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1. Light-driven processes: key players of the functional biodiversity in microalgae

Author

Falciatore, Angela, Bailleul, Benjamin, Boulouis, Alix, Bouly, Jean-Pierre, Bujaldon, Sandrine, Cheminant-Navarro, Soizic, Choquet, Yves, de Vitry, Catherine, Eberhard, Stephan, Jaubert, Marianne, Kuras, Richard, Lafontaine, Ingrid, Landier, Sophie, Selles, Julien, Vallon, Olivier, and Wostrikoff, Katia

Subjects
Microalgae, Biodiversity, Chlamydomonas reinhardtii, Marine diatoms, Photosynthesis, Photoperception, Chloroplast biology, Biology (General), QH301-705.5
Abstract

Microalgae are prominent aquatic organisms, responsible for about half of the photosynthetic activity on Earth. Over the past two decades, breakthroughs in genomics and ecosystem biology, as well as the development of genetic resources in model species, have redrawn the boundaries of our knowledge on the relevance of these microbes in global ecosystems. However, considering their vast biodiversity and complex evolutionary history, our comprehension of algal biology remains limited. As algae rely on light, both as their main source of energy and for information about their environment, we focus here on photosynthesis, photoperception, and chloroplast biogenesis in the green alga Chlamydomonas reinhardtii and marine diatoms. We describe how the studies of light-driven processes are key to assessing functional biodiversity in evolutionary distant microalgae. We also emphasize that integration of laboratory and environmental studies, and dialogues between different scientific communities are both timely and essential to understand the life of phototrophs in complex ecosystems and to properly assess the consequences of environmental changes on aquatic environments globally.

Published
2022
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3. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

