Physiological Consequences of protein translocation stress in Bacillus subtilis Bernal-Cabas, M.
DOI:
10.33612/diss.143818857
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Publication date: 2020
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Bernal-Cabas, M. (2020). Physiological Consequences of protein translocation stress in Bacillus subtilis. https://doi.org/10.33612/diss.143818857
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Chapter 9
Acknowledgements
Biography
List of publications
Acknowledgements
Those who have come to know me over the years know that I am a huge cycling fan. What I am currently feeling must be similar to how a cyclist feels in the last stages of the Tour de France, having trained for several months and after three weeks of racing, with many victories, losses, and mishaps along the way. Most cyclists that make it to the Tour of France just dream to make it there, and winning it is an added bonus, just like for Tadej Pogačar, who surprisingly won the Tour de France this year. To me, doing this PhD and having completed it, feels just like winning the Tour de France. Even though the parallel between cycling and doing a PhD might not seem completely clear, I have compiled several reasons that explain this connection. First of all, in order to stay on your bike, you have to keep pedaling. Otherwise you lose momentum and fall off your bike. Similarly, during your PhD you have to keep momentum by innovating and pushing boundaries of science to create new knowledge. Secondly, cycling is unpredictable just like a PhD. A cyclist can have trained for many months and be at the top of their game before the start of a big race. However, a small fall, a stomach issue, or an old injury can hinder even the best cyclist from performing their best, as was the case for Egan Bernal after he won the Tour de France in 2019 but had to drop out of the race this year after a back injury. Similarly, in a PhD you start with a project and an idea in mind. You plan and develop your work and experiments around this idea. However, even with all the best preparation things rarely go according to plan. Initially, the main objective of my PhD was to unlock the Tat pathway for the secretion of heterologous proteins, and in an ideal scenario this would have been the outcome of my thesis. Unfortunately, this was not the outcome I obtained. Nonetheless, we were able to obtain significant progress understanding and characterizing the effects of high-level protein secretion in the physiology of B. subtilis. Lastly, cycling is a sport of suffering, and as Eddie Mercx said “Cyclists live with pain. If you can't handle it you will win nothing. The race is won by the rider who can suffer the most”. Likewise, in science there is a lot of suffering, lots of experiments that never work, unexplainable results, long hours, unclear data sets, and paper rejections. Nevertheless, in both a PhD and in cycling, suffering is not only a means to achieve a reward, but also a motivator to persevere, improve, and flourish. Finally, to win a race, the team leader of the cycling teams requires the support and help of his “domestiques”. The domestiques are in charge off shielding the leader from the wind and providing him with food and water during
the race. Similarly, I have been lucky enough to have the support of everybody I have mentioned in these acknowledgments to help me complete my PhD.
First of all, I would like to thank my supervisor, Jan Maarten. Thank you for choosing me for this PhD position and giving me this amazing opportunity. Because of your trust in me, support, guidance, and mentorship, I have learned so much more than what I could possibly have imagined in the last 5 years. You have taught me not only how to be a better scientist and writer, but also how to work well under pressure and think outside the box. I am glad I had the opportunity to share with you so many amazing conferences and meetings. I am looking forward to sharing everything I learned from you in the next step of my career.
I would also like to thank my co-supervisor Girbe. Thank you so much for all the useful comments, observations, and help you provided during my PhD. Your curiosity and enthusiasm sparked many new experiments and ideas that made this thesis more interesting and significant. It was wonderful to also share with you so many nice conversations about running and teaching. Thank you for being my co-supervisor.
A big thank you to the reading committee, Prof. Arnold Driessen, Prof. Oscar Kuipers, and Prof. Colin Robinson,for taking the time to assess and approve my thesis.
