Julian M Hibberd

Julian M Hibberd
University of Cambridge | Cam · Department of Plant Sciences

PhD

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228
Publications
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Publications

Publications (228)
Preprint
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Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C 4 photosynthesis due to its evolutionary proximity to Arabidopsis. Here, we present a high-quality genome sequence of G. gynandra , anchored onto 17 main super-scaffolds with a total length of 740 Mb, an N50 of 42...
Article
In biological discovery and engineering research there is a need to spatially and/or temporally regulate transgene expression. However, the limited availability of promoter sequences that are uniquely active in specific tissue‐types and/or at specific times often precludes co‐expression of multiple transgenes in precisely‐controlled developmental c...
Preprint
Leaves of shade avoiding plants like Arabidopsis thaliana change their growth pattern and position in response to a low red to far-red ratio (LRFR) that is encountered in dense plant communities. In LRFR, transcription factors of the phytochrome interacting family (PIFs) are de-repressed. PIFs induce auxin production, which is required to promote l...
Article
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Grafting is possible in both animals and plants. Although in animals the process requires surgery and is often associated with rejection of non-self, in plants grafting is widespread, and has been used since antiquity for crop improvement¹. However, in the monocotyledons, which represent the second largest group of terrestrial plants and include ma...
Article
Full-text available
In C4 plants, the enzymatic machinery underpinning photosynthesis can vary, with, for example, three distinct C4 acid decarboxylases being used to release CO2 in the vicinity of RuBisCO. For decades, these decarboxylases have been used to classify C4 species into three biochemical sub‐types. However, more recently, the notion that C4 species mix an...
Preprint
Full-text available
Plants are essential for life on Earth converting light into chemical energy in the form of sugars. To adjust for changes in light intensity and quality, and to become as efficient as possible in harnessing light, plants utilize multiple light receptors, signaling, and acclimation mechanisms. In addition to altering plant metabolism, development an...
Article
Reducing photorespiration in C3 crops could significantly increase rates of photosynthesis and yield. One method to achieve this would be to integrate C4 photosynthesis into C3 species. This objective is challenging as it involves engineering incompletely understood traits into C3 leaves including complex changes to their biochemistry, cell biology...
Article
Chloroplasts are best known for their role in photosynthesis, but they also allow nitrogen and sulphur assimilation, amino acid, fatty acid, nucleotide and hormone synthesis. How chloroplasts develop is therefore relevant to these diverse and fundamental biological processes, but also to attempts at their rational redesign. Light is strictly requir...
Article
Full-text available
C4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C4 photosynthesis from its ancestral C3 pathway can help us better understand the generic principles of the evolution of complex traits and guide the engineering of C3 crops for higher yields. Here, we used the genus Flaveria that contains C3, C3–C4, C4-...
Article
Full-text available
The engineering of C4 photosynthetic activity into the C3 plant rice has the potential to nearly double rice yields. To engineer a two‐cell photosynthetic system in rice, the rice bundle sheath (BS) must be rewired to enhance photosynthetic capacity. Here, we show that BS chloroplast biogenesis is enhanced when the transcriptional activator, Oryza...
Article
Full-text available
When exposed to high light, plants produce reactive oxygen species (ROS). In Arabidopsis thaliana , local stress such as excess heat or light initiates a systemic ROS wave in phloem and xylem cells dependent on NADPH oxidase/respiratory burst oxidase homolog (RBOH) proteins. In the case of excess light, although the initial local accumulation of RO...
Preprint
Full-text available
Leaves comprise multiple cell types but our knowledge of the patterns of gene expression that underpin their functional specialization is fragmentary. Our understanding and ability to undertake rational redesign of these cells is therefore limited. We aimed to identify genes associated with the incompletely understood bundle sheath of C 3 plants, w...
Article
Full-text available
Leaves comprise multiple cell types but our knowledge of the patterns of gene expression that underpin their functional specialization is fragmentary. Our understanding and ability to undertake rational redesign of these cells is therefore limited. We aimed to identify genes associated with the incompletely understood bundle sheath of C3 plants, wh...