Abdullah, Natasha, Abraao, Marcos, Adel, Ait-hamlat, Afaq, Muhammad, Al-Quaddoomi, Faisal S., Alam, Ireen, Albuquerque, Gabriela E., Alexiev, Alex, Ali, Kalyn, Alvarado-Arnez, Lucia E., Aly, Sarh, Amachee, Jennifer, Amorim, Maria G., Ampadu, Majelia, Amran, Muhammad Al-Fath, An, Nala, Andrew, Watson, Andrianjakarivony, Harilanto, Angelov, Michael, Antelo, Verónica, Aquino, Catharine, Aranguren, Álvaro, Araujo, Luiza F., Vasquez Arevalo, Hitler Francois, Arevalo, Jenny, Arnan, Carme, Alvarado Arnez, Lucia Elena, Arredondo, Fernanda, Arthur, Matthew, Asenjo, Freddy, Aung, Thomas Saw, Auvinet, Juliette, Aventin, Nuria, Ayaz, Sadaf, Baburyan, Silva, Bakere, Abd-Manaaf, Bakhl, Katrin, Bartelli, Thais F., Batdelger, Erdenetsetseg, Baudon, François, Becher, Kevin, Bello, Carla, Benchouaia, Médine, Benisty, Hannah, Benoiston, Anne-Sophie, Benson, Joseph, Benítez, Diego, Bernardes, Juliana, Bertrand, Denis, Beurmann, Silvia, Bitard-Feildel, Tristan, Bittner, Lucie, Black, Christina, Blanc, Guillaume, Blyther, Brittany, Bode, Toni, Boeri, Julia, Boldgiv, Bazartseren, Bolzli, Kevin, Bordigoni, Alexia, Borrelli, Ciro, Bouchard, Sonia, Bouly, Jean-Pierre, Boyd, Alicia, Branco, Gabriela P., Breschi, Alessandra, Brindefalk, Björn, Brion, Christian, Briones, Alan, Buczansla, Paulina, Burke, Catherine M., Burrell, Aszia, Butova, Alina, Buttar, Irvind, Bynoe, Jalia, Bönigk, Sven, Bøifot, Kari O., Caballero, Hiram, Cai, Xiao Wen, Calderon, Dayana, Cantillo, Angela, Carbajo, Miguel, Carbone, Alessandra, Cardenas, Anais, Carrillo, Katerine, Casalot, Laurie, Castro, Sofia, Castro, Ana V., Castro, Astred, Castro, Ana Valeria B., Cawthorne, Simone, Cedillo, Jonathan, Chaker, Salama, Chalangal, Jasna, Chan, Allison, Chasapi, Anastasia I., Chatziefthimiou, Starr, Chaudhuri, Sreya Ray, Chavan, Akash Keluth, Chavez, Francisco, Chem, Gregory, Chen, Xiaoqing, Chen, Michelle, Chen, Jenn-Wei, Chernomoretz, Ariel, Chettouh, Allaeddine, Cheung, Daisy, Chicas, Diana, Chiu, Shirley, Choudhry, Hira, Chrispin, Carl, Ciaramella, Kianna, Cifuentes, Erika, Cohen, Jake, Coil, David A., Collin, Sylvie, Conger, Colleen, Conte, Romain, Corsi, Flavia, Cossio, Cecilia N., Costa, Ana F., Cuebas, Delisia, D’Alessandro, Bruno, Dahlhausen, Katherine E., Darling, Aaron E., Das, Pujita, Davenport, Lucinda B., David, Laurent, Davidson, Natalie R., Dayama, Gargi, Delmas, Stéphane, Deng, Chris K., Dequeker, Chloé, Desert, Alexandre, Devi, Monika, Dezem, Felipe S., Dias, Clara N., Donahoe, Timothy Ryan, Dorado, Sonia, Dorsey, LaShonda, Dotsenko, Valeriia, Du, Steven, Dutan, Alexandra, Eady, Naya, Eisen, Jonathan A., Elaskandrany, Miar, Epping, Lennard, Escalera-Antezana, Juan P., Ettinger, Cassie L., Faiz, Iqra, Fan, Luice, Farhat, Nadine, Faure, Emile, Fauzi, Fazlina, Feigin, Charlie, Felice, Skye, Ferreira, Laís Pereira, Figueroa, Gabriel, Fleiss, Aubin, Flores, Denisse, Velasco Flores, Jhovana L., Fonseca, Marcos A.S., Foox, Jonathan, Forero, Juan Carlos, Francis, Aaishah, French, Kelly, Fresia, Pablo, Friedman, Jacob, Fuentes, Jaime J., Galipon, Josephine, Garcia, Mathilde, Garcia, Laura, García, Catalina, Geiger, Annie, Gerner, Samuel M., Ghose, Sonia L., Giang, Dao Phuong, Giménez, Matías, Giovannelli, Donato, Githae, Dedan, Gkotzis, Spyridon, Godoy, Liliana, Goldman, Samantha, Gonnet, Gaston H., Gonzalez, Juana, Gonzalez, Andrea, Gonzalez-Poblete, Camila, Gray, Andrew, Gregory, Tranette, Greselle, Charlotte, Guasco, Sophie, Guerra, Juan, Gurianova, Nika, Haehr, Wolfgang, Halary, Sebastien, Hartkopf, Felix, Hastings, Jaden J.A., Hawkins-Zafarnia, Arya, Hazrin-Chong, Nur Hazlin, Helfrich, Eric, Hell, Eva, Henry, Tamera, Hernandez, Samuel, Hernandez, Pilar Lopez, Hess-Homeier, David, Hittle, Lauren E., Hoan, Nghiem Xuan, Holik, Aliaksei, Homma, Chiaki, Hoxie, Irene, Huber, Michael, Humphries, Elizabeth, Hyland, Stephanie, Hässig, Andrea, Häusler, Roland, Hüsser, Nathalie, Petit, Robert A., III, Iderzorig, Badamnyambuu, Igarashi, Mizuki, Iqbal, Shaikh B., Ishikawa, Shino, Ishizuka, Sakura, Islam, Sharah, Islam, Riham, Ito, Kohei, Ito, Sota, Ito, Takayuki, Ivankovic, Tomislav, Iwashiro, Tomoki, Jackson, Sarah, Jacobs, JoAnn, James, Marisano, Jaubert, Marianne, Jerier, Marie-Laure, Jiminez, Esmeralda, Jinfessa, Ayantu, De Jong, Ymke, Joo, Hyun Woo, Jospin, Guilllaume, Kajita, Takema, Ahmad Kassim, Affifah Saadah, Kato, Nao, Kaur, Amrit, Kaur, Inderjit, de Souza Gomes Kehdy, Fernanda, Khadka, Vedbar S., Khan, Shaira, Khavari, Mahshid, Ki, Michelle, Kim, Gina, Kim, Hyung Jun, Kim, Sangwan, King, Ryan J., Knights, Kaymisha, KoLoMonaco, Giuseppe, Koag, Ellen, Kobko-Litskevitch, Nadezhda, Korshevniuk, Maryna, Kozhar, Michael, Krebs, Jonas, Kubota, Nanami, Kuklin, Andrii, Kumar, Sheelta S., Kwong, Rachel, Kwong, Lawrence, Lafontaine, Ingrid, Lago, Juliana, Lai, Tsoi Ying, Laine, Elodie, Laiola, Manolo, Lakhneko, Olha, Lamba, Isha, de Lamotte, Gerardo, Lannes, Romain, De Lazzari, Eleonora, Leahy, Madeline, Lee, Hyunjung, Lee, Yunmi, Lee, Lucy, Lemaire, Vincent, Leong, Emily, Leung, Marcus H.Y., Lewandowska, Dagmara, Li, Chenhao, Liang, Weijun, Lin, Moses, Lisboa, Priscilla, Litskevitch, Anna, Liu, Eric Minwei, Liu, Tracy, Livia, Mayra Arauco, Lo, Yui Him, Losim, Sonia, Loubens, Manon, Lu, Jennifer, Lykhenko, Olexandr, Lysakova, Simona, Mahmoud, Salah, Majid, Sara Abdul, Makogon, Natalka, Maldonado, Denisse, Mallari, Krizzy, Malta, Tathiane M., Mamun, Maliha, Manoir, Dimitri, Marchandon, German, Marciniak, Natalia, Marinovic, Sonia, Marques, Brunna, Mathews, Nicole, Matsuzaki, Yuri, Matthys, Vincent, May, Madelyn, McComb, Elias, Meagher, Annabelle, Melamed, Adiell, Menary, Wayne, Mendez, Katterinne N., Mendez, Ambar, Mendy, Irène Mauricette, Meng, Irene, Menon, Ajay, Menor, Mark, Meoded, Roy, Merino, Nancy, Meydan, Cem, Miah, Karishma, Mignotte, Mathilde, Miketic, Tanja, Miranda, Wilson, Mitsios, Athena, Miura, Ryusei, Miyake, Kunihiko, Moccia, Maria D., Mohan, Natasha, Mohsin, Mohammed, Moitra, Karobi, Moldes, Mauricio, Molina, Laura, Molinet, Jennifer, Molomjamts, Orgil-Erdene, Moniruzzaman, Eftar, Moon, Sookwon, de Oliveira Moraes, Isabelle, Moreno, Mario, Mosella, Maritza S., Moser, Josef W., Mozsary, Christopher, Muehlbauer, Amanda L., Muner, Oasima, Munia, Muntaha, Munim, Naimah, Muscat, Maureen, Mustac, Tatjana, Muñoz, Cristina, Nadalin, Francesca, Naeem, Areeg, Nagy-Szakal, Dorottya, Nakagawa, Mayuko, Narce, Ashanti, Nasu, Masaki, Navarrete, Irene González, Naveed, Hiba, Nazario, Bryan, Nedunuri, Narasimha Rao, Neff, Thomas, Nesimi, Aida, Ng, Wan Chiew, Ng, Synti, Nguyen, Gloria, Ngwa, Elsy, Nicolas, Agier, Nicolas, Pierre, Nika, Abdollahi, Noorzi, Hosna, Nosrati, Avigdor, Noushmehr, Houtan, Nunes, Diana N., O’Brien, Kathryn, O’Hara, Niamh B., Oken, Gabriella, Olawoyin, Rantimi A., Oliete, Javier Quilez, Olmeda, Kiara, Oluwadare, Tolulope, Oluwadare, Itunu A., Ordioni, Nils, Orpilla, Jenessa, Orrego, Jacqueline, Ortega, Melissa, Osma, Princess, Osuolale, Israel O., Osuolale, Oluwatosin M., Ota, Mitsuki, Oteri, Francesco, Oto, Yuya, Ounit, Rachid, Ouzounis, Christos A., Pakrashi, Subhamitra, Paras, Rachel, Pardo-Este, Coral, Park, Young-Ja, Pastuszek, Paulina, Patel, Suraj, Pathmanathan, Jananan, Patrignani, Andrea, Perez, Manuel, Peros, Ante, Persaud, Sabrina, Peters, Anisia, Phillips, Adam, Pineda, Lisbeth, Pizzi, Melissa P., Plaku, Alma, Plaku, Alketa, Pompa-Hogan, Brianna, Portilla, María Gabriela, Posada, Leonardo, Priestman, Max, Prithiviraj, Bharath, Priya, Sambhawa, Pugdeethosal, Phanthira, Pugh, Catherine E., Pulatov, Benjamin, Pupiec, Angelika, Pyrshev, Kyrylo, Qing, Tao, Rahiel, Saher, Rahmatulloev, Savlatjon, Rajendran, Kannan, Ramcharan, Aneisa, Ramirez-Rojas, Adan, Rana, Shahryar, Ratnanandan, Prashanthi, Read, Timothy D., Rehrauer, Hubert, Richer, Renee, Rivera, Alexis, Rivera, Michelle, Robertiello, Alessandro, Robinson, Courtney, Rodríguez, Paula, Rojas, Nayra Aguilar, Roldán, Paul, Rosario, Anyelic, Roth, Sandra, Ruiz, Maria, Boja Ruiz, Stephen Eduard, Russell, Kaitlan, Rybak, Mariia, Sabedot, Thais S., Sabina, Mahfuza, Saito, Ikuto, Saito, Yoshitaka, Malca Salas, Gustavo Adolfo, Salazar, Cecilia, San, Kaung Myat, Sanchez, Jorge, Sanchir, Khaliun, Sankar, Ryan, de Souza Santos, Paulo Thiago, Saravi, Zulena, Sasaki, Kai, Sato, Yuma, Sato, Masaki, Sato, Seisuke, Sato, Ryo, Sato, Kaisei, Sayara, Nowshin, Schaaf, Steffen, Schacher, Oli, Schinke, Anna-Lena M., Schlapbach, Ralph, Schori, Christian, Schriml, Jason R., Segato, Felipe, Sepulveda, Felipe, Serpa, Marianna S., De Sessions, Paola F., Severyn, Juan C., Shaaban, Heba, Shakil, Maheen, Shalaby, Sarah, Shari, Aliyah, Shim, Hyenah, Shirahata, Hikaru, Shiwa, Yuh, Siam, Rania, Da Silva, Ophélie, Silva, Jordana M., Simon, Gwenola, Singh, Shaleni K., Sluzek, Kasia, Smith, Rebecca, So, Eunice, Andreu Somavilla, Núria, Sonohara, Yuya, Rufino de Sousa, Nuno, Souza, Camila, Sperry, Jason, Sprinsky, Nicolas, Stark, Stefan G., La Storia, Antonietta, Suganuma, Kiyoshi, Suliman, Hamood, Sullivan, Jill, Supie, Arif Asyraf Md, Suzuki, Chisato, Takagi, Sora, Takahara, Fumie, Takahashi, Naoya, Takahashi, Kou, Takeda, Tomoki, Takenaka, Isabella K., Tanaka, Soma, Tang, Anyi, Man Tang, Yuk, Tarcitano, Emilio, Tassinari, Andrea, Taye, Mahdi, Terrero, Alexis, Thambiraja, Eunice, Thiébaut, Antonin, Thomas, Sade, Thomas, Andrew M., Togashi, Yuto, Togashi, Takumi, Tomaselli, Anna, Tomita, Masaru, Tomita, Itsuki, Tong, Xinzhao, Toth, Oliver, Toussaint, Nora C., Tran, Jennifer M., Truong, Catalina, Tsonev, Stefan I., Tsuda, Kazutoshi, Tsurumaki, Takafumi, Tuz, Michelle, Tymoshenko, Yelyzaveta, Urgiles, Carmen, Usui, Mariko, Vacant, Sophie, Valentine, Brandon, Vann, Laura E., Velter, Fabienne, Ventorino, Valeria, Vera-Wolf, Patricia, Vicedomini, Riccardo, Suarez-Villamil, Michael A., Vincent, Sierra, Vivancos-Koopman, Renee, Wan, Andrew, Wang, Cindy, Warashina, Tomoro, Watanabe, Ayuki, Weekes, Samuel, Werner, Johannes, Westfall, David, Wieler, Lothar H., Williams, Michelle, Wolf, Silver A., Wong, Brian, Wong, Yan Ling, Wong, Tyler, Wright, Rasheena, Wunderlin, Tina, Yamanaka, Ryota, Yang, Jingcheng, Yano, Hirokazu, Yeh, George C., Yemets, Olena, Yeskova, Tetiana, Yoshikawa, Shusei, Zafar, Laraib, Zhang, Yang, Zhang, Shu, Zhang, Amy, Zheng, Yuanting, Zubenko, Stas, Danko, David, Bezdan, Daniela, Afshin, Evan E., Ahsanuddin, Sofia, Bhattacharya, Chandrima, Butler, Daniel J., Chng, Kern Rei, Donnellan, Daisy, Hecht, Jochen, Jackson, Katelyn, Kuchin, Katerina, Karasikov, Mikhail, Lyons, Abigail, Mak, Lauren, Meleshko, Dmitry, Mustafa, Harun, Mutai, Beth, Neches, Russell Y., Ng, Amanda, Nikolayeva, Olga, Nikolayeva, Tatyana, Png, Eileen, Ryon, Krista A., Sanchez, Jorge L., Sierra, Maria A., Thomas, Dominique, Young, Ben, Abudayyeh, Omar O., Alicea, Josue, Bhattacharyya, Malay, Blekhman, Ran, Castro-Nallar, Eduardo, Cañas, Ana M., Chatziefthimiou, Aspassia D., Crawford, Robert W., De Filippis, Francesca, Deng, Youping, Desnues, Christelle, Dias-Neto, Emmanuel, Dybwad, Marius, Elhaik, Eran, Ercolini, Danilo, Frolova, Alina, Gankin, Dennis, Gootenberg, Jonathan S., Graf, Alexandra B., Green, David C., Hajirasouliha, Iman, Hernandez, Mark, Iraola, Gregorio, Jang, Soojin, Kahles, Andre, Kelly, Frank J., Kyrpides, Nikos C., Łabaj, Paweł P., Lee, Patrick K.H., Ljungdahl, Per O., Mason-Buck, Gabriella, McGrath, Ken, Mongodin, Emmanuel F., Moraes, Milton Ozorio, Nagarajan, Niranjan, Nieto-Caballero, Marina, Oliveira, Manuela, Ossowski, Stephan, Osuolale, Olayinka O., Özcan, Orhan, Paez-Espino, David, Rascovan, Nicolás, Richard, Hugues, Rätsch, Gunnar, Schriml, Lynn M., Semmler, Torsten, Sezerman, Osman U., Shi, Leming, Shi, Tieliu, Song, Le Huu, Suzuki, Haruo, Court, Denise Syndercombe, Tighe, Scott W., Udekwu, Klas I., Ugalde, Juan A., Vassilev, Dimitar I., Vayndorf, Elena M., Velavan, Thirumalaisamy P., Wu, Jun, Zambrano, María M., Zhu, Jifeng, Zhu, Sibo, and Mason, Christopher E.