I would also like to thank all the people involved in the Protein Factory consortium. It was a wonderful experience to have participated in this consortium and to attend multiple courses, conferences, and seminars across Europe. In particular, I would like to thank Ane and Minia. Gracias por su amistad, apoyo, y cariño durante los últimos años. Fue un placer trabajar con ustedes y poder compartir tantos momentos, como el nacimiento de Antonio y que Javi se haya unido a la familia. Les mando un gran abrazo y las quiero montones (y mi madre les manda a decir que ahora hablo con acento español). No se como habría podido lograr este PhD sin su amistad y apoyo. No veo la hora de darles un super abrazo. Ste, thanks for your help with the protein localization database. I would also like to thank you for sharing with the dinner club all the amazing food you prepared. It was a great honor to have been part of Protein Factory with you. Sierd, thank you for all your help during Protein Factory. You helped
make this consortium one of the best experiences in my life. I am so glad we have crossed paths.
I would also like to thank the people at the University of Greifswald (Dr. Becher, Sandra, Claudia, Jurgen, and Andreas) for welcoming me into their team and helping me so much with the sample preparation and data analysis for the proteomics paper. Also, I would like to thank my collaborators at TU Dresden (Dr. Diana Wolf and Dr. Thorsten Mascher) for all your help with LiaH. Finally, I would like to thank Dr. Juan Alfonso Ayala: thank you so much for your help and encouragement over the last years. Thank you for also inviting Eric and me to Madrid. I am looking forward to seeing you soon.
I would like to thank my dearest paranymphs. Giorgio, you were the first person that welcomed me in MolBac. You have been through thick and thin with me during the past few years. You helped me find my love for cooking and taught me so many wonderful amazing recipes. Also, you cooked for me so many times the most amazing food I have ever had. I will never forget all the dinner club gatherings, the Molbac parties, our trip to Italy. However (and fortunately) not everything has been food related. You have also taught me so much about science, friendship, life, and perseverance. You are a brilliant scientist and a wonderful friend. I am so blessed to have crossed paths with you. Suru, thank you for love, patience, and kindness. Thanks again for designing this amazing thesis cover. This PhD journey wouldn’t have been nearly as amazing if I hadn’t met you, and I am also almost certain I would have never finished this thesis if you hadn’t help me discover my love for coffee. Thank you for your support in the last kilometers of this race. I am looking forward to going to Nepal with you. Marina, mil gracias por tu amistad, cariño, apoyo, entusiasmo y compañía durante todo este tiempo. Me encanta haberte conocido y haber compartido tantos momentos contigo. Infinitas gracias por todo el queso, no habría podido sobrevivir esta tesis sin una buena dosis de Manchego. No veo la hora de que nos vayamos a andar en bici unos buenos días.
I would like to thank my teammates, the people from MolBac. I am so incredibly grateful that I had the opportunity to have an amazing time with you and also share so many life events; weddings, graduations, birthdays, engagements, births, and many other milestones. All of you have made a significant impact in my life and I hope I was able to have some impact in your
life as well. Marinesilla, gracias por tu apoyo durante todos estos años; ha sido una gran alegría poder haber vivido tantos momentos juntas. Gracias por haber estado siempre allí cuando más te necesitaba. Elisa, thank you for your friendship, support, and encouragement over the last few years. I am looking forward to having many cappuccinos with you. Andrea, gracias por tu apoyo en los últimos años. Gracias por todas tus enseñanzas sobre la vida, yoga y meditación. Todo lo que me enseñaste me ha ayudado a transformar mi vida, y no veo la hora de seguir mejorando. Bimal, thank you so much for your help and support over the last months. It has been amazing to have worked with you, and of course it has been a blast to get to know you. Pragyi thank you for all the delicious food you have prepared for us. Eric and I look forward to visiting you and Bimal in Nepal. Marco, hermano, trabajar contigo fue uno de los mejores momentos del PhD. También fui muy afortunada de haber compartido tantos momentos contigo (Venezia, Milano, y el Giro d’Italia!!). Te deseo lo mejor en tu PhD. Rocío, gracias por todos los momentos que compartimos juntas, por todo tu apoyo, ayuda, y por haber organizado tantos eventos