December 2023

A year end summary: As Britney once sang “…but now we are stronger than yesterday (2023), now it’s nothing but our way…”

Reflecting on the passing year, 2023 has been a year of transformation and challenges that hopefully made us stronger than ever. Let’s begin with some unfiltered truths. Our journey this year was far from smooth, marked by transitional hurdles.

Our new lab at RUB in June 2023

Moving an entire lab from one place to another, including almost all lab members was a major challenge that brought us to our own limits. Major delays, considering wet lab work (e.g., we’ve been waiting more than six months for our water taps in our lab, to be able to normally work in it) and office place (Suayb got his office one year after his arrival), navigating a new environment, and grappling with shifts in administration and colleague dynamics made this year a test of resilience for all of us. Transitioning from the vibrant and forward-thinking environment of ZMBP in Tübingen, it was evident to all of us that our experience in Bochum would offer a “unique” perspective and bring about notable differences. Still, it held many surprises, for all of us, even the ones that have been experiencing the “German system” before. One prevailing realization was the nature of hierarchical structures, where departments and domains seemed ingrained. At times, it felt like an uphill battle against this entrenched mindset. But amidst these challenges, there’s a growing understanding that breaking free from these old structures is crucial for progress. At least we slowly got used to everything which is essential to improve and change certain structures. We will see what the future holds for TheÜstünLab!

Unfortunately, challenging times often reveal the genuine nature of human kind. We’ve observed that expressions of gratitude, acts of kindness, and displays of emotional intelligence are regrettably rare. At times, whether glancing through the news or observing our immediate environment, it appeared as though the essence of humanity was fading. We‘ve seen many memes & quotes about that “humanity is dead” – let’s hope 2024 will convince us of the contrary. 2023 left us contemplating the way forward towards cultivating a more empathetic and compassionate society in 2024. In more simple words – let’s just move on.

Manuel is receiving his poster award at MPMI in Providence.

So let’s stop with the unfiltered truth- and move on to the bright side. Amidst the turbulence, there were also bright spots for our lab. Members of the lab have been traveling to various conferences (Paris, Mendel Early Career Symposium in Vienna, 2024 MPMI in Providence, GRC Plant Proteolysis, ICPP in Lyon, invited seminars in Freiburg & Heidelberg) provided invaluable experiences. Manuel‘s poster award at the MPMI conference, catching up with old friends, and forging new friendships within the proteostasis community really brightened up the ride. 

Manuel during his Plant Immunity Lecture.

Another very bright spot was our engagement in teaching at RUB. TheÜstünLab led two plant science courses (one with other plant groups and one on plant-microbe interactions). It has been a very fun and rewarding journey for Manuel & Suayb to organize and supervise the courses. Manuel’s exceptional supervision and active involvement in our lab course, “Plant Cell Biology meets Plant-Pathogen interactions,” marked a significant milestone, positioning TheUstunLab prominently within the teaching landscape at RUB. Encountering the enthusiastic and talented bachelor and master students at RUB filled us with excitement. We’re thrilled to extend our involvement in additional teaching responsibilities in 2024. Furthermore, we eagerly anticipate welcoming bachelor and master students to our lab! It’s a lot of work for us but witnessing students’ growing interest in science and their evolution into prospective scientists is immensely rewarding! By far our teaching experience and interaction with the students have been the highlight of 2023!

Additionally, contributions to research papers, forging new collaborations, and the submission of a major grant, along with the approval of the confocal grant (yes, we have a fancy confocal now!) and Gautier’s preprint, signified progress and promise for future endeavors. You can find more on our research activities here.

As we bid farewell to 2023, it’s not just a year concluded; it’s a chapter filled with lessons, challenges, defeats but also victories. Sad and happy memories, things we simply want to forget and events/encounters we want to cherish. We move forward to 2024, wiser, and more resolute in our pursuit of breaking barriers, fostering community, and advancing research in our shared field. Let’s stay open to the surprises that 2024 has in store for us!

