathogen Interactions, Mutation, Spike Glycoprotein, Coronavirus, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Coronavirus Infections
Abstract

The current SARS‐CoV‐2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID‐19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS‐CoV‐2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS‐CoV‐2 would offer significant relief, although vaccine developers have warned that design, testing and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (i), but the earliest vaccines were based on the live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS‐CoV‐2 will mutate and may naturally attenuate over time (ii). What makes the current pandemic unique is that, thanks to state‐of‐the‐art nucleic acid sequencing technologies, we can follow in detail how SARS‐CoV‐2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS‐CoV‐2 variants across the globe should be of key interest in our fight against the pandemic.

Published
2020
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13. Retraction: "Reactome Array: Forging a Link between Metabolome and Genome"

Author

BELOQUI, ANA, GUAZZARONI, MARÍA EUGENIA, PAZOS, FLORENCIO, VIEITES, JOSÉ M., GODOY, MARTA, GOLYSHINA, OLGA V., CHERNIKOVA, TATYANA N., WALICZEK, AGNES, SILVA-ROCHA, RAFAEL, AL-RAMAHI, YAMAL, LA CONO, VIOLETTA, MENDEZ, CARMEN, SALAS, JOSÉ A., SOLANO, ROBERTO, YAKIMOV, MICHAIL M., TIMMIS, KENNETH N., GOLYSHIN, PETER N., and FERRER, MANUEL

Published
2010

16. Reactome Array: Forging a Link between Metabolome and Genome

Author

Beloqui, Ana, Guazzaroni, María-Eugenia, Pazos, Florencio, Vieites, José M., Godoy, Marta, Golyshina, Olga V., Chernikova, Tatyana N., Waliczek, Agnes, Silva-Rocha, Rafael, Al-ramahi, Yamal, La Cono, Violetta, Mendez, Carmen, Salas, José A., Solano, Roberto, Yakimov, Michail M., Timmis, Kenneth N., Golyshin, Peter N., and Ferrer, Manuel

Published
2009
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20. The urgent need for microbiology literacy in society