para el laboratorio. Haber podido compartir tantos momentos especiales contigo fue una gran experiencia. Te deseo lo mejor en el futuro. Usma, thank you for all the coffee and medical conversations that we had, I am looking forward to visiting you in Edinburgh. Yare, gracias por todos los momentos que compartimos juntas y todas las películas que vimos en Pathé. Te deseo lo mejor en tu defensa. Francis, working with you has been wonderful. Thank you for your generosity and support. Francisco, Elias, Laura, Solomon, Jolien, Dennis, and Rense, I am so glad I had the opportunity to get to know you; thanks for your enthusiasm and having shared so many experiences with me. Thank you to my lovely officemates Jolanda and Min for making our office so cozy and productive. I had a great time working with you, and I will miss you dearly. Sjouke, thank you so much for your positive vibes, for all the nice conversations that we had about coffee and life. Tim, it was a great fun to work with you. Thank you for all the help and advice you gave me. I am looking forward to seeing you soon. Toby, thanks for listening to me and for sharing all the sourdough and cooking tips. I wish you all the best in the upcoming years. Xin, thank you for support throughout the PhD and for helping me with proteomics I am looking forward to seeing you soon. Aysegul, Mafalda, Lisanne, Yanyan, and Marjolein, thank you for all the nice conversations. I wish you all the best in the rest of your PhD. To my former students Robert, Simone, Patrick, Danielle,and Bente, having the opportunity to work with you was one of the highlights of my PhD. I am so proud of the persons you have become. I would also thank the
people downstairs, Gaby, Eleni, Lu, Arezoo, and Rita. Thanks for all the wonderful conversations and help. I am so glad I had the opportunity to work with you. Hermie, thanks for all the feedback and interesting questions regarding my thesis. I am sure they will help me with the thesis defense. Finally, I would like to thank all the staff at the Department of Medical Microbiology, Ank, Carolin, Henk, Guido, Bert, and Mike. Your friendliness, willingness to help, and contributions were indispensable to help me complete this PhD.
Thank you to all the people who decided to make Groningen a stop during their Eurotrips. We really appreciate that you took the time to come to this city. Jessifer, gracias por venirme a visitar a mi pueblo. La pasamos buenísimo. Gracias por tu apoyo en los últimos meses. Te quiero un montón. Tati y Cami, no veo la hora de verlos, y felicitaciones por la nueva adición a su familia. A mis tíos, Pedro y Amparito, los quiero infinitamente, muchas gracias por consentirme tanto y por haberme visitado acá y haber ido a nuestro matrimonio en Canadá. Cuento los segundos para verlos nuevamente. Logan, it has been wonderful getting to know you. I am so glad you are part of our lives. And of course, thank you for stopping by, it was so wonderful you biked from Amsterdam to Groningen, I hope to do the same in the near future. I am looking forward to seeing you and Steph soon. Adele, thank you for all your support during this crazy journey.
I would also thank my wonderful friend, Hana. Babes, we met in the moment God wanted us to, and it could not have worked any better. Even though you are on the other side of the world, I can’t wait to visit you in Malaysia and meet your beautiful sons. I love you, and I wish you all the happiness in the world.
To our friends in Groningen, Maya and Stathis, thank you for your support, generosity, and friendship. I am so glad we met in Dutch class. It was been a pleasure to get to know you and to meet Valeria. Nataly, que bendición fue conocerte en esa clase de scientific writing. Me encanta nuestro parche ‘cedritos’. Ana Carolina, thanks for all the advice and strategic lunches we had together. Natalia, Xime, Lili, Diego, Pao, y Raúl, gracias por todos los momentos que compartimos juntos. Krum, Ingrid, and Ronald, thank you for helping me enhance my athletic abilities and helping me get in the best shape of my life. Dr. van Willigen and Dr. Gansevoort, thank you for all your help and support over the last few years. Ali en
Jan, bedankt dat jullie de beste buren zijn. Eric en ik hebben het geluk dat we naast jullie wonen. Ik kan niet wachten om iets met jullie te vieren. Trijne, bedankt voor alle Nederlandse lessen. Samen met jou is leren een enorm plezier. Ik ben zo blij dat ik je ken en dat ik van je kan leren. I would also like to thank the people at the Launch Café for welcoming me and for all the interesting conversations. Silvia, thank you so much for all the coaching sessions and for helping me figure out the next step in my career.
