Dr Steve Kelly
Research Interests
Photosynthesis, Evolution, Gene expression, Bioinformatics
Photosynthesis is the primary energy source for life on earth. While the biochemistry and cell biology of photosynthesis are well understood, little is known of how the genes that mediate photosynthesis are regulated. Our research aims to address this knowledge gap by identifying the molecular regulators and mechanisms that control the expression of photosynthesis genes in the world’s most important food crops, the grasses. This work combines comparative genomics, evolutionary biology, high-throughput assays and genetic engineering.
For up-to-date details on research interests and publications please see the lab website.
If you are interested in joining our group please get in touch by email including your CV and a short paragraph outlining the project area that you are interested in.
Publications
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Publishing ethics in the era of paper mills.
October 2020|Journal article|Biol Open -
Installation of C4 photosynthetic pathway enzymes in rice using a single construct.
October 2020|Journal article|Plant biotechnology journalIntroduction of a C<sub>4</sub> photosynthetic mechanism into C<sub>3</sub> crops offers an opportunity to improve photosynthetic efficiency, biomass and yield in addition to potentially improving nitrogen and water use efficiency. To create a two-cell metabolic prototype for an NADP-malic enzyme type C<sub>4</sub> rice, we transformed Oryza sativa spp.japonica cultivar Kitaake with a single construct containing the coding regions of carbonic anhydrase, phosphoenolpyruvate (PEP) carboxylase, NADP-malate dehydrogenase, pyruvate orthophosphate dikinase and NADP-malic enzyme from Zea mays, driven by cell-preferential promoters. Gene expression, protein accumulation and enzyme activity were confirmed for all five transgenes, and intercellular localization of proteins was analysed. <sup>13</sup> CO<sub>2</sub> labelling demonstrated a 10-fold increase in flux though PEP carboxylase, exceeding the increase in measured in vitro enzyme activity, and estimated to be about 2% of the maize photosynthetic flux. Flux from malate via pyruvate to PEP remained low, commensurate with the low NADP-malic enzyme activity observed in the transgenic lines. Physiological perturbations were minor and RNA sequencing revealed no substantive effects of transgene expression on other endogenous rice transcripts associated with photosynthesis. These results provide promise that, with enhanced levels of the C<sub>4</sub> proteins introduced thus far, a functional C<sub>4</sub> pathway is achievable in rice. -
The economics of endosymbiotic gene transfer and the evolution of organellar genomes
October 2020|Journal article<jats:title>Abstract</jats:title><jats:p>The endosymbiosis of the bacterial progenitors of mitochondrion and the chloroplast are landmark events in the evolution of life on earth. While both organelles have retained substantial proteomic and biochemical complexity, this complexity is not reflected in the content of their genomes. Instead, the organellar genomes encode fewer than 5% of genes found in living relatives of their ancestors. While some of the 95% of missing organellar genes have been discarded, many have been transferred to the host nuclear genome through a process known as endosymbiotic gene transfer. Here we demonstrate that the energy liberated or consumed by a cell as a result of endosymbiotic gene transfer can be sufficient to provide a selectable advantage for retention or nuclear-transfer of organellar genes in eukaryotic cells. We further demonstrate that for realistic estimates of protein abundances, organellar protein import costs, host cell sizes, and cellular investment in organelles that it is energetically favourable to transfer the majority of organellar genes to the nuclear genome. Moreover, we show that the selective advantage of such transfers is sufficiently large to enable such events to rapidly reach fixation. Thus, endosymbiotic gene transfer can be advantageous in the absence of any additional benefit to the host cell, providing new insight into the processes that have shaped eukaryotic genome evolution.</jats:p><jats:sec><jats:title>One sentence summary</jats:title><jats:p>The high copy number of organellar genomes renders endosymbiotic gene transfer energetically favourable for the vast majority of organellar genes.</jats:p></jats:sec> -
RuBisCO adaptation is more limited by phylogenetic constraint than by catalytic trade-off in plants
September 2020|Journal article<jats:title>Abstract</jats:title><jats:p>RuBisCO assimilates CO<jats:sub>2</jats:sub> to form the sugars that fuel life on earth. Correlations between RuBisCO kinetic traits across species have led to the proposition that RuBisCO adaptation is constrained by catalytic trade-offs. However, these analyses did not consider the phylogenetic context of the enzymes that were analysed. Thus, it is possible that the observed correlations between RuBisCO kinetic traits are an artefact of the presence of phylogenetic signal in RuBisCO kinetics and the phylogenetic relationship between the species that were sampled. Here, we conducted a phylogenetically resolved analysis of RuBisCO kinetics and show that there is significant phylogenetic signal in all carboxylase kinetic traits, and significant phylogenetic signal in the Michaelis constant for O<jats:sub>2</jats:sub> in species that conduct C<jats:sub>3</jats:sub> photosynthesis. When accounting for this phylogenetic non-independence between enzymes, we show that the catalytic trade-off between carboxylase turnover and the Michaelis constant for CO<jats:sub>2</jats:sub> is weak (~30 % dependency) and that the correlations between all other RuBisCO kinetic traits are either not-significant or marginal (<9 % dependency). Finally, we demonstrate that phylogenetic constraints have limited RuBisCO evolution to a greater extent than catalytic trade-offs. Thus, RuBisCO adaptation in angiosperms is predominantly limited by phylogenetic constraint (most likely caused by a slow rate of molecular evolution) and a partial trade-off between carboxylase turnover and the Michaelis constant for CO<jats:sub>2</jats:sub>.</jats:p> -