Article
Full-text available
We generated antisense constructs targeting two of the five Rubisco small subunit genes (OsRBCS2 and 4) which account for between 30-40% of the RBCS transcript abundance in leaf blades. The constructs were driven by a maize phosphoenolpyruvate carboxylase (PEPC) promoter known to have enriched expression in mesophyll cells (MCs). In the resulting l...
Preprint
Full-text available
C4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C4 photosynthesis from its ancestral C3 pathway can help us better understand the generic principles of the evolution of complex trait and guide the engineering of C3 crops for higher yields. Here, we used the genus Flaveria that contains C3, C3-C4, C4-l...
Article
Full-text available
C4 photosynthesis evolved repeatedly from the ancestral C3 state, improving photosynthetic efficiency by ~50%. In most C4 lineages, photosynthesis is compartmented between mesophyll and bundle sheath cells, but how gene expression is restricted to these cell types is poorly understood. Using the C3 model Arabidopsis thaliana, we identified cis-elem...
Preprint
Full-text available
We generated antisense constructs targeting two of the five Rubisco small subunit genes (OsRBCS2 and 4) which account for between 30-40% of the RBCS transcript abundance in leaf blades. The constructs were driven by a maize phosphoenolpyruvate carboxylase (PEPC) promoter known to have enriched expression in mesophyll cells (MCs). In the resulting l...
Preprint
Full-text available
When exposed to high light plants produce reactive oxygen species (ROS). In Arabidopsis thaliana local accumulation of ROS preferentially takes place in bundle sheath strands, but little is known about how this response takes place. Using rice and the ROS probes diaminobenzidine and 2',7'-dichlorodihydrofluorescein diacetate, we found that after ex...
Preprint
Full-text available
The efficient C4 pathway is based on strong up-regulation of genes found in C3 plants, but also compartmentation of their expression into distinct cell-types such as the mesophyll and bundle sheath. Transcription factors associated with these phenomena have not been identified. To address this, we undertook genome-wide analysis of transcript accumu...
Preprint
Full-text available
Introduction of a C 4 photosynthetic pathway into C 3 rice ( Oryza sativa ) requires installation of a biochemical pump that concentrates CO 2 at the site of carboxylation in modified bundle sheath cells. To investigate the feasibility of this, we generated a quadruple line that simultaneously expresses four of the core C 4 photosynthetic enzymes f...
Preprint
Full-text available
Convergent trait evolution is a recurrent phenomenon in all domains of the tree of life. While some convergent traits are caused by simple sequence changes, many are associated with extensive changes to the sequence and regulation of large cohorts of genes. It is unknown how organisms traverse this expansive genotype space to assemble such complex...
Article
Full-text available
Fluorescent reporters have facilitated non‐invasive imaging in multiple plant species and thus allowed the analysis of processes ranging from gene expression and protein localization to cellular patterning. However, in rice, a globally important crop and model species, there are relatively few reports of fluorescent proteins being used in leaves. F...
Article
Full-text available
The engineering process of C4 photosynthesis into C3 plants requires an increased activity of phosphoenolpyruvate carboxylase (PEPC) in the cytosol of leaf mesophyll cells. The literature varies on the physiological effect of transgenic maize (Zea mays) PEPC (ZmPEPC) leaf expression in Oryza sativa (rice). Therefore, to address this issue, leaf–atm...
Article
Full-text available
The majority of plants use C3 photosynthesis, but over 60 independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle-sheath cells. We performed DNaseI sequencing to identify genome-wide profiles of transcription factor binding in leaves of the C4...
Article
Full-text available
Achieving global food security for the estimated 9 billion people by 2050 is a major scientific challenge. Crop productivity is fundamentally restricted by the rate of fixation of atmospheric carbon. The dedicated enzyme, RubisCO, has a low turnover and poor specificity for CO2. This limitation of C3 photosynthesis (the basic carbon-assimilation pa...
Article
Full-text available
Laser Capture Microdissection is a powerful tool that allows thin slices of specific cell types to be separated from one another. However, the most commonly used protocol, which involves embedding tissue in paraffin wax, results in severely degraded RNA. Yields from low abundance cell types of leaves are particularly compromised. We reasoned that t...
