Welcome to the Knop Lab!

Welcome to the Knop Lab!

Systems biology, meiosis and signal transduction

Research in our lab focuses on the processes that regulate cellular morphogenesis and cell signaling. These are very active and rapidly evolving areas of research that are driven by work conducted with model organisms such as yeast, flies or worms. The studies provide important conceptual and experimental input into work conducted with medically relevant mammalian systems.

Cell differentiation processes are associated with cellular pathways that regulate structural functions and metabolic changes necessary that the cell can adopt its new role. Using yeast we study cell differentiation in meiosis, where yeast cell are prone to assemble spores inside the boundaries of the original cell. We also study the cellular response to external stimuli such as the yeast mating pheromone. This leads to stimulation of the cell via MAP kinase signaling pathways and to a polarization necessary for cell-to-cell fusion.

The small size of the yeast genome and the rich spectrum of available methods make this organism an ideal model system to decipher the machinery or the mechanistic principles behind these processes. The goal of our work is to obtain a systems-level understanding of the main molecular processes behind the regulatory as well as the structural aspects.

An important driver of our work is the ability to observe cellular processes by microscopic imaging methods, such as live cell imaging. Here we seek to continuously expand our methods in order to be able to image protein functions in more details. We use methods such as fluorescence cross-correlation spectroscopy (FCS/FCCS), fluorescence lifetime imaging (FLIM) and other so-called F-techniques, in order to obtain to information about bio-molecules and their interaction partners in their natural environment. We combine these functional high-content imaging methods with genetic and genomic approaches to explore the processes of interest.

We currently focus on the following areas:

1. We would like to understand the extent by which spatial partitioning of cells by reaction-diffusion mechanisms does contribute to the regulation of signal transduction processes.
2. We would like to understand the evolutionary dimension of molecular mechanisms. By comparing the situation in related species we can obtain insight into the constraints that shape particular processes.
3. We develop new approaches and microscopic methods in order to improve systemic studies towards the function of proteins within complex processes using novel high-content imaging or screening methods.

Selected Publications with corresponding authorship:

Multiplexed protein stability (MPS) profiling of terminal degrons using fluorescent timer libraries in Saccharomyces cerevisiae. Reinbold C, Kong KE, Kats I, Khmelinskii A, Knop M. Methods Enzymol. 2023;686:321-344. doi: 10.1016/bs.mie.2023.02.017. Epub 2023 Apr 4. PMID. 37532406

Scalable RT-LAMP-based SARS-CoV-2 testing for infection surveillance with applications in pandemic prepardeness. Lou D, Meurer M, Ovchinnikova S, Burk R, Denzler A, Herbst K, Papaioannou IA, Duan Y, Jacobs ML, Witte V, Ürge D, Kirrmaier D, Krogemann M, Gubicza K, Boerner K, Bundschuh C, Weidner NM, Merle U, Knorr B, Welker A, Denkinger CM, Schnitzler P, Kräusslich HG, Dao Thi VL, De Allegri M, Nguyen HT, Deckert A, Anders S, Knop M. EMBO Rep. 2023 May 4;24(5):e57162. doi:10.15252/embr.202357162.Epub 2023 Mar23.PMID36951170 Free PMC article.

Up-regulation of ubiquitin-proteasome activity upon loss of NatA-dependent N-terminal acetylation. Kats I, Reinbold C, Kschonsak M, Khmelinskii A, Armbruster L, Ruppert T, Knop M. Life Sci Alliance. 2021 Nov 11;5(2):e202000730. doi: 10.26508/lsa.202000730. Print 2022 Feb. PMID: 34764209 Free PMC article.

Sex without crossing over in the yeast Saccharomycodes ludwigii. Papaioannou IA, Dutreux F, Peltier FA, Maekawa H, Delhomme N, Bardhan A, Friedrich A, Schacherer J, Knop M. Genome Biol. 2021 Nov 3;22(1):303. doi: 10.1186/s13059-021-02521-w. PMID: 34732243 Free PMC article.