Published
2021
Full Text
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7. A global metagenomic map of urban microbiomes and antimicrobial resistance

Author

Danko, David, primary, Bezdan, Daniela, additional, Afshin, Evan E., additional, Ahsanuddin, Sofia, additional, Bhattacharya, Chandrima, additional, Butler, Daniel J., additional, Chng, Kern Rei, additional, Donnellan, Daisy, additional, Hecht, Jochen, additional, Jackson, Katelyn, additional, Kuchin, Katerina, additional, Karasikov, Mikhail, additional, Lyons, Abigail, additional, Mak, Lauren, additional, Meleshko, Dmitry, additional, Mustafa, Harun, additional, Mutai, Beth, additional, Neches, Russell Y., additional, Ng, Amanda, additional, Nikolayeva, Olga, additional, Nikolayeva, Tatyana, additional, Png, Eileen, additional, Ryon, Krista A., additional, Sanchez, Jorge L., additional, Shaaban, Heba, additional, Sierra, Maria A., additional, Thomas, Dominique, additional, Young, Ben, additional, Abudayyeh, Omar O., additional, Alicea, Josue, additional, Bhattacharyya, Malay, additional, Blekhman, Ran, additional, Castro-Nallar, Eduardo, additional, Cañas, Ana M., additional, Chatziefthimiou, Aspassia D., additional, Crawford, Robert W., additional, De Filippis, Francesca, additional, Deng, Youping, additional, Desnues, Christelle, additional, Dias-Neto, Emmanuel, additional, Dybwad, Marius, additional, Elhaik, Eran, additional, Ercolini, Danilo, additional, Frolova, Alina, additional, Gankin, Dennis, additional, Gootenberg, Jonathan S., additional, Graf, Alexandra B., additional, Green, David C., additional, Hajirasouliha, Iman, additional, Hastings, Jaden J.A., additional, Hernandez, Mark, additional, Iraola, Gregorio, additional, Jang, Soojin, additional, Kahles, Andre, additional, Kelly, Frank J., additional, Knights, Kaymisha, additional, Kyrpides, Nikos C., additional, Łabaj, Paweł P., additional, Lee, Patrick K.H., additional, Leung, Marcus H.Y., additional, Ljungdahl, Per O., additional, Mason-Buck, Gabriella, additional, McGrath, Ken, additional, Meydan, Cem, additional, Mongodin, Emmanuel F., additional, Moraes, Milton Ozorio, additional, Nagarajan, Niranjan, additional, Nieto-Caballero, Marina, additional, Noushmehr, Houtan, additional, Oliveira, Manuela, additional, Ossowski, Stephan, additional, Osuolale, Olayinka O., additional, Özcan, Orhan, additional, Paez-Espino, David, additional, Rascovan, Nicolás, additional, Richard, Hugues, additional, Rätsch, Gunnar, additional, Schriml, Lynn M., additional, Semmler, Torsten, additional, Sezerman, Osman U., additional, Shi, Leming, additional, Shi, Tieliu, additional, Siam, Rania, additional, Song, Le Huu, additional, Suzuki, Haruo, additional, Court, Denise Syndercombe, additional, Tighe, Scott W., additional, Tong, Xinzhao, additional, Udekwu, Klas I., additional, Ugalde, Juan A., additional, Valentine, Brandon, additional, Vassilev, Dimitar I., additional, Vayndorf, Elena M., additional, Velavan, Thirumalaisamy P., additional, Wu, Jun, additional, Zambrano, María M., additional, Zhu, Jifeng, additional, Zhu, Sibo, additional, Mason, Christopher E., additional, Abdullah, Natasha, additional, Abraao, Marcos, additional, Adel, Ait-hamlat, additional, Afaq, Muhammad, additional, Al-Quaddoomi, Faisal S., additional, Alam, Ireen, additional, Albuquerque, Gabriela E., additional, Alexiev, Alex, additional, Ali, Kalyn, additional, Alvarado-Arnez, Lucia E., additional, Aly, Sarh, additional, Amachee, Jennifer, additional, Amorim, Maria G., additional, Ampadu, Majelia, additional, Amran, Muhammad Al-Fath, additional, An, Nala, additional, Andrew, Watson, additional, Andrianjakarivony, Harilanto, additional, Angelov, Michael, additional, Antelo, Verónica, additional, Aquino, Catharine, additional, Aranguren, Álvaro, additional, Araujo, Luiza F., additional, Vasquez Arevalo, Hitler Francois, additional, Arevalo, Jenny, additional, Arnan, Carme, additional, Alvarado Arnez, Lucia Elena, additional, Arredondo, Fernanda, additional, Arthur, Matthew, additional, Asenjo, Freddy, additional, Aung, Thomas Saw, additional, Auvinet, Juliette, additional, Aventin, Nuria, additional, Ayaz, Sadaf, additional, Baburyan, Silva, additional, Bakere, Abd-Manaaf, additional, Bakhl, Katrin, additional, Bartelli, Thais F., additional, Batdelger, Erdenetsetseg, additional, Baudon, François, additional, Becher, Kevin, additional, Bello, Carla, additional, Benchouaia, Médine, additional, Benisty, Hannah, additional, Benoiston, Anne-Sophie, additional, Benson, Joseph, additional, Benítez, Diego, additional, Bernardes, Juliana, additional, Bertrand, Denis, additional, Beurmann, Silvia, additional, Bitard-Feildel, Tristan, additional, Bittner, Lucie, additional, Black, Christina, additional, Blanc, Guillaume, additional, Blyther, Brittany, additional, Bode, Toni, additional, Boeri, Julia, additional, Boldgiv, Bazartseren, additional, Bolzli, Kevin, additional, Bordigoni, Alexia, additional, Borrelli, Ciro, additional, Bouchard, Sonia, additional, Bouly, Jean-Pierre, additional, Boyd, Alicia, additional, Branco, Gabriela P., additional, Breschi, Alessandra, additional, Brindefalk, Björn, additional, Brion, Christian, additional, Briones, Alan, additional, Buczansla, Paulina, additional, Burke, Catherine M., additional, Burrell, Aszia, additional, Butova, Alina, additional, Buttar, Irvind, additional, Bynoe, Jalia, additional, Bönigk, Sven, additional, Bøifot, Kari O., additional, Caballero, Hiram, additional, Cai, Xiao Wen, additional, Calderon, Dayana, additional, Cantillo, Angela, additional, Carbajo, Miguel, additional, Carbone, Alessandra, additional, Cardenas, Anais, additional, Carrillo, Katerine, additional, Casalot, Laurie, additional, Castro, Sofia, additional, Castro, Ana V., additional, Castro, Astred, additional, Castro, Ana Valeria B., additional, Cawthorne, Simone, additional, Cedillo, Jonathan, additional, Chaker, Salama, additional, Chalangal, Jasna, additional, Chan, Allison, additional, Chasapi, Anastasia I., additional, Chatziefthimiou, Starr, additional, Chaudhuri, Sreya Ray, additional, Chavan, Akash Keluth, additional, Chavez, Francisco, additional, Chem, Gregory, additional, Chen, Xiaoqing, additional, Chen, Michelle, additional, Chen, Jenn-Wei, additional, Chernomoretz, Ariel, additional, Chettouh, Allaeddine, additional, Cheung, Daisy, additional, Chicas, Diana, additional, Chiu, Shirley, additional, Choudhry, Hira, additional, Chrispin, Carl, additional, Ciaramella, Kianna, additional, Cifuentes, Erika, additional, Cohen, Jake, additional, Coil, David A., additional, Collin, Sylvie, additional, Conger, Colleen, additional, Conte, Romain, additional, Corsi, Flavia, additional, Cossio, Cecilia N., additional, Costa, Ana F., additional, Cuebas, Delisia, additional, D’Alessandro, Bruno, additional, Dahlhausen, Katherine E., additional, Darling, Aaron E., additional, Das, Pujita, additional, Davenport, Lucinda B., additional, David, Laurent, additional, Davidson, Natalie R., additional, Dayama, Gargi, additional, Delmas, Stéphane, additional, Deng, Chris K., additional, Dequeker, Chloé, additional, Desert, Alexandre, additional, Devi, Monika, additional, Dezem, Felipe S., additional, Dias, Clara N., additional, Donahoe, Timothy Ryan, additional, Dorado, Sonia, additional, Dorsey, LaShonda, additional, Dotsenko, Valeriia, additional, Du, Steven, additional, Dutan, Alexandra, additional, Eady, Naya, additional, Eisen, Jonathan A., additional, Elaskandrany, Miar, additional, Epping, Lennard, additional, Escalera-Antezana, Juan P., additional, Ettinger, Cassie L., additional, Faiz, Iqra, additional, Fan, Luice, additional, Farhat, Nadine, additional, Faure, Emile, additional, Fauzi, Fazlina, additional, Feigin, Charlie, additional, Felice, Skye, additional, Ferreira, Laís Pereira, additional, Figueroa, Gabriel, additional, Fleiss, Aubin, additional, Flores, Denisse, additional, Velasco Flores, Jhovana L., additional, Fonseca, Marcos A.S., additional, Foox, Jonathan, additional, Forero, Juan Carlos, additional, Francis, Aaishah, additional, French, Kelly, additional, Fresia, Pablo, additional, Friedman, Jacob, additional, Fuentes, Jaime J., additional, Galipon, Josephine, additional, Garcia, Mathilde, additional, Garcia, Laura, additional, García, Catalina, additional, Geiger, Annie, additional, Gerner, Samuel M., additional, Ghose, Sonia L., additional, Giang, Dao Phuong, additional, Giménez, Matías, additional, Giovannelli, Donato, additional, Githae, Dedan, additional, Gkotzis, Spyridon, additional, Godoy, Liliana, additional, Goldman, Samantha, additional, Gonnet, Gaston H., additional, Gonzalez, Juana, additional, Gonzalez, Andrea, additional, Gonzalez-Poblete, Camila, additional, Gray, Andrew, additional, Gregory, Tranette, additional, Greselle, Charlotte, additional, Guasco, Sophie, additional, Guerra, Juan, additional, Gurianova, Nika, additional, Haehr, Wolfgang, additional, Halary, Sebastien, additional, Hartkopf, Felix, additional, Hawkins-Zafarnia, Arya, additional, Hazrin-Chong, Nur Hazlin, additional, Helfrich, Eric, additional, Hell, Eva, additional, Henry, Tamera, additional, Hernandez, Samuel, additional, Hernandez, Pilar Lopez, additional, Hess-Homeier, David, additional, Hittle, Lauren E., additional, Hoan, Nghiem Xuan, additional, Holik, Aliaksei, additional, Homma, Chiaki, additional, Hoxie, Irene, additional, Huber, Michael, additional, Humphries, Elizabeth, additional, Hyland, Stephanie, additional, Hässig, Andrea, additional, Häusler, Roland, additional, Hüsser, Nathalie, additional, Petit, Robert A., additional, Iderzorig, Badamnyambuu, additional, Igarashi, Mizuki, additional, Iqbal, Shaikh B., additional, Ishikawa, Shino, additional, Ishizuka, Sakura, additional, Islam, Sharah, additional, Islam, Riham, additional, Ito, Kohei, additional, Ito, Sota, additional, Ito, Takayuki, additional, Ivankovic, Tomislav, additional, Iwashiro, Tomoki, additional, Jackson, Sarah, additional, Jacobs, JoAnn, additional, James, Marisano, additional, Jaubert, Marianne, additional, Jerier, Marie-Laure, additional, Jiminez, Esmeralda, additional, Jinfessa, Ayantu, additional, De