Thorsten Allers

Contact

• workRoom D114 School of Life Sciences
  Queen's Medical Centre
  Nottingham
  NG7 2UH
  UK
• work0115 823 0304
• fax0115 823 0338
• thorsten.allers@nottingham.ac.uk
• http://www.nottingham.ac.uk/life-sciences/people/thorsten.allers

Biography

• BA, Genetics, University of Cambridge (1989)
• PhD, Cell and Molecular Biology, University of Edinburgh (1994)
• Research Assistant, University of Edinburgh (1994-1995)
• Visiting Postdoctoral Fellow, National Cancer Institute, NIH, USA (1995-2001)
• Wellcome Trust Postdoctoral Fellow, University of Nottingham (2001-2002)
• Royal Society University Research Fellow (2002-2007, renewed 2007-2010)
• Lecturer, University of Nottingham (2010-2014)
• Associate Professor, University of Nottingham (2014-2018)
• Professor, University of Nottingham (2018-present)

Teaching Summary

I teach a 3rd year module 'Ageing, Sex and DNA Repair' (C43629) in the spring semester. In this module, I examine how the process of ageing is related to DNA damage, study the cellular mechanisms… read more

Research Summary

We are using genetics and biochemistry to understand how DNA replication, recombination and repair operate in the Archaea.

Archaea are the third domain of life alongside bacteria and eukaryotes. Archaea live in extremely harsh environments such as boiling acid pools or salt lakes, which pose enormous challenges for growth and DNA stability. For more information on Archaea, see https://youtu.be/hw-ij3822DY

^{Salt works at Red Sea, Israel, and acid pool in Yellowstone National Park, USA}

We are interested in how DNA replication, recombination and repair have evolved to meet these challenges, and how they operate in an evolutionary lineage that is fundamentally distinct from bacteria and eukaryotes.

^{The tree of life has three domains}

Archaea show many similarities to eukaryotic cells, particularly in the proteins used for DNA replication, repair and recombination. Studies of the archaea may therefore help with the dissection of more complex eukaryotic systems.

We have developed genetic and biochemical systems using Haloferax volcanii as a model organism. Haloferax volcanii was isolated from the Dead Sea and is an obligate halophile.

^{Haloferax volcanii was isolated from the Dead Sea. It is easily grown in the lab}

Haloferax volcanii grows aerobically at 45°C in media containing 2.5 M NaCl, it can be cultivated in the laboratory with ease. Many genetic and biochemical tools are available for Haloferax volcanii.

^{Sampling for Haloferax volcanii from the Dead Sea}

Genetic and biochemical tools for Haloferax volcanii include a markerless gene knockout system, several auxotrophic and antibiotic-resistance markers, reporter genes, an inducible promoter and plasmid vectors for protein over-expression.

^{Genetic and biochemical tools for Haloferax volcanii}

Our research is focused on four areas: DNA replication origins, homologous recombination, DNA double-strand break repair, and DNA helicases.

DNA replication origins

DNA replication initiates at defined sites on the chromosome called origins. Bacteria, which have small circular chromosomes, have one replication origin. Eukaryotes have large linear chromosomes, therefore they require many replication origins.

^{DNA replication initiates at origins}

Archaea have small circular chromosomes like bacteria, but have several replication origins like eukaryotes. The DNA replication machinery used in archaea and eukaryotes is strikingly similar.

^{DNA replication machinery}

The chromosome of Haloferax volcanii has several DNA replication origins. We are investigating how DNA replication initiates at these origins and how this process is regulated.

^{Haloferax volcanii laboratory strain H26 has four replication origins, but none is needed for DNA replication}

Intriguingly, Haloferax volcanii does not need DNA replication origins. In fact, a mutant strain lacking all origins grows significantly faster than the wild type. We have discovered that cells without origins use homologous recombination to initiate DNA replication.

^{Cells without origins grow faster than wild-type, but the (tryptophan-inducible) radA gene is essential}

Homologous recombination

Homologous recombination is an important pathway of DNA repair, it is also used to restart stalled DNA replication and to generate genetic diversity. Homologous recombination involves the exchange of DNA strands of identical sequence.