Author

Timmis, Kenneth N. [0000-0002-0066-4670], Cavicchioli, Ricardo [0000-0001-8989-6402], García, José Luis [0000-0002-9238-2485], Nogales, Balbina [0000-0001-5769-9500], Chavarría, Max [0000-0001-5901-3576], Stein, Lisa [0000-0001-5095-5022], McGenity, Terry J. [0000-0002-1497-8822], Webster, Nicole [0000-0002-4753-5278], Singh, Brajesh K. [0000-0003-4413-4185], Handelsman, Jo [0000-0003-3488-5030], Lorenzo, Víctor de [0000-0002-6041-2731], Pruzzo, Carla [0000-0002-1280-4677], Timmis, James Kenneth [0000-0002-7773-0859], Danchin, Antoine [0000-0002-6350-5001], Gilbert, Jack [0000-0001-7920-7001], Lal, Rup [0000-0001-8364-8547], Sessitsch, Angela [0000-0003-0137-930X], Bonfante, Paola [0000-0003-3576-8530], Gram Lone [0000-0002-1076-5723], Ron, Eliora [0000-0003-2615-8685], Karahan, Z. Ceren [0000-0001-7727-3363], Van Der Meer, Jan Roelof [0000-0003-1485-3082], Jahn, Dieter [0000-0002-4064-9205], Harper, Lucy [0000-0001-9909-0103], Timmis, Kenneth N., Cavicchioli, Ricardo, García, José Luis, Nogales, Balbina, Chavarría, Max, Stein, Lisa, McGenity, Terry J., Webster, Nicole, Singh, Brajesh K., Handelsman, Jo, Lorenzo, Víctor de, Pruzzo, Carla, Timmis, James Kenneth, Ramos, Juan L., Verstraete, Willy, Jetten, Mike S. M., Danchin, Antoine, Huang, Wei, Gilbert, Jack, Lal, Rup, Santos, Helena, Lee, S. Y., Sessitsch, Angela, Bonfante, Paola, Gram, Lone, Lin, Raymond T.P., Ron, Eliora, Karahan, Z. Ceren, Van Der Meer, Jan Roelof, Artunkal, Seza, Jahn, Dieter, Harper, Lucy, Timmis, Kenneth N. [0000-0002-0066-4670], Cavicchioli, Ricardo [0000-0001-8989-6402], García, José Luis [0000-0002-9238-2485], Nogales, Balbina [0000-0001-5769-9500], Chavarría, Max [0000-0001-5901-3576], Stein, Lisa [0000-0001-5095-5022], McGenity, Terry J. [0000-0002-1497-8822], Webster, Nicole [0000-0002-4753-5278], Singh, Brajesh K. [0000-0003-4413-4185], Handelsman, Jo [0000-0003-3488-5030], Lorenzo, Víctor de [0000-0002-6041-2731], Pruzzo, Carla [0000-0002-1280-4677], Timmis, James Kenneth [0000-0002-7773-0859], Danchin, Antoine [0000-0002-6350-5001], Gilbert, Jack [0000-0001-7920-7001], Lal, Rup [0000-0001-8364-8547], Sessitsch, Angela [0000-0003-0137-930X], Bonfante, Paola [0000-0003-3576-8530], Gram Lone [0000-0002-1076-5723], Ron, Eliora [0000-0003-2615-8685], Karahan, Z. Ceren [0000-0001-7727-3363], Van Der Meer, Jan Roelof [0000-0003-1485-3082], Jahn, Dieter [0000-0002-4064-9205], Harper, Lucy [0000-0001-9909-0103], Timmis, Kenneth N., Cavicchioli, Ricardo, García, José Luis, Nogales, Balbina, Chavarría, Max, Stein, Lisa, McGenity, Terry J., Webster, Nicole, Singh, Brajesh K., Handelsman, Jo, Lorenzo, Víctor de, Pruzzo, Carla, Timmis, James Kenneth, Ramos, Juan L., Verstraete, Willy, Jetten, Mike S. M., Danchin, Antoine, Huang, Wei, Gilbert, Jack, Lal, Rup, Santos, Helena, Lee, S. Y., Sessitsch, Angela, Bonfante, Paola, Gram, Lone, Lin, Raymond T.P., Ron, Eliora, Karahan, Z. Ceren, Van Der Meer, Jan Roelof, Artunkal, Seza, Jahn, Dieter, and Harper, Lucy

Abstract

Microbes and their activities have pervasive, remarkably profound and generally positive effects on the functioning, and thus health and well‐being, of human beings, the whole of the biological world, and indeed the entire surface of the planet and its atmosphere. Collectively, and to a significant extent in partnership with the sun, microbes are the life support system of the biosphere. This necessitates their due consideration in decisions that are taken by individuals and families in everyday life, as well as by individuals and responsible bodies at all levels and stages of community, national and planetary health assessment, planning, and the formulation of pertinent policies. However, unlike other subjects having a pervasive impact upon humankind, such as financial affairs, health, and transportation, of which there is a widespread understanding, knowledge of relevant microbial activities, how they impact our lives, and how they may be harnessed for the benefit of humankind – microbiology literacy – is lacking in the general population, and in the subsets thereof that constitute the decision makers. Choices involving microbial activity implications are often opaque, and the information available is sometimes biased and usually incomplete, and hence creates considerable uncertainty. As a consequence, even evidence‐based ‘best’ decisions, not infrequently lead to unpredicted, unintended, and sometimes undesired outcomes. We therefore contend that microbiology literacy in society is indispensable for informed personal decisions, as well as for policy development in government and business, and for knowledgeable input of societal stakeholders in such policymaking. An understanding of key microbial activities is as essential for transitioning from childhood to adulthood as some subjects currently taught at school, and must therefore be acquired during general education. Microbiology literacy needs to become part of the world citizen job description. To facilitate th

Published
2019

29. Bacterial tRNA landscape revisited.

Author

Pust, Marie‐Madlen, Timmis, Kenneth N., and Tümmler, Burkhard

Subjects
*TRANSFER RNA, *GENETIC code, *BACTERIAL metabolism, *BACTERIAL physiology, *NUCLEOSIDES
Abstract

