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Chair of Cell and Developmental Biology (Zoology I)

kramer lab

The major aim of our research is to understand how spatial aspects of mRNA metabolism contribute to the posttranscriptional regulation of gene expression in eukaryotes.

Research synopsis

In the Kramer lab, we use Trypanosomes as a system to study mRNA metaoblism pathways. Trypanosomes are close to the root of the last common eukaryotic ancestor and research helps to understand how eukaryote-specific features of mRNA metabolism have evolved. In addition, differences between trypanosomes and mammals can be exploited for drug development against Kinetoplastida-caused diseases. We are specialised in employing imaging based methods, such as smFISH, of which we have pioneered several variants that allow to detect transcription and decay intermediates as well as compactness of mRNAs. We have a strong background in RNA granules: the first purification of starvation stress granules was done in trypanosomes, using the peripheral cytoskeleton as a molecular sieve. Currently, the lab interest is divided two-fold: (i) we study nuclear pores, mRNA export and its contrrol mechanisms and (ii) we study the novel mRNA decapping enzyme ALPH1, also with the focus of employing this enzyme as a drug target.

Selected recent publications

Kramer,S., Karolak,N.K., Odenwald,J., Gabiatti,B., Castañeda Londoño,P.A., Zavřelová,A., Freire,E.R., Almeida,K.S., Braune,S., Moreira,C., et al. (2023) A unique mRNA decapping complex in trypanosomes. Nucleic Acids Res., 10.1093/nar/gkad497. PMID37309887

Moreira, C. M. do N. et al. (2022) Impact of inherent biases built into proteomic techniques: Proximity labeling and affinity capture compared. J Biol Chem 102726  PMID: 36410438

Londono, P. A. C., Banholzer, N., Bannerman, B. P. & Kramer, S. (2021) Is mRNA decapping activity of ApaH like phosphatases (ALPH’s) the reason for the loss of cytoplasmic ALPH’s in all eukaryotes but Kinetoplastida? doi:10.21203/rs.3.rs-192222/v1. PMID: 34162332

Kramer, S., Meyer-Natus, E., Stigloher, C., Thoma, H., Schnaufer, A. and Engstler M. (2020) Parallel monitoring of RNA abundance, localisation and compactness with correlative single molecule FISH on LR White embedded samples. Nucleic Acids Res 49, gkaa1142- PMID: 33275141

Goos C, Dejung M, Wehman AM, Meyer-Natus E, Schmidt J, SunterJ , Engstler M, Butter F and Kramer S. (2019) Trypanosomes can initiate nuclear export co-transcriptionally. Nucleic Acid research, in press PMID:30418648

Kramer S and McLennan AG. (2018) The complex enzymology of mRNA decapping: enzymes of four classes cleave pyrophosphate bounds.WIREs RNA 38, e1511–17. PMID:30345629

Kramer S (2017). The ApaH-like phosphatase TbALPH1 is the major mRNA decapping enzyme of trypanosomes. PLoS Pathog 13: e1006456 PMID:28628654

Kramer S (2017). Simultaneous detection of mRNA transcription and decay intermediates by dual colour single mRNA FISH on subcellular resolution. Nucleic Acids Res 45: e49 PMID:27940558

full list of publications

NEWs

Visitors from Brazil

11th-13th of September, 2023

Osvaldo Pompilio de Melo Neto from Instituto Aggeu Magalhães/Fundação Oswaldo Cruz and Fabiola Holetz from FIOCRUZ - PARANÁ
 have been visiting the lab. Osvaldo gave a great talk about trypanosome translation initiation factors and we had phantastic scientific discussions, on projects of ongoing and future colaborations.

Nancy Standart visits for Bernardos PhD progress report

21-22th August 2022

Bernardo gave a wonderful talk. Thanks to all members of the thesis commitee and in particular to Nancy, for very helpful input and discussions. 

Susanne in Brazil

Jun 2023

Susanne visits our long-term collaborator Fabiola Holetz at the Carlos Chagas Insitute in Curitiba.

Labmeeting in Prague

9th of February, 2023

Johanna und Susanne visit Prague, to discuss APEX and Co with Martin, SIqi und Farnaz. 

спасибо GORBI

30th August 2022

... the Kramer lab would not exist without you.

RIP

Nuclear export in Potsdam

Jul 2022

Johanna and Bernardo present their work at the DGZ meeting "Life at the edge: the nuclear envelope and nucleocytoplasmic transport".

Visitors from Prague

11th to 13th May, 2022

Our collaborators from Martin Zoltners lab in Prague visited. We had a great and productive time together, discussing our joined project and plans for the next grant application. 

Discussing ALPH in Warsaw

7th Dec 2021

Start up meeting in Warsaw with Maria GoRNA and Martin Zolter to plan how to employ ALPH as a drug target.