NO GAMETOPHORES 2 is a novel regulator of the 2D to 3D growth transition in the moss Physcomitrium patens
July 2020|Journal article<jats:title>SUMMARY</jats:title><jats:p>The colonization of land by plants was one of the most transformative events in the history of life on Earth. The transition from water, which coincided with and was likely facilitated by the evolution of 3-dimensional (3D) growth, enabled the generation of morphological diversity on land. In many plants, the transition from 2-dimensional (2D) to 3D growth occurs during embryo development. However, in the early divergent moss <jats:italic>Physcomitrium patens</jats:italic> (formerly <jats:italic>Physcomitrella patens</jats:italic>), 3D growth is preceded by an extended filamentous phase that can be maintained indefinitely. Here, we describe the identification of the cytokinin-responsive <jats:italic>NO GAMETOPHORES 2</jats:italic> (<jats:italic>PpNOG2</jats:italic>) gene, which encodes a shikimate o- hydroxycinnamoyltransferase. In mutants lacking <jats:italic>PpNOG2</jats:italic> function, transcript levels of <jats:italic>CLAVATA</jats:italic> and <jats:italic>SCARECROW</jats:italic> genes are significantly reduced, excessive gametophore initial cells are produced, and buds undergo premature developmental arrest. Our results suggest that PpNOG2 functions in the ascorbic acid pathway leading to cuticle formation, and that NOG2-related genes were co-opted into the lignin biosynthesis pathway after the divergence of bryophytes and vascular plants. We present a revised model of 3D growth in which PpNOG2 comprises part of a feedback mechanism that is required for the modulation of gametophore initial cell frequency. We also propose that the 2D to 3D growth transition in <jats:italic>P. patens</jats:italic> is underpinned by complex auxin-cytokinin crosstalk that is regulated, at least in part, by changes in flavonoid metabolism.</jats:p> -
Benchmarking Orthogroup Inference Accuracy: Revisiting Orthobench
July 2020|Journal article<jats:title>Abstract</jats:title><jats:p>Orthobench is the standard benchmark to assess the accuracy of orthogroup inference methods. It contains 70 expert curated reference orthogroups (RefOGs) that span the Bilateria and cover a range of different challenges for orthogroup inference. Here we leveraged improvements in tree inference algorithms and computational resources to re-interrogate these RefOGs and carry out an extensive phylogenetic delineation of their composition. This phylogenetic revision altered the membership of 31 of the 70 RefOGs, with 24 subject to extensive revision and a further 7 that required minor changes. We further used these revised and updated RefOGs to provide an assessment of the orthogroup inference accuracy of widely used orthogroup inference methods. Finally, we provide an open-source benchmarking suite to support the future development and use of the Orthobench benchmark.</jats:p><jats:sec><jats:title>Significance statement</jats:title><jats:p>Orthogroup inference forms the foundation of comparative genomic analysis. Benchmarks to evaluate performance are essential to enable these methods to be compared and stimulate further method development. Here we present an update to the orthobench benchmark database and provide a comparative performance evaluation of commonly used orthogroup inference methods.</jats:p></jats:sec> -
The Quest for Orthologs benchmark service and consensus calls in 2020.
July 2020|Journal article|Nucleic acids researchThe identification of orthologs-genes in different species which descended from the same gene in their last common ancestor-is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.Animals, Humans, Mice, Rats, Proteome, Consensus, Genomics, Phylogeny, Multigene Family, Software, Benchmarking -
Multiple Metabolic Innovations and Losses Are Associated with Major Transitions in Land Plant Evolution.
May 2020|Journal article|Current biology : CBInvestigating the evolution of plant biochemistry is challenging because few metabolites are preserved in fossils and because metabolic networks are difficult to experimentally characterize in diverse extant organisms. We report a comparative computational approach based on whole-genome metabolic pathway databases of eight species representative of major plant lineages, combined with homologous relationships among genes of 72 species from streptophyte algae to angiosperms. We use this genomic approach to identify metabolic gains and losses during land plant evolution. We extended our findings with additional analysis of 305 non-angiosperm plant transcriptomes. Our results revealed that genes encoding the complete biosynthetic pathway for brassinosteroid phytohormones and enzymes for brassinosteroid inactivation are present only in spermatophytes. Genes encoding only part of the biosynthesis pathway are present in ferns and lycophytes, indicating a stepwise evolutionary acquisition of this pathway. Nevertheless, brassinosteroids are ubiquitous in land plants, suggesting that brassinosteroid biosynthetic pathways differ between earlier- and later-diverging lineages. Conversely, genes for gibberellin biosynthesis and inactivation using methyltransferases are found in all land plant lineages. This suggests that bioactive gibberellins might be present in bryophytes, although they have yet to be detected experimentally. We also found that cytochrome P450 oxidases involved in cutin and suberin production are absent in genomes of non-angiosperm plants that nevertheless do contain these biopolymers. Overall, we identified significant differences in crucial metabolic processes between angiosperms and earlier-diverging land plants and resolve details of the evolutionary history of several phytohormone and structural polymer biosynthetic pathways in land plants.
Graduate Students
Contact Details
| E: | steven.kelly@plants.ox.ac.uk |
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+44 (0) 1865 275123 |
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| Lab website |