Summary: The updated Wobble Hypothesis reasonably explains why some 40 tRNA species are sufficient to decode the 61 amino acid codons of the Universal Genetic Code. However, we still have no clue why eubacteria lack tRNA isoacceptors with ANN anticodons, whereas eukaryotes universally lack eight GNN anticodons, only one of which is also absent in bacteria. Direct tRNA sequencing could resolve the patterns of nucleoside modification that had been driving the divergent evolution in prokaryotes and eukaryotes, but this task will require the development of AI‐supported base‐callers that can recognize modified nucleosides without any subsequent analytical verification. Our knowledge of the bacterial tRNA landscape is moreover broadened by the recent discovery of antisense tRNAs and tRNA‐derived fragments that should be examined in their roles for gene expression, translation, bacterial physiology or metabolism. [ABSTRACT FROM AUTHOR]

Published
2022
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30. A purple acidophilic di-ferric DNA ligase from Ferroplasma

Author

Ferret, Manuel, Golyshina, Olga V., Beloqui, Ana, Bottger, Lars H., Andreu, Jose M., Polaina, Julio, De Lacey, Antonio L., Trautwein, Alfred X., Timmis, Kenneth N., and Golyshin, Peter N.

Subjects
DNA-ligand interactions -- Physiological aspects, Ligases -- Physiological aspects, Sulfur bacteria -- Physiological aspects, Science and technology
Abstract

We describe here an extraordinary purple-colored DNA ligase, LigFa, from the acidophilic ferrous iron-oxidizing archaeon Ferroplasma acidiphilum, a di-ferric enzyme with an extremely low pH activity optimum. Unlike any other DNA ligase studied to date, LigFa contains two [Fe.sup.3+]-tyrosinate centers and lacks any requirement for either [Mg.sup.2+] or [K.sup.+] for activity. DNA ligases from closest phylogenetic and ecophysiological relatives have normal pH optima (6.0-7.5), lack iron, and require [Mg.sup.2+]/[K.sup.+] for activity. Ferric iron retention is pH-dependent, with release resulting in partial protein unfolding and loss of activity. Reduction of the [Fe.sup.3+] to [Fe.sup.2+] results in an 80% decrease in DNA substrate binding and an increase in the pH activity optimum to 5.0. DNA binding induces significant conformational change around the iron site(s), suggesting that the ferric irons of LigFa act both as structure organizing and stabilizing elements and as Lewis acids facilitating DNA binding at low pH. iron metalloenzyme | Picrophilus torridus | Sulfolobus acidocaldarius | Thermoplasma acidophilum | Ferroplasma acidiphilum

Published
2008

33. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis

Author

Schneiker, Susanne, dos Santos, Vítor AP Martins, Bartels, Daniela, Bekel, Thomas, Brecht, Martina, Buhrmester, Jens, Chernikova, Tatyana N, Denaro, Renata, Ferrer, Manuel, Gertler, Christoph, Goesmann, Alexander, Golyshina, Olga V, Kaminski, Filip, Khachane, Amit N, Lang, Siegmund, Linke, Burkhard, McHardy, Alice C, Meyer, Folker, Nechitaylo, Taras, Pühler, Alfred, Regenhardt, Daniela, Rupp, Oliver, Sabirova, Julia S, Selbitschka, Werner, Yakimov, Michail M, Timmis, Kenneth N, Vorhölter, Frank-Jörg, Weidner, Stefan, Kaiser, Olaf, and Golyshin, Peter N

Published
2006
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34. Analysis of storage lipid accumulation in Alcanivorax borkumensis: evidence for alternative triacylglycerol biosynthesis routes in bacteria

Author

Kalscheuer, Rainer, Stoveken, Tim, Malkus, Ursula, Reichelt, Rudolf, Golyshin, Peter N., Sabirova, Julia S., Ferret, Manuel, Timmis, Kenneth N., and Steinbuchel, Alexander

Subjects
Lipids -- Analysis, Biosynthesis -- Research, Triglycerides -- Research, Marine bacteria -- Research, Biological sciences
Abstract