^{Strand exchange is catalysed by RadA, which polymerises on DNA}

Recombination is carried out by RecA-family recombinases, which catalyse the strand exchange of homologous DNA sequences. Archaeal and eukaryotic recombinases are very similar to each other. We are investigating how recombination in archaea is carried out by RadA.

^{RecA-family recombinases from archaea, bacteria and eukaryotes}

In archaea such as Haloferax volcanii, homologous recombination is carried out with assistance by RadB protein. RadB is related to RadA and the two proteins interact with each other. But unlike RadA, RadB cannot carry out strand exchange. We are investigating the role of RadB.

^{RadB is related to RadA but cannot catalyse strand exchange}

DNA double-strand break repair

Double-stranded breaks in DNA are very dangerous and can lead to cell death or cancer. This type of DNA damage is detected by the Mre11-Rad50 complex, it binds directly to the broken end and helps to coordinate DNA repair.

^{Mre11-Rad50 complex binds to DNA double strand breaks}

We are investigating how the repair of DNA double-strand breaks is carried out in archaea. Intriguingly, deletion of the mre11 or rad50 genes makes Haloferax volcanii more resistant to DNA damage, but the cells recover more slowly.

^{Cells after irradiation with UV light}

After DNA damage, the chromosome of Haloferax volcanii is reorganized into a compacted shape. This process is catalysed by the Mre11-Rad50 complex and may help with the rapid recovery from DNA double-strand breaks.

^{Chromosomal DNA is compacted after DNA damage}

DNA helicases

Helicases are enzymes that separate the two complementary strands of an DNA or RNA duplex. Helicases play many important roles in the cell during processes such as transcription, DNA replication and repair. Mutations in helicase genes are frequently associated with cancer.

^{Helicases such as Hel308 unwind DNA}

Hel308 is a helicase that is conserved across metazoans (multicellular animals) and archaea, but is absent from bacteria and fungi. Hel308 helicase is involved in DNA repair and recombination. We are investigating the role of Hel308 in Haloferax volcanii.

Current lab members Rebecca Lever, Patricia Perez Arnaiz, Laura Mitchell,Thorsten Allers, Victoria Smith, Ambika Dattani, Nathan Jones and Çağla Tosun

Former lab members

2017 Hannah Marriott, Nathan Jones, Patricia Perez Arnaiz, Alexandra Schindl, Laura Mitchell,Thorsten Allers, Jaime Hughes, Rebecca Lever, RisatHaque and Dasha Ausiannikava

2015 Dasha Ausiannikava, Hannah Marriott, Laura Mitchell, Rebecca Gamble-Milner, Charlie Wickham-Smith, Thorsten Allers and Leonardo Oliveira

2013 Rebecca Milner, Thorsten Allers and Kayleigh Wardell

2008 Zhenhong (Belinda) Duan, Michelle Hawkins, Stéphane Delmas, Thorsten Allers, Amy Stroud and Sam Haldenby

Selected Publications

• WHITE MF and ALLERS T, 2018. DNA repair in the Archaea - an emerging picture. FEMS microbiology reviews. 42(4), 514-526
• AUSIANNIKAVA D, MITCHELL L, MARRIOTT H, SMITH V, HAWKINS M, MAKAROVA KS, KOONIN EV, NIEDUSZYNSKI CA and ALLERS T, 2018. Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii. Molecular biology and evolution. 35(8), 1855-1868
• WARDELL K, HALDENBY S, JONES N, LIDDELL S, NGO GHP and ALLERS T, 2017. RadB acts in homologous recombination in the archaeon Haloferax volcanii, consistent with a role as recombination mediator. DNA repair. 55, 7-16
• HAWKINS, M., MALLA, S., BLYTHE, M.J., NIEDUSZYNSKI, C.A. and ALLERS, T., 2013. Accelerated growth in the absence of DNA replication origins. Nature. 503, 544-547

• View all publications

We are accepting applications year-round for PhD and MRes studentships. More details are available on FindAPhD, specific projects include:

• DNA replication, recombination and repair in Archaea
• Discovering new DNA repair enzymes using archaea as a model for mammals

I teach a 3rd year module 'Ageing, Sex and DNA Repair' (C43629) in the spring semester. In this module, I examine how the process of ageing is related to DNA damage, study the cellular mechanisms that have evolved to repair damage, and explain how defects in these repair pathways can lead to mutation, cancer, ageing and death. The topics covered include:

• Theories of ageing, the role of DNA damage
• Direct repair of DNA damage
• Base and nucleotide excision repair, mismatch repair
• The eukaryotic cell cycle and checkpoints
• Homologous recombination in bacteria, yeast and higher eukaryotes
• Non-homologous end joining and V(D)J recombination

I also teach a 2nd year module 'Bacterial Genes and Development' (C42418) in the spring semester. The convenor for this module is Professor Liz Sockett. Together we examine the different mechanisms of gene regulation in bacteria and their viruses. The topics I cover include:

• RNA polymerase and the regulation of transcription
• The lac operon and transcription attenuation
• Bacterial sporulation
• Bacteriophage lambda

• HAQUE RU, PARADISI F and ALLERS T, 2019. Haloferax volcanii as immobilised whole cell biocatalyst: new applications for halophilic systems. Applied microbiology and biotechnology. (In Press.)
• BRAUN F, THOMALLA L, VAN DER DOES C, QUAX TEF, ALLERS T, KAEVER V and ALBERS SV, 2019. Cyclic nucleotides in archaea: Cyclic di-AMP in the archaeon Haloferax volcanii and its putative role. MicrobiologyOpen. e829 (In Press.)
• KELLY SA, MAGILL DJ, MEGAW J, SKVORTSOV T, ALLERS T, MCGRATH JW, ALLEN CCR, MOODY TS and GILMORE BF, 2019. Characterisation of a solvent-tolerant haloarchaeal (R)-selective transaminase isolated from a Triassic period salt mine. Applied microbiology and biotechnology. (In Press.)
• BLOMBACH F, AUSIANNIKAVA D, FIGUEIREDO AM, SOLOVIEV Z, PRENTICE T, ZHANG M, ZHOU N, THALASSINOS K, ALLERS T and WERNER F, 2018. Structural and functional adaptation of Haloferax volcanii TFEα/β. Nucleic acids research. 46(5), 2308-2320
• AUSIANNIKAVA D, MITCHELL L, MARRIOTT H, SMITH V, HAWKINS M, MAKAROVA KS, KOONIN EV, NIEDUSZYNSKI CA and ALLERS T, 2018. Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii. Molecular biology and evolution. 35(8), 1855-1868
• WHITE MF and ALLERS T, 2018. DNA repair in the Archaea - an emerging picture. FEMS microbiology reviews. 42(4), 514-526
• AUSIANNIKAVA D and ALLERS T, 2017. Diversity of DNA Replication in the Archaea. Genes. 8(2), 56
• STACHLER AE, TURGEMAN-GROTT I, SHTIFMAN-SEGAL E, ALLERS T, MARCHFELDER A and GOPHNA U, 2017. High tolerance to self-targeting of the genome by the endogenous CRISPR-Cas system in an archaeon. Nucleic acids research. 45(9), 5208-5216
• WARDELL K, HALDENBY S, JONES N, LIDDELL S, NGO GHP and ALLERS T, 2017. RadB acts in homologous recombination in the archaeon Haloferax volcanii, consistent with a role as recombination mediator. DNA repair. 55, 7-16
• GOPHNA U, ALLERS T and MARCHFELDER A, 2017. Finally, Archaea Get Their CRISPR-Cas Toolbox. Trends in microbiology. 25(6), 430-432
• MAIER L, BENZ J, FISCHER S, ALSTETTER M, JASCHINSKI K, HILKER R, BECKER A, ALLERS T, SOPPA J and MARCHFELDER A, 2015. Deletion of the Sm1 encoding motif in the lsm gene results in distinct changes in the transcriptome and enhanced swarming activity of Haloferax cells. Biochimie. 117, 129-37
• STRILLINGER E, GRÖTZINGER SW, ALLERS T, EPPINGER J and WEUSTER-BOTZ D, 2015. Production of halophilic proteins using Haloferax volcanii H1895 in a stirred-tank bioreactor. Applied microbiology and biotechnology. 100(3), 1183-95