Jong, Ymke, additional, Joo, Hyun Woo, additional, Jospin, Guilllaume, additional, Kajita, Takema, additional, Ahmad Kassim, Affifah Saadah, additional, Kato, Nao, additional, Kaur, Amrit, additional, Kaur, Inderjit, additional, de Souza Gomes Kehdy, Fernanda, additional, Khadka, Vedbar S., additional, Khan, Shaira, additional, Khavari, Mahshid, additional, Ki, Michelle, additional, Kim, Gina, additional, Kim, Hyung Jun, additional, Kim, Sangwan, additional, King, Ryan J., additional, KoLoMonaco, Giuseppe, additional, Koag, Ellen, additional, Kobko-Litskevitch, Nadezhda, additional, Korshevniuk, Maryna, additional, Kozhar, Michael, additional, Krebs, Jonas, additional, Kubota, Nanami, additional, Kuklin, Andrii, additional, Kumar, Sheelta S., additional, Kwong, Rachel, additional, Kwong, Lawrence, additional, Lafontaine, Ingrid, additional, Lago, Juliana, additional, Lai, Tsoi Ying, additional, Laine, Elodie, additional, Laiola, Manolo, additional, Lakhneko, Olha, additional, Lamba, Isha, additional, de Lamotte, Gerardo, additional, Lannes, Romain, additional, De Lazzari, Eleonora, additional, Leahy, Madeline, additional, Lee, Hyunjung, additional, Lee, Yunmi, additional, Lee, Lucy, additional, Lemaire, Vincent, additional, Leong, Emily, additional, Lewandowska, Dagmara, additional, Li, Chenhao, additional, Liang, Weijun, additional, Lin, Moses, additional, Lisboa, Priscilla, additional, Litskevitch, Anna, additional, Liu, Eric Minwei, additional, Liu, Tracy, additional, Livia, Mayra Arauco, additional, Lo, Yui Him, additional, Losim, Sonia, additional, Loubens, Manon, additional, Lu, Jennifer, additional, Lykhenko, Olexandr, additional, Lysakova, Simona, additional, Mahmoud, Salah, additional, Majid, Sara Abdul, additional, Makogon, Natalka, additional, Maldonado, Denisse, additional, Mallari, Krizzy, additional, Malta, Tathiane M., additional, Mamun, Maliha, additional, Manoir, Dimitri, additional, Marchandon, German, additional, Marciniak, Natalia, additional, Marinovic, Sonia, additional, Marques, Brunna, additional, Mathews, Nicole, additional, Matsuzaki, Yuri, additional, Matthys, Vincent, additional, May, Madelyn, additional, McComb, Elias, additional, Meagher, Annabelle, additional, Melamed, Adiell, additional, Menary, Wayne, additional, Mendez, Katterinne N., additional, Mendez, Ambar, additional, Mendy, Irène Mauricette, additional, Meng, Irene, additional, Menon, Ajay, additional, Menor, Mark, additional, Meoded, Roy, additional, Merino, Nancy, additional, Miah, Karishma, additional, Mignotte, Mathilde, additional, Miketic, Tanja, additional, Miranda, Wilson, additional, Mitsios, Athena, additional, Miura, Ryusei, additional, Miyake, Kunihiko, additional, Moccia, Maria D., additional, Mohan, Natasha, additional, Mohsin, Mohammed, additional, Moitra, Karobi, additional, Moldes, Mauricio, additional, Molina, Laura, additional, Molinet, Jennifer, additional, Molomjamts, Orgil-Erdene, additional, Moniruzzaman, Eftar, additional, Moon, Sookwon, additional, de Oliveira Moraes, Isabelle, additional, Moreno, Mario, additional, Mosella, Maritza S., additional, Moser, Josef W., additional, Mozsary, Christopher, additional, Muehlbauer, Amanda L., additional, Muner, Oasima, additional, Munia, Muntaha, additional, Munim, Naimah, additional, Muscat, Maureen, additional, Mustac, Tatjana, additional, Muñoz, Cristina, additional, Nadalin, Francesca, additional, Naeem, Areeg, additional, Nagy-Szakal, Dorottya, additional, Nakagawa, Mayuko, additional, Narce, Ashanti, additional, Nasu, Masaki, additional, Navarrete, Irene González, additional, Naveed, Hiba, additional, Nazario, Bryan, additional, Nedunuri, Narasimha Rao, additional, Neff, Thomas, additional, Nesimi, Aida, additional, Ng, Wan Chiew, additional, Ng, Synti, additional, Nguyen, Gloria, additional, Ngwa, Elsy, additional, Nicolas, Agier, additional, Nicolas, Pierre, additional, Nika, Abdollahi, additional, Noorzi, Hosna, additional, Nosrati, Avigdor, additional, Nunes, Diana N., additional, O’Brien, Kathryn, additional, O’Hara, Niamh B., additional, Oken, Gabriella, additional, Olawoyin, Rantimi A., additional, Oliete, Javier Quilez, additional, Olmeda, Kiara, additional, Oluwadare, Tolulope, additional, Oluwadare, Itunu A., additional, Ordioni, Nils, additional, Orpilla, Jenessa, additional, Orrego, Jacqueline, additional, Ortega, Melissa, additional, Osma, Princess, additional, Osuolale, Israel O., additional, Osuolale, Oluwatosin M., additional, Ota, Mitsuki, additional, Oteri, Francesco, additional, Oto, Yuya, additional, Ounit, Rachid, additional, Ouzounis, Christos A., additional, Pakrashi, Subhamitra, additional, Paras, Rachel, additional, Pardo-Este, Coral, additional, Park, Young-Ja, additional, Pastuszek, Paulina, additional, Patel, Suraj, additional, Pathmanathan, Jananan, additional, Patrignani, Andrea, additional, Perez, Manuel, additional, Peros, Ante, additional, Persaud, Sabrina, additional, Peters, Anisia, additional, Phillips, Adam, additional, Pineda, Lisbeth, additional, Pizzi, Melissa P., additional, Plaku, Alma, additional, Plaku, Alketa, additional, Pompa-Hogan, Brianna, additional, Portilla, María Gabriela, additional, Posada, Leonardo, additional, Priestman, Max, additional, Prithiviraj, Bharath, additional, Priya, Sambhawa, additional, Pugdeethosal, Phanthira, additional, Pugh, Catherine E., additional, Pulatov, Benjamin, additional, Pupiec, Angelika, additional, Pyrshev, Kyrylo, additional, Qing, Tao, additional, Rahiel, Saher, additional, Rahmatulloev, Savlatjon, additional, Rajendran, Kannan, additional, Ramcharan, Aneisa, additional, Ramirez-Rojas, Adan, additional, Rana, Shahryar, additional, Ratnanandan, Prashanthi, additional, Read, Timothy D., additional, Rehrauer, Hubert, additional, Richer, Renee, additional, Rivera, Alexis, additional, Rivera, Michelle, additional, Robertiello, Alessandro, additional, Robinson, Courtney, additional, Rodríguez, Paula, additional, Rojas, Nayra Aguilar, additional, Roldán, Paul, additional, Rosario, Anyelic, additional, Roth, Sandra, additional, Ruiz, Maria, additional, Boja Ruiz, Stephen Eduard, additional, Russell, Kaitlan, additional, Rybak, Mariia, additional, Sabedot, Thais S., additional, Sabina, Mahfuza, additional, Saito, Ikuto, additional, Saito, Yoshitaka, additional, Malca Salas, Gustavo Adolfo, additional, Salazar, Cecilia, additional, San, Kaung Myat, additional, Sanchez, Jorge, additional, Sanchir, Khaliun, additional, Sankar, Ryan, additional, de Souza Santos, Paulo Thiago, additional, Saravi, Zulena, additional, Sasaki, Kai, additional, Sato, Yuma, additional, Sato, Masaki, additional, Sato, Seisuke, additional, Sato, Ryo, additional, Sato, Kaisei, additional, Sayara, Nowshin, additional, Schaaf, Steffen, additional, Schacher, Oli, additional, Schinke, Anna-Lena M., additional, Schlapbach, Ralph, additional, Schori, Christian, additional, Schriml, Jason R., additional, Segato, Felipe, additional, Sepulveda, Felipe, additional, Serpa, Marianna S., additional, De Sessions, Paola F., additional, Severyn, Juan C., additional, Shakil, Maheen, additional, Shalaby, Sarah, additional, Shari, Aliyah, additional, Shim, Hyenah, additional, Shirahata, Hikaru, additional, Shiwa, Yuh, additional, Da Silva, Ophélie, additional, Silva, Jordana M., additional, Simon, Gwenola, additional, Singh, Shaleni K., additional, Sluzek, Kasia, additional, Smith, Rebecca, additional, So, Eunice, additional, Andreu Somavilla, Núria, additional, Sonohara, Yuya, additional, Rufino de Sousa, Nuno, additional, Souza, Camila, additional, Sperry, Jason, additional, Sprinsky, Nicolas, additional, Stark, Stefan G., additional, La Storia, Antonietta, additional, Suganuma, Kiyoshi, additional, Suliman, Hamood, additional, Sullivan, Jill, additional, Supie, Arif Asyraf Md, additional, Suzuki, Chisato, additional, Takagi, Sora, additional, Takahara, Fumie, additional, Takahashi, Naoya, additional, Takahashi, Kou, additional, Takeda, Tomoki, additional, Takenaka, Isabella K., additional, Tanaka, Soma, additional, Tang, Anyi, additional, Man Tang, Yuk, additional, Tarcitano, Emilio, additional, Tassinari, Andrea, additional, Taye, Mahdi, additional, Terrero, Alexis, additional, Thambiraja, Eunice, additional, Thiébaut, Antonin, additional, Thomas, Sade, additional, Thomas, Andrew M., additional, Togashi, Yuto, additional, Togashi, Takumi, additional, Tomaselli, Anna, additional, Tomita, Masaru, additional, Tomita, Itsuki, additional, Toth, Oliver, additional, Toussaint, Nora C., additional, Tran, Jennifer M., additional, Truong, Catalina, additional, Tsonev, Stefan I., additional, Tsuda, Kazutoshi, additional, Tsurumaki, Takafumi, additional, Tuz, Michelle, additional, Tymoshenko, Yelyzaveta, additional, Urgiles, Carmen, additional, Usui, Mariko, additional, Vacant, Sophie, additional, Vann, Laura E., additional, Velter, Fabienne, additional, Ventorino, Valeria, additional, Vera-Wolf, Patricia, additional, Vicedomini, Riccardo, additional, Suarez-Villamil, Michael A., additional, Vincent, Sierra, additional, Vivancos-Koopman, Renee, additional, Wan, Andrew, additional, Wang, Cindy, additional, Warashina, Tomoro, additional, Watanabe, Ayuki, additional, Weekes, Samuel, additional, Werner, Johannes, additional, Westfall, David, additional, Wieler, Lothar H., additional, Williams, Michelle, additional, Wolf, Silver A., additional, Wong, Brian, additional, Wong, Yan Ling, additional, Wong, Tyler, additional, Wright, Rasheena, additional, Wunderlin, Tina, additional, Yamanaka, Ryota, additional, Yang, Jingcheng, additional, Yano, Hirokazu, additional, Yeh, George C., additional, Yemets, Olena, additional, Yeskova, Tetiana, additional, Yoshikawa, Shusei, additional, Zafar, Laraib, additional, Zhang, Yang, additional, Zhang, Shu, additional, Zhang, Amy, additional, Zheng, Yuanting, additional, and Zubenko, Stas, additional

