Plant Science Research Weekly: March 1, 2024

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Review: SynBio takes on roots and the rhizosphere

This is an excellent introduction to how synthetic biology can be used to program plants for climate resilience by engineering them to respond predictably and in ways beyond those that evolution has explored, through the use of controllable synthetic gene circuits. Ragland et al. describe how precise and specific transcription factors can target synthetic promoter elements with little bleed-through to other genes, providing very fine  and predictable control of gene expression and eliminating confounding pleiotropic effects. Combining these elements as Boolean logic gates can produce expression patterns in cells where conditions are absent (NOR gates) or NIMPLY gates where expression occurs where one circuit is on and the other off. After describing some of these synthetic gene circuits, the article discusses how they can be used to modify root system architecture, anatomy, and nutrient uptake. Several key genes have been identified with large impacts on root development, such as lateral root initiation or gravity setpoint angle, which in turn affect water and nutrient uptake. Genes that affect nutrient uptake, soil penetrance, and exudation of molecules into the soil are also promising candidates for synthetic biology-based engineering. Finally, plant productivity can be promoted by the potentially quicker engineering of soil microbes, with examples discussed that can impact plant biotic and abiotic interactions, as well as nutrient acquisition. Through the use of the design-build-test-learn cycle, its likely that we’ll be seeing rapid progress in the engineering of plant root systems. (Summary by Mary Williams @PlantTeaching)  Nature Comms. 10.1038/s41467-024-45272-5

Review: Long noncoding RNAs and the art of being influential without protein

Advances in sequencing technologies have led to a tremendous growth in the number of long noncoding RNAs (lncRNAs) being identified in plants, but identifying their function lags behind. Here, Ramirez Gonzales and Blom et al. draw on lessons from studies in mammalian systems and highlight several known functions of lncRNAs. One of the more well-known plant lncRNA is COLD ASSISTED INTRONIC NONCODING RNA (COLDAIR), a component of the vernalization response that affects histone methylation and transcriptional silencing at FLOWERING LOCUS C (FLC). Other lncRNAs in plants and mammals also have epigenetic effects including chromatin methylation. As nucleic acids, lncRNAs can directly interact with DNA and RNA including microRNAs (miRNAs) through base pairing. One of the better-known examples of this involves the interaction between the lncRNA INDUCED BY PHOSPHATE STARVATION1 (IPS1) and miR399. This interaction prevents miR399 from binding to its “real” target, the mRNA PHO2, thus regulating phosphate uptake. Other lncRNA functions that are discussed include splicing, other forms of transcriptional regulation, and acting as a mobile signal. Besides being a really clear and thorough overview of lncRNAs, this review highlights potential applications of lncRNAs in plants. (Summary by Mary Williams @PlantTeaching) Trends Plant Sci. 10.1016/j.tplants.2024.01.006

Review: Development and evolution of the Asteraceae inflorescence

Asteraceae, also known as Compositae or the daisy family, is one of the largest plant families and comprises 10% of all flowering plants. Members of this family are found in habitats worldwide. The unique inflorescence, called a capitulum, is a key innovation of the family and contributes to its success. This highly compressed head-like structure can consist of a single flower but usually is composed of multiple florets. In this new review, Zhang and Elomaa delve into the development and evolution of the capitulum, shedding light on molecular and genetic studies that have expanded our understanding of its formation such as exploring the patterning and maturation of florets within the capitulum, including the iconic phyllotactic arrangement of florets in Fibonacci numbers of spirals. While much has been uncovered about the capitulum’s evolution and organization, there is still a large numberr of species to explore. The paper emphasizes Asteraceae’s potential as a model for evolutionary developmental studies, utilizing its diverse morphology and genetic networks to advance crop breeding efforts.  (Summary by Villő Bernád) New Phytol. 10.1111/nph.19590

Moss phenotype unaffected by removal of repetitive sequences from genome

Genome complexity in multicellular organisms is often associated with repetitive sequences from Transposable Elements (TEs). TE function, importance for genome integrity, and dispensability have not been completely characterized.  In prokaryotes and simple eukaryotes, genome synthesis (production of synthetic chromosomes and genomes) has proven to be a useful tool to understand genome organisation and function. As a prelude to the development of synthetic genomes in a multicellular organism. Physcomitrium (Physcomitrella) patens is a well-established multicellular model organism that is more complex than unicellular organisms due to greater genome size, gene number and epigenetic diversity. Chen and collaborators investigated the effect of decreased repetitive sequences by eliminating 55.8% of a 155 kb region of chromosome 18 in Physcomitrella. They used various methods to reassemble the DNA, including homologous recombination which was highly effective. Surprisingly, the phenotype of the transformed plant was comparable to the wild type (WT) even when growing under salt and osmotic stress. There was not much difference in histone marks related to active transcription between the synthetic and WT genomic regions, however marks associated with TEs abundance (H3K9me2) were almost completely removed, probably due to the lack of repetitive elements. On the other hand, chromatin interaction did show changes in the redesigned and neighbouring regions, demonstrating that genome redesign can alter chromosome conformation. These studies show that repetitive sequences can be removed without affecting morphology, development, and stress resistance, paving the way for the Synthetic Moss (SynMoss) project. (Summary by Rigel Salinas-Gamboa @Rigelitactica). Nature Plants 10.1038/s41477-023-01595-7