Joined Lab-Meeting in Prague

Sep 2021

We had our first in-person meeting since Corona: with our collaborators from the Zoltner lab at the Biocev near Prague. Zoom can never replace real meetings.

We have moved to our new lab!

2nd and 3rd June, 2021

This week we have moved into our new lab and we even found a place for the picture that we inherited. There are still some small issues to sort out, but in principle the lab is already fully functional and we look forwards to testing it with exciting experiments. 

14 DAYS of Quarantine

April/May 2021

Covid once again, Lisa got the virus, but nobody else got infected :-). Here are images from our (almost) daily quarantine Zoom Meetings.

First PhD defence of the Kramer lab

14th April 2021

The Kramer lab has its first Doktor! Carina Goos successfully defended her Thesis. Many congratulations, Carina!

RNA 2019

June, 2019

We met with our Polish Collaboraters from the laboratory of Maria Gorna at the RNA society meeting in Krakow. Together we will unravel the secrets of the trypanosome decapping enzyme !

RESEARCH TOPICS

mRNA granules

Many non-polysomal mRNAs aggregate into RNA granules, large ribonucleoprotein particles. What is the composition and function of RNA granules and how are they regulated?

mRNA decay

The first step in mRNA decay is the removal of the 5' cap. In trypanosomes, this is done by a highly unusual enzyme, an ApaH like phosphatase.

mRNA export

We recently found that trypanosomes can export their mRNAs co-transcriptionally.

CURRENT LAB MEMBERS

Silke Braune

Carolin Schlitz

PhD, Postdoc

José Carlos Quilles Junior (2022-2023)

ncRNAs in Leishmania

Paula Castaneda Londono (2022)

In vitro characterisation of the mRNA decapping enzyme ALPH1

Claudia Moreira (2019)

Establishing novel proximity labelling techniques (Postdoc)

Carina Goos (2017 / Defense 2021)

Purification and characterisation of trypanosome nuclear periphery granules

Master Students

Lilith Babilon/Ruis (2023)

Functional analysis of the mRNA decapping complex in Trypanosoma brucei

Johanna Odenwald (2021)

Interactions and Function of a novel mRNA decapping enzyme from Trypanosoma brucei

Andrea Reichert (2018)

Untersuchungen zur Funktion der spezifischen Lokalisation des T. brucei mRNA-Decapping-Enzyms

Nadja Sauer (2016) 

In vivo Markierung von mRNAs in RNP Granula durch photoaktivierbare, abstandsabhängige Biotinylierung: Etablierung der Methode

Hanna Thoma (2016)

Warum sind für ribosomale Proteine kodierende mRNAs aus Stress-Granula ausgeschlossen?

Christina Julia Lorenz (2015, extern in Cambridge)

Identification of interaction partners of the DEAD-box RNA helicase DHH1 in Trypanosoma brucei

Nina Krienitz (2015, extern Cambridge and Dundee)

Implementation of a novel cryomilling method to analyse protein and RNA interactions of the poly(A)-binding proteins in Trypanosoma brucei

Melanie Fritz (2014)

Zusammensetzung und Ultrastruktur von Stress-Granula in Trypanosoma brucei brucei

Bachelor Students

Amelie Eder (2022)

Untersuchungen zum Interaktom des Trypanosomen mRNA Decapping Enzyms ALPH1

Marko Korb (2022)

Serum-Abhängigkeit von Trypanosoma brucei brucei Kulturen: Untersuchungen zur Reduktion der benötigten FCS-Konzentration

Lisa Marie-Hofacker (2021)

Etablierung einer induzierbaren Bio-ID Methode in Trypanosoma brucei

Nicole Banholzer (2019)

Charakterisierung eines neuen mRNA Decapping-Enzyms aus Trypanosomen

Anna Sophie Kreis (2019)

Etablierung einer Methode zur mRNA-Visualisierung mittels CRISPR/dCAS13

Laura Gauglitz (2018)

Etablierung einer neuen BioID Methode in Trypanosomen

Laura Peters (2017)

Warum sind mRNAs, die für ribosomale Proteine kodieren, aus Stress-Granula ausgeschlossen?

Till Elharrar (2015)

Validierung der Lokalisation zu ‘Nuclear periphery granules’ von neu identifizierten Proteinkandidaten

Nadja Sauer (2014)

Überprüfung neuer Stressgranula-Protein-Kandidaten in Trypanosoma brucei

Daja Schichler (2014)

Analyse von RNA-Granula in Trypanosoma brucei

Melanie Fritz (2012)

Charakterisierung von Stress-Granula in Trypanosoma brucei brucei

Mario Hofweber (2012)

Ist das trypanosomale P-body Protein SCD6 ein Multimer?

Internship

Johanna Meyer (2023)

Nico Ankenbrand (2022)

Delara Shahidi (2021)

Sisco Jung (2021)

Frederik Heim

Corinna Kronenthaler

Johannes Schmidt

Bilal Tetik

Susheela Behera

FUNDING