Published
2021
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8. An antimicrobial origin of targeting peptides to endosymbiotic organelles

Author

Garrido, Clotilde, Caspari, Oliver D., Choquet, Yves, Wollman, Francis-André, and Lafontaine, Ingrid

Abstract

Mitochondria and chloroplasts emerged from primary endosymbiosis. Most endosymbiont proteins have subsequently been expressed in the nucleo-cytosol of the host and organelle-targeted via the acquisition of N-terminal presequences, whose evolutionary origin remains enigmatic. Using a quantitative assessment of their physico-chemical properties, we show that organelle targeting peptides, which are distinct from signaling peptides targeting other subcellular compartments, group with a subset of antimicrobial peptides. We demonstrate that extant antimicrobial peptides target a fluorescent reporter to either the mitochondria or the chloroplast in the green alga Chlamydomonas reinhardtii and, conversely, that extant targeting peptides display antimicrobial activity. Thus, we provide conclusive computational and functional evidence for an evolutionary link between organelle-targeting and antimicrobial peptides. Our results support the view that resistance of bacterial progenitors of organelles to the attack of host antimicrobial peptides, has been instrumental in eukaryogenesis and in the subsequent emergence of photosynthetic eukaryotes.

Published
2020
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10. Genome evolution in yeasts

Author

Dujon, Bernard, Sherman, David, Fischer, Gilles, Durrens, Pascal, Casaregola, Serge, Lafontaine, Ingrid, de Montigny, Jacky, Marck, Christian, Neuveglise, Cecile, Talla, Emmanuel, Goffard, Nicolas, Frangeul, Lionel, Aigle, Michel, Anthouard, Veronique, Babour, Anna, Barbe, Valerie, Barnay, Stephanie, Blanchin, Sylvie, Beckerich, Jean-Marie, Beyne, Emmanuelle, Bleykasten, Claudine, Boisrame, Anita, Boyer, Jeanne, Cattolico, Laurence, Confanioleri, Fabrice, de Daruvar, Antoine, Despons, Laurence, Fabre, Emmanuelle, Fairhead, Cecile, Ferry-Dumazet, Helene, Groppi, Alexis, Hantraye, Florence, Hennequin, Christophe, Jauniaux, Nicolas, Joyet, Philippe, Kachouri, Rym, Kerrest, Alix, Koszul, Romain, Lemaire, Marc, Lesur, Isabelle, Ma, Laurence, Muller, Heloise, Nicaud, Jean-Marc, Nikolski, Macha, Oztas, Sophie, Ozier-Kalogeropoulos, Odile, Pellenz, Stefan, Potier, Serge, Richard, Guy-Franck, Straub, Marie-Laure, Suleau, Audrey, Swennen, Dominique, Tekaia, Fredj, Wesolowski-Louvel, Micheline, Westhof, Eric, Wirth, Benedicte, Zeniou-Meyer, Maria, Zivanovic, Ivan, Bolotin-Fukuhara, Monique, Thierry, Agnes, Bouchier, Christiane, Caudron, Bernard, Scarpelli, Claude, Gaillardin, Claude, Weissenbach, Jean, Wincker, Patrick, and Souciet, Jean-Luc

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

Author(s): Bernard Dujon (corresponding author) [1]; David Sherman [5, 6]; Gilles Fischer [1]; Pascal Durrens [6, 7]; Serge Casaregola [8]; Ingrid Lafontaine [1]; Jacky de Montigny [9]; Christian Marck [10]; [...]

