Protein root discovery seals future of climate-proof plants

Researchers have discovered a protein that seals plant roots to regulate the uptake of nutrients and water from the soil, the discovery could help develop climate proof crops that require less water and chemical fertilizers.

Researchers from the University of Nottingham identified new components of the lignin barrier in plant roots and the specific function of dirigent proteins (DPs), located in the root endodermis that control water and nutrient uptake. Their findings have been published today in Science Direct.

Plant roots function by absorbing mineral nutrients and water from the soil and also controlling their proper balance in the plant. This control is exerted by a specialised layer of root tissue called the endodermis.

The endodermis contains a barrier to the movement of solutes and water that is made of lignin, the same material present in wood. This impermeable barrier blocks the uncontrolled movement of material into the root, by forming a tight seal between cells. This seal ensures the only pathway for nutrients and water to be taken up by roots is through the cells of the endodermis. This allows full cellular control over what enters and leaves the plant via the roots.

This research has identified new components of the lignin deposition machinery that focus on the function of dirigent proteins (DPs), located in the root endodermis. These proteins act in coordination with other described root regulatory components to direct and organize the correct deposition of lignin in the endodermis allowing the plant to ensure it receives the optimum balance of nutrients from the soil.

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Roots are capable of measuring heat on their own

Plant roots have their own thermometer to measure the temperature of the soil around them and they adjust their growth accordingly. Through extensive experiments, a team led by Martin Luther University Halle-Wittenberg (MLU), was able to demonstrate that roots have their own temperature sensing and response system. In a new study in The EMBO Journal, the scientists also provide a new explanation for how roots themselves detect and react to higher temperatures. The results could help develop new approaches for plant breeding.

The researchers used climate chambers to investigate how the plant model organism thale cress and the two