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Associate Professor Anthony Poole

Contact

Department: Biomolecular Interaction Centre

Email: anthony.poole@canterbury.ac.nz

Office:

Languages: English, Japanese, Swedish

About
Research / Creative works
Networks
Projects
Methods & Equipment

Fields of Research

  • Cell evolution
  • RNA world
  • Origin of DNA
  • Genome evolution
  • Molecular Evolution
  • RNA evolution
  • Metagenomics
  • Eukaryote origins

Researcher Summary

My research group is interested in understanding how complex molecular systems evolve.

One project in the lab is the evolution of translation initiation in bacteria. We have streamlined E. coli translation initiation by removing two steps in the pathway by which protein synthesis initiates, and let our strains adapt via culturing during a long term evolution experiment. This work is currently being undertaken by MSc student Alannah Rickerby.

PhD student Alicia Lai has evolved a lineage of bacteria that performs RNA editing. Our work shows that editing can evolve under conditions favouring genetic drift, suggesting that greater complexity is a product of low-fidelity evolution.

We have been using comparative genomics and transcriptomics to examine evolution of small RNAs. We find that only a few RNAs appear genuinely ancient (i.e. tracing back to the earliest stages of life), with the vast majority appearing to have much shorter evolutionary histories. As part of this, we have pioneered a phylogeny-informed approach to identification of noncoding RNAs.

With Prof. Jun Ogawa and team at Kyoto University, we are working to engineer E. coli that can produce DNA via an alternative pathway to the ubiquitous ribonucleotide reductase pathway, which all life uses to generate DNA building blocks from RNA. This work may tell us if DNA could have evolved via a simpler route than the complex reaction performed by ribonucleotide reductases.

Subject Area: Disciplines

  • Biology: Ecology, Evolution and Behaviour: Evolution; Microbiology
  • Biology: Molecular, Cellular and Whole Organism Biology: Genetics; Genomics/Bioinformatics; Molecular Biology

Prizes and Awards

  • Royal Swedish Academy of Sciences Research Fellow ( 2007 - 2011)
  • Rutherford Discovery Fellowship ( 2011 - 2021)

