LABORATORY OF PROTEIN METABOLISM

Wojciech Pokrzywa Lab

Who we are

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 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 exophergenesis

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 ( exophergenesis) represents a transgenerational metabolic/resource management system that supports embryos in utero. Currently, we investigate the mechanism of exopher formation and the regulation of exophergenesis 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

November 2022 | New preprint
published

Putative degron sites in filaggrin protein

Together with the group of Dr. Danuta Owsiak-Gutowska from the University of Gdańsk, we released a preprint where we shed some light on the degradation routes of filaggrin, an important protein in the pathogenesis of atopic dermatitis.

We show the involvement of the proteasome in filaggrin turnover and we describe filaggrin's potential degron sites and their effect on its mutated variants associated with the disease.

November 2022 | A Fulbrighter from our lab

Fulbright cover

We would like to congratulate our Ph.D. student Natalia on receiving the prestigious Fulbright Junior Research Award for the research stay at the Dana-Farber Cancer Institute in Boston.

November 2022 | New article
published

Aldicarb sensitivity assay

We are pleased that our collaboration with Prof. Rafał Płoski from the Medical University of Warsaw and Prof. Maria Mazurkiewicz-Bełdzińska from the Medical University of Gdańsk has resulted in a joint publication where we link an uncharacterized neurological disease with an ultra-rare mutation in FEM1C ubiquitin ligase.

In our article, we present the first evidence from an animal model, Caenorhabditis elegans nematode, suggesting that a mutation in the conserved FEM1C Asp126 position causes a neurodevelopmental disorder in humans.

October 2022 | Our presence
at the Rare Disease Congres

Wojciech presenting at the Rare Disease Congres

We are very grateful for the invitation to the Rare Disease Congres in Cracow from the Jesteśmy Pod Ścianą Foundation, an NGO supporting patients with rare diseases. Our PI, Wojciech, and Ph.D. student, Natalia, presented our research on an uncharacterized neurodevelopmental disorder caused by an ultra-rare mutation in the FEM1C ubiquitin ligase and chorea-acanthocytosis. We hope that our research will contribute to a better understanding of the molecular mechanisms underlying these diseases.

October 2022 | Our presence
at the FNP conference

Wojciech at the FNP conference

Our PI, Wojciech, presented the poster about our study that hit the cover of the prestigious EMBO Journal at the 4th Interdisciplinary FNP Conference, organized by our funding agency - the Foundation for Polish Science. We are very grateful for the obtained funds which enabled our research and hope for more exciting discoveries.

September 2022 | Lecture at the 26th Science Festival in Warsaw

Science Festival in Warsaw

Like last year, we were delighted to participate in the Science Festival in Warsaw, a well-recognized science popularization event in Poland. We unveiled some of the secrets of Caenorhabditis elegans and discussed its role in aging research. Students also had an opportunity to test their knowledge as we prepared a quiz with prizes.


We hope that we passed some of our fascination with this tiny creature to our listeners, and our lecture provided insight into the complex mechanisms of aging and the role of Caenorhabditis elegans in studying them.

September 2022 | M.Sc. thesis defense

Konrad after his defence

Congratulations to our M.Sc. student Konrad for graduating with a Master’s degree in Biotechnology at the University of Warsaw!


Konrad wrote his thesis about the role of human CHIP ubiquitin ligase in nucleolar protein recovery after heat stress and co-authored our recent preprint. We are very proud of you and wish you many more successes!

September 2022 | New grant
awarded

Logo of the Ministry of Education and Science

We are delighted to announce that we were awarded the Social Responsibility of Science (Społeczna Odpowiedzialność Nauki) grant from the Ministry of Education and Science for developing an educational computer game about protein degradation processes in the cell.


As we believe that science should break out of its ivory tower and be widely accessible, the aim of the proposed computer game would be to explain how cells maintain protein homeostasis and why its disruption may lead to disease. Stay tuned!

September 2022 | Our presence
at the C. elegans conference

Worm Meeting Basel

Katarzyna, our Ph.D. student, gave a talk on our soon-to-be-released study on muscular exopheresis in Caenorhabditis elegans at the Basel Worm Meeting.

We are delighted that it gained a lot of attention of the worm community and cannot wait to publish it.

Publications

2022

In silico analysis of the profilaggrin sequence indicates alterations in the stability, degradation route, and intracellular protein fate in filaggrin null mutation carriers
Paul A.A., Szulc N.A., Kobiela A., Brown S.J., Pokrzywa W.* & Owsiak-Gutowska D.*
Research Square
doi: 10.21203/rs.3.rs-2302890/v1 

A novel de novo FEM1C variant is linked to 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.*
Human Molecular Genetics
doi: 10.1093/hmg/ddac276 

A dimer-monomer switch controls CHIP-dependent substrate ubiquitylation and processing
Balaji V., Müller L., Lorenz R., Kevei E., Zhang W.H., Santiago U., Gebauer J., Llamas E., Vilchez D., Camacho C.J., Pokrzywa W. & Hoppe T.
Molecular Cell
doi: 10.1016/j.molcel.2022.08.003 

Ferritin-mediated iron detoxification promotes hypothermia survival in Caenorhabditis elegans and murine neurons
Pekec T., Lewandowski J., Komur A.A., Sobańska D., Guo Y., Świtońska-Kurkowska K., Małecki J.M., Dubey A.A., Pokrzywa W, Frankowski M., Figiel M. & Ciosk R.
Nature Communications
doi: 10.1038/s41467-022-32500-z 

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 is linked to 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 Prof. 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.

Konrad Kowalski, 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.

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

Principal Investigator

Wojciech Pokrzywa, Ph.D., D.Sc. 

Phone: +48 22 597 07 43
E-mail: wpokrzywa@iimcb.gov.pl

Laboratory Manager

Anna Grabowska, Ph.D.

Phone: +48 22 597 07 77
E-mail: agrabowska@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 

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