娩佾樽

PhD project - Elucidating the mechanisms of cell cycle control in the Archaea using the hyperthermophilic crenarchaeon Sulfolobus islandicus as a model organism

Introduction
Our knowledge about the taxonomic diversity of the Archaea domain has expanded greatly in the recent years thanks to advances in DNA sequencing approaches, with over 30 phyla now described. The Archaea are widespread, they include some of the most abundant organisms on Earth and are crucial for nutrient cycling and ecology (1). Moreover, the acquired knowledge about archaeal diversity has provided new insights into the evolution of eukaryotes (2). Despite all of the above, very little is known about archaeal physiology and particularly about cell cycle regulation. The cell cycle is the series of events in which cells obtain mass, replicate their genome and segregate into two daughter cells. Cell cycle control is crucial for all living organisms and there is ample knowledge of bacterial and eukaryote cell cycles where multiple players have been described and several mechanisms are known to participate (3, 4). In contrast, only two proteins are reported to regulate cell cycle progression in archaea at the transcriptional level: the first one is CdrS (5), which activates cell division genes in euryarchaea; the second is aCcr-1, which we have recently characterized and inhibits cell division and chromosome partitioning in the Sulfolobales (6).
Project
We use the hyperthermophilic crenarchaeon Sulfolobus islandicus as our research model because it is amenable to genetic manipulation and has an ESCRT-based cell division machinery with defined cell cycle phases and strictly controlled chromosome copies, replication and segregation, traits that are also present in eukaryotes (7). The aim of this project is to identify and characterize additional players participating in the transcriptional regulation of cell cycle progression in Sulfolobus and to identify additional mechanisms involved in cell cycle control. Furthermore, we want to expand our understanding of cell cycle regulation to other taxons of the Archaea. We envisage to apply different approaches including genetics, fluorescence microscopy, biochemical assays and phylogenomics. The results obtained will be relevant for the understanding of archaeal biology and can give evolutionary insight into the function and origin of eukaryotic cell division.
Profile of applicants
Applicants should hold a Master’s degree in any field of Life Sciences. A background in prokaryote molecular biology, cell biology, biochemistry or bioinformatics is preferred, but not mandatory. Medium to high proficiency in English is required.
Environment
You will join the Microbial Immunity group ( https://www1.bio.ku.dk/english/research/fg/peng/ ) headed by Professor Xu Peng at the University of Copenhagen, Denmark. We are an international
group investigating diverse aspects of archaeal biology, with particular focus in virus-host interactions within the hyperthermophilic crenarchaea and a strong background in microbial immunity. The group has experience with archaeal and bacterial CRISPR-Cas systems and its viral counterparts, the anti-CRISPRs.  The laboratory has all equipment and expertise to grow and genetically engineer Sulfolobus and its viruses. Other than Sulfolobus, the lab has experience with CRISPR-Cas systems of gram-positive, acidophilic bacteria (e.g. Lactobacillus, Streptococcus). As a PhD student at our group, you will be exposed to different topics related to microbiology and participate in frontier research projects. Additionally, the University of Copenhagen is among the top 30 universities internationally with a strong PhD student network.
Applications
Aspirants that had their visa application rejected by the U.S.A. immigration are encouraged to submit an application with us.
Applications should be addressed to peng@bio.ku.dk and include a full CV and motivation statement. Additional questions about the project or the position can be addressed to Li Xuyang (xuyang.li@bio.ku.dk) or Laura Martínez Alvarez (laura.martinez@bio.ku.dk).
References
1.         Tahon G, Geesink P, Ettema TJG. 2021. Expanding Archaeal Diversity and Phylogeny: Past, Present, and Future. Annual Review of Microbiology 75:359–381.
2.         Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Bäckström D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJG. 2017. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541:353–358.
3.         Bähler J. 2005. Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet 39:69–94.
4.         Margolin W, Bernander R. 2004. How Do Prokaryotic Cells Cycle? Current Biology 14:R768–R770.
5.         Darnell CL, Zheng J, Wilson S, Bertoli RM, Bisson-Filho AW, Garner EC, Schmid AK. 2020. The Ribbon-Helix-Helix Domain Protein CdrS Regulates the Tubulin Homolog ftsZ2 To Control Cell Division in Archaea. mBio 11:e01007-20.
6.         Li X, Lozano-Madueño C, Martínez-Alvarez L, Peng X. 2022. A clade of RHH proteins ubiquitous in Sulfolobales and their viruses regulates cell cycle progression. bioRxiv https://doi.org/10.1101/2022.07.28.501860.
7.         Bernander R. 2007. The cell cycle of Sulfolobus. Mol Microbiol 66:557–562.
8.         Tesson F, Hervé A, Mordret E, Touchon M, d’Humières C, Cury J, Bernheim A. 2022. Systematic and quantitative view of the antiviral arsenal of prokaryotes. 1. Nat Commun 13:2561.
9.         Doron S, Melamed S, Ofir G, Leavitt A, Lopatina A, Keren M, Amitai G, Sorek R. 2018. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359:eaar4120.
10.         Gao L, Altae-Tran H, Böhning F, Makarova KS, Segel M, Schmid-Burgk JL, Koob J, Wolf YI, Koonin EV, Zhang F. 2020. Diverse enzymatic activities mediate antiviral immunity in prokaryotes. Science 369:1077–1084.
11.         Pawluk A, Davidson AR, Maxwell KL. 2018. Anti-CRISPR: discovery, mechanism and function. Nat Rev Microbiol 16:12–17.
12.         Makarova KS, Wolf YI, Iranzo J, Shmakov SA, Alkhnbashi OS, Brouns SJJ, Charpentier E, Cheng D, Haft DH, Horvath P, Moineau S, Mojica FJM, Scott D, Shah SA, Siksnys V, Terns MP, Venclovas Č, White MF, Yakunin AF, Yan W, Zhang F, Garrett RA, Backofen R, van der Oost J, Barrangou R, Koonin EV. 2020. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants. 2. Nat Rev Microbiol 18:67–83.
13.         He F, Bhoobalan-Chitty Y, Van LB, Kjeldsen AL, Dedola M, Makarova KS, Koonin EV, Brodersen DE, Peng X. 2018. Anti-CRISPR proteins encoded by archaeal lytic viruses inhibit subtype I-D immunity. Nat Microbiol 3:461–469.
14.         Bhoobalan-Chitty Y, Johansen TB, Di Cianni N, Peng X. 2019. Inhibition of Type III CRISPR-Cas Immunity by an Archaeal Virus-Encoded Anti-CRISPR Protein. Cell 179:448-458.e11.
15.         Athukoralage JS, McMahon SA, Zhang C, Grüschow S, Graham S, Krupovic M, Whitaker RJ, Gloster TM, White MF. 2020. An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity. Nature 577:572–575.