LABORATORIUM METABOLIZMU BIAŁEK

Wojciech Pokrzywa

Kim jesteśmy

We are a research lab located at the International Institute of Molecular and Cell Biology in Warsaw, one of the best research institutions in Poland.

We focus on the mechanisms of protein metabolism - maintenance of the balance between the synthesis and degradation of proteins. We explore the regulation of translation, ubiquitin-proteasome system, chaperone network, and muscular exophers in proteostasis. However, we are sometimes intrigued by topics outside this list.

In Pokrzywa lab, we use a combination of biochemical, microscopic, molecular genetics, and bioinformatics techniques, supported by mammalian cell assays and the nematode Caenorhabditis elegans.

Research

Scheme of impact of cold on transcriptome and proteome
Cellular adaptation to cold

To counteract cold, organisms developed various types of responses, ranging from cold avoidance to adaptation. The latter strategy is used by hibernating animals, which, in extreme cases, can survive subzero temperatures for many days. We focus on deciphering mechanisms altering the abundance and types of cellular messenger RNAs and proteins, as these kinds of molecules are critical for the live-or-die decision of the cell. As in some disease states, like stroke, cooling can facilitate a patient's recovery, understanding how cells adapt to cold has the potential to influence treatments of human disorders.

Scheme of myosin assembly
Stress-induced myosin folding and assembly mechanisms

Little is known about the regulation of muscle-specific response programs that coordinate protein quality control upon mechanical stress and in human disease. We established a Caenorhabditis elegans-centered array of experimental approaches for the in-depth investigation of myosin-directed stress induction mechanisms. The long-term objective of this project is to understand how protein folding and degradation networks are coordinated with the dynamics of myosin assembly, muscle integrity, and repair in the context of mechanical stress. 

Scheme of methionine metabolism
The regulation of methionine metabolism by the ubiquitin-proteasome system

Methylation is the modification that various cellular molecules, from nucleic acids to proteins to lipids, undergo. It is central to the regulation of many biological processes, including gene expression, signaling, protein synthesis and lipid metabolism. The long-term goal of this project is to understand how the ubiquitin-proteasome system modulates cellular methylation potential. Congenital methylation disorders are a group of rarely described and probably largely unrecognized disorders involving transmethylation processes. We also model these human diseases on Caenorhabditis elegans to understand the molecular basis involved in the dysfunction of methylation pathway enzymes and their impact on physiology.

Scheme of muscular exopheresis
Mechanisms of muscular exopheresis

We discovered that large extracellular vesicles, termed exophers, that attribute in neurons and cardiomyocytes and carry damaged subcellular components, are released by muscles to support embryonic growth in Caenorhabditis elegans. Our results demonstrate that an exopher formation (exopheresis) represents a transgenerational metabolic/resource management system that supports embryos in utero. Currently, we investigate the mechanism of exopher formation and the regulation of exopheresis at the molecular level. 

Schema of E3 ligase complex
E3 ligase complexes in the integration of proteostasis and aging

From their synthesis to destruction, the fate of eukaryotic proteins is supervised by the ubiquitin-proteasome system (UPS). Cooperation of E3 ligases, essential components of the UPS that recognize damaged or misfolded proteins, can lead to the formation of alternative ubiquitylation structures that aid in directing substrate specificity. We investigate how specific E3 ligase pairs determine substrate recruitment and ubiquitin chain formation to coordinate proteolytic networks. Understanding the function and identifying the signals that coordinate the interaction between E3 ligases will provide information on how proteolytic networks are tuned to maintain cellular proteostasis in health and disease.


News

June 2022 | Our article published in EMBO Journal

EMBO graphical abstract

Our article has just been published in the prestigious EMBO Journal. We are thrilled, as it will be featured on the cover of August issue of the EMBO Journal!

We focused on the CHIP ubiquitin ligase enzyme – a quality control factor responsible for the regulation and degradation of multiple protein targets, including those implicated in the pathogenesis of neurodegenerative diseases or cancer. We described a potential regulatory process enabling switching on/off activity of CHN-1, a worm analog of human CHIP, to maintain cellular homeostasis. We also identified a set of its new potential substrates, including AHCY‐1, a key enzyme involved in methylation - a process responsible e.g., for determining if particular DNA instructions would be processed or regulating proteins and lipids.

June 2022 | Degronopedia hit 1000 queries

conference photo

We are delighted that our recently released web server degronopedia.com has just passed 1000 queries!

