Suayib Üstün

The Üstün lab receives funding to study the “Manipulation of protein translation by pathogenic bacteria”. Postdoc and PhD positions are available.

Protein homeostasis embodies a delicate balance between protein synthesis and breakdown, representing the dynamic cycle of protein “life and death.” About one-third of newly formed proteins undergo degradation. Consequently, the processes of protein translation and turnover are rigorously controlled to uphold cellular function and viability. Hence, regulating protein homeostasis in reaction to environmental cues has become a crucial strategy to manage disturbances spanning from aging to pathological conditions in both animals and plants. To allow rapid, versatile, and cost-efficient responses to sudden environmental changes, eukaryotes utilize reversible translational arrest caused by compartmentalization of transcripts in cytosolic membraneless aggregates formed by phase separation. One such type of aggregates are processing bodies (PBs), dynamic ribonucleoprotein aggregates conserved among eukaryotes. PBs are involved in translational arrest, mRNA decay and both RNA and protein quality control and regulate several developmental processes and responses to abiotic stresses. However, our knowledge of how and under which conditions PBs are formed as well as if PBs are hijacked by pathogens to manipulate protein translation is unknown.

Our team aims to delve deeper into how pathogens disrupt this mechanism. Through the generous support of approximately 565,000 euros from the Boehringer Ingelheim Foundation, as part of the “Rise Up!” funding program, the project is set to commence on August 1, 2024, and span a duration of three years.

Human pathogens like salmonella or legionella, as well as viruses, have been demonstrated to impact protein synthesis. Initial investigations led the Üstün lab indicate that plant pathogenic bacteria similarly influence protein synthesis, with this alteration being implicated in disease progression. In our upcoming project titled “Manipulation of protein translation as a virulence strategy of pathogenic bacteria,” we aim to further explore this phenomenon. To this end we have advertised a Postdoc and a PhD position. The postdoc will focus on  how PBs are hijacked by bacterial infection to alter global protein translation and what mRNAs are sequestered and repressed in translation. The PhD candidate will address how bacterial effectors induce the formation of PBs to understand the mechanism of PB assembly and analyse the composition of PBs during infection. More details about the positions, requirements and deadlines for application can be found in the job adverts. Apply if you are interested in proteostasis and would like to work in an international, innovative and inclusive team!

All in all, through this endeavor, we anticipate elucidating the comprehensive understanding of how proteostasis, specifically at the level of protein translation, governs immune responses and is consequently manipulated by pathogenic bacteria. Grasping the underlying molecular intricacies of translation modulation in disease settings will pave the way for innovative approaches to tackling diseases and environmental adversities.

 

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

PhD Position in Plant Proteostasis Research

Our group is still searching for a PhD candidate in the SFB1101 funded project “Specificity of proteasome regulation by tail-anchored transcription factors”. Within this project we have identified two transcription factors that regulate proteasome gene expression during bacterial infection and other proteotoxic stresses (Langin et al., unpublished). Interaction studies with both transcription factors revealed various proteins implicated in their degradation via the ERAD system and trafficking to the nucleus from the ER. Currently, we are looking into additional target genes of these transcription factors as they seem to mediate the trade-off between proteasome activation, growth, and defense.

The project is for three years with a possibility of a one year extension. Starting date is expected to be March or April 2023 but negotiable. Application deadline is the 9.01.2023. We are looking forward to receiving your application with the subject line “Application PhD-SFB1101 ANR: 1379” as a composite pdf-file in English. Please include a letter of motivation with your research interests, CV, name, and addresses of at least two referees via email: suayb.uestuen@rub.de

Postdoc position available in plant microbiome and autophagy research

Our group is still searching for a postdoc to continue our ERC funded research on “how the microbiome influences plant autophagy”. In the ERC project DIVERSIPHAGY we want to obtain a holistic picture of the role of autophagy in plant-microbe interactions by utilizing bacterial, genetic, and cellular diversity. So far, we have identified that (i) root microbiota are inducing autophagy in roots and shoots, (ii) commensal bacteria can compensate impaired growth in autophagy mutants and (iii) specific bacteria are enriched/depleted using microbial profiling under autophagy modulated conditions. We would like to continue this project with a postdoc experienced in plant microbiome research who will lead this part of the ERC funded project. PhD candidates with proven expertise in plant-microbiome research are also welcome to apply. The position is for 2 years, with a possibility to prolong it for another 2 years. The position is available immediately and open until a suitable candidate is found. For more details about the position and project see the ad below or contact suayib.uestuen@zmbp.uni-tuebingen.de

Britney survived 2007 and is finally free! We handled 2021 and will handle 2022!