The Marchantia transcription factor atlas

Marchantia’s power as a model organism continues to grow! Here, Ramoni et al. have investigated the expression pattern of the proximal promoters of most of its 450 transcription factor (TF)-encoding genes. The promoter elements were fused to nuclear-localized fluorescent reporters and introduced into plants. The authors provide the expression data of the constructs in a useful and accessible website, https://mpexpatdb.org/. Each TF promoter construct is shown along with chlorophyll fluorescence and a constitutive plasma membrane marker, which can be toggled on and off independently. Focusing on 218 genes, they identified five expression-pattern based clusters, with many of the genes preferentially expressed in the stem-cell zone or the dividing and differentiating cell zone. They also examined cell-specific and dynamic patterns of expression, and correlated these results with those obtained through other methods such as transcriptomics. As well as providing a great resource for further studies, this work has already provided insights into Marchantia development, including a suite of genes expressed in the stem-cell zone that are distinct from genes expressed in vascular plant meristems. (Summary by Mary Williams @PlantTeaching) Plant Cell 10.1093/plcell/koae053

Novel lignin-based extracellular barrier in glandular trichome

This is a fascinating story by Hao et al., which takes us from phenotype to novel insights by looking at glandular trichomes in cucumber. Cucumber fruits often have a silica-based white powder deposited on their surface, but this is missing from the yellow green peel (ygp) mutant. Staining shows that the silica is deposited on the surface of glandular trichomes of wild-type plants but not on the mutants. The YGP gene encodes MYB36, which in Arabidopsis is a master regulator of Casparian strip formation. The Casparian strip is a lignin-based apoplastic barrier that controls apoplastic movement in the root endodermis. Transcriptomic analysis showed that in the ygp mutant one of the most down-regulated genes is CASP1, which is a direct target of MYB26 and in the endodermis is a scaffold protein for Casparian strip formation. The authors looked at the expression pattern of CASP1 in cucumber and found that it is highly expressed in the neck cells of glandular trichomes. Additional experiments showed that in the neck region, there is an apoplastic accumulation of lignin as has been observed in the Casparian strip. The authors propose a model in which there is an apoplastic barrier in the neck region of glandular trichomes that keeps the silica exudate on the surface of these cells, but in the ypg mutant is missing, allowing this exudate to move apoplasticaly away from the surface. Finally, they identified similar structures of glandular trichomes of several other species. Given the usefulness of several compounds produced by glandular trichomes, it will be interesting to see if these new insights can be applied commercially. (Summary by Mary Williams @PlantTeaching) Nature Plants 10.1038/s41477-024-01626-x

Using emmer wheat to discover genes involved in drought tolerance

Wheat is a major global crop, but its yields are severely compromised by drought, thus developing varieties with a higher drought tolerance is important. Emmer wheat (Triticum turgidum) is a wheat ancestor that contains more genetic diversity than cultivated varieties, so it can be used in genome wide association studies (GWAS) to discover alleles associated with higher drought tolerance. Here Yang et al. grew 107 emmer wheat accessions to the three-leaf stage, and then transferred them to well-watered and water-stressed conditions for a further four weeks. For each accession, they measured biomass, root length, root area and root volume in both conditions and calculated drought tolerance indexes for each trait by dividing the value in the water-stressed condition by that in the well-watered condition. These drought tolerance indexes were used as input for a GWAS and an expression GWAS (eGWAS), which allows identification of loci associated with changes in gene expression between well-watered and water-stressed conditions. Integrating these strategies identified 86 quantitative trait loci (QTLs) and 190 expression QTLs. Interestingly, one contained the SUMO protease OTS1, and silencing or knocking this out in emmer wheat increased the drought tolerance indexes. Hence, OST1 has a potential to improve wheat drought tolerance. (Summary by Rose McNelly @Rose_McN) New Phytol. 10.1111/nph.19589

Peptide GOLVEN10 alters root development and noduletaxis

For many years, biologists argued about whether plants have peptide hormones like animals have, and ever since it was first shown that plant peptides do have hormone-like functions, I’ve said a little cheer as new functions are discovered (Yay plants!). A few years ago, Sonali Roy and colleagues wrote an excellent Teaching Tool on this topic (Small and mighty: Peptide hormones in plant biology) which I encourage you to read and share. Here, Roy et al. demonstrate a new role for the GOLVEN10 peptide in Medicago truncatula. Previous work identified roles for GOLVEN (GLV) peptides in root development; GLV overexpression leads to a wavy root and golven means “waves” in Dutch. The authors found that in Medicago, GLV10 is expressed in nodule-initiation sites and under the control of the NODULE INCEPTION (NIN) transcription factor. They found that application of GLV10 peptide to roots caused a decrease in nodule number, independent of effects on the symbiont. Interestingly, they also found a shift in position of the nodules and lateral roots along the root axis away from the root base, and that GLV10-treated roots had more, shorter cortical cells. Consistent with this finding, analysis of genes regulated by GLV10 showed that cell-cycle and cytoskeleton-related genes are differentially expressed. Thus, GLV10 is a regulator of nodule placement, or, by analogy to phyllotaxis, “nodultaxis”. (Summary by Mary Williams @PlantTeaching) Plant J. 10.1111/tpj.16626