Moreover, our PhD student Natalia gave two successful talks about it - at the EMBO Workshop Protein Termini in Bergen, Norway and virtually at the Dana-Farber Seminar Series. We are looking forward to introduce some new features soon, so stay tuned!

May 2022 | New preprint published

DEGRONOPEDIA logo

We published a preprint where we introduce DEGRONOPEDIA - a web server allowing for degron screening. 


Degrons are short linear motifs critical for selective protein degradation. Our tool provides complex degron information (i.a. nearby residues that may be ubiquitinated, post-translational modifications, disorder) and allows for Machine Learning predictions of protein termini stability.

DEGRONOPEDIA can be freely accessed at degronopedia.com 

May 2022 | Our presence at two major conferences

Travel grant awardees

Our study on CHIP/UFD-2 molecular cooperation has been presented at the Ubiquitin & Friends Symposium in Vienna and GRK2243 Symposium in Würzburg by our talented Ph.D. students - Aniruddha Das and Pankaj Thapa.

We are very pleased how warmly it was received by the scientific community as expressed by the Travel Grant awarded to Aniruddha for one of the best presented posters. 

Photo: @SFB_TPDvienna, Twitter

May 2022 | New preprint published

CHIP scheme

We released a preprint where we describe the engagement of the ubiquitin ligase CHIP by the nucleolus in response to proteotoxic stress.

These observations may be relevant in elucidating the mechanisms of nucleolar proteostasis and in the biology of cancer, whose development is influenced by nucleolar stress response pathways. Our study provides a solid basis for further exploring CHIP function in the nucleolus.

April 2022 | New preprint published

Omega bends plot

We released a preprint describing the first case of neurodevelopmental disorder in a patient with a de novo missense variant in a degron-binding pocket of E3 ubiquitin ligase FEM1C. We used Caenorhabditis elegans as a model of the disease - mutant worms, similarly to the patient, also developed locomotion impairments.

This study was carried out in collaboration with the group of Prof. Rafal Ploski from the Medical University of Warsaw. We are looking forward to further fruitful collaborative research on possible mechanisms of pathogenicity underlying this mutation.

February 2022 | New grant awarded

NCN logo

We are very pleased to inform that PI of our group - Wojciech Pokrzywa has obtained the five-year SONATA-BIS grant from the National Science Centre.


In the next years we will focus on mechanisms of protein adaptation to escape premature degradation by the ubiquitin-proteasome system. We are very excited for this new avenue of research!

January 2022 | New preprint published

Preprint figure

In our recent preprint, we show that defects in red pulp macrophages - cells responsible for maintaining blood homeostasis - occur early in aging and disrupt iron turnover, contributing to elderly anemia.

November 2021 | New grants awarded

PRELUDIUM grant awardees

We are delighted to announce that two of our Ph.D. students received their own PRELUDIUM grants from the National Science Centre (NCN).

Natalia Szulc will study how the cullin-RING ubiquitin ligase complexes avoid premature degradation, and Pankaj Thapa will investigate the molecular mechanism of the activity switch of the ubiquitin ligase CHIP.

Publications

2022

A heterotypic assembly mechanism regulates CHIP E3 ligase activity
Das, A., Thapa, P., Santiago, U., Shanmugam, N., Banasiak, K., Dabrowska, K., Nolte, H., Szulc, N.A., Gathungu, R. M., Cysewski, D., Krueger, M., Dadlez, M., Nowotny, M., Camacho, C. J., Hoppe, T., & Pokrzywa, W.*
EMBO Journal
doi: 10.15252/embj.2021109566 

fingeRNAt - a novel tool for high-throughput analysis of nucleic acid-ligand interactions
Szulc, N.A.*, Mackiewicz, Z., Bujnicki, J.M., & Stefaniak F.
PLOS Computational Biology
doi: 10.1371/journal.pcbi.1009783 

DEGRONOPEDIA - a web server for proteome-wide inspection of degrons
Szulc N.A.*, Stefaniak F., Piechota M., Cappannini A., Bujnicki J.M. & Pokrzywa W.*
bioRxiv
doi: 10.1101/2022.05.19.492622 

CHIP ubiquitin ligase is involved in the nucleolar stress management
Piechota M.*, Biriczova L., Kowalski K., Szulc N.A. & Pokrzywa W.*
bioRxiv
doi: 10.1101/2022.05.17.492288

