Ellis studied Natural Sciences in Cambridge, focusing on Chemistry, Biochemistry and Plant Sciences. He then went on to the John Innes Centre for his PhD, working in Biological Chemistry on carbohydrate enzymes and algae under the supervision of Rob Field. Ellis then moved to the Scripps Institution of Oceanography at the University of California - San Diego to work on bacterial natural product discovery in the lab of Brad Moore. Ellis joined Oxford, working with Steve Kelly on Eukaryotic synthetic biology, before he was awarded a Glasstone Independent Research Fellowship to work on algal natural products, also holding a Junior Research Fellowship at New College, Oxford. In 2019 Ellis was awarded a Nottingham Research Fellowship to continue his work on algal natural products in the School of Chemistry.
Algal Natural Products
Algae are well known to make complex natural products, notable when they are released during a harmful algal bloom. They also encode the capacity for the synthesis of many as yet undiscovered compounds in their genomes. In order to investigate the molecules they maker, we are using high throughput chemoinformatic strategies to discover these new compounds. This involves the growth of a wide range of algae, simple extraction of the cultures and LCMS2. The data is analysed using the GNPS pipeline to compare the metabolites produced among the different samples and to compare to the libraries of known compounds. Using all of this information we can prioritise new compounds produced by these algae for purification and structure elucidation. We are currently applying this strategy to investigating the natural products made by euglenoid algae.
Euglena expresses a wide range of carbohydrate-active enzymes, suggesting an unexpectedly high capacity for the synthesis of complex carbohydrates for a single-celled organism. Aside from the enzymes involved in the synthesis of the β-glucan storage polysaccharide (paramylon) and for the synthesis of N-glycans, there are many enzymes related to those involved in plant cell wall biosynthesis. Analysis of the sugar nucleotide pool showed that there are the substrates necessary for synthesis of complex polysaccharides. Lectin-and antibody-based profiling of whole cells and extracted carbohydrates shows a complex galactan, xylan and aminosugar based surface. Work is ongoing to characterise the nature of the complex polysaccharides produced by these cells.
Genomics of Euglena
The genome of Euglena is highly complex for a simple free living cell. The total amount of DNA is similar to that of Human cells and there are more genes encoded. It is not clear why Euglena needs all these genes. The aim of this project is to sequence related Euglena, at transcriptomic, genomic and metagenomic levels. Euglena controls gene expression at post transcriptionally, meaning that the transcriptome at any given time is a good representation of the genome, and avoids the difficulties of sequencing their large complex genome. Comparing the gene between different species will help us to understand the capacity of these cells.
Euglena cells have a complex metabolism, able to grow using photosynthesis, osmotrophy or eukaryovory. Euglena contain a secondary plastid, derived from a green algae, and acquired by a free living ancestor. E. gracilis can survive after destruction of this plastid, unlike other photosynthetic organisms. In order to understand this complex metabolism in Euglena we are using a range of metabolic profiling techniques. this has revealed the different pathways used by Euglena under alternative conditions and may be used to optimise growth for production of a range of products.
GANESAN, A, ALDHOLMI, MOHAMMED, AHMAD, RIZWAN, CARRETERO-MOLINA, DANIEL, PEREZ-VICTORIA, IGNACIO, MARTIN, JESUS, REYES, FERNANDO, GENILLOUD, OLGA, GOURBEYRE, LEA, GEFFLAUT, THIERRY, CARLSSON, HANNE, MAKLAKOV, ALEXEI, FIELD, ROBERT A, O'NEILL, ELLIS, WILKINSON, BARRIE and O'CONNELL, MARIA, 2022. Euglenatides, Potent Antiproliferative Cyclic Peptides Isolated from the Freshwater Photosynthetic Microalga Euglena gracilis. Angewandte Chemie (International ed. in English).