I would also like to thank my friends from back home. No matter where I am, whenever I talk to you, I feel home. Cata, me alegra infinitamente que nos hayamos conocido durante el pregrado. Hemos vivido muchas cosas juntas durante los últimos 14 años (como vuela el tiempo). Te quiero mucho y te deseo lo mejor del mundo. No sé qué habría hecho sin tu apoyo durante la última fase de este doctorado. No veo la hora de vernos próximamente. Nati, mil gracias por tu ayuda formateando la tesis. Gracias por todo el apoyo y cariño que me has brindado. Te quiero mucho. Vane, gracias por la gran amistad que me has brindado durante los últimos veinte y tantos años. No puedo creer a donde no ha llevado la vida. Estoy muy orgullosa de la persona en que te has convertido. Jois, mil gracias por tu amistad y por los excelentes consejos durante todos estos años. Sanch y Nico, gracias por acompañarme todos estos años. Haber crecido con ustedes y haber compartido tantos momentos juntos ha sido uno de los mejores momentos de mi vida. Ale, gracias por tu apoyo y amistad durante todos estos años. Felipe, gracias por todos los reencuentros. Verte cada vez que voy a Bogotá es uno de los mejores momentos en cada uno de mis viajes (sobre todo si es ciclovía). Me encanta hablar contigo sobre deporte y vida sana. Espero que puedas venir a visitar la tierra de las bicicletas prontamente.
To my Canadian friends. Jules, thanks for your unconditional friendship and support over the last years. You have been my inspiration, and because of you I have also become a better scientist and geneticist. Thank you for coming to visit me here and for going to all the way from Australia to our wedding in Colombia. I can’t wait to come to Vancouver and have a good yoga session with you, followed by coffee and Israeli food. Jing, thank you so much for teaching me how to crochet. I am completely hooked now. I don’t think I would have survived the quarantine, thesis writing, submission, or defense prep without crocheting every night for
an hour. I am looking forward to seeing you in Canada and visiting your new place. I hope you can also visit here as soon as COVID allows us to.
A sincere thank you to the adopted members of our family. Jeremy, you have become a member of our family here in the Netherlands. You have been there for us no matter how or when. I am so glad we ended up meeting on that WIRE trip and that Eric recognized your Canadian accent from several kilometers away. Your generosity and kindness have made us feel at home here in the Netherlands. Your academic and personal advice have helped me immensely throughout my PhD. Most importantly, thank you for welcoming us into your house any time and any day. Of course, I want to thank your wonderful cats Nygma and Tippi for being so loving and providing lots of pet therapy (like the wonderful hair massage I got from Tippi). We love you dearly and we wish you all the best in life. Alison (or should I just say dude), I love you so much, and I thank God for putting you in my life. Thank you so much for being such an integral part of our family. You are the sister I never had, and words can’t express how much I love having you in my life. I can’t wait to see what life has in store for us. I am so blessed, dude.
I would also like to thank my amazing parents. Papi y Mami, mil gracias por su amor, paciencia y cariño durante todos estos años. Sin su apoyo incondicional nada de esto habría sucedido. Estoy increíblemente agradecida por todos los sacrificios que han hecho por mi para que pudiera perseguir mis sueños. Los extraño infinitamente, y no veo la hora de verlos nuevamente. A mi hermano, Juan Sebastián, estoy muy orgullosa de la persona que te has convertido y te deseo lo mejor del mundo en Interpol. Tom and Jo-Ann, thank you so much for your love and support over the last few years. I am so incredibly grateful and lucky that I get to be part of your wonderful family. None of this would have been possible without you. Thank you for your endless love and support throughout the years. I love you.
Last but not least, I want to dedicate this thesis to my amazing and wonderful husband Eric Maximilian. This achievement is also yours. Thank you so much for encouraging me to follow my dreams and for leaving your life behind in Canada to follow me here. You make me the happiest woman on this planet with your infinite love, kindness, patience, and jokes. Thank you for being my best friend and partner in crime. Thank you for always believing in me and
for always being there for me. I wish you all the best in the beginning of your PhD. I will be there to support you at every step along the way, the same way you did for me. I am eternally grateful that I am your wife, I am so incredibly blessed. I love you so much mi cielo hermoso.
And just to wrap up this long acknowledgement, I would like to quote one of my favorite Arcade Fire songs, which summarizes the last 10 years of my life better than I could ever write myself.