Cross-enrichment of-siderophore secreting rhizobacteria improves iron nutrition and yield of peanut intercropped with maize

Intercropping, the system of growing at least two crops simultaneously, increases crop productivity and ecological sustainability. An intercropping system of peanut (Arachis hypogaea L.) and maize (Zea mays) has been previously found to improve the yield of peanut, specifically its iron nutrition and photosynthetic efficiency. Here, Wang et al. investigated the role of the rhizosphere microbiome in the increased iron nutrition observed in peanut/maize intercropping systems. They used 16S rRNA amplicon sequencing to explore the microbiome communities of peanut and maize in monocropping and intercropping systems. They found a convergence between maize and peanut microbiomes in the intercropping system. Interestingly, siderophore-producing Pseudomonas spp. was cross-enriched from maize to peanut and found to be associated with improved iron nutrition in peanut. The authors conclude that the improved yield of peanut observed in the peanut-maize intercropping system is associated with the cross-enrichment of rhizosphere microbiomes from maize. These findings highlight the potential role of rhizosphere microbiomes in intercropping systems and provide insights into the possibility of exploring such systems to boost crop yield and productivity.  (Summary by Abdulkabir Omeiza Abdulmalik @Omeiza_PlantDoc) Nature Comms. 10.1038/s41467-024-45207-0

Application of silicate enhances plant growth-promoting rhizobacteria network complexity in sugarcane rhizosphere

Silicon (Si) plays a significant role in helping plants to mitigate biotic and abiotic stress. Previous studies have shown that the application of Si also influences the microbial communities in the rhizosphere. However, the extent to which Si shapes the dynamics of plant growth promoting rhizobacteria (PGPR) in the rhizosphere is less explored. Here, Leite et al. investigated the influence of silicon on the PGPR community in the sugarcane rhizosphere.  They assessed the PGPR community within the rhizosphere of three sugarcane genotypes in the presence (Si+) and absence (Si-) of Si in the form of silicate. Specifically, the authors used 16S rRNA sequencing to evaluate the richness, diversity, composition, co-occurrence network, and niche occupancy of the PGPR community. Although the results showed no significant influence of the treatments and the genotypes on the richness and diversity of the PGPR, they found varied effects of the Si treatment across the three genotypes. Two of the three genotypes showed increased network complexity in the presence of Si, indicating that the effect of the Si treatment may be genotype dependent. The authors concluded that Si application increases the complexity of microbial networks with the potential to increase plant growth. These findings highlight the possibility of increasing PGPR interaction networks as a recipe for sustainable agriculture. (Summary by Abdulkabir Omeiza Abdulmalik @Omeiza_PlantDoc) Rhizosphere 10.1016/j.rhisph.2024.100855

Effect of plant-derived versus animal-derived fertilizers on the rhizosphere microbiome

Yu et al. conducted a meta-analysis of published 16S rRNA gene amplicon sequenced soil samples to compare the effects of plant-based fertilizers (e.g. compost, seaweed fertilizer) versus animal-based fertilizers (e.g., dung, manure) versus control, unfertilized samples on soil microbial diversity and function. Their analysis showed that the fertilizer source significantly influences microbial functional profiles and the metabolic pathways and biogeochemical cycle processes that are upregulated. The authors validated these findings experimentally by investigating the effect of the four fertilizer sources (fermented pig or chicken manure, fermented tree leaves or tea slag)  on pakchoi (Brassica chinensis L.) All fertilizers showed a significant increase in plant growth versus unfertilized treatment and confirmed the findings of their meta-analysis on the impact of soil microbial function. Both types of fertilizers increased the stability of rhizosphere microbial communities, but in different ways. The animal-derived fertilizer mainly enriched genes related to nitrogen cycling while the plant-derived fertilizer enriched genes related to carbon fixation, carbon degradation, and methane metabolism. However, in samples treated with animal-derived fertilizers there was an increased abundance of antibiotic resistance genes and viruses related to human disease. Given the risks to human health conferred by animal-derived fertilizer samples, the authors conclude that plant-derived fertilizers are safer for sustainable crop production. (Summary by Abdulkabir Omeiza Abdulmalik @Omeiza_PlantDoc) Appl. Environ. Microbiol. 10.1128/aem.01719-23

 

Strategy-I plants exploit the distinct chemical activities of coumarins to maximize Fe acquisition

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Paffrath et al. explore the main physiological roles of coumarins released in response to iron deficiency under different environmental pHs.  

https://doi.org/10.1093/plcell/koad279

By Ricardo F. H. Giehl, Leibniz Institute of Plant Genetics & Crop Plant Research (IPK), Germany.