A novel de novo FEM1C variant as a potential cause of neurodevelopmental disorder with absent speech, pyramidal signs, and limb ataxia
Dubey A.A., Krygier M., Szulc N.A., Rutkowska K., Kosinska J., Pollak A., Rydzanicz M., Kmiec T., Mazurkiewicz-Beldzinska M., & Pokrzywa W.*, Ploski R.*
bioRxiv
doi: 10.1101/2022.04.24.489208

Impaired iron recycling from erythrocytes is an early iron-dependent hallmark of aging
Mandal, P. K., Slusarczyk P., Zurawska G., Cybulska M., Krawczyk O., Mikula M., Herman S., Lenartowicz M., Serwa R., Pokrzywa W., & Mleczko-Sanecka K.
bioRxiv
doi: 10.1101/2022.01.16.476518 

2021

fingeRNAt - a novel tool for high-throughput analysis of nucleic acid-ligand interactions
Szulc, N.A.*, Mackiewicz, Z., Bujnicki, J.M., & Stefaniak F.
bioRxiv
doi: 10.1101/2021.12.23.474073 

Heterotypic assembly mechanism regulates CHIP E3 ligase activity
Das, A., Thapa, P., Santiago, U., Shanmugam, N., Banasiak, K., Dabrowska, K., Nolte, H., Szulc, N.A., Gathungu, R. M., Cysewski, D., Krueger, M., Dadlez, M., Nowotny, M., Camacho, C. J., Hoppe, T., & Pokrzywa, W.*
bioRxiv
doi: 10.1101/2021.08.20.457118 

Muscle-derived exophers promote reproductive fitness
Turek, M., Banasiak, K., Piechota, M., Shanmugam, N., Macias, M., Śliwińska, M. A., Niklewicz, M., Kowalski, K., Nowak, N., Chacinska, A., & Pokrzywa, W.*
EMBO reports
doi: 10.15252/embr.202052071 

Maintaining proteostasis under mechanical stress
Höhfeld, J., Benzing, T., Bloch, W., Fürst, D.O., Gehlert, S., Hesse, M., Hoffmann, B., Hoppe, T., Huesgen, P.F., Köhn, M., Kolanus, W., Merkel, R., Niessen, C. M., Pokrzywa, W., Rinschen, M.M., Wachten, D., & Warscheid, B.
EMBO reports
doi: 10.15252/embr.202152507 

The dose-dependent pleiotropic effects of the UBB+1 ubiquitin mutant
Banasiak, K., Szulc, N.A., & Pokrzywa, W.*
Frontiers in Molecular Biosciences
doi: 10.3389/fmolb.2021.650730 

2020

The ubiquitin-conjugating enzyme UBE2K determines neurogenic potential through histone H3 in human embryonic stem cells
Fatima, A., Irmak, D., Noormohammadi, A., Rinschen, M.M., Das, A., Leidecker, O., Schindler, C., Sánchez-Gaya, V., Wagle, P., Pokrzywa, W., Hoppe, T., Rada-Iglesias, A., & Vilchez, D.
Communications Biology
doi: 10.1038/s42003-020-0984-3 

Ubiquitin signaling regulates RNA biogenesis, processing, and metabolism
Thapa, P., Shanmugam, N., & Pokrzywa, W.*
BioEssays
doi: 10.1002/bies.201900171

CHIP ubiquitylates NOXA and induces its lysosomal degradation in response to DNA damage
Albert, M.-C., Brinkmann, K., Pokrzywa, W., Günther, S. D., Krönke, M., Hoppe, T., & Kashkar, H.
Cell Death & Disease
doi: 10.1038/s41419-020-02923-x 

Bioshell 3.0: Library for processing structural biology data
Macnar, J.M., Szulc, N.A., Kryś, J.D., Badaczewska-Dawid, A.E., & Gront, D.
Biomolecules
doi: 10.3390/biom10030461 

Pathogenic variants in the myosin chaperone UNC-45B cause progressive myopathy with eccentric cores
Donkervoort, S., Kutzner, C. E., Hu, Y., Lornage, X., Rendu, J., Stojkovic, T., Baets, J., Neuhaus, S.B., Tanboon, J., Maroofian, R., Bolduc, V., Mroczek, M., Conijn, S., Kuntz, N. L., Töpf, A., Monges, S., Lubieniecki, F., McCarty, R. M., Chao, K. R., Governali, S., Böhm, J., Boonyapisit, K., Malfatti, E., Sangruchi, T., Horkayne-Szakaly, I., Hedberg-Oldfors, C., Efthymiou, S., Noguchi, S., Djeddi, S., Iida, A., di Rosa, G., Fiorillo, C., Salpietro, V., Darin, N., Faure, J., Houlden, H., Oldfors, A., Nishino, I., de Ridder, W., Straub, V., Pokrzywa, W., Laporte, J., Foley, R., Romero, N.B., Ottenheijm, C., Hoppe, T., & Bönnemann, C.G.
The American Journal of Human Genetics
doi: 10.1016/j.ajhg.2020.11.002 