Research/Scholarly/Creative Works

  • Adair KL., Lindgreen S., Poole AM., Young LM., Bernard-Verdier M., Wardle DA. and Tylianakis JM. (2019) Above and belowground community strategies respond to different global change drivers. Scientific Reports 9(1) http://dx.doi.org/10.1038/s41598-019-39033-4. (Journal Articles)
  • Coombes D., Moir JWB., Poole AM., Cooper TF. and Dobson RCJ. (2019) The fitness challenge of studying molecular adaptation. Biochemical Society Transactions 47(5): 1533-1542. http://dx.doi.org/10.1042/BST20180626. (Journal Articles)
  • Hoeppner MP., Denisenko E., Gardner PP., Schmeier S. and Poole AM. (2018) An evaluation of function of multicopy noncoding RNAs in mammals using ENCODE/FANTOM data and comparative genomics. Molecular Biology and Evolution 35(6): 1451-1462. http://dx.doi.org/10.1093/molbev/msy046. (Journal Articles)
  • Sagulenko E., Nouwens A., Webb RI., Green K., Yee B., Morgan G., Leis A., Lee KC., Butler MK. and Chia N. (2017) Nuclear pore-like structures in a compartmentalized bacterium. PLoS ONE 12(2) http://dx.doi.org/10.1371/journal.pone.0169432. (Journal Articles)
  • Allison JR., Lechner M., Hoeppner MP. and Poole AM. (2016) Positive selection or free to vary? Assessing the functional significance of sequence change using molecular dynamics. PLoS ONE (early access online) http://dx.doi.org/10.1371/journal.pone.0147619. (Journal Articles)
  • Poole AM. and Gribaldo S. (2016) Eukaryotic origins: how and when was the mitochondrion acquired? Cold Spring Harbor Perspectives in Biology (early access online) http://dx.doi.org/10.1101/cshperspect.a015990. (Journal Articles)
  • Poole AM., Jeffares DC., Hoeppner MP. and Penny D. (2016) Does the Ribosome Challenge our Understanding of the RNA World? Journal of Molecular Evolution 82(1): 1-4. http://dx.doi.org/10.1007/s00239-015-9720-x. (Journal Articles)
  • Umu SU., Poole AM., Dobson RCJ. and Gardner PP. (2016) Avoidance of stochastic RNA interactions can be harnessed to control protein expression levels in bacteria and archaea. eLife 5 e13479 http://dx.doi.org/10.7554/eLife.13479. (Journal Articles)
  • Poole AM., Lundin D. and Rytkönen KT. (2015) The evolution of early cellular systems viewed through the lens of biological interactions. Frontiers in Microbiology 6: 1144. http://dx.doi.org/10.3389/fmicb.2015.01144. (Journal Articles)
  • Catchpole RJ. and Poole AM. (2014) Horizontal gene transfer: Antibiotic genes spread far and wide. eLife 3 e05244 http://dx.doi.org/10.7554/eLife.05244. (Journal Articles)
  • Lindgreen S., Umu SU., Lai ASW., Eldai H., Liu W., McGimpsey S., Wheeler N., Biggs PJ., Thomson NR. and Barquist L. (2014) Robust identification of noncoding RNA from transcriptomes requires phylogenetically-informed sampling. PLoS Computational Biology 10(10) e1003907 http://dx.doi.org/10.1371/journal.pcbi.1003907. (Journal Articles)
  • Poole AM., Horinouchi N., Catchpole RJ., Si D., Hibi M., Tanaka K. and Ogawa J. (2014) The case for an early biological origin of DNA. Journal of Molecular Evolution 79(5-6): 204-212. http://dx.doi.org/10.1007/s00239-014-9656-6. (Journal Articles)
  • Brindefalk B., Desailly BH., Yeats C., Orengo C., Werner F. and Poole AM. (2013) Evolutionary history of the TBP-domain superfamily. Nucleic Acids Research 41(5): 2832-2845. http://dx.doi.org/10.1093/nar/gkt045. (Journal Articles)
  • Massaro M., Sainudiin R., Merton D., Briskie JV., Poole AM. and Hale ML. (2013) Human-Assisted Spread of a Maladaptive Behavior in a Critically Endangered Bird. PLoS ONE 8(12) e79066: 7. http://dx.doi.org/10.1371/journal.pone.0079066. (Journal Articles)
  • Overballe-Petersen S., Harms K., Orlando LA., Mayar JV., Rasmussen S., Dahl TW., Rosing MT., Poole AM., Sicheritz-Pontén T. and Brunak S. (2013) Bacterial natural transformation by highly fragmented and damaged DNA. Proceedings of the National Academy of Sciences USA 110(49): 19860-19865. http://dx.doi.org/10.1073/pnas.1315278110. (Journal Articles)