Marine hydrocarbonoclastic bacteria, like Alcanivorax borkumensis, play a globally important role in bioremediation of petroleum oil contamination in marine ecosystems. Accumulation of storage lipids, serving as endogenous carbon and energy sources during starvation periods, might be a potential adaptation mechanism for coping with nutrient limitation, which is a frequent stress factor challenging those bacteria in their natural marine habitats. Here we report on the analysis of storage lipid biosynthesis in A. borkumensis strain SK2. Triacylglycerols (TAGs) and wax esters (WEs), but not poly(hydroxyalkanoic acids), are the principal storage lipids present in this and other hydrocarbonoelastie bacterial species. Although so far assumed to be a characteristic restricted to gram-positive actinomycetes, substantial accumulation of TAGs corresponding to a fatty acid content of more than 23% of the cellular dry weight is the first characteristic of large-scale de novo TAG biosynthesis in a gram-negative bacterium. The acyltransferase AtfA1 (ABO_2742) exhibiting wax ester synthase/acyl-coenzyme A'diacylglycerol acyltransferase (WS/DGAT) activity plays a key role in both TAG and WE biosynthesis, whereas AtfA2 (ABO_1804) was dispensable for storage lipid formation. However, reduced but still substantial residual TAG levels in atfA1 and atfA2 knockout mutants compellingly indicate the existence of a yet unknown WS/DGAT-independent alternative TAG biosynthesis route. Storage lipids of A. borkumensis were enriched in saturated fatty acids and accumulated as insoluble intracytoplasmic inclusions exhibiting great structural variety. Storage lipid accumulation provided only a slight growth advantage during short-term starvation periods but was not required for maintaining viability and long-term persistence during extended starvation phases.

Published
2007

35. The cellular machinery of Ferroplasma acidiphilum is iron-protein-dominated

Author

Ferrer, Manuel, Golyshina, Olga V., Beloqui, Ana, Golyshin, Peter N., and Timmis, Kenneth N.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Manuel Ferrer (corresponding author) [1]; Olga V. Golyshina [2]; Ana Beloqui [1]; Peter N. Golyshin [2, 3, 5]; Kenneth N. Timmis [2, 3, 4, 5] Ferroplasma is a genus [...]

Published
2007
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36. The importance of naturally attenuated SARS-CoV-2in the fight against COVID-19

Author

Armengaud, Jean, Delaunay-Moisan, Agnès, Thuret, Jean Yves, van Anken, Eelco, Acosta-Alvear, Diego, Aragón, Tomás, Arias, Carolina, Blondel, Marc, Braakman, Ineke, Collet, Jean François, Courcol, René, Danchin, Antoine, Deleuze, Jean François, Lavigne, Jean Philippe, Lucas, Sophie, Michiels, Thomas, Moore, Edward R.B., Nixon-Abell, Jonathon, Rossello-Mora, Ramon, Shi, Zheng Li, Siccardi, Antonio G., Sitia, Roberto, Tillett, Daniel, Timmis, Kenneth N., Toledano, Michel B., van der Sluijs, Peter, Vicenzi, Elisa, Armengaud, Jean, Delaunay-Moisan, Agnès, Thuret, Jean Yves, van Anken, Eelco, Acosta-Alvear, Diego, Aragón, Tomás, Arias, Carolina, Blondel, Marc, Braakman, Ineke, Collet, Jean François, Courcol, René, Danchin, Antoine, Deleuze, Jean François, Lavigne, Jean Philippe, Lucas, Sophie, Michiels, Thomas, Moore, Edward R.B., Nixon-Abell, Jonathon, Rossello-Mora, Ramon, Shi, Zheng Li, Siccardi, Antonio G., Sitia, Roberto, Tillett, Daniel, Timmis, Kenneth N., Toledano, Michel B., van der Sluijs, Peter, and Vicenzi, Elisa