2018

Ubiquitylation pathways in insulin signaling and organismal homeostasis
Balaji, V., Pokrzywa, W., & Hoppe, T.
BioEssays
doi: 10.1002/bies.201700223 

The ubiquitin ligase UBR5 suppresses proteostasis collapse in pluripotent stem cells from Huntington’s disease patients
Koyuncu, S., Saez, I., Lee, H. J., Gutierrez-Garcia, R., Pokrzywa, W., Fatima, A., Hoppe, T., & Vilchez, D.
Nature Communications
doi: 10.1038/s41467-018-05320-3 

2017

Chaperone-directed ubiquitylation maintains proteostasis at the expense of longevity
Pokrzywa, W., Lorenz, R., & Hoppe, T.
Worm
doi: 10.1080/21624054.2017.137140 

CHIPped balance of proteostasis and longevity
Pokrzywa, W., & Hoppe, T.
Oncotarget
doi: 10.18632/oncotarget.22101 

Repair or destruction - an intimate liaison between ubiquitin ligases and molecular chaperones in proteostasis
Kevei, É., Pokrzywa, W., & Hoppe, T.
FEBS Letters
doi: 10.1002/1873-3468.12750 

Facilities

In the Pokrzywa lab, in addition to standard equipment and a coffee machine, we have several state-of-the-art research instruments for worms and proteins analysis, including:

WormLab® Imaging System

ScreenChip™ System

wMicroTracker

CherryTemp

ZEISS Axio Zoom.V16 Fluorescence Microscope

ÄKTA Go Protein Purification System


Funding

Logos of funding agencies
Open grants
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Closed grants
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Team

Principal Investigator

Photo of Dr. Wojciech Pokrzywa

Wojciech Pokrzywa, Ph.D., D.Sc.

During his Ph.D. studies at the Catholic University of Louvain, Belgium, Wojciech Pokrzywa investigated the function of the ubiquitin-proteasome system in regulating membrane protein localization in yeast. In 2009, he joined the laboratory of Thorsten Hoppe at the University of Cologne, Germany, where he studied the mechanisms of proteostasis during development and aging in Caenorhabditis elegans.
In mid-2017, he started his own research group in Warsaw focusing on the mechanisms of protein metabolism regulation.

Lab Members

Photo of lab members

Senior Researchers 

Małgorzata Piechota, Ph.D.


POSTDOCTORAL RESEARCHERS

Abhishek Dubey, Ph.D.

Laboratory Support Specialists 

Anna Grabowska, Ph.D.

Marta Niklewicz, M.Sc.

Lilla Biriczová, M.Sc.

Graduate Students

Aniruddha Das, M.Sc.

Pankaj Thapa, M.Sc.
Pratik Kumar Mandal, M.Sc.

Katarzyna Banasiak, M.Sc.

Natalia Szulc, M.Sc.

Anwesha Sarkar, M.Sc.


Undergraduate Students

Konrad Kowalski, B.Sc.

Join Us

Are you interested in molecular mechanisms of proteostasis? Are you looking for a passionate group of scientists with an exceptionally friendly working atmosphere? Why not join the Pokrzywa lab?

We are always looking for highly motivated individuals eager to pursue research in our group. If you are interested in possible future opportunities, please send us your CV.


If you are elligible, we encourage you to contact head of the lab - Wojciech Pokrzywa and apply for the POLONEZ BIS fellowship.  


Contact

Laboratory Manager

Anna Grabowska, Ph.D.

Phone: +48 22 597 07 77
Email: agrabowska@iimcb.gov.pl

Principal Investigator

Wojciech Pokrzywa, Ph.D., D.Sc. 

Phone: +48 22 597 07 43
Email: wpokrzywa@iimcb.gov.pl

Address

Laboratory of Protein Metabolism

International Institute of Molecular and Cell Biology in Warsaw

4 Ks. Trojdena Street

02-109 Warsaw, Poland 

IIMCB logo