• BRENDEL J, STOLL B, LANGE SJ, SHARMA K, LENZ C, STACHLER A, MAIER L, RICHTER H, NICKEL L, SCHMITZ RA, RANDAU L, ALLERS T, URLAUB H, BACKOFEN R and MARCHFELDER A, 2014. A complex of Cas proteins 5, 6, and 7 is required for the biogenesis and stability of crRNAs in Haloferax volcanii. The Journal of biological chemistry. 289(10), 7164-77
• TIMPSON, L.M., LILIENSIEK, A.-K., ALSAFADI, D., CASSIDY, J., SHARKEY, M.A., LIDDELL, S., ALLERS, T. and PARADISI, F., 2013. A comparison of two novel alcohol dehydrogenase enzymes (adh1 and adh2) from the extreme halophile haloferax volcanii Applied Microbiology and Biotechnology. 97(1), 195-203
• DELMAS, S., DUGGIN, I.G.L and ALLERS, T., 2013. DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii Molecular Microbiology. 87(1), 168-179
• KAMINSKI L, LURIE-WEINBERGER MN, ALLERS T, GOPHNA U and EICHLER J, 2013. Phylogenetic- and genome-derived insight into the evolution of N-glycosylation in Archaea. Molecular phylogenetics and evolution. 68(2), 327-39
• YUAN H, LIU X, HAN Z, ALLERS T, HOU J and LIU J, 2013. RecJ-like protein from Pyrococcus furiosus has 3'-5' exonuclease activity on RNA: implications for proofreading of 3'-mismatched RNA primers in DNA replication. Nucleic acids research. 41(11), 5817-26
• HAWKINS, M., MALLA, S., BLYTHE, M.J., NIEDUSZYNSKI, C.A. and ALLERS, T., 2013. Accelerated growth in the absence of DNA replication origins. Nature. 503, 544-547
• FISCHER S, JOHN VON FREYEND S, SABAG-DAIGLE A, DANIELS CJ, ALLERS T and MARCHFELDER A, 2012. Assigning a function to a conserved archaeal metallo-β-lactamase from haloferax volcanii. Extremophiles : life under extreme conditions. 16(2), 333-43
• STROUD A, LIDDELL S and ALLERS T, 2012. Genetic and biochemical identification of a novel single-stranded dna-binding complex in haloferax volcanii. Frontiers in microbiology. 3, 224
• NAOR A, THIAVILLE PC, ALTMAN-PRICE N, COHEN-OR I, ALLERS T, DE CRÉCY-LAGARD V and GOPHNA U, 2012. A genetic investigation of the keops complex in halophilic archaea. Plos one. 7(8), e43013
• LEIGH, J.A., ALBERS, S.-V., ATOMI, H. and ALLERS, T., 2011. Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales FEMS Microbiology Reviews. 35(4), 577-608
• ALLERS T, 2011. Swapping Genes To Survive - A New Role For Archaeal Type Iv Pili. Molecular Microbiology. 82(4), 789-91
• LESTINI, R., DUAN, Z. and ALLERS, T., 2010. The archaeal Xpf/Mus81/FANCM homolog Hef and the Holliday junction resolvase Hjc define alternative pathways that are essential for cell viability in Haloferax volcanii DNA Repair. 9(9), 994-1002
• FISCHER, SUSAN, BENZ, JULIANE, SPÄTH, BETTINA, MAIER, LISA-KATHARINA, STRAUB, JULIA, GRANZOW, MICHAELA, RAABE, MONIKA, URLAUB, HENNING, HOFFMANN, JAN, BRUTSCHY, BERND, ALLERS, THORSTEN and SOPPA, J&, 2010. The archaeal Lsm protein binds to small RNAs. The Journal of biological chemistry. 285(45), 34429-38
• ALLERS, THORSTEN, 2010. Overexpression and purification of halophilic proteins in Haloferax volcanii. Bioengineered bugs. 1(4), 288-290
• HARTMAN, AMBER L, NORAIS, CÉDRIC, BADGER, JONATHAN H, DELMAS, STÉPHANE, HALDENBY, SAM, MADUPU, RAMANA, ROBINSON, JEFFREY, KHOURI, HODA, REN, QINGHU, LOWE, TODD M, MAUPIN-FURLOW, JULIE and POHLS, 2010. The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon. PloS one. 5(3), e9605
• ALLERS, T., BARAK, S., LIDDELL, S., WARDELL, K. and MEVARECH, M., 2010. Improved strains and plasmid vectors for conditional overexpression of His-tagged proteins in Haloferax volcanii Applied and Environmental Microbiology. 76(6), 1759-1769