 Background: Although iron (Fe) is abundant in the Earth’s crust, the availability of this micronutrient to plants is often low under slightly acidic to alkaline pH conditions. Non-graminaceous species, such as Arabidopsis (Arabidopsis thaliana), rely on the “strategy I” Fe acquisition mechanism, which requires the reduction of Fe(III) prior to uptake. These plants are typically more prone to high pH-induced Fe deficiency because Fe(III) reductase activity is pH sensitive, such as that of FERRIC REDUCTION OXIDASE2 (FRO2). Iron acquisition in species employing the reduction-based strategy is often supported by the release of coumarins, secondary metabolites derived from the phenylpropanoid pathway.

 Questions: Do the redox-active coumarins secreted by Fe-deficient A. thaliana plants contribute to ferric Fe reduction in roots? If so, how this function is linked to FRO2? How are coumarin composition and the chemical activities of distinct coumarins modulated by environmental pH?

 Findings: With chemical complementation experiments and by disrupting single steps of the coumarin biosynthesis pathway in the fro2 mutant, we revealed that coumarins play a physiologically relevant role in Fe(III) reduction. We demonstrated that sideretin is the dominant chemical reductant in Arabidopsis and, with FRO2, contributes to generating Fe(II) for root uptake under acidic conditions. At alkaline pH, transcription factor MYB72 shifts coumarin biosynthesis away from sideretin and toward fraxetin. Under these conditions, instead of ferric Fe reduction, the predominant function of fraxetin is to provide soluble Fe(III) substrates for FRO2.

Next steps: Future studies are needed to determine whether there is genetic variability for coumarin-mediated ferric Fe reduction and to characterize the putative role of MYB72 in pH-dependent modulation of coumarin composition. Furthermore, it will be of interest to investigate whether and how coumarin-mediated Fe(III) reduction affects the root microbiota.

Reference:

Vanessa Paffrath, Yudelsy A. Tandron Moya, Günther Weber, Nicolaus von Wirén and Ricardo F.H. Giehl. (2023). A major role of coumarin-dependent ferric iron reduction in strategy I-type iron acquisition in Arabidopsis. https://doi.org/10.1093/plcell/koad279

One gene for taller, stiffer and high-yield rice

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Wang et al. reveal that MYB110 serves as a phosphate-dependent negative regulator of plant height that could be manipulated to boost lodging resistance and yield.

https://doi.org/10.1093/plcell/koad268

Tingting Wang,1 Ming Yan,2 Mian Gu,1 Guohua Xu1

1 National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China

2 MOA Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Shanghai Agrobiological Gene Center, Shanghai 201106, China

Background: The semi-dwarf architecture of the ‘Green Revolution’ crop varieties, which confers remarkably enhanced lodging resistance, is a fundamental basis for high yield. To further boost yield, developing novel crop varieties with higher plant height and improved lodging resistance could be a potential solution. Plant height is tightly regulated by the availability of phosphate (Pi), an essential nutrient for plant growth and development, yet the underlying mechanism remains obscure.

Question: What are the molecular mechanisms by which rice plants coordinately regulate plant height and lodging resistance in response to varied Pi availabilities?

Findings: An R2R3-type MYB transcription factor in rice (Oryza sativa), OsMYB110, is a Pi-dependent negative regulator of plant height. Inactivation of OsMYB110 increased culm diameter and bending resistance, leading to enhanced lodging resistance in spite of increased plant height. We demonstrated that OsMYB110 is a direct target of OsPHR2 (PHOSPHATE STARVATION RESPONSE 2), the central regulator of Pi starvation signaling network in rice, and is responsible for OsPHR2-induced suppression of plant height. The response of plant height to Pi-limiting stress was largely compromised upon OsMYB110 inactivation. Strikingly, the grain yield of osmyb110 mutants was elevated under both high- and low-Pi regimes. Furthermore, we identified two indica-japonica divergent haplotypes based on single-nucleotide polymorphisms in the putative promoter of OsMYB110, which correlates with OsMYB110 transcript level and plant height in response to Pi availability.

Next steps: We plan to introduce the OsMYB110 haplotype with lower expression, which confers enhanced plant height and lodging resistance, into widely planted rice cultivars by generating near isogenic lines.