It was a very intense, crazy, and exhausting year, with lots of ups and downs for our lab, but we managed to survive. We faced happy moments, difficult situations, rejections, and acceptance. This is just a small reflection about our lab life in 2021.

Publish, don’t perish.

Full of hopes we started 2021, posting our first preprint on biorxiv, in which we describe how a bacterial effector counteracts host autophagy by degrading an autophagy component, a project led by PhD student Jia Xuan Leong. We have spent more than 6 years to finalize this story, and this project made its way through various labs across the world, including Germany (Erlangen, Grossbeeren, Tübingen), Sweden (Uppsala) and the US. In the end we were excited to submit it in March to get peer reviewed. The process was very long (we lost 9 months), edifying (reviews improved our manuscript), but also painful. It showed us again that our publication system (or certain journals) may need a revamp. Luckily, there are very good other alternatives available out there and we are currently under review. Fingers crossed that 2022 starts with positive news. Fortunately, we received also good news regarding publications in 2021: one of the preprints with contributions from the Ustun Lab was accepted just before Christmas, you’ll soon hear from it. In 2022 we hope to finish Gautier’s and Paul’s stories and publish them as a preprint. Fingers crossed!

Our lab grows.

Managing a lab with various lab members and different projects is already challenging. Recruiting new team members to start their new projects is always a difficult task. The pandemic doesn’t make it easier. Nevertheless, beginning 2021, we started our search, and with the help of the entire lab we found new members, Shanshuo Zhu and Shiji Hou, to kickstart the ERC project DIVERSIPHAGY. Shanshuo and Shiji have promising results in their projects so far, and we hope to continue this in 2022. We also started a completely new project on the role of “P-Bodies in bacterial infection” with Manuel Gonzalez Fuente, who joined our lab as a postdoc with his own DFG funding from the Walter Benjamin Programme. All in all, it is great to see the group growing, different projects progressing and developing, even though we had limited space in the lab (thanks to the pandemic). The new year will again bring some changes to our group: We are very happy to welcome another postdoc in the new year, Margot Raffeiner (former PhD student in the Börnke Lab), who will join our ERC team, working on the autophagy degradome. Sadly, Shiji had to leave our lab by the end of the year, and we are currently trying to find a new postdoc to study plant microbiome and its influence on degradation pathways (you can find the ad here). Let’s see what other major changes will happen in 2022…to be continued!

Money, money, money.

Regarding grants for our lab, the year was pretty much focused to get approval for our project (“Specificity of proteasome regulation during plant immunity”) in the CRC1101 (“Molecular encoding of specificity in plant processes”), a research center, including labs from University of Tübingen, Heidelberg, Hohenheim and MPI Tubingen. Our lab was in a fortunate situation, as our PhD student Gautier Langin, working in this project since 2019, obtained exciting results that made it easy to develop the proposal for the third funding period of the CRC1101. After a positive evaluation in the summer, we got the final approval by the end of November. Full credits should go to all the amazing PhD students & Postdocs working in the different projects of the CRC1101 (I personally think that this always comes up short). Without their contributions the CRC1101 wouldn’t be there where it is now!