SCHORN, MICHELLE A., VERHOEVEN, STEFAN, RIDDER, LARS, HUBER, FLORIAN, ACHARYA, DEEPA D., AKSENOV, ALEXANDER A., ALETI, GAJENDER, MOGHADDAM, JAMSHID AMIRI, ARON, ALLEGRA T., AZIZ, SAEFUDDIN, BAUERMEISTER, ANELIZE, BAUMAN, KATHERINE D., BAUNACH, MARTIN, BEEMELMANNS, CHRISTINE, BEMAN, J. MICHAEL, BERLANGA-CLAVERO, MARIA VICTORIA, BLACUTT, ALEX A., BODE, HELGE B., BOULLIE, ANNE, BREJNROD, ASKER, BUGNI, TIM S., CALTEAU, ALEXANDRA, CAO, LIU, CARRION, VICTOR J., CASTELO-BRANCO, RAQUEL, CHANANA, SHAURYA, CHASE, ALEXANDER B., CHEVRETTE, MARC G., COSTA-LOTUFO, LETICIA V., CRAWFORD, JASON M., CURRIE, CAMERON R., CUYPERS, BART, DANG, TAM, DE ROND, TRISTAN, DEMKO, ALYSSA M., DITTMANN, ELKE, DU, CHAO, DROZD, CHRISTOPHER, DUJARDIN, JEAN-CLAUDE, DUTTON, RACHEL J., EDLUND, ANNA, FEWER, DAVID P., GARG, NEHA, GAUGLITZ, JULIA M., GENTRY, EMILY C., GERWICK, LENA, GLUKHOV, EVGENIA, GROSS, HARALD, GUGGER, MURIEL, GUILLEN MATUS, DULCE G., HELFRICH, ERIC J. N., HEMPEL, BENJAMIN-FLORIAN, HUR, JAE-SEOUN, IORIO, MARIANNA, JENSEN, PAUL R., KANG, KYO BIN, KAYSSER, LEONARD, KELLEHER, NEIL L., KIM, CHUNG SUB, KIM, KI HYUN, KOESTER, IRINA, KOENIG, GABRIELE M., LEAO, TIAGO, LEE, SEOUNG RAK, LEE, YI-YUAN, LI, XUANJI, LITTLE, JESSICA C., MALONEY, KATHERINE N., MAENNLE, DANIEL, MARTIN H., CHRISTIAN, MCAVOY, ANDREW C., METCALF, WILLAM W., MOHIMANI, HOSEIN, MOLINA-SANTIAGO, CARLOS, MOORE, BRADLEY S., MULLOWNEY, MICHAEL W., MUSKAT, MITCHELL, NOTHIAS, LOUIS-FELIX, O'NEILL, ELLIS C., PARKINSON, ELIZABETH I., PETRAS, DANIEL, PIEL, JORN, PIERCE, EMILY C., PIRES, KARINE, REHER, RAPHAEL, ROMERO, DIEGO, ROPER, M. CAROLINE, RUST, MICHAEL, SAAD, HAMADA, SAENZ, CARMEN, SANCHEZ, LAURA M., SORENSEN, SOREN JOHANNES, SOSIO, MARGHERITA, SUSSMUTH, RODERICH D., SWEENEY, DOUGLAS, TAHLAN, KAPIL, THOMSON, REGAN J., TOBIAS, NICHOLAS J., TRINDADE-SILVA, AMARO E., VAN WEZEL, GILLES P., WANG, MINGXUN, WELDON, KELLY C., ZHANG, FAN, ZIEMERT, NADINE, DUNCAN, KATHERINE R., CRUESEMANN, MAX, ROGERS, SIMON, DORRESTEIN, PIETER C., MEDEMA, MARNIX H. and VAN DER HOOFT, JUSTIN J. J., 2021. A community resource for paired genomic and metabolomic data mining NATURE CHEMICAL BIOLOGY. 17(4), 363-368
O'NEILL, ELLIS, 2020. Mining Natural Product Biosynthesis in Eukaryotic Algae MARINE DRUGS. 18(2),
EBENEZER, THANKGOD E., ZOLTNER, MARTIN, BURRELL, ALANA, NENAROKOVA, ANNA, NOVÁK VANCLOVÁ, ANNA M. G., PRASAD, BINOD, SOUKAL, PETR, SANTANA-MOLINA, CARLOS, O’NEILL, ELLIS, NANKISSOOR, NERISSA N., VADAKEDATH, NITHYA, DAIKER, VIKTOR, OBADO, SAMSON, SILVA-PEREIRA, SARA, JACKSON, ANDREW P., DEVOS, DAMIEN P., LUKEŠ, JULIUS, LEBERT, MICHAEL, VAUGHAN, SUE, HAMPL, VLADIMΊR, CARRINGTON, MARK, GINGER, MICHAEL L., DACKS, JOEL B., KELLY, STEVEN and FIELD, MARK C., 2019. Transcriptome, proteome and draft genome of Euglena gracilis: BMC Biology BMC Biology. 17(1), 11