• DELMAS, S., SHUNBURNE, L., NGO, H.-P. and ALLERS, T., 2009. Mre11-Rad50 promotes rapid repair of DNA damage in the polyploid archaeon Haloferax volcanii by restraining homologous recombination PLoS Genetics. 5(7), e1000552
• HALDENBY, SAM, WHITE, MALCOLM F and ALLERS, THORSTEN, 2009. RecA family proteins in archaea: RadA and its cousins. Biochemical Society Transactions. 37(Pt 1), 102-7
• OH, S.D, JESSOP, L, LAO, J.P, ALLERS, T and LICHTEN, M. AND HUNTER, N., 2009. Stabilization and Electrophoretic Analysis of Meiotic Recombination Intermediates in Saccharomyces cerevisiae. In: KEENEY, S., ed., Meiosis: Molecular and Genetic Methods Methods in Molecular Biology, Vol. 557. Humana Press. 209-234
• HÖLZLE, A., FISCHER, S., HEYER, R., SCHÜTZ, S., ZACHARIAS, M., WALTHER, P., ALLERS, T. and MARCHFELDER, A., 2008. Maturation of the 5S rRNA 5′ end is catalyzed in vitro by the endonuclease tRNase Z in the archaeon H. volcanii RNA. 14(5), 928-937
• NORAIS, C., HAWKINS, M., HARTMAN, A.L., EISEN, J.A., MYLLYKALLIO, H. and ALLERS, T., 2007. Genetic and physical mapping of DNA replication origins in Haloferax volcanii PLoS Genetics. 3(5), e77
• MEVARECH, M. and ALLERS, T., 2007. Genetics. In: GARRETT, R.A. and KLENK, H.-P., eds., Archaea: Evolution, Physiology and Molecular Biology Malden, MA: Blackwell Publishing. 125-136
• LARGE, A., STAMME, C., LANGE, C., DUAN, Z., ALLERS, T., SOPPA, J. and LUND, P.A., 2007. Characterization of a tightly controlled promoter of the halophilic archaeon Haloferax volcanii and its use in the analysis of the essential cct1 gene Molecular Microbiology. 66(5), 1092-1106
• GUY, C.P., HALDENBY, S., BRINDLEY, A., WALSH, D.A., BRIGGS, G.S., WARREN, M.J., ALLERS, T. and BOLT, E.L., 2006. Interactions of RadB, a DNA repair protein in archaea, with DNA and ATP Journal of Molecular Biology. 358(1), 46-56
• BREUERT, S., ALLERS, T., SPOHN, G. and SOPPA, J., 2006. Regulated polyploidy in halophilic archaea. PLoS ONE. 1(1), e92
• ALLERS, T. and MEVARECH, M., 2005. Archaeal genetics — the third way Nature Reviews: Genetics. 6(1), 58-73
• JESSOP, L., ALLERS, T. and LICHTEN, M., 2005. Infrequent co-conversion of markers flanking a meiotic recombination initiation site in Saccharomyces cerevisiae Genetics. 169(3), 1353-1367
• ALLERS, T., NGO, H.-P., MEVARECH, M. and LLOYD, R.G., 2004. Development of additional selectable markers for the halophilic Archaeon Haloferax volcanii based on the leuB and trpA genes Applied and Environmental Microbiology. 70(2), 943-953
• ALLERS, T. and NGO, H.-P., 2003. Genetic analysis of homologous recombination in Archaea: Haloferax volcanii as a model organism Biochemical Society Transactions. 31(3), 706-709
• ALLERS, T. and LICHTEN, M., 2001. Differential timing and control of noncrossover and crossover recombination during meiosis Cell. 106(1), 47-57
• ALLERS, T. and LICHTEN, M., 2001. Intermediates of yeast meiotic recombination contain heteroduplex DNA Molecular Cell. 8(1), 225-231
• ALLERS, T and LICHTEN, M, 2000. A method for preparing genomic DNA that restrains branch migration of Holliday junctions. Nucleic Acids Research. 28(2), e6
• ALLERS, T and LEACH, D R, 1995. DNA palindromes adopt a methylation-resistant conformation that is consistent with DNA cruciform or hairpin formation in vivo. Journal of Molecular Biology. 252(1), 70-85