Abstract

The current SARS-CoV-2 pandemic is wreaking havoc throughout the world and has rapidly become a global health emergency. A central question concerning COVID-19 is why some individuals become sick and others not. Many have pointed already at variation in risk factors between individuals. However, the variable outcome of SARS-CoV-2 infections may, at least in part, be due also to differences between the viral subspecies with which individuals are infected. A more pertinent question is how we are to overcome the current pandemic. A vaccine against SARS-CoV-2 would offer significant relief, although vaccine developers have warned that design, testing and production of vaccines may take a year if not longer. Vaccines are based on a handful of different designs (i), but the earliest vaccines were based on the live, attenuated virus. As has been the case for other viruses during earlier pandemics, SARS-CoV-2 will mutate and may naturally attenuate over time (ii). What makes the current pandemic unique is that, thanks to state-of-the-art nucleic acid sequencing technologies, we can follow in detail how SARS-CoV-2 evolves while it spreads. We argue that knowledge of naturally emerging attenuated SARS-CoV-2 variants across the globe should be of key interest in our fight against the pandemic.

Published
2020

37. The long journey towards standards for engineering biosystems: Are the Molecular Biology and the Biotech communities ready to standardise?

Author

European Commission, National Science Foundation (US), Beal, Jacob, Goñi-Moreno, Ángel, Myers, Chris, Hecht, Ariel, Vicente, María del Carmen, Parco, María, Schmidt, Markus, Timmis, Kenneth N., Baldwin, Geoff, Friedrichs, Steffi, Freemont, Paul, Kiga, Daisuke, Ordozgoiti, Elena, Rennig, Maja, Rios, Leonardo, Tanner, Kristie, Lorenzo, Víctor de, Porcar, Manuel, European Commission, National Science Foundation (US), Beal, Jacob, Goñi-Moreno, Ángel, Myers, Chris, Hecht, Ariel, Vicente, María del Carmen, Parco, María, Schmidt, Markus, Timmis, Kenneth N., Baldwin, Geoff, Friedrichs, Steffi, Freemont, Paul, Kiga, Daisuke, Ordozgoiti, Elena, Rennig, Maja, Rios, Leonardo, Tanner, Kristie, Lorenzo, Víctor de, and Porcar, Manuel

Abstract

Standards are the basis of technology: they allow rigorous description and exact measurement of properties, reliable reproducibility and a common “language” that enables different communities to work together. Molecular biology was in part created by physicists; yet, the field did not inherit the focus on the quantitation, the definition of system boundaries and the robust, unequivocal language that is characteristic of the other natural sciences. However, synthetic biology (SynBio) increasingly requires scientific, technical, operational and semantic standards for the field to become a full‐fledged engineering discipline with a high level of accuracy in the design, manufacturing and performance of biological artefacts. Although the benefits of adopting standards are clear, the community is still largely reluctant to accept them, owing to concerns about adoption costs and losses in flexibility.

Published
2020

38. Mutation in a 'tesB-like' hydroxyacyl-coenzyme A-specific thioesterase gene causes hyperproduction of extracellular polyhydroxyalkanoates by Alcanivorax borkumensis SK2

Author

Sabirova, Julia S., Ferrer, Manuel, Lunsdorf, Heinrich, Wray, Victor, Kalscheuer, Rainer, Steinbuchel, Alexander, Timmis, Kenneth N., and Golyshin, Peter N.

Subjects
Gene mutations -- Research, Polyhydroxyalkanoates -- Research, Genetic research, Biological sciences
Abstract

A novel mutant of the marine oil-degrading bacterium Alcanivorax borkumensis SK2, containing a mini-Tn5 transposon disrupting a 'tesB-like' acyl-coenzyme A (CoA) thioesterase gene, was found to hyperproduce polyhydroxyalkanoates (PHA), resulting in the extracellular deposition of this biotechnologically important polymer when grown on alkanes. The tesB-like gene encodes a distinct novel enzyme activity, which acts exclusively on hydroxylated acyl-CoAs and thus represents a hydroxyacyl-CoA-specific thioesterase. Inactivation of this enzyme results in the rechanneling of CoA-activated hydroxylated fatty acids, the cellular intermediates of alkane degradation, towards PHA production. These findings may open up new avenues for the development of simplified biotechnological processes for the production of PHA as a raw material for the production of bioplastics.

Published
2006

39. Proteomic insights into metabolic adaptations in Alcanivorax borkumensis induced by alkane utilization

Author

Sabirova, Julia S., Ferrer, Manuel, Regenhardt, Daniela, Timmis, Kenneth N., and Golyshin, Peter N.