Tired of online meetings

Usually, in the pre-pandemic era, we would report about exciting meetings, international conferences, and networking events as well as huge social events. Especially not having any international conferences is affecting early career researchers a lot: It is crucial to present your science, to meet new people (future employees, collaborators, friends). Some of our lab members never went to international conferences. This is an essential part of building your own network and preparing yourself for your future. As much as online conferences are a great distraction, and a way to communicate your science (if you don’t present only published things), it misses the “social” part as most social interactions on Zoom or other platforms are impersonal. Our own lab meetings and journal clubs improved a lot when we started having in person meetings again. Our highlight of an in-person meeting was in November, when Yasin Dagdas, group leader at GMI Vienna, visited us, to participate in Gautier’s thesis advisory committee. We had great discussions about Gautier’s PhD project and future publication strategy that helped him a lot to focus his research. We hope for 2022 to have more in person meetings and small conferences.

Happy (we really mean this!) new year to everyone

Indeed, it was a very intense, tiring, sometimes exciting and sometimes challenging year for our team. We are glad that 2021 is over and we hope that 2022 brings many positive news (soon!) and experiences. The new year will definitely bring new adventures, big changes and challenges to the Üstün Lab but no doubt that our amazing team will manage this together.

The Üstün Lab is wishing everyone a happy new year and a fantastic start into 2022!

Highlights of the year

  • Publishing our first preprint
  • Welcoming new team members
  • Yasin’s visit for Gautier’s TAC
  • EURO2020 and kicktipp barbecue
  • CRC1101 grant approved
  • Having in person lab meetings again
  • AlphaFold
  • Results from various proteomics experiments
  • our first scRNAseq experiment
  • Christmas dinner & cocktails
  • Suayb doing something with R 
  • Will tell you in 2022

Flops of the year:

  • Rejected paper after 9 months
  • Pandemic, pandemic, pandemic
  • Online conferences (cancelled MPMI),

The Üstün Lab receives funding to continue research on the “regulation of proteasome in plants” within the CRC1101 “Molecular encoding of specificity in plant processes”

In November ,the German Research Foundation (DFG) announced that our collaborative research center, CRC1101, will get funded for an additional 4 years. In total 14 CRCs in Germany were approved and will start in 01.01.2022. You can find more information in the official press release from the DFG: https://www.dfg.de/service/presse/pressemitteilungen/2021/pressemitteilung_nr_48/index.html

The CRC1101 is integrating several group from ZMBP, University Tübingen, Max-Planck-Society (MPG) at the Tübingen campus and associated research groups of the Centre for Organismal Studies (COS) of the University of Heidelberg. Within the CRC1101 the research groups study how specificity of biological processes is achieved on molecular-mechanistic level. The CRC1101 is divided in four research areas: (A) “Specificity by Subcellular Sorting”, (B) “Specificity through Regulators of Growth and Development”, (C) “RNA-Mediated Specificity” and (D) “Receptor-Mediated Specificity”, in which the encoding of specificity of diverse processes will be studied.

The project of the Üstün Lab is within project area (A), Specificity of Subcellular Sorting, in which we study how a pair of NAC transcription factors regulate the proteasome during proteotoxic stress in plants. The proteasome is involved in plant defence and is therefore exploited by pathogens. In the second funding period of the CRC1101, we have shown that a pair of NAC transcription factors regulate proteotoxic stress during bacterial infection, are essential for plant defence, and are degraded by the proteasome (most likely by the ERAD pathway). We aim to elucidate (i) which other target genes are regulated by NACs, (ii) by which factors NACs are posttranslationally regulated, (iii) how subcellular sorting of NACs functions, and (iv) how NACs specifically modulate target genes. This should decipher how NACs integrate different signals to balance the trade-off between proteasome regulation and defence.

This project was initiated by PhD student Gautier Langin, who started his PhD in March 2019, and is continuing his research on the proteasome regulation in plants. His efforts led to several new findings and laid the foundation to be a part of the 3rd funding period of the CRC1101. Gautier will focus on the characterization of both transcription factors, with an emphasis on their posttranslational regulation during proteotoxic stress, for the next year. We are very happy to be able to continue our research on both NAC transcription factors and the proteasome in the next 4 years.

Co-localization study of one of the transcription factors with an E3 ligase at the ER.