Reference:

Tingting Wang, Yi Jin, Lixiao Deng, Feng Li, Zhiyuan Wang, Yuanyuan Zhu, Yufeng Wu, Hongye Qu, Shunan Zhang, Ying Liu, Hanwei Mei, Lijun Luo, Ming Yan,*, Mian Gu*, Guohua Xu* (2023) Transcription factor MYB110 regulates plant height, lodging resistance and grain yield in rice. https://doi.org/10.1093/plcell/koad268

 

Working towards your goals one step at a time: An interview with Plant Physiology monitoring editor Alistair McCormick

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By Jiawen Chen, PhD, Plant Physiology Assistant Features Editor

Alistair McCormick is a Professor in Plant Engineering Biology at the University of Edinburgh (UK). He obtained his PhD at the University of KwaZulu Natal (South Africa), where he worked on sink regulation of photosynthesis in sugarcane, with Derek Watt and Michael Cramer. After postdocs in Oxford, Cambridge and the John Innes Centre (UK), he became a PI at the University of Edinburgh as a Chancellor’s Fellow in 2013 and was promoted to Professor in 2023. His lab researches photosynthesis in plants, algae and cyanobacteria using a synthetic/engineering biology approach, with key focuses on improving photosynthetic efficiencies in C3 plants, and enhancing the carbon sequestration potential and production of high value compounds in micro-algae.

CAREER

How did you first become interested in plant science and in becoming a scientist?

When I first started my BSc, I wanted to do science and to be a medic. My undergraduate degree back in Durban, South Africa (University of KwaZulu Natal) was a mixture of ecology and cell biology or molecular biology. It was when I started working on sugarcane in my master’s degree (Plant Biotechnology, University of Stellenbosch) and continued this in my PhD (University of KwaZulu Natal), that I started developing this passion for plant science.

So how did you become involved in the sugarcane project when at first you weren’t really looking at plant science?

In the fourth and final year of my honours degree I successfully applied for an internship at the South African Sugarcane Research Institute (SASRI), which is part of SASA, the South African Sugar Association. SASRI has a good lab, they have tissue culture facilities and link up with breeders, but do blue skies research as well. I was in a win-win situation working at an institute that did both applied and fundamental research. I did my MSc and PhD at SASRI, and focused on understanding the source-sink relationship in sugarcane. This was really fun, because we got to start playing with new molecular tools like microarrays and mixed that up with proper physiology measurements in plants. It was great as the facilities were so good. It’s probably still one of the better equipped research labs that I’ve worked in, and I think that comes down to industry support and the talented group of scientists there.

As that project was looking at photosynthesis, is that how you came on to researching carbon concentrating mechanisms (CCMs)?

Sugarcane is C4 of course, so I got involved in studying the C4 concentrating mechanism (CCM) during my MSc and PhD, but it was only when I got to the UK for my second and third postdocs that I discovered pyrenoids. I started working with algae and cyanobacteria in my second postdoc in Chris Howe’s lab in Cambridge, and focused on pyrenoids and carboxysomes in my third postdoc with Alison Smith at the John Innes Centre (JIC). This was part of a large collaborative project funded by BBSRC-NSF, to introduce a pyrenoid-based CCM into plants to enhance photosynthesis. This has become the Combining Algal and Plant Photosynthesis (CAPP) Consortium, which has been going since 2010. In 2013, I applied for a Chancellor’s Fellowship at Edinburgh, and Alison Smith basically handed over the reins to me for the pyrenoid work, which was really great. The core group of CAPP currently consists of Luke Mackinder at York, and Martin Jonikas and Ned Wingreen at Princeton.

How do you manage a large consortium like that, with people approaching a similar goal from different perspectives and different labs?

I think it has worked well because of communication between the core group members. For many years now we have been meeting up every three months for an online call, and usually one or two members of the labs present their recent findings. It’s not competitive, but when you see another lab has discovered something new it’s really exciting. This helps to motivate future work and to focus going forward in a particular way. You start rethinking about challenges you might be having and, as such, everyone helps each other. For us, we’ve found three months is usually a good period in which to make progress and put together new data that you can share. We’ve had many successes I think, partly from just keeping those meetings going and keeping all the members of the CAPP groups informed.

Did you always want to be a PI?

Not at all, really. I’ve always worked in terms of my next goal. When I was nearing the end of my PhD, I was very focused on what I wanted to do next, and I wanted to do a postdoc. I wasn’t thinking about being a PI at that point. Then through my first two postdoc projects, I suppose I subconsciously felt that it was the trajectory of where I was going, but I wasn’t thinking about it seriously. I think many postdocs might feel this way. For example, they may feel they don’t have enough in terms of publications or experience. Then I think literally in the first month that I joined Alison Smith’s group at the JIC, she said, “What are you doing next?” Being put on the spot, I said, “I suppose I’d like to be a PI,” and she said, “Well you’d better start applying for fellowships.” She was a really good mentor, and that helped to put me on the PI path. Then it basically came down to putting applications together and getting used to that process of applying and going up to the next level, which I think, like anything, once you get used to the details it’s not that scary, and you just have to try your best.

Other than Alison’s great mentorship, who had a big influence on your career and how does that influence your own ways of mentorship?