Published
2004
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11. Evolutionary History of Peptidases Involved in the Processing of Organelle-Targeting Peptides.

Author

Garrido, Clotilde, Wollman, Francis-André, and Lafontaine, Ingrid

Subjects
PEPTIDASE, PEPTIDES, HORIZONTAL gene transfer, BACTERIAL transformation, MITOCHONDRIAL proteins, ENDOSYMBIOSIS
Abstract

Most of the proteins present in mitochondria and chloroplasts, the organelles acquired via endosymbiotic events, are encoded in the nucleus and translated into the cytosol. Most of such nuclear-encoded proteins are specifically recognized via an N-terminal-encoded targeting peptide (TP) and imported into the organelles via a translocon machinery. Once imported, the TP is degraded by a succession of cleavage steps ensured by dedicated peptidases. Here, we retrace the evolution of the families of the mitochondrial processing peptidase (MPP), stromal processing peptidase (SPP), presequence protease (PreP), and organellar oligo-peptidase (OOP) that play a central role in TP processing and degradation across the tree of life. Their bacterial distributions are widespread but patchy, revealing unsurprisingly complex history of lateral transfers among bacteria. We provide evidence for the eukaryotic acquisition of MPP, OOP, and PreP by lateral gene transfers from bacteria at the time of the mitochondrial endosymbiosis. We show that the acquisition of SPP and of a second copy of OOP and PreP at the time of the chloroplast endosymbiosis was followed by a differential loss of one PreP paralog in photosynthetic eukaryotes. We identified some contrasting sequence conservations between bacterial and eukaryotic homologs that could reflect differences in the functional context of their peptidase activity. The close vicinity of the eukaryotic peptidases MPP and OOP to those of several bacterial pathogens, showing antimicrobial resistance, supports a scenario where such bacteria were instrumental in the establishment of the proteolytic pathway for TP degradation in organelles. The evidence for their role in the acquisition of PreP is weaker, and none is observed for SPP, although it cannot be excluded by the present study. [ABSTRACT FROM AUTHOR]

Published
2022
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17. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

Author

Afshinnekoo, Ebrahim, Ahsanuddin, Sofia, Ghedin, Elodie, Read, Timothy, Fraser, Claire, Dudley, Joel, Bowler, Christopher, Mason, Christopher E., Chernomoretz, Ariel, Stolovitzky, Gustavo, Łabaj, Paweł P., Graf, Alexandra B., Darling, Aaron, Burke, Catherine, Noushmehr, Houtan, Dias-Neto, Emmanuel, Guo, Yongli, Xie, Zhi, Lee, Patrick K. H., Shi, Leming, Ruiz-Perez, Carlos A., Zambrano, Maria Mercedes, Siam, Rania, Ouf, Amged, Richard, Hugues, Lafontaine, Ingrid, Wieler, Lothar H., Semmler, Torsten, Prithiviraj, Bharath, Nedunuri, Narasimha, Mehr, Shaadi, Banihashemi, Kambiz, Lista, Florigio, Anselmo, Anna, Suzuki, Haruo, Kuroda, Makoto, Yamashita, Riu, Sato, Yukoto, Kaminuma, Eli, Aranda, Celia M. Alpuche, Martinez, Jesus, Dada, Christopher, Dybwad, Marius, Oliveira, Manuela, Schuster, Stephan, Siwo, Geoffrey H., Jang, Soojin, Seo, Sung Chul, Hwang, Sung Ho, Ossowski, Stephan, Bezdan, Daniela, Chaker, Salama, Chatziefthimiou, Aspassia D., Udekwu, Klas, Liungdahl, Per, Sezerman, Ugur, Meydan, Cem, Elhaik, Eran, Gonnet, Gaston, Schriml, Lynn M., Mongodin, Emmanuel, Huttenhower, Curtis, Gilbert, Jack, Eisen, Jonathan, Hirschberg, David, Hernandez, Mark, McGrath, Ken, McGrath, Leanne, Gray, Andrew, Osuolale, Olayinka, Segata, Nicola, Fillo, Silvia, Iraola, Gregorio, Zhou, Yiming, Chang, Yujun, Li, Yang, Zhend, Yuanting, Hou, Wanwan, Ramirez, Adan, Cepeda, Martha, Desnues, Christelle, Rascovan, Nicolas, Baron, Colin, Nagarajan, Niranjan, Ercolini, Danilo, Menary, Wayne, Tighe, Scott, Donia, Mohamed, Levy, Shawn, Benito, Joseph, Jones, Angela, Kasarskis, Andrew, Maritz, Julia, Jorgensen, Ellen, Neches, Russell, Livelli, Tom, Barnetche, Jesus Martinez, Pasolli, Edoardo, Greenfield, Nick, Hasan, Nur, Brownstein, John, Nozick, Linda, Michels, Harold, Schriml, Lynn, Brownstein, Catherine, Garbarino, Jeanne, Lyons, Abby, Zhu, Jeff, Genome Center [UC Davis], University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), American University in Cairo, Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Robert Koch Institute [Berlin] (RKI), Centre for Infection Medicine, Institute of Microbiology and Epizootics, Health Corps Italian Army, Department of Molecular Biology, Immunology and Experimental Medicine, Army Medical and Veterinary Research Center, Integrative Biology Unit, Parco Tecnologico Padano, Department of Environmental Science and Engineering, Graduate School of Science and Engineering, Department of Population Medicine and Diagnostic Sciences, Cornell University [New York], Dynamique cellulaire et moléculaire de la muqueuse respiratoire, Université de Reims Champagne-Ardenne (URCA)-IFR53-Institut National de la Santé et de la Recherche Médicale (INSERM), Biostatistics Department, Harvard School of Public Health, Institute for genomic and systems biology, Argonne National Laboratory [Lemont] (ANL), Department of Ecology and Evolution [Chicago], University of Chicago, Alfred P. Sloan Foundation [2015-13964], National Institutes of Health [F31GM111053, R01NS076465, R25EB020393], Promega, CosmosID, Illumina, Copan, QIAGEN, University of California-University of California, Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Acibadem University Dspace, Afshinnekoo, Ebrahim, Ahsanuddin, Sofia, Ghedin, Elodie, Read, Timothy, Fraser, Claire, Dudley, Joel, Bowler, Christopher, Mason, Christopher E., Chernomoretz, Ariel, Stolovitzky, Gustavo, Łabaj, Paweł P., Graf, Alexandra B., Darling, Aaron, Burke, Catherine, Noushmehr, Houtan, Dias-Neto, Emmanuel, Guo, Yongli, Xie, Zhi, Lee, Patrick K. H., Shi, Leming, Ruiz-Perez, Carlos A., Zambrano, Maria Mercede, Siam, Rania, Ouf, Amged, Richard, Hugue, Lafontaine, Ingrid, Wieler, Lothar H., Semmler, Torsten, Prithiviraj, Bharath, Nedunuri, Narasimha, Mehr, Shaadi, Banihashemi, Kambiz, Lista, Florigio, Anselmo, Anna, Suzuki, Haruo, Kuroda, Makoto, Yamashita, Riu, Sato, Yukoto, Kaminuma, Eli, Aranda, Celia M. Alpuche, Martinez, Jesu, Dada, Christopher, Dybwad, Mariu, Oliveira, Manuela, Schuster, Stephan, Siwo, Geoffrey H., Jang, Soojin, Seo, Sung Chul, Hwang, Sung Ho, Ossowski, Stephan, Bezdan, Daniela, Chaker, Salama, Chatziefthimiou, Aspassia D., Udekwu, Kla, Liungdahl, Per, Sezerman, Ugur, Meydan, Cem, Elhaik, Eran, Gonnet, Gaston, Schriml, Lynn M., Mongodin, Emmanuel, Huttenhower, Curti, Gilbert, Jack, Eisen, Jonathan, Hirschberg, David, Hernandez, Mark, Mcgrath, Ken, Mcgrath, Leanne, Gray, Andrew, Osuolale, Olayinka, Segata, Nicola, Fillo, Silvia, Iraola, Gregorio, Zhou, Yiming, Chang, Yujun, Li, Yang, Zhend, Yuanting, Hou, Wanwan, Ramirez, Adan, Cepeda, Martha, Desnues, Christelle, Rascovan, Nicola, Baron, Colin, Nagarajan, Niranjan, Ercolini, Danilo, Menary, Wayne, Tighe, Scott, Donia, Mohamed, Levy, Shawn, Benito, Joseph, Jones, Angela, Kasarskis, Andrew, Maritz, Julia, Jorgensen, Ellen, Neches, Russell, Livelli, Tom, Barnetche, Jesus Martinez, Pasolli, Edoardo, Greenfield, Nick, Hasan, Nur, Brownstein, John, Nozick, Linda, Michels, Harold, Schriml, Lynn, Brownstein, Catherine, Garbarino, Jeanne, Lyons, Abby, and Zhu, Jeff