"If I could have it back, all the time that we wasted, I'd only waste it again"-The suburbs
Thank you again,
Biography
María Margarita Bernal-Cabas was born in the Andean capital of Bogotá, Colombia. From 2006 to 2011, she studied at the Universidad de los Andes in Colombia with a full scholarship, and she graduated with a BSc in Microbiology. During this time, she went on an academic exchange for 5 months at the University of Oklahoma, where she took several classes in microbiology and biochemistry, and did an internship with Dr. Bradley Stevenson. During the final year of her undergraduate degree, she also completed an internship with the group of Dr. Cesar Arias at the Universidad El Bosque in Bogotá. This was followed by a second internship with the Bacterial Cell Division and Antimicrobial Resistance group of Dr. Juan Alfonso Ayala Serrano at the Centro de Biologia Molecular Severo Ochoa in Madrid. Subsequently, from 2011 to 2014, she attended the University of Alberta in Canada, where she graduated with a MSc. in Microbiology and Biotechnology. During this time, she worked under the supervision of Dr. Tracy Raivio. The title of her thesis was ‘The Cpx pathway causes changes in peptidoglycan structure, turnover, and recycling’. In October 2015, she started her PhD research at the department of Medical Microbiology at the University Medical Center Groningen, under the supervision of Prof. Jan Maarten van Dijl. During the first three years of her Ph.D., Margarita was part of the Horizon 2020 ‘Protein Factory’ Innovative Training Network (ITN), whose objective was to engineer a new generation of super-secreting strains. In her PhD thesis, Margarita investigated and characterized the physiological changes of B. subtilis in response to high-level protein production by employing a combinatory approach consisting of ‘omics’, biochemical, and molecular methods. Her research resulted in the work described in this thesis. In her free time, Margarita enjoys long distance and performance cycling, weight training, discovering new recipes, reading, and travelling.
List of publications
Bernal-Cabas M., Antelo M, Prajapati B., Ganuza-Quesada A., Schilling T., Grasso S., Maaβ S., Otto A., G. Buist, Becher D., Dijl JM. In the Cave of Wonders – 15N metabolic labeling provides new insights in cell physiology during twin-arginine translocation in Bacillus subtilis. Journal of Proteomics Research. Manuscript to be submitted.
Bernal-Cabas M., Miethke M, Wolf D., Antelo M, Aguilar Suarez R., Otto A., Becher D., Dijl JM. Cell envelope adaptation and minimal Tat translocation are functionally intertwined. Biochemica et Biophysica Acta (BBA)-Molecular Cell Research. 1867, 118719 (2020).
Prajapati B., Bernal-CabasM., SchafferM., BartelJ., RathH., SteilL., MäderU., van Dijl JM. Double trouble: Bacillus depends on a functional Tat machinery to avoid severe oxidative stress and starvation upon entry into a NaCl-depleted environment. Biochemica et Biophysica Acta (BBA)-Molecular Cell Research. Submitted.
Antelo-Varela M., Aguilar Suárez R., Bartel J., Bernal-Cabas M., Stobernack T., Sura T., van Dijl JM., Sandra Maaß., Becher D. Membrane modulation of super-secreting ‘midiBacillus’ expressing the major Staphylococcus aureus antigen -a mass-spectrometry based absolute quantification approach. Frontiers in Bioengineering and Biotechnology. 8, 1-15 (2020). Antelo-Varela M., Bartel J., Quesada-Gamuza A., Appel K., Bernal-Cabas M., Sura T., Otto A., Rasmussen m., Dijl J.M., Nielsen A., Maaß S., Becher D. Ariadne’s thread in the Analytical Labiryinth of Membrane Proteins- Integration of Targeted and Shotgun proteomics for Global Absolute Quantification of Membrane Proteins: exemplified in Bacillus subtilis during osmostress. Analytical Chemistry. 91, 11972-11980 (2019).
Bernal-Cabas, M., Ayala Serrano JA., Raivio TL. The Cpx envelope stress response modifies peptidoglycan cross-linking via the L,D-transpeptidase LdtD and the novel protein YgaU. Journal of Bacteriology. 197.603–61 (2015)