TheÜstünLab

Publish don’t perish! – TheÜstünLab publication activities in 2023

As 2023 winds down after an incredibly eventful year, the global scientific community is in its familiar rhythm of gathering the fruits of their labor. Researchers worldwide are wrapping up their manuscripts, sending them off to journals, or sharing them on platforms like bioRxiv. Within the last two weeks we have seen many labs preprinting papers, some of them having multiple new exciting stories that will have a huge impact in plant science. Witnessing this evolution within the plant science community is truly remarkable, especially as more scientists embrace the principles of open science by endorsing preprints. Despite the transitions from Tübingen to Bochum and the inevitable hiccups that followed, our momentum still persists. #TheUstunLab has been productive in 2023 and published one research paper, two reviews, one commentary in Nature Plants, two collaborative preprints on nanodomains and plant autophagy

In 2022 and 2023, we have been busy writing reviews about the “Interplay between autophagy and proteasome during proteasome turnover” and “The Plant Ubiquitin-Proteasome as a target for microbial manipulation”.

Our first review that appeared in Trends in Plant Science discusses the intricate relationship between two essential cellular degradation pathways: the ubiquitin-proteasome system (UPS) and autophagy. It highlights their individual roles in maintaining cellular homeostasis by clearing malfunctioning or unneeded proteins and reveals their interdependence, which was historically overlooked. We propose future directions to better understand and dissect the interplay of both pathways.

You can find more details here: https://doi.org/10.1016/j.tplants.2023.01.013

In our second invited review in Annual Review of Phytopathology, we describe how the ubiquitin-proteasome system regulates different immunity-related processes and how pathogens (bacteria, viruses, fungi) subvert this to promote disease. Pathogens use intricate tactics to manipulate the UPS, affecting plant immune responses. They utilize effectors to influence the degradation or stability of proteins involved in plant defense. However, this interplay is complex; the UPS is essential for effective plant defense, yet pathogens rely on its proper function for their pathogenicity. This complexity indicates that our understanding remains superficial. Thus, we propose in our review that it is vital to comprehend how the proteasome and its components are finely tuned at various levels. You can read more here:

https://www.annualreviews.org/doi/10.1146/annurev-phyto-021622-110443

Which brings us to our latest published preprint “ER-anchored protein sorting controls the fate of two proteasome activators for intracellular organelle communication during proteotoxic stress”, the SFB1101 funded PhD work of Gautier Langin. As proposed in our review about the proteasome and its role in plant immune reactions, we tried to decipher how proteotoxicity, caused by pathogens, diseases, organelle stress, and Co. is regulated. We show that the proteasome autoregulatory feedback loop acts as a gatekeeper to facilitate the communication between nucleus and chloroplast. In our study we revealed that the ER-anchored protein sorting system (ERAPS) controls the proteasomal degradation or nuclear translocation of proteasome activators NAC53 and NAC78. While both transcription factors activate the proteasome gene expression, they repress photosynthesis-associated nuclear genes during proteotoxicity. It appears that this trade-off is highly “conserved” as other stress conditions and developmental cues also lead to similar responses. We think that our findings also provide a new conceptual framework for understanding the integral role of transcription factors in managing cellular proteostasis under environmental stress, suggesting conservation of these mechanisms across kingdoms. But this is just a small summary and teaser 🙂 We promise it will be a good read over the Christmas holidays, lots of data, and possible future implications on other trade-offs between the proteasome and energy metabolism.

You can find the link here: https://www.biorxiv.org/content/10.1101/2023.12.11.571118v1

If you want to have a quick summary of our paper you can find this on the new biorxiv “addon” ScienceCast (https://sciencecast.org/casts/dypf9lriqtaz) that provides AI-generated summaries for expert and general audience – it is a fantastic tool and surely will help as to disseminate our research.

We are grateful for every feedback, comments and suggestions regarding our manuscript that we will certainly keep in mind before we submit in January 2024. Please don’t hesitate to contact us – we are always happy to discuss science!

TheUstunlab will certainly try to keep its spirit high in 2024 by finalizing papers (e.g., our Autophagy-Auxin-Vacuoles manuscript, cell-type specific autophagy) and participating in collaborative manuscripts on proteostasis (one will appear in the “Compelling Open Questions in Plant Proteolysis Research” in the focus issue on plant proteolysis in The Plant Cell). Hope that all of you won’t have too much stress the days before Christmas and remember: do not submit to journals before christmas 🙂

Happy Holidays to everyone!

TheUstunLab