During my PhD I had two excellent supervisors, Derek Watt and Mike Cramer. Mike Cramer is at the University of Cape Town and Derek works for SASA. They both taught me molecular and physiology skills, and how to write. The evolution from being an undergraduate to writing at a PhD level is a big step. For my first postdoc, Nick Kruger was fantastic in terms of getting me involved in Arabidopsis and just generally getting me up to speed with the UK research community. Chris Howe in Cambridge then gave me a lot of freedom to explore different research avenues, which helped develop my confidence and independence. We were trying to build photovoltaic cells, using cyanobacteria and algae to generate electricity, which was really fun, interdisciplinary collaborative research, and good for outreach activities. I was fortunate to be involved in several good publications there, too. I think each of them taught me different things and what I do now is a conglomeration of it all. You watch your supervisors, and you learn what they do best.

Have you found doing research in the UK quite different from South Africa, and how did you find that transition?

Some of the labs in South Africa are really top notch. In general, though, the level of funding available is much lower than you have in the UK. In South Africa there’s a lot of applied research, and ecology and phylogenetic characterization research. Molecular biology is rarer compared to the UK, as it’s more expensive to do. I think moving to the UK and seeing the scope of the research community was something that took a bit of getting used to, as well as getting to understand the funding landscape. I don’t currently have plans to move back to South Africa, but in terms of collaborating with researchers in South Africa, I do look for opportunities to link up with local labs.

Do you have any advice for early career researchers (ECRs) for their general career development?

I think keeping focused on the details of your immediate next goal is a good thing to do, and so far it’s worked well for me. So, as a PhD student, it might be the key experiments you need to do to publish a specific research chapter as a good paper. This helps when you become a postdoc, where you’ll be focused on getting your suite of papers together or your next big publication and filling up your CV. As you progress in your career to being a PI, the details of your goals naturally become more long-term and complex, for instance the milestones you want to achieve in a three-year project. But overall, I think if you get into a habit of finding and paying attention to the important details upfront, it makes things easier overall.

RESEARCH

What kinds of different projects is your lab working on? How did you get started on all of them and how are all of these different paths developing?

We work with plants, algae, and cyanobacteria and we’ve got projects in each of these areas. For plant work, we collaborate with the CAPP group to introduce the pyrenoid into plants. With algae, we’re part of an sLoLa consortium with Saul Purton (UCL), Alison Smith (Cambridge), and Attila Molnar (Edinburgh) working on redesigning the algal plastid genome. With cyanobacteria, we’ve been building engineering toolkits for a while now, and have collaborated with several companies in the UK. We’ve worked with ScotBio on the blue pigment protein phycocyanin. We’re currently working with a company in Oxford called CyanoCapture to engineer a fast-growing cyanobacterial strain for enhance CO2 capture. The strain is really great to work with – with most model species you often wait up to 10 days to get colonies, but now we get colonies in 2-3 days. The cycle of “design, build, test, learn” is much accelerated.

Did the toolkit generation start from a necessity because you were working on a project?

Because I had such good fun with cyanobacteria when I was working in Chris’s lab, I decided I’d like to start a branch of cyanobacterial work in my lab. So, I teamed up with Chris and ScotBio, and we initially got a small proof of concept grant from PHYCONET (the predecessor of AlgaeUK) and built a MoClo kit, CyanoGate, which no one had done for cyanobacteria yet. During that time we recruited several excellent PhD and MSc students, who helped to further develop the kit and use it for various applications, for example, expressing a more thermotolerant variant of phycocyanin. We’ve also collaborated with David Lea-Smith at the University of East Anglia to start building a whole genome knockout library for model species Synechocystis sp. PCC 6803 (https://cyanosource.ac.uk). Most recently we’ve been working with this fast-growing strain, Synechocystis sp. PCC 11901. I feel I’ve been very fortunate as this branch of my lab has grown from strength to strength.

When do you think there might be a crop plant with a CO2-concentrating mechanism?

Our ambitious short-term goal is to get our first proof of concept pyrenoid-based CCM in Arabidopsis up and running in the next two years. In addition, we have two PhD students in the lab working on engineering various algal CCM components into tobacco and rice, respectively. As such, we’re testing out different species to decide on the specific crop that we want to commit to. If we get our proof of concept working, I would hope we can transfer this into a crop in the following five years.

What do you think is the most exciting development in plant biology in recent years?

Based on personal experience, I feel the recent improvements in microscopy tools have been game changing. We’ve been very fortunate to work with Ben Engel on cryo-electron tomography and with David Seung and Sam Zeeman on serial block-face electron microscopy approaches. These technologies are just so exciting in terms of being able to see, from a 3D perspective, the impact of heterologous proteins on plant chloroplast architecture. In the future, I hope we’ll be able to better automate these approaches, so we can quickly visualise and segment proteins and sub-cellular structures, and that such tools will become more abundantly available to the wider plant research community.

EDITING AND PUBLISHING

How much time do you spend on average in your role as editor, and how do you balance this with all your other tasks?