  • Thureborn P., Lundin D., Plathan J., Poole AM., Sjöberg BM. and Sjöling S. (2013) A Metagenomics Transect into the Deepest Point of the Baltic Sea Reveals Clear Stratification of Microbial Functional Capacities. PLoS ONE 8(9) e74983 http://dx.doi.org/10.1371/journal.pone.0074983. (Journal Articles)
  • Curtis BA., Tanifuji G., Burki F., Gruber A., Irimia M., Maruyama S., Arias MC., Ball SG., Gile GH. and Hirakawa Y. (2012) Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. Nature 492: 59-65. http://dx.doi.org/10.1038/nature11681. (Journal Articles)
  • Hoeppner MP. and Poole AM. (2012) Comparative Genomics of Eukaryotic Small Nucleolar RNAs Reveals Deep Evolutionary Ancestry Amidst Ongoing Intragenomic Mobility. BMC Evolutionary Biology 12: 183. http://dx.doi.org/10.1186/1471-2148-12-183. (Journal Articles)
  • Hoeppner MP., Gardner PP. and Poole AM. (2012) Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life. PLoS Computational Biology 8 e1002752 http://dx.doi.org/10.1371/journal.pcbi.1002752. (Journal Articles)
  • Lundin D., Poole AM., Sjöberg BM. and Högbom M. (2012) Use of Structural Phylogenetic Networks for Classification of the Ferritin-like Superfamily. The Journal of Biological Chemistry 287(24): 20565-20575. http://dx.doi.org/10.1074/jbc.M112.367458. (Journal Articles)
  • Neumann N. and Poole AM. (2012) Evolution of phagotrophy. In McGraw-Hill (Ed.), McGraw-Hill Yearbook of Science & Technology: 80-83. New York: McGraw-Hill. (Chapters)
  • Poole AM., Kobayashi T. and Ganley AR. (2012) A positive role for yeast extrachromosomal rDNA circles? BioEssays 34(9): 725-729. http://dx.doi.org/10.1002/bies.201200037. (Journal Articles)
  • Poole AM., Stouffer DB. and Tylianakis JM. (2012) Ecosystomics': ecology by sequencer. Trends in Ecology and Evolution 27(6): 309-310. http://dx.doi.org/10.1016/j.tree.2012.03.008. (Journal Articles)
  • Poole AM. (2011) On Alternative Biological Scenarios for the Evolutionary Transitions to DNA and Biological Protein Synthesis. In Egel R; Lankenau DH; Mulkidjanian AY (Ed.), Origins of Life: The Primal Self-Organization: 209-223. Berlin: Springer. http://dx.doi.org/10.1007/978-3-642-21625-1_10. (Chapters)
  • Poole AM. and Neumann N. (2011) Reconciling an archaeal orgin of eukaryotes with engulfment: a biologically plausible update of the Eocyte hypothesis. Research in Microbiology 162(1): 71-76. http://dx.doi.org/10.1016/j.resmic.2010.10.002. (Journal Articles)
  • Gardner PP., Bateman A. and Poole AM. (2010) SnoPatrol: how many snoRNA genes are there? Journal of Biology 9(1): 4pp. (Journal Articles)
  • Gribaldo S., Poole AM., Daubin V., Forterre P. and Brochier-Armanet C. (2010) The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse? Nature Reviews Microbiology 8: 743-752. http://dx.doi.org/10.1038/nrmicro2426. (Journal Articles)
  • Lundin D., Gribaldo S., Torrents E., Sjöberg BM. and Poole AM. (2010) Ribonucleotide reduction - horizontal transfer of a required function spans all three domains. BMC Evolutionary Biology 10: 383. http://dx.doi.org/10.1186/1471-2148-10-383. (Journal Articles)
  • Neumann N., Lundin D. and Poole AM. (2010) Comparative genomic evidence for a complete nuclear pore complex in the last eukaryotic common ancestor. PLoS ONE 5(10) e13241 http://dx.doi.org/10.1371/journal.pone.0013241. (Journal Articles)
  • Poole AM. (2010) Eukaryote Evolution: The Importance of the Stem Group. In Caetano-Anolles G (Ed.), Evolutionary Genomics and Systems Biology: 63-80. Chicester: John Wiley & Sons. (Chapters)
  • Hoeppner MP., White S., Jeffares DC. and Poole AM. (2009) Evolutionarily stable association of intronic snoRNAs and microRNAs with their host genes. Genome Biology and Evolution 1(1): 420-428. http://dx.doi.org/10.1093/gbe/evp045. (Journal Articles)
  • Lundin D., Torrents E., Poole AM. and Sjoberg BM. (2009) RNRdb, a curated database of the universal enzyme family ribonucleotide reductase, reveals a high level of misannotation in sequences deposited to Genbank. BMC Genomics 10(589): 8pp. http://dx.doi.org/10.1186/1471-2164-10-589. (Journal Articles)