Timer-based proteomic profiling of the ubiquitin-proteasome system reveals a substrate receptor of the GID ubiquitin ligase. Kong KE, Fischer B, Meurer M, Kats I, Li Z, RÃƒÂ¼hle F, Barry JD, Kirrmaier D, Chevyreva V, San Luis BJ, Costanzo M, Huber W, Andrews BJ, Boone C, Knop Mhttps://pubmed.ncbi.nlm.nih.gov/33974913/, Khmelinskii A. Mol Cell. 2021 Jun 3;81(11):2460-2476.e11. doi: 10.1016/j.molcel.2021.04.018. Epub 2021 May 10. PMID: 33974913 Free PMC article.

Single-Color Fluorescence Lifetime Cross-Correlation Spectroscopy In Vivo. Ã…Â tefl M, Herbst K, RÃƒÂ¼bsam M, Benda A, Knop M. Biophys J. 2020 Oct 6;119(7):1359-1370. doi: 10.1016/j.bpj.2020.06.039. Epub 2020 Aug 20. PMID: 32919495 Free PMC article.

A colorimetric RT-LAMP assay and LAMP-sequencing for detecting SARS-CoV-2 RNA in clinical samples. Dao Thi VL, Herbst K, Boerner K, Meurer M, Kremer LP, Kirrmaier D, Freistaedter A, Papagiannidis D, Galmozzi C, Stanifer ML, Boulant S, Klein S, Chlanda P, Khalid D, Barreto Miranda I, Schnitzler P, KrÃƒÂ¤usslich HG, Knop M, Anders S. Sci Transl Med. 2020 Aug 12;12(556):eabc7075. doi: 10.1126/scitranslmed.abc7075. Epub 2020 Jul 27. PMID: 32719001 Free PMC article.

CRISPR-Cas12a-assisted PCR tagging of mammalian genes. Fueller J, Herbst K, Meurer M, Gubicza K, Kurtulmus B, Knopf JD, Kirrmaier D, Buchmuller BC, Pereira G, Lemberg MK, Knop M. J Cell Biol. 2020 Jun 1;219(6):e201910210. doi: 10.1083/jcb.201910210. PMID: 32406907 Free PMC article.

Pooled clone collections by multiplexed CRISPR-Cas12a-assisted gene tagging in yeast. Buchmuller BC, Herbst K, Meurer M, Kirrmaier D, Sass E, Levy ED, Knop M. Nat Commun. 2019 Jul 4;10(1):2960. doi: 10.1038/s41467-019-10816-7. PMID: 31273196 Free PMC article

Bicoid gradient formation mechanism and dynamics revealed by protein lifetime analysis. Durrieu L, Kirrmaier D, Schneidt T, Kats I, Raghavan S, Hufnagel L, Saunders TE, Knop M. Mol Syst Biol. 2018 Sep 4;14(9):e8355. doi: 10.15252/msb.20188355. PMID: 30181144 Free PMC article.

Genome-wide C-SWAT library for high-throughput yeast genome tagging. Meurer M, Duan Y, Sass E, Kats I, Herbst K, Buchmuller BC, Dederer V, Huber F, Kirrmaier D, Štefl M, Van Laer K, Dick TP, Lemberg MK, Khmelinskii A, Levy ED, Knop M. Nat Methods. 2018 Aug;15(8):598-600. doi: 10.1038/s41592-018-0045-8. Epub 2018 Jul 9. PMID: 29988096

Mapping Degradation Signals and Pathways in a Eukaryotic N-terminome. Kats I, Khmelinskii A, Kschonsak M, Huber F, Knieß RA, Bartosik A, Knop M. Mol Cell. 2018 May 3;70(3):488-501.e5. doi: 10.1016/j.molcel.2018.03.033. PMID: 29727619

SPIM: high NA high resolution isotropic light-sheet imaging in cell culture dishes. Theer P, Dragneva D, Knop M. Sci Rep. 2016 Sep 13;6:32880. doi: 10.1038/srep32880. PMID: 27619647 Free PMC article.

Protein Abundance Control by Non-coding Antisense Transcription. Huber F, Bunina D, Gupta I, Khmelinskii A, Meurer M, Theer P, Steinmetz LM, Knop M. Cell Rep. 2016 Jun 21;15(12):2625-36. doi: 10.1016/j.celrep.2016.05.043. Epub 2016 Jun 9. PMID: 27292640 Free PMC article.