Subjects
Lipoproteins -- Research, Proteolipids -- Research, Bacterial proteins -- Research, Operons -- Structure, Operons -- Research, Biological sciences
Abstract

Alcanivorax borkumensis is a ubiquitous marine petroleum oil-degrading bacterium with an unusual physiology specialized for alkane metabolism. This 'hydrocarbonoclastic' bacterium degrades an exceptionally broad range of alkane hydrocarbons but few other substrates. The proteomic analysis presented here reveals metabolic features of the hydrocarbonoclastic lifestyle. Specifically, hexadecane-grown and pyruvate-grown cells differed in the expression of 97 cytoplasmic and membrane-associated proteins whose genes appeared to be components of 46 putative operon structures. Membrane proteins up-regulated in alkane-grown cells included three enzyme systems able to convert alkanes via terminal oxidation to fatty acids, namely, enzymes encoded by the well-known alkB1 gene cluster and two new alkane hydroxylating systems, a P450 cytochrome monooxygenase and a putative flavin-binding monooxygenase, and enzymes mediating [beta]-oxidation of fatty acids. Cytoplasmic proteins up-regulated in hexadecane-grown cells reflect a central metabolism based on a fatty acid diet, namely, enzymes of the glyoxylate bypass and of the gluconeogenesis pathway, able to provide key metabolic intermediates, like phosphoenolpyruvate, from fatty acids. They also include enzymes for synthesis of riboflavin and of unsaturated fatty acids and cardiolipin, which presumably reflect membrane restructuring required for membranes to adapt to perturbations induced by the massive influx of alkane oxidation enzymes. Ancillary functions up-regulated included the lipoprotein releasing system (Lol), presumably associated with biosurfactant release, and polyhydroxyalkanoate synthesis enzymes associated with carbon storage under conditions of carbon surfeit. The existence of three different alkane-oxidizing systems is consistent with the broad range of oil hydrocarbons degraded by A. borkumensis and its ecological success in oil-contaminated marine habitats.

Published
2006

40. Stratified prokaryote network in the oxic-anoxic transition of a deep-sea halocline

Author

Daffonchio, Daniele, Borin, Sara, Brusa, Tullio, Brusetti, Lorenzo, van der Wielen, Paul W. J. J., Bolhuis, Henk, Yakimov, Michail M., D'Auria, Giuseppe, Giuliano, Laura, Marty, Danielle, Tamburini, Christian, McGenity, Terry J., Hallsworth, John E., Sass, Andrea M., Timmis, Kenneth N., Tselepides, Anastasios, de Lange, Gert J., Hubner, Andreas, Thomson, John, Varnavas, Soterios P., Gasparoni, Francesco, Gerber, Hans W., Malinverno, Elisa, Corselli, Cesare, Garcin, Jean, McKew, Boyd, Golyshin, Peter N., Lampadariou, Nikolaos, Polymenakou, Paraskevi, Calore, Daniele, Cenedese, Stefano, Zanon, Fabio, and Hoog, Sven

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Daniele Daffonchio (corresponding author) [1]; Sara Borin [1]; Tullio Brusa [1]; Lorenzo Brusetti [1]; Paul W. J. J. van der Wielen [2]; Henk Bolhuis [2]; Michail M. Yakimov [3]; [...]

Published
2006
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42. Expression of a temperature-sensitive esterase in a novel chaperone-based Escherichia coli strain

Author

Ferrer, Manuel, Chernikova, Tatyana N., Golyshin, Peter N., and Timmis, Kenneth N.

Subjects
Escherichia coli -- Research, Recombinant proteins -- Analysis, Biological sciences
Abstract

A new principle for expression of heat-sensitive recombinant proteins in Escherichia coli at temperatures close to 4 degrees C. was experimentally evaluated. The successful use of a chaperone-based E. coli strain to express heat-labile recombinant proteins at temperatures below the theoretical minimum growth temperature of a common E. coli strain (7.5 degrees C.) is reported.