Preprint
Full-text available
The majority of plants use C 3 photosynthesis, but over sixty independent lineages of angiosperms have evolved the C 4 pathway. In most C 4 species, photosynthesis gene expression is compartmented between mesophyll and bundle sheath cells. We performed DNaseI-SEQ to identify genome-wide profiles of transcription factor binding in leaves of the C 4...
Article
Full-text available
The influence of reduced glycine decarboxylase complex (GDC) activity on leaf-atmosphere CO2 and 13CO2 exchange was tested in transgenic Oryza sativa with the knocked down (KD) of the GDC H-subunit in the leaf M cells. Leaf measurements on transgenic (gdch-KD) and wild-type (WT) plants were carried out in the light under photorespiratory and low-ph...
Preprint
Full-text available
Background C 4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C 4 photosynthesis from its ancestral C 3 pathway can help us to better understand the generic principles of complex trait evolution and guide engineering of C 3 crops for higher yields. We used the genus Flaveria that contains C 3 , C 3 -C 4...
Preprint
Full-text available
In multicellular organisms the specification of distinct tissues within organs allows compartmentation of complex processes. However, the mechanisms that allow gene expression to be restricted to such tissues are poorly understood. To better understand this process, we focused on bundle sheath expression of the gene encoding the MYB76 transcription...
Article
Full-text available
The bundle sheath provides a conduit linking veins and mesophyll cells. In C3 Arabidopsis thaliana it also plays important roles in oxidative stress and sulphur metabolism. However, the mechanisms responsible for the patterns of gene expression that underpin these metabolic specialisations are poorly understood. Here we used the A. thaliana SULTR2;...
Article
Full-text available
Droplet-based microfluidics has been used to facilitate high-throughput analysis of individual prokaryote and mammalian cells. However, there is a scarcity of similar workflows applicable to rapid phenotyping of plant systems where phenotyping analyses typically are time-consuming and low-throughput. We report on-chip encapsulation and analysis of...
Data
Sorting of M. polymorpha protoplasts. Bright field and fluorescence micrographs of microdroplets sorted into positive and negative channels based on their mVenus fluorescence intensity. Scale bars; 50 μm. (PDF)
Data
Encapsulation of A. thaliana protoplasts. A) Bright field and (B) chlorophyll fluorescence micrographs of individual A. thaliana leaf protoplasts encapsulated in microdroplets. (C) Representative photomultiplier tube (PMT) readout of chlorophyll fluorescence intensity represented as arbitrary fluorescent units (AFU) recorded over 17.5 s. Each line...
Article
Full-text available
Engineering C4 photosynthesis into C3 crops could substantially increase their yield by alleviating photorespiratory losses. This objective is challenging because the C4 pathway involves complex modifications to the biochemistry, cell biology and anatomy of leaves. Forward genetics has provided limited insight into the mechanistic basis of these pr...
Article
Full-text available
C4 photosynthesis has evolved repeatedly from the ancestral C3 state to generate a carbon concentrating mechanism that increases photosynthetic efficiency. This specialised form of photosynthesis is particularly common in the PACMAD clade of grasses, and is used by many of the world's most productive crops. The C4 cycle is accomplished through cell...
Preprint
It has been proposed that introducing C 4 photosynthesis into C 3 crops would increase yield. The simplest scheme in- volves concentrating carbon originating from the cytosol in the chloroplast stroma of mesophyll cells without altering leaf or cell anatomy. Photosynthetic efficiency would then strongly depend on the chloroplast envelope permeabili...
Article
If the highly efficient C4 photosynthesis pathway could be transferred to crops with the C3 pathway there could be yield gains of up to 50%. It has been proposed that the multiple metabolic and developmental modifications associated with C4 photosynthesis are underpinned by relatively few master regulators that have allowed the evolution of C4 phot...
Preprint
Full-text available
Engineering C4 photosynthesis into C3 crops such as rice or wheat could substantially increase their yield by alleviating photorespiratory losses1,2. This objective is challenging because the C4 pathway involves complex modifications to the biochemistry, cell biology and anatomy of leaves3. Forward genetics has provided limited insight into the mec...
Preprint
Full-text available
C 4 photosynthesis has evolved repeatedly from the ancestral C 3 state to generate a carbon concentrating mechanism that increases photosynthetic efficiency. This specialised form of photosynthesis is particularly common in the PACMAD clade of grasses, and is used by many of the world’s most productive crops. The C 4 cycle is accomplished through c...