Subjects
0301 basic medicine, Microbiology (medical), Built environment, Antimicrobial resistance markers, [SDV]Life Sciences [q-bio], 030106 microbiology, BIOINFORMÁTICA, Biosynthetic gene cluster, Genomics, Biology, Meeting Report, Microbiology, Biosynthetic gene clusters, Microbiome, Next-generation sequencing, 12. Responsible consumption, Metagenomic, 03 medical and health sciences, Data visualization, Urban planning, Databases, Genetic, 11. Sustainability, City Planning, Architecture, Environmental planning, Ecosystem, Metadesign, business.industry, Antimicrobial resistance marker, Biotechnology, 030104 developmental biology, Research Design, 13. Climate action, Metagenomics, Public Health, Sample collection, business, Human
Abstract

International audience; The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities.

Published
2016
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19. Additional Layer of Regulation via Convergent Gene Orientation in Yeasts.

Author

Gilet, Jules, Conte, Romain, Torchet, Claire, Benard, Lionel, and Lafontaine, Ingrid

Abstract

Convergent gene pairs can produce transcripts with complementary sequences. We had shown that mRNA duplexes form in vivo in Saccharomyces cerevisiae via interactions of mRNA overlapping 3′-ends and can lead to posttranscriptional regulatory events. Here we show that mRNA duplex formation is restricted to convergent genes separated by short intergenic distance, independently of their 3′-untranslated region (UTR) length. We disclose an enrichment in genes involved in biological processes related to stress among these convergent genes. They are markedly conserved in convergent orientation in budding yeasts, meaning that this mode of posttranscriptional regulation could be shared in these organisms, conferring an additional level for modulating stress response. We thus investigated the mechanistic advantages potentially conferred by 3′-UTR mRNA interactions. Analysis of genome-wide transcriptome data revealed that Pat1 and Lsm1 factors, having 3′-UTR binding preference and participating to the remodeling of messenger ribonucleoprotein particles, bind differently these messenger-interacting mRNAs forming duplexes in comparison to mRNAs that do not interact (solo mRNAs). Functionally, messenger-interacting mRNAs show limited translational repression upon stress. We thus propose that mRNA duplex formation modulates the regulation of mRNA expression by limiting their access to translational repressors. Our results thus show that posttranscriptional regulation is an additional factor that determine s the order of coding genes. [ABSTRACT FROM AUTHOR]

Published
2020
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21. A Molecular Portrait of De Novo Genes in Yeasts

Author

Vakirlis, Nikolaos, primary, Hebert, Alex S, additional, Opulente, Dana A, additional, Achaz, Guillaume, additional, Hittinger, Chris Todd, additional, Fischer, Gilles, additional, Coon, Joshua J, additional, and Lafontaine, Ingrid, additional

Published
2017
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23. Comparative genomics of protoploid Saccharomycetaceae

Author

Souciet, Jean-Luc, Dujon, Bernard, Gaillardin, Claude, Johnston, Mark, Baret, Philippe V., Cliften, Paul, Sherman, David J., Weissenbach, Jean, Westhof, Eric, Wincker, Patrick, Jubin, Claire, Poulain, Julie, Barbe, Valerie, Segurens, Beatrice, Artiguenave, Francois, Anthouard, Veronique, Vacherie, Benoit, Val, Marie-Eve, Fulton, Robert S., Minx, Patrick, Wilson, Richard, Durrens, Pascal, Jean, Geraldine, Marck, Christian, Martin, Tiphaine, Nikolski, Macha, Rolland, Thomas, Seret, Marie-Line, Casaregola, Serge, Despons, Laurence, Fairhead, Cecile, Fischer, Gilles, Lafontaine, Ingrid, Leh, Veronique, Lemaire, Marc, de Montigny, Jacky, Neuveglise, Cecile, Thierry, Agnes, Blanc-Lenfle, Isabelle, Bleykasten, Claudine, Diffels, Julie, Fritsch, Emilie, Frangeul, Lionel, Goeffon, Adrien, Jauniaux, Nicolas, Kachouri-Lafond, Rym, Payen, Celia, Potier, Serge, Pribylova, Lenka, Ozanne, Christophe, Richard, Guy-Franck, Sacerdot, Christine, Straub, Marie-Laure, and Talla, Emmanuel

Subjects
Nucleotide sequence -- Analysis, Genomics -- Analysis, Brewer's yeast -- Genetic aspects, Health
Published
2009

24. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

Author

Chernomoretz, Ariel, Stolovitzky, Gustavo, Labaj, Pawel P., Graf, Alexandra B., Darling, Aaron, Burke, Catherine, Noushmehr, Houtan, Moraes, Milton Ozorio, Dias-Neto, Emmanuel, Guo, Yongli, Xie, Zhi, Lee, Patrick, Shi, Leming, Ruiz-Perez, Carlos A., Mercedes Zambrano, Maria, Siam, Rania, Ouf, Amged, Richard, Hugues, Lafontaine, Ingrid, Wieler, Lothar H., Semmler, Torsten, Ahmed, Niyaz, Prithi-viraj, Bharath, Nedunuri, Narasimha, Mehr, Shaadi, Banihashemi, Kambiz, Lista, Florigio, Anselmo, Anna, Suzuki, Haruo, Kuroda, Makoto, Yamashita, Riu, Sato, Yukoto, Kaminuma, Eli, Alpuche Aranda, Celia M., Martinez, Jesus, Dada, Christopher, Dybwad, Marius, Oliveira, Manuela, Schuster, Stephan, Siwo, Geoffrey H., Jang, Soojin, Seo, Sung Chul, Hwang, Sung Ho, Ossowski, Stephan, Bezdan, Daniela, Chaker, Salama, Chatziefthimiou, Aspassia D., Udekwu, Klas, Ljungdahl, Per, Sezerman, Ugur, Meydan, Cem, Elhaik, Eran, Gonnet, Gaston, Schriml, Lynn M., Mongodin, Emmanuel, Huttenhower, Curtis, Gilbert, Jack, Mason, Christopher E., Eisen, Jonathan, Hirschberg, David, Hernandez, Mark, Chernomoretz, Ariel, Stolovitzky, Gustavo, Labaj, Pawel P., Graf, Alexandra B., Darling, Aaron, Burke, Catherine, Noushmehr, Houtan, Moraes, Milton Ozorio, Dias-Neto, Emmanuel, Guo, Yongli, Xie, Zhi, Lee, Patrick, Shi, Leming, Ruiz-Perez, Carlos A., Mercedes Zambrano, Maria, Siam, Rania, Ouf, Amged, Richard, Hugues, Lafontaine, Ingrid, Wieler, Lothar H., Semmler, Torsten, Ahmed, Niyaz, Prithi-viraj, Bharath, Nedunuri, Narasimha, Mehr, Shaadi, Banihashemi, Kambiz, Lista, Florigio, Anselmo, Anna, Suzuki, Haruo, Kuroda, Makoto, Yamashita, Riu, Sato, Yukoto, Kaminuma, Eli, Alpuche Aranda, Celia M., Martinez, Jesus, Dada, Christopher, Dybwad, Marius, Oliveira, Manuela, Schuster, Stephan, Siwo, Geoffrey H., Jang, Soojin, Seo, Sung Chul, Hwang, Sung Ho, Ossowski, Stephan, Bezdan, Daniela, Chaker, Salama, Chatziefthimiou, Aspassia D., Udekwu, Klas, Ljungdahl, Per, Sezerman, Ugur, Meydan, Cem, Elhaik, Eran, Gonnet, Gaston, Schriml, Lynn M., Mongodin, Emmanuel, Huttenhower, Curtis, Gilbert, Jack, Mason, Christopher E., Eisen, Jonathan, Hirschberg, David, and Hernandez, Mark

Abstract

The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium is a novel, interdisciplinary initiative comprised of experts across many fields, including genomics, data analysis, engineering, public health, and architecture. The ultimate goal of the MetaSUB Consortium is to improve city utilization and planning through the detection, measurement, and design of metagenomics within urban environments. Although continual measures occur for temperature, air pressure, weather, and human activity, including longitudinal, cross-kingdom ecosystem dynamics can alter and improve the design of cities. The MetaSUB Consortium is aiding these efforts by developing and testing metagenomic methods and standards, including optimized methods for sample collection, DNA/RNA isolation, taxa characterization, and data visualization. The data produced by the consortium can aid city planners, public health officials, and architectural designers. In addition, the study will continue to lead to the discovery of new species, global maps of antimicrobial resistance (AMR) markers, and novel biosynthetic gene clusters (BGCs). Finally, we note that engineered metagenomic ecosystems can help enable more responsive, safer, and quantified cities.