I usually spend about one or two hours a week on it. Once you get used to the process, it’s usually quite enjoyable and not that arduous to be an editor. Sometimes there are challenging situations, for example, when reviewers are late or disagree, and that can take a little bit of extra time to work through. For Plant Physiology, we can set up consultation sessions online with reviewers or other editors. This is really useful, as you can have relatively quick discussions on issues, and make sure everyone is in agreement and that your final decision is supported. It’s quite a fun and fulfilling process.

Do you choose postdocs and students as reviewers?

Not typically, but sometimes if the first authors of highly relevant papers are postdocs, and I would invite them. I would normally go for the last author unless I knew the postdoc, but often what happens is the last author might be busy and they recommend a postdoc or even a PhD student to review, in which case, I would send an invitation. I’ve found that postdocs and PhD students often do a solid job at reviewing because they are very thorough. Overall, I think getting ECRs involved in the review process is really good. At Plant Physiology, reviewers are given a star rating depending on how well or how timely their reviews are. So, if an ECR gets a high rating, they will likely get invited again in the future.

Do you have any thoughts on the way scientific publishing has developed, is evolving and where it may go?

One area of concern is the peer review process. I think the increasing number of publications is overburdening research communities and putting the peer review process under massive stress.  Monetizing peer review might help, but I’m not sure if there’s an appetite for this from publishers. You could see a future where only certain journals continue with traditional peer review, while others move to a preprint-like scenario, like bioRxiv, where a paper’s quality and impact is measured only by a crowd-sourcing approach; for example, a metric could be how often the paper is read and cited. This could be a good way forward, you could build a standardized base platform for robust data that doesn’t need to go through the typical peer review process. For example, a PhD chapter that doesn’t have sufficiently novel data for a high-impact publication, but nonetheless contains good science could be published on this kind of platform and just go through editorial review. Perhaps changes like this could support the ongoing need to publish work and help ease the pressure on traditional peer review.

Read more interviews of Plant Physiology editors here.

About the author

Jiawen Chen is a postdoctoral researcher at the KU Leuven (Belgium), in the lab of Bram van de Poel. She is interested in plant metabolism and is currently studying the ethylene biosynthesis pathway in Marchantia polymorpha. She obtained her PhD from the John Innes Centre in Norwich (UK) with David Seung, where she worked on the biochemistry of starch granule initiation in Arabidopsis and wheat. She is an Assistant Features Editor for Plant Physiology for the term 2023-2024.

The Membrane-bound Transcription Factor GmNTL1 Promotes Salt Tolerance in Soybean

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Zhang et al. identified a membrane-bound NAC transcription factor GmNTL that can be oxidized and released from the endoplasmic reticulum to the nucleus, thereby regulating downstream target genes to promote salt tolerance in soybean.

Plant Cell https://doi.org/10.1093/plcell/koad250

Wenxiao Zhang, Wenjiao Zhi, Hong Qiao, Jingjing Huang, Shuo Li, Qing Lu , Nan Wang, Qiang Li, Qian Zhou, Jiaqi Sun, Yuting Bai, Xiaojian Zheng, Mingyi Bai, Frank Van Breusegem, Fengning Xiang

Background: Worldwide, soybean (Glycine max) production is often adversely affected by salinity. Reactive oxygen species (ROS) are key signaling molecules that enable cells to rapidly respond to different stimuli, regulating plant growth and development by mediating oxidative post-translational modifications (OxiPTMs) of proteins. Thus, identifying the underlying mechanisms of redox regulation and its contribution to various physiological processes is a current research hotspot.

Question: The membrane-bound NAC WITH TRANS-MEMBRANE MOTIF1-LIKE (NTL) transcription factors play critical roles in plant responses to various environmental stimuli. However, how GmNTLs translocate to the nucleus and regulate salt tolerance remains unclear.

A model for the role of GmNTL1 in H2O2-mediated induction of gene expression under salt stress.

Findings: Our study reports that GmNTL1 is released from the endoplasmic reticulum (ER) and translocates to the nucleus upon NaCl or hydrogen peroxide (H2O2) treatment. Salt-induced H2O2 production increases GmNTL1 nuclear import and DNA-binding activity by oxidizing cysteine 247. Furthermore, GmNTL1 oxidation directly activates the expression of RESPIRATORY BURST OXIDASE HOMOLOG B (GmRbohB) genes, affecting the production of H2O2, thereby forming a feed-forward loop to fine-tune GmNTL1 activity. In addition, the oxidation of GmNTL1 further activates the expression of CATION H+ EXCHANGER 1 (GmCHX1)/SALT TOLERANCE-ASSOCIATED GENE ON CHROMOSOME 3 (GmSALT3) and Na+/H+ EXCHANGER 1 (GmNHX1), reducing root Na+ accumulation and improving soybean salt tolerance.

Next Steps: Given that OxiPTMs are highly dynamic and interconvertible, we will next focus on analyzing the reduction mechanisms of GmNTL1. Understanding how GmNTL1 regulates cellular redox dynamics will generate new ideas to elucidate soybean salt stress responses.