  • Penny D., Hoeppner MP., Poole AM. and Jeffares DC. (2009) An Overview of the Introns-First Theory. Journal of Molecular Evolution 69(5): 527-540. http://dx.doi.org/10.1007/s00239-009-9279-5. (Journal Articles)
  • Poole AM. (2009) Horizontal gene transfer and the earliest stages of the evolution of life. Research in Microbiology 160(7): 473-480. http://dx.doi.org/10.1016/j.resmic.2009.07.009. (Journal Articles)
  • Poole AM. (2009) How the endosymbiont got its cell. New Zealand Science Review 66(1): 28-33. (Journal Articles)
  • Freyhult E., Edvardsson S., Tamas I., Moulton V. and Poole AM. (2008) Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics - assessment and update. BMC Research Notes 1: 49. http://dx.doi.org/10.1186/1756-0500-1-49. (Journal Articles)
  • Takeuchi N., Salazar L., Poole AM. and Hogeweg P. (2008) The evolution of strand preference in simulated RNA replicators with strand displacement: Implications for the origin of transcription. Biology Direct 3: 33. http://dx.doi.org/10.1186/1745-6150-3-33. (Journal Articles)
  • Tamas I., Wernegreen JJ., Nystedt B., Kauppinen SN., Darby AC., Gomez-Valero L., Lundin D., Poole AM. and Andersson SGE. (2008) Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts. Proceedings of the National Academy of Science USA 105(39): 14934-14939. http://dx.doi.org/10.1073/pnas.0806554105. (Journal Articles)
  • Poole A. and Penny D. (2007) Eukaryote evolution: engulfed by speculation. Nature 447(7147): 913. http://dx.doi.org/10.1038/447913a. (Journal Articles)
  • Poole AM. and Penny D. (2007) Evaluating hypotheses for the origin of eukaryotes. BioEssays 29(1): 74-84. http://dx.doi.org/10.1002/bies.20516. (Journal Articles)
  • Poole AM. and Penny D. (2007) Response to Dagan and Martin. BioEssays 29(6): 611-614. http://dx.doi.org/10.1002/bies.20577. (Journal Articles)
  • Poole AM. and Willerslev E. (2007) Can identification of a fourth domain of life be made from sequence data alone, and could it be done on Mars? Astrobiology 7(5): 801-814. http://dx.doi.org/10.1089/ast.2006.0094. (Journal Articles)
  • Neumann N., Jeffares DC. and Poole AM. (2006) Outsourcing the nucleus: nuclear pore complex genes are no longer encoded in nucleomorph genomes. Evolutionary Bioinformatics 2: 23-34. (Journal Articles)
  • Poole AM. (2006) Did group II intron proliferation in an endosymbiont-bearing archaeon create eukaryotes? Biology Direct 7(1): 36. http://dx.doi.org/10.1186/1745-6150-1-36. (Journal Articles)
  • Poole AM. (2006) Getting from an RNA world to modern cells just got a little easier. BioEssays 28(2): 105-108. http://dx.doi.org/10.1002/bies.20367. (Journal Articles)
  • Poole AM., Hode T., Brandenburg A., Hjalmarson A. and Holm NG. (2006) Life Up North: Meeting report: Nordic Astrobiology 2006: Origins & Distribution of Life in the Universe. Astrobiology 6(6): 815-818. http://dx.doi.org/10.1089/ast.2006.6.815. (Journal Articles)
  • Poole AM. and Logan DT. (2005) Modern mRNA Proofreading and Repair: Clues that the Last Universal Common Ancestor Possessed an RNA Genome? Molecular Biology and Evolution 22(6): 1444-1455. http://dx.doi.org/10.1093/molbev/msi132. (Journal Articles)
  • Poole AM. (2004) Is all that junk really regulatory RNA? Nature Reviews Genetics 5. (Journal Articles)
  • Collins LJ., Poole AM. and Penny D. (2003) Using ancestral sequences to uncover potential gene homologues. Applied Bioinformatics 2(3 (Supplement)) S85-95. (Journal Articles)
  • Collins LJ., Poole AM. and Penny D. (2003) Using ancestral sequences to uncover potential gene homologues.. Applied bioinformatics 2(3 Suppl). (Journal Articles)
  • Edvardsson S., Gardner PP., Poole AM., Hendy MD., Penny D. and Moulton V. (2003) A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction. Bioinformatics 19(7): 865-873. http://dx.doi.org/10.1093/bioinformatics/btg080. (Journal Articles)
  • Penny D. and Poole AM. (2003) Lateral gene transfer: some theoretical aspects. NZ BioScience 12: 32-35. (Journal Articles)
  • Penny D., Hendy MD. and Poole AM. (2003) Testing fundamental evolutionary hypotheses. Journal of Theoretical Biology 223(3): 377-385. (Journal Articles)