Published
2004

44. A dual lethal system to enhance containment of recombinant micro-organisms

Author

Torres, Begona, Jaenecke, Susanne, Timmis, Kenneth N., Garcia, Jose L., and Diaz, Eduardo

Subjects
Cells -- Genetic aspects, Cells -- Physiological aspects, Chromosomes -- Genetic aspects, Chromosomes -- Physiological aspects, Gene expression -- Physiological aspects, Gene mutations -- Environmental aspects, Gene mutations -- Physiological aspects, Lethal mutation -- Physiological aspects, Microbiology -- Research, Microorganisms -- Environmental aspects, Microorganisms -- Genetic aspects, Microorganisms -- Physiological aspects, Biological sciences
Abstract

Active containment systems based on the controlled expression of a lethal gene are designed to increase containment of recombinant micro-organisms used for environmental applications. A major drawback in containment is the existence of mutations that generate surviving cells that cease to respond to the toxic effect of the lethal function. In this work the authors have developed for the first time a strategy to reduce the problem of mutations and increase the efficiency of containment based on the combination of two lethal functions acting on different cellular targets of major concern in containment, DNA and RNA, and whose expression is under control of different regulatory signals. To engineer the dual gene containment circuit, two toxin--antitoxin pairs, i.e. the colicin E3--immunity E3 and the EcoRI restriction--modification systems, were combined. The genes encoding the immunity E3 and the EcoRI methyltransferase proteins (antitoxins) were stably inserted into the chromosome of the host cell, whereas the broad-host-range lethal genes encoding the colicin E3 RNase and the EcoRI restriction endonuclease (toxins) were flanking the contained trait in a plasmid. This dual lethal cassette decreased gene transfer frequencies, through killing of the recipient cells, by eight orders of magnitude, which provides experimental evidence that the anticipated containment level due to the combination of single containment systems is generally achieved. Survivors that escaped killing were analysed and the mutational events involved were characterized.

Published
2003

45. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenyl-polluted soil

Author

Nogales, Balbina, Moore, Edward R.B., Llobet-Brossa, Enrique, Rossello-Mora, Ramon, Amann, Rudolf, and Timmis, Kenneth N.

Subjects
Soil microbiology -- Research, Polymerase chain reaction -- Usage, Microbial populations -- Analysis, Biological sciences
Abstract

Most soil bacteria are adequately represented in clone libraries prepared from either rRNA or rDNA. These libraries are used to identify bacteria using PCR rather than traditional culture methods.

Published
2001

47. The importance of naturally attenuated SARS‐CoV‐2in the fight against COVID‐19

Author

Armengaud, Jean, primary, Delaunay‐Moisan, Agnès, additional, Thuret, Jean‐Yves, additional, van Anken, Eelco, additional, Acosta‐Alvear, Diego, additional, Aragón, Tomás, additional, Arias, Carolina, additional, Blondel, Marc, additional, Braakman, Ineke, additional, Collet, Jean‐François, additional, Courcol, René, additional, Danchin, Antoine, additional, Deleuze, Jean‐François, additional, Lavigne, Jean‐Philippe, additional, Lucas, Sophie, additional, Michiels, Thomas, additional, Moore, Edward R. B., additional, Nixon‐Abell, Jonathon, additional, Rossello‐Mora, Ramon, additional, Shi, Zheng‐Li, additional, Siccardi, Antonio G., additional, Sitia, Roberto, additional, Tillett, Daniel, additional, Timmis, Kenneth N., additional, Toledano, Michel B., additional, van der Sluijs, Peter, additional, and Vicenzi, Elisa, additional

Published
2020
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48. A second [2Fe-2S] ferredoxin from Sphingomonas sp. strain RW1 can function as an electron donor for the dioxin dioxygenase

Author

Armengaud, Jean, Gaillard, Jacques, and Timmis, Kenneth N.

Subjects
Bacterial genetics -- Physiological aspects, Dioxin -- Physiological aspects, Electron donor-acceptor complexes -- Physiological aspects, Proteins -- Analysis, Biological sciences
Abstract

Results demonstrate that ferredoxin Fdx3 identified in Sphingomonas sp. strain RW1 can serve as an electron donor for the dioxin dioxygenase. Data are also presented comparing Fdx3 with Fdx1 ferredoxin.

Published
2000

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