News in 2021: Three preprints, including the first research paper from our Lab: “Self-ubiquitination of a pathogen type-III effector traps and blocks the autophagy machinery to promote disease”

2021 has been a very exciting and productive year for our lab so far with one major manuscript from our lab and two other contributions together with the Hafrén (SLU Uppsala) about virus-proteasome interaction and Börnke Lab (IGZ Großbeeren) about bacterial effector XopS. We have finally finished one of our major stories about how a bacterial effector from Xanthomonas traps the autophagy machinery to cause disease:” “Self-ubiquitination of a pathogen type-III effector traps and blocks the autophagy machinery to promote disease”. You can find the updated link to the preprint here:

https://www.biorxiv.org/content/10.1101/2021.03.17.435853v2

The XopL journey:

Our journey on Xanthomonas effector XopL started in 2015 when we conducted Y2H screenings with various Xanthomonas effectors to identify new host targets. This approach was pretty successful as we identified many interesting putative host targets (including the proteasome). However, as usual, it takes a long time to verify these interactions and also its biological relevance (it took as almost 6 years!). In the same screen we also identified that another bacterial effector, XopS, interacted with WRKY40 transcription factor, which in the end resulted in the fantastic story “The Xanthomonas type-III effector protein XopS stabilizes CaWRKY40a to regulate defense hormone responses and preinvasion immunity in pepper” from the Börnke Lab, led by first author Margot Raffeiner. Read more about it here: https://www.biorxiv.org/content/10.1101/2021.03.31.437833v1

The Y2H screen yielded that XopL might interact with SH3P2, a component of the autophagy machinery. However, at this time, we were not really motivated to study these interactions, as the expression of XopL and also SH3P2 was pretty tricky in plants and things did not develop as quick as we thought. Meanwhile, when I started to do my postdoc in Sweden, SLU Uppsala, we found out that Pseudomonas, activated autophagy for proteasome degradation (and most likely other stuff) to promote its virulence (http://www.plantcell.org/content/30/3/668). These findings together with the interaction data of XopL and SH3P2 prompted us to investigate whether Xanthomonas utilizes autophagy in a similar or different manner for its own benefit (in the DFG funded Emmy Noether project).

My talented and super motivated PhD student Jia Xuan Leong joined our lab last year as a master student and was able to show that, in contrast to Pseudomonas, Xanthomonas blocks autophagy in an effector-dependent manner to enhance its pathogenicity. We then went on and screened a couple of effectors for their ability to block autophagy. We analysed XopJ, XopS and XopD, as they have known effects on proteolytic degradation pathways and of course included XopL, because of its ability to interact with SH3P2. Fortunately, it turned out that XopL is able to suppress autophagy which made us very confident that we have to further characterize its function. However, our major concern was that previous reports stated that XopL is not a major virulence factor of Xanthomonas.

Fortunately, with the help of Mary Beth Mudgett and her amazing lab, we were able to show that XopL is one of the major virulence factors required for the virulence of Xanthomonas in tomato and roq1 N. benthamiana. Interestingly, this effect is only present when plants are dip-inoculated and not when they are syringe-inoculated.Thanks again for the Mudgett Lab for this great contribution!

Meanwhile we got a bit confused, as we realized that XopL is also degraded by autophagy. XopL associates with selective autophagy receptor NBR1/Joka2 which mediates the degradation of XopL. So far NBR1/Joka2 was known to degrade aggregates (aggrephagy), viral proteins and intracellular pathogens (xenophagy) but not bacterial effector proteins. We further discovered that XopL undergoes self-ubiquitination in vitro and in planta, at Lysine 191. Although, mutation of this lysine stabilizes XopL, XopL is still ubiquitinated in plants. We assume (and have also indications) that other lysines within XopL are ubiquitinated.

But how does XopL suppress its own degradation to act as a virulence factor? We went back to our “old” interaction data and confirmed the interaction between XopL and SH3P2 using different techniques. Because XopL is a member of the IpaH3 E3 ligase family, we hypothesized that XopL might degrade SH3P2 and thereby block autophagy. Indeed, in vitro ubiquitination assays (performed by talented PhD Student Margot Raffeiner from the Börnke lab) revealed that XopL ubiquitinates SH3P2 and mediates its degradation by the proteasome. The role of SH3P2 in the literature was still a bit controversial, as it has multiple functions. However, we show that SH3P2 from Nicotiana benthamiana is partially required for autophagy. Autophagosome formation during autophagy induction seems impacted.