  • Poole AM., Phillips MJ. and Penny D. (2003) Prokaryote and eukaryote evolvability. Biosystems 69(2-3): 163-185. http://dx.doi.org/10.1016/S0303-2647(02)00131-4. (Journal Articles)
  • Poole AM. (2002) My name is LUCA — The Last Universal Common Ancestor. ActionBioscience. (Journal Articles)
  • Poole AM. (2002) What is the Last Universal Common Ancestor (LUCA)? ActionBioscience. (Journal Articles)
  • Poole AM., Logan DT. and Sjöberg BM. (2002) The evolution of the ribonucleotide reductases: much ado about oxygen. Journal of Molecular Evolution 55(2): 180-196. http://dx.doi.org/10.1007/s00239-002-2315-3. (Journal Articles)
  • Poole A. and Penny D. (2001) Does endo-symbiosis explain the origin of the nucleus? Nature Cell Biology 3(8) E173 http://dx.doi.org/10.1038/35087102. (Journal Articles)
  • Poole A., Penny D. and Sjoberg BM. (2001) Confounded cytosine! Tinkering and the evolution of DNA. Nature Reviews Molecular Cell Biology 2: 147-151. http://dx.doi.org/10.1038/35052091. (Journal Articles)
  • Jeffares DC. and Poole AM. (2000) Were bacteria the first forms of life on Earth? ActionBioscience. (Journal Articles)
  • Poole AM. (2000) Bakterierna var inte först. Forskning och Framsteg 5: 46-51. (Journal Articles)
  • Poole AM., Penny D. and Sjöberg BM. (2000) Methyl-RNA: an evolutionary bridge between RNA and DNA? Chemistry & Biology 7(12) R207-R216 http://dx.doi.org/10.1016/S1074-5521(00)00042-9. (Journal Articles)
  • Penny D. and Poole AM. (1999) The nature of the last universal common ancestor. Current Opinion in Genetics & Development 9(6): 672-677. http://dx.doi.org/10.1016/S0959-437X(99)00020-9. (Journal Articles)
  • Poole A., Jeffares D. and Penny D. (1999) Early evolution: Prokaryotes, the new kids on the block. BioEssays 21(10): 880-889. http://dx.doi.org/10.1002/(SICI)1521-1878(199910)21:10<880::AID-BIES11>3.0.CO;2-P. (Journal Articles)
  • Poole AM., Jeffares D. and Penny D. (1999) Early evolution: prokaryotes, the new kids on the block. BioEssays 21(10): 880-889. http://dx.doi.org/10.1002/(SICI)1521-1878(199910)21:10<880::AID-BIES11>3.0.CO;2-P. (Journal Articles)
  • Jeffares DC., Poole AM. and Penny D. (1998) Relics from the RNA world. Journal of Molecular Evolution 46(1): 18-36. http://dx.doi.org/10.1007/PL00006280. (Journal Articles)
  • Poole AM., Jeffares DC. and Penny D. (1998) The path from the RNA world. Journal of Molecular Evolution 46(1): 1-17. http://dx.doi.org/10.1007/PL00006275. (Journal Articles)
  • Akiyama Y., Hosoya T., Poole AM. and Hotta Y. (1996) The gcm-motif: a novel DNA-binding motif conserved in Drosophila and mammals. Proceedings of the National Academy of Sciences of the United States of America (PNAS) 93(25): 14912-14916. (Journal Articles)
  • Akiyama Y., Hosoya T., Poole AM. and Hotta Y. (1996) The gem-motif: A novel DNA-binding motif conserved in Drosophila and mammals. Proceedings of the National Academy of Sciences of the United States of America 93(25): 14912-14916. http://dx.doi.org/10.1073/pnas.93.25.14912. (Journal Articles)
  • Jeffares DC., Poole AM. and Penny D. (1995) Pre-rRNA processing and the path from the RNA world. Trends in Biochemical Sciences 20(8): 298-299. http://dx.doi.org/10.1016/S0968-0004(00)89053-2. (Journal Articles)

Editorial Work

  • Actionbioscience Editorial Board Member ( 2003 - 2021)
  • Biology Direct Editorial Board Member ( 2006 - 2021)

Review and Refereeing

  • Proceedings of the National Academy of Sciences USA; Molecular Biology & Evolution; Trends in Ecology & Evolution; BMC Evolutionary Biology; Bioinformatics; Journal of Molecular Evolution; Journal of Theoretical Biology; BioEssays; Astrobiology ( 2006 - 2021)

Research Groups

  • Biomathematics Research Centre

Future Research

  • Evolution of RNA editing
  • Comparative genomics of the eukaryote cell
  • Comparative genomics of small RNAs
  • Origin & evolution of cells
  • Soil metagenomics

Key Methodologies

  • Molecular biology
  • Comparative genomics
  • Long term evolution experiments
  • Evolutionary theory
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