Reference:

Wenxiao Zhang, Wenjiao Zhi, Hong Qiao, Jingjing Huang, Shuo Li, Qing Lu, Nan Wang, Qiang Li, Qian Zhou, Jiaqi Sun, Yuting Bai, Xiaojian Zheng, Mingyi Bai, Frank Van Breusegem, Fengning Xiang. (2023). H2O2-dependent oxidation of the transcription factor GmNTL1 promotes salt tolerance in soybean. https://doi.org/10.1093/plcell/koad250.

Review: Integrating cellular electron microscopy with multimodal data to explore biology across space and time

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Fifty years ago (1974), Albert Claude, Christian de Duve, and George Palade were awarded the Nobel Prize for their discoveries on the structural and functional organization of the cell, which Claude eloquently framed by writing, “We have entered the cell, the mansion of our birth, and started the inventory of our acquired wealth.” In the subsequent fifty years, amazing new tools and technologies have greatly enhanced our understanding of our cellular inventory. McCafferty et al. have skillfully crafted a comprehensive overview of these methods, beautifully weaving together how they complement each other to provide extraordinary insights into cell structures and compositions in space and time. I particularly enjoyed how the authors melded multiple imaging technologies together along with computational and modeling approaches. As one of several examples, they show using Chlamydomonas how fluorescent microscopy can be combined with ultrastructure expansion microscopy, soft X-ray tomography, cross-linking and co-expression mass spectrometry, single-particle analysis, alpha fold structure prediction, proximity labeling and molecular dynamics modeling. This is a fascinating and inspiring article that makes me eager to see where the next 50 years will take us. (Summary by Mary Williams @PlantTeaching) Cell  10.1016/j.cell.2024.01.005

Review. Mycorrhizal symbiosis: Genomics, ecology, and agricultural application

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This outstanding Tansley review by Martin and van der Heijden spans the scale of research on mycorrhizal symbiosis from molecules to ecosystems, and spans time from the earliest encroachment of plants and fungi onto land to the future applications of our understanding. This very comprehensive review is a great resource to anyone with an interest in mycorrhizal symbiosis. I particularly appreciate their objective approach to addressing some of the potentially overhyped topics. For example, the idea of plants communicating and displaying altruistic behaviors through common mycorrhizal networks is intriguing, but the evidence for such effects is small. The authors also look at the potential for improving plant productivity through mycorrhizal inoculation. Although some studies have shown growth enhancement, the range of responses is huge and highly dependent on many factors that are difficult to identify and control. Mycorrhizal symbiosis impacts on and by climate change are also discussed, as are the many questions that require further research. (Summary by Mary Williams @PlantTeaching) New Phytol. 10.1111/nph.19541

Oxygen supply dictates growth and metabolism in young leaves

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When thinking of hypoxia or low oxygen in plants, the image that often comes to mind is one of flooding stress. However, it’s not just plants exposed to excess of water that face hypoxia. Even in growing plants, hypoxia sensing and the existence of hypoxic niches play a vital role in their development. Young, actively growing leaves have different metabolic needs compared to mature leaves, characterized by high respiration rates and thus high oxygen consumption. Yet a functional connection between internal oxygen sensing and a metabolic shift in developing plants is unexplored. In this intriguing study, Triozzi et al. uncovered the existence of cyclic hypoxia in young leaves. The authors found that the expression of hypoxia-responsive genes (HRGs) exhibits diurnal fluctuations, with peak expression at night. Using a combination of genetic and pharmacological approaches and transcriptional reporters, in combination with oxygen-modified atmosphere treatments, they demonstrated that diurnal variations in HRGs occur independently of light and clock inputs and are actually regulated by oxygen levels. Through the measurement of internal oxygen levels, the authors reveal that young leaves, and not old leaves, experience a drop in oxygen during the night. This nocturnal oxygen dip and the associated hypoxia signaling cascade, which is ERFVII-dependent, causes a shift in metabolism from aerobic to hypoxic metabolism, which is important to modulate leaf growth at at different times of the day. (Summary by Thomas Depaepe @thdpaepe) Mol. Plant 10.1016/j.molp.2024.01.006

Phase separation determining meiotic interference-sensitive meiotic crossover formation

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In sexual reproduction, meiosis creates new combinations between homologs and diversifies the genetic information among gametes and progenies. Most meiotic crossovers (COs) are mediated by a group of ZMM factors, including HUMAN ENHANCER of INVASION-10 (HEI10), which is suggested to concentrate at CO sites to form larger foci for crossover interference. However, how HEI10 is recruited to the CO site is still unclear. Here, Wang et al. showed Arabidopsis HEI10 undergoes liquid-liquid phase separation (LLPS) and its condensation depends on its residue Ser70. The HEI10 promoted the ubiquitination-dependent degradation of the interacting REPLICATION PROTEIN A (RPA1a) in the LLPS of CO sites through the early pachytene phase. This study also provides clues about how HEI10 controls class I meiotic crossover formation and can be relevant in most eukaryotes. (Summary by Yueh Cho @YuehCho1984) PNAS. 10.1073/pnas.2310542120.