Preprint
Full-text available
The bundle sheath provides a conduit linking veins and mesophyll cells. In C 3 Arabidopsis thaliana it also plays important roles in oxidative stress and sulphur metabolism. However, the mechanisms responsible for the patterns of gene expression that underpin these metabolic specialisations are poorly understood. Here we used the A. thaliana SULTR2...
Preprint
Full-text available
Droplet-based microfluidics has been used to facilitate high throughput analysis of individual prokaryote and mammalian cells. However, there is a scarcity of similar workflows applicable to rapid phenotyping of plant systems. We report on-chip encapsulation and analysis of protoplasts isolated from the emergent plant model Marchantia polymorpha at...
Article
Full-text available
During C 4 photosynthesis, CO 2 is concentrated around the enzyme RuBisCO. The net effect is to reduce photorespiration while increasing water and nitrogen use efficiencies. Species that use C 4 photosynthesis have evolved independently from their C 3 ancestors on more than 60 occasions. Along with mimicry and the camera-like eye, the C 4 pathway t...
Preprint
Full-text available
Introductory paragraph Much of biology is associated with convergent traits, and it is challenging to determine the extent to which underlying molecular mechanisms are shared across phylogeny. By analyzing plants representing eighteen independent origins of C 4 photosynthesis, we quantified the extent to which this convergent trait utilises identic...
Preprint
Full-text available
In C 4 plants the enzymatic machinery underpinning photosynthesis can vary, with for example, three distinct C 4 acid decarboxylases being used to release CO 2 in the vicinity of RuBisCO. For decades, these decarboxylases have been used to classify C 4 species into three biochemical sub-types. However, more recently the notion that C 4 species mix...
Article
Full-text available
Most terrestrial plants use C3 photosynthesis to fix carbon. In multiple plant lineages a modified system known as C4 photosynthesis has evolved. To better understand the molecular patterns associated with induction of C4 photosynthesis, the genus Flaveria that contains C3 and C4 species was used. A base to tip maturation gradient of leaf anatomy w...
Article
C4 photosynthesis is a carbon-concentrating mechanism that increases delivery of carbon dioxide to RuBisCO and as a consequence reduces photorespiration. The C4 pathway is therefore beneficial in environments that promote high photorespiration. This pathway has evolved many times, and involves restricting gene expression to either mesophyll or bund...
Preprint
Full-text available
Photosynthesis is compromised in most plants because an enzymatic side-reaction fixes O 2 instead of CO 2 . The energetic cost of oxygenation led to the evolution of C 4 photosynthesis. In almost all C 4 leaves compartmentation of photosynthesis between cells reduces oxygenation and so increases photosynthetic efficiency. Here we report that spatia...
Preprint
Full-text available
Most terrestrial plants use C 3 photosynthesis to fix carbon. In multiple plant lineages a modified system known as C 4 photosynthesis has evolved. To better understand the molecular patterns associated with induction of C 4 photosynthesis the genus Flaveria that contains C 3 and C 4 species was used. A base to tip maturation gradient of leaf anato...
Article
A recent survey of transcript abundance in wheat grains found accumulation of mRNAs encoding key enzymes of C4 photosynthesis. However, this is not the same as showing that the C4 pathway operates in these tissues.
Article
C4 photosynthesis acts as a carbon concentrating mechanism that leads to large increases in photosynthetic efficiency. The C4 pathway is found in more than 60 plant lineages¹ but the molecular enablers of this evolution are poorly understood. In particular, it is unclear how non-photosynthetic proteins in the ancestral C3 system have repeatedly bec...
Article
Half a century after the discovery of a plant photosynthetic pathway termed C4, researchers are working to engineer this efficient pathway into crops such as rice to maintain food security.
Article
Full-text available
TransRate is a tool for reference-free quality assessment of de novo transcriptome assemblies. Using only the sequenced reads and the assembly as input, we show multiple common artifacts of de novo transcriptome assembly can be readily detected. These include chimeras, structural errors, incomplete assembly and base errors. TransRate evaluates thes...