Published
2016
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25. Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus

Author

Vakirlis, Nikolaos, primary, Sarilar, Véronique, additional, Drillon, Guénola, additional, Fleiss, Aubin, additional, Agier, Nicolas, additional, Meyniel, Jean-Philippe, additional, Blanpain, Lou, additional, Carbone, Alessandra, additional, Devillers, Hugo, additional, Dubois, Kenny, additional, Gillet-Markowska, Alexandre, additional, Graziani, Stéphane, additional, Huu-Vang, Nguyen, additional, Poirel, Marion, additional, Reisser, Cyrielle, additional, Schott, Jonathan, additional, Schacherer, Joseph, additional, Lafontaine, Ingrid, additional, Llorente, Bertrand, additional, Neuvéglise, Cécile, additional, and Fischer, Gilles, additional

Published
2016
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26. A Molecular Portrait of De Novo Genes in Yeasts.

Author

Vakirlis, Nikolaos, Hebert, Alex S, Opulente, Dana A, Achaz, Guillaume, Hittinger, Chris Todd, Fischer, Gilles, Coon, Joshua J, and Lafontaine, Ingrid

Abstract

New genes, with novel protein functions, can evolve "from scratch" out of intergenic sequences. These de novo genes can integrate the cell's genetic network and drive important phenotypic innovations. Therefore, identifying de novo genes and understanding how the transition from noncoding to coding occurs are key problems in evolutionary biology. However, identifying de novo genes is a difficult task, hampered by the presence of remote homologs, fast evolving sequences and erroneously annotated protein coding genes. To overcome these limitations, we developed a procedure that handles the usual pitfalls in de novo gene identification and predicted the emergence of 703 de novo gene candidates in 15 yeast species from 2 genera whose phylogeny spans at least 100 million years of evolution. We validated 85 candidates by proteomic data, providing new translation evidence for 25 of them through mass spectrometry experiments. We also unambiguously identified the mutations that enabled the transition from noncoding to coding for 30 Saccharomyces de novo genes. We established that de novo gene origination is a widespread phenomenon in yeasts, only a few being ultimately maintained by selection. We also found that de novo genes preferentially emerge next to divergent promoters in GC-rich intergenic regions where the probability of finding a fortuitous and transcribed ORF is the highest. Finally, we found a more than 3-fold enrichment of de novo genes at recombination hot spots, which are GC-rich and nucleosomefree regions, suggesting that meiotic recombination contributes to de novo gene emergence in yeasts. [ABSTRACT FROM AUTHOR]

Published
2018
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29. The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest

Author

Kunze, Gotthard, primary, Gaillardin, Claude, additional, Czernicka, Ma¿gorzata, additional, Durrens, Pascal, additional, Martin, Tiphaine, additional, Böer, Erik, additional, Gabaldón, Toni, additional, Cruz, Jose A, additional, Talla, Emmanuel, additional, Marck, Christian, additional, Goffeau, André, additional, Barbe, Valérie, additional, Baret, Philippe, additional, Baronian, Keith, additional, Beier, Sebastian, additional, Bleykasten, Claudine, additional, Bode, Rüdiger, additional, Casaregola, Serge, additional, Despons, Laurence, additional, Fairhead, Cécile, additional, Giersberg, Martin, additional, Gierski, Przemys¿aw Piotr, additional, Hähnel, Urs, additional, Hartmann, Anja, additional, Jankowska, Dagmara, additional, Jubin, Claire, additional, Jung, Paul, additional, Lafontaine, Ingrid, additional, Leh-Louis, Véronique, additional, Lemaire, Marc, additional, Marcet-Houben, Marina, additional, Mascher, Martin, additional, Morel, Guillaume, additional, Richard, Guy-Franck, additional, Riechen, Jan, additional, Sacerdot, Christine, additional, Sarkar, Anasua, additional, Savel, Guilhem, additional, Schacherer, Joseph, additional, Sherman, David J, additional, Stein, Nils, additional, Straub, Marie-Laure, additional, Thierry, Agnès, additional, Trautwein-Schult, Anke, additional, Vacherie, Benoit, additional, Westhof, Eric, additional, Worch, Sebastian, additional, Dujon, Bernard, additional, Souciet, Jean-Luc, additional, Wincker, Patrick, additional, Scholz, Uwe, additional, and Neuvéglise, Cécile, additional

Published
2014
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33. Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries.

Author

Gillet-Markowska, Alexandre, Richard, Hugues, Fischer, Gilles, and Lafontaine, Ingrid

Subjects
STRUCTURAL bioinformatics, ANALYSIS of variance, MATHEMATICAL sequences, HUMAN genome, BLOOD testing
Abstract

Motivation: The detection of structural variations (SVs) in short-range Paired-End (PE) libraries remains challenging because SV breakpoints can involve large dispersed repeated sequences, or carry inherent complexity, hardly resolvable with classical PE sequencing data. In contrast, large insert-size sequencing libraries (Mate-Pair libraries) provide higher physical coverage of the genome and give access to repeat-containing regions. They can thus theoretically overcome previous limitations as they are becoming routinely accessible. Nevertheless, broad insert size distributions and high rates of chimerical sequences are usually associated to this type of libraries, which makes the accurate annotation of SV challenging. Results: Here, we present Ulysses, a tool that achieves drastically higher detection accuracy than existing tools, both on simulated and real mate-pair sequencing datasets from the 1000 Human Genome project. Ulysses achieves high specificity over the complete spectrum of variants by assessing, in a principled manner, the statistical significance of each possible variant (duplications, deletions, translocations, insertions and inversions) against an explicit model for the generation of experimental noise. This statistical model proves particularly useful for the detection of low frequency variants. SV detection performed on a large insert Mate-Pair library from a breast cancer sample revealed a high level of somatic duplications in the tumor and, to a lesser extent, in the blood sample as well. Altogether, these results show that Ulysses is a valuable tool for the characterization of somatic mosaicism in human tissues and in cancer genomes. [ABSTRACT FROM AUTHOR]

Published
2015
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38. UGE1and UGE2Regulate the UDP-Glucose/UDP-Galactose Equilibrium in Cryptococcus neoformans

Author

Moyrand, Fre´de´rique, Lafontaine, Ingrid, Fontaine, Thierry, and Janbon, Guilhem

Abstract

ABSTRACTThe genome of the basidiomycete pathogenic yeast Cryptococcus neoformanscarries two UDP-glucose epimerase genes (UGE1and UGE2). UGE2maps within a galactose cluster composed of a galactokinase homologue gene and a galactose-1-phosphate uridylyltransferase. This clustered organization of the GALgenes is similar to that in most of the hemiascomycete yeast genomes and in Schizosaccharomyces pombebut is otherwise not generally conserved in the fungal kingdom. UGE1has been identified as necessary for galactoxylomannan biosynthesis and virulence. Here, we show that UGE2is necessary for C. neoformanscells to utilize galactose as a carbon source at 30°C but is not required for virulence. In contrast, deletion of UGE1does not affect cell growth on galactose at this temperature. At 37°C, a uge2?mutant grows on galactose in a UGE1-dependent manner. This compensation by UGE1of UGE2mutation for growth on galactose at 37°C was not associated with upregulation of UGE1transcription or with an increase of the affinity of the enzyme for UDP-galactose at this temperature. We studied the subcellular localization of the two enzymes. Whereas at 30°C, Uge1p is at least partially associated with intracellular vesicles and Uge2p is on the plasma membrane, in cells growing on galactose at 37°C, Uge1p colocalizes with Uge2p to the plasma membrane, suggesting that its activity is regulated through subcellular localization.

Published
2008
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39. Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae

Author

Boyer, Jeanne, Badis, Gwenaël, Fairhead, Cécile, Talla, Emmanuel, Hantraye, Florence, Fabre, Emmanuelle, Fischer, Gilles, Hennequin, Christophe, Koszul, Romain, Lafontaine, Ingrid, Ozier-Kalogeropoulos, Odile, Ricchetti, Miria, Richard, Guy-Franck, Thierry, Agnès, and Dujon, Bernard

Abstract

We have screened the genome of Saccharomyces cerevisiae for fragments that confer a growth-retardation phenotype when overexpressed in a multicopy plasmid with a tetracycline-regulatable (Tet-off) promoter. We selected 714 such fragments with a mean size of 700 base-pairs out of around 84,000 clones tested. These include 493 in-frame open reading frame fragments corresponding to 454 distinct genes (of which 91 are of unknown function), and 162 out-of-frame, antisense and intergenic genomic fragments, representing the largest collection of toxic inserts published so far in yeast.

Published
2004
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