 

Finally, after huge efforts (I am really sorry that you had to perform so many bacterial growth assays ) Jia Xuan could show that loss of SH3P2 and Joka2/NBR1 is beneficial for Xanthomonas growth (also loss of general autophagy) and can even restore the reduced growth of a Xanthomonas strain lacking autophagy suppressor XopL. Taken together, we conclude that Xanthomonas effector XopL acts as a bait to trap and dampen the autophagy pathway resulting in enhance pathogenicity of Xanthomonas. We provide a unique mechanism how a bacterial effector undergoes self-ubiquitination to trick the autophagy machinery. We think that during this process XopL is partially sacrificed and degraded in order to access and dampen autophagy responses.

 

XopL belongs to the IpaH3 E3 ligase family with members in Salmonella & Shigella. Are these effectors also undergoing self-ubiquitination and do NBR1 homologue in animals recognize bacterial effectors? Superimposing XopL (brown) and IpaH3 (blue) structures reveal possible ubiquitination sites (green) in IpaH3 in the same region within the LRR domain. It might be interesting to look if this mechanism is conserved across kingdoms.

Kudos to first author Jia Xuan Leong who did an amazing job during the last year. She was so persistent, especially doing all the bacterial growths and silencing assays. I am so proud what you have achieved and sure that we‘ll discover more in the next years! We are thankful to everyone who contributed to this exciting project and grateful for generous funding by the DFG Emmy Noether Program.

PhD and Postdoc Positions in the ERC funded Project DIVERSIPHAGY

The Ustun Lab is searching for new members to start our ERC funded project DIVERSIPHAGY-Utilizing diversity to decipher the role of autophagy in plant-microbe interactions. Within this project we want to obtain a holistic view of how autophagy plays a role in plant-microbe interactions utilizing bacterial, genetic and cellular diversity with an emphasis on cell-type and organ-specific autophagy responses. For one of the postdoc position prior experiences with methods to study plant/root-microbe interactions (pathogenic or beneficial), microbial reconstitution assays (SynComs) or microbiome analysis are advantageous. For the other Postdoc position experience in general plant molecular biology is expected. Here, cell biological experience is beneficial but not required. A master’s degree in molecular biology, biochemistry or corresponding is required for PhD candidates. No prior experience with autophaghy is expected. You can find more information below in the advertisement. The positions are available from 03/2021 (with flexible starting date) and application deadline is the 8th of Jan 2021 (might be extended if no suitable candidates are available). Please send the application via email to suayib.uestuen@zmbp.uni-tuebingen.de.

Suayb Üstün receives ERC Starting Grant to study the role of autophagy in plant-microbe interactions. Postdoc and PhD positions are available in 2021.

In September, Suayb Üstün received the ERC Starting Grants from the European Research Council (ERC) for his project DIVERSIPHAGY. The grant of up to 1.5 million euros is awarded for a period of five years. Suayb Üstün will investigate the role of regulated degradation and recycling processes in the interaction of plants and pathogenic microbes in the “DIVERSIPHAGY” project.

In the ERC project “Utilizing diversity to decipher the role of autophagy in plant-microbe interactions” (DIVERSIPHAGY), Üstün aims to elucidate the role of autophagy in the interaction between plants and microbes. Plants are constantly exposed to beneficial and pathogenic microbes. In order to obtain a comprehensive picture of the role of autophagy, it is necessary to include its diversity in the investigations. The picture becomes even more complex considering cell-type specific responses in host plants. DIVERSIPHAGY includes all organisms, processes and factors that influence autophagy in plant-microbe interaction. To this end, state-of-the-art technologies such as the analysis of the entire protein inventory of the cells, the so-called proteomes, all metabolic products, the metabolites, or even single-cell RNA sequencing technology will be used. Üstün intends to transfer the results to crops in order to generate resistance to bacterial pathogens.

The start of DIVERSIPHAGY will be in 2021. Stay tuned for job postings for postdoctoral researchers and PhD positions.