Alpi Group

Cell signaling pathways are essential for every organism to maintain cell homeostasis, cell behavior, and to adjust cellular physiology in response to internal cues and external stimuli. Our major scientific focus is to understand signaling mediated by the ubiquitin system. My lab aims to functionally dissect these ubiquitin signaling pathways and their molecular machines to gain insight into their physiology and understand how their deregulation promotes cellular transformation and disease.

1) Ubiquitin system and protein dynamic in red blood cell development (erythropoiesis)
Erythrocytes play a vital role in all vertebrates through their oxygen delivery function. The cellular differentiation from haematopoietic stem cells/progenitors to mature erythrocytes, called erythropoiesis, is one of the most striking examples of protein remodelling. Throughout this developmentally programmed process erythrocyte-specific proteins are expressed, whereas all cellular organelles and the majority of proteins of progenitors are stepwise eliminated, ultimately forming the proteome of mature erythrocytes consisting of nearly 98% of haemoglobin.

The ubiquitin system is central for targeted protein degradation by the proteasome and lysosomal systems and may also play important regulatory roles in erythrocyte differentiation. We recently employed genetic screens, RNA-Seq, and mass spectrometry-based proteomics (in collaboration with Matthias Mann Department, and Mitch Weiss lab, St Jude’s Children Research Institute, Memphis) to identify key players in the ubiquitin system required for erythropoiesis.

Figure 1: Temporal global proteome analysis across erythropoiesis. Human erythroid progenitor cells (HUDEP2) were subjected to an in vitro differentiation protocol and global proteomes assessed after indicated maturation times (day 0 to 12). The Heat map shows z-scored protein abundances (log2 DIA intensities) and hierarchical clustering of the differentially expressed proteins during progressing erythroid maturation.

2) Ubiquitin system in Xenophagy
Autophagy is an essential cellular process that mediates the delivery of cellular cargo to the lysosome for degradation. Originally thought to be a non-specific process, it became clear that it is highly regulated and induced by various stress conditions to remove damaged or excessive cellular components. This also includes the targeted removal of invaded pathogens/microbes, a special form of autophagy called xenophagy, as part of a host cell defense regime (Figure 2).

Figure 2: Model of Xenophagy of cytosolic Salmonella. The invaded bacterium resides in a Salmonella-containing vacuole (SCV). The membrane of a subset of SCVs is damaged and the bacterium is exposed to the cytosol, recognized and targeted by the ubiquitin machinery forming a “ubiquitin coat”. Autophagy cargo receptors assemble on the ubiquitin coat and recruit autophagosomes by binding to membrane-linked LC3/GABARAPs and ultimately forming autolysosomes, where Salmonella is degraded.

A central part of xenophagy is the ubiquitin system. It is required to mark pathogens with ubiquitin molecules that serves as signal to initiate the formation of double-membrane autophagosome structures and lysosomal destruction. The functional role of several E3 ubiquitin ligases has been associated with xenophagy of different pathogens including Salmonella and Legionella. However, there is only a limited understanding of how these E3 ligases are activated and regulated during the process of xenophagy. Building on our recent work on Ariadne RBR E3 ligases (Scott et al. 2016; Kelsall et al., 2013), we currently focus our investigation on the Ariadne family member ARIH1, and aim to elucidate the molecular mechanism of ARIH1 in xenophagy (DFG funded project in collaboration with Christian Behrends, LMU). In collaboration with Alejandro Rojas (Austral University, Chile) we explore nanobody technology to generate a tool-box to monitor autophagosome biogenesis.

Members of the team:

Christine Baumann, Technician
Oliver Czarnecki, Master student
Karthik V. Gottemukkala, Master student
Judith Müller, Technician
Ishita Tripathi, PhD student (DFG funded)

External Funding:

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