Incomplete proteasomal degradation of green fluorescent proteins in the context of tandem fluorescent protein timers. Khmelinskii A, Meurer M, Ho CT, Besenbeck B, Füller J, Lemberg MK, Bukau B, Mogk A, Knop M. Mol Biol Cell. 2016 Jan 15;27(2):360-70. doi: 10.1091/mbc.E15-07-0525. Epub 2015 Nov 25. PMID: 26609072 Free PMC article.

Protein quality control at the inner nuclear membrane. Khmelinskii A, Blaszczak E, Pantazopoulou M, Fischer B, Omnus DJ, Le Dez G, Brossard A, Gunnarsson A, Barry JD, Meurer M, Kirrmaier D, Boone C, Huber W, Rabut G, Ljungdahl PO, Knop M. Nature. 2014 Dec 18;516(7531):410-3. doi: 10.1038/nature14096. PMID: 25519137 Free PMC article.

PSFj: know your fluorescence microscope. Theer P, Mongis C, Knop M. Nat Methods. 2014 Oct;11(10):981-2. doi: 10.1038/nmeth.3102. PMID: 25264772 No abstract available.

Analytical model for macromolecular partitioning during yeast cell division. Kinkhabwala A, Khmelinskii A, Knop M. BMC Biophys. 2014 Sep 23;7:10. doi: 10.1186/s13628-014-0010-6. eCollection 2014. PMID: 25737777 Free PMC article.

Spindle pole body-anchored Kar3 drives the nucleus along microtubules from another nucleus in preparation for nuclear fusion during yeast karyogamy. Gibeaux R, Politi AZ, Nédélec F, Antony C, Knop M. Genes Dev. 2013 Feb 1;27(3):335-49. doi: 10.1101/gad.206318.112. PMID: 23388829 Free PMC article.

Tandem fluorescent protein timers for in vivo analysis of protein dynamics. Khmelinskii A, Keller PJ, Bartosik A, Meurer M, Barry JD, Mardin BR, Kaufmann A, Trautmann S, Wachsmuth M, Pereira G, Huber W, Schiebel E, Knop M. Nat Biotechnol. 2012 Jun 24;30(7):708-14. doi: 10.1038/nbt.2281. PMID: 22729030

Quantitative fluorescence imaging of protein diffusion and interaction in living cells. Capoulade J, Wachsmuth M, Hufnagel L, Knop M. Nat Biotechnol. 2011 Aug 7;29(9):835-9. doi: 10.1038/nbt.1928. PMID: 21822256

Segregation of yeast nuclear pores. Khmelinskii A, Keller PJ, Lorenz H, Schiebel E, Knop M. Nature. 2010 Jul 22;466(7305):E1. doi: 10.1038/nature09255. PMID: 20651645

Evolution of mutational robustness in the yeast genome: a link to essential genes and meiotic recombination hotspots. Keller PJ, Knop M. PLoS Genet. 2009 Jun;5(6):e1000533. doi: 10.1371/journal.pgen.1000533. Epub 2009 Jun 26. PMID: 19557188 Free PMC article.

The SpoMBe pathway drives membrane bending necessary for cytokinesis and spore formation in yeast meiosis. Maier P, Rathfelder N, Maeder CI, Colombelli J, Stelzer EH, Knop M. EMBO J. 2008 Sep 17;27(18):2363-74. doi: 10.1038/emboj.2008.168. Epub 2008 Aug 28. PMID: 18756268 Free PMC article.

Spatial regulation of Fus3 MAP kinase activity through a reaction-diffusion mechanism in yeast pheromone signalling. Maeder CI, Hink MA, Kinkhabwala A, Mayr R, Bastiaens PI, Knop M. Nat Cell Biol. 2007 Nov;9(11):1319-26. doi: 10.1038/ncb1652. Epub 2007 Oct 21. PMID: 17952059

Evolution of the hemiascomycete yeasts: on life styles and the importance of inbreeding. Knop M. Bioessays. 2006 Jul;28(7):696-708. doi: 10.1002/bies.20435. PMID: 16929561 Review.

Spore number control and breeding in Saccharomyces cerevisiae: a key role for a self-organizing system. Taxis C, Keller P, Kavagiou Z, Jensen LJ, Colombelli J, Bork P, Stelzer EH, Knop M. J Cell Biol. 2005 Nov 21;171(4):627-40. doi: 10.1083/jcb.200507168. Epub 2005 Nov 14. PMID: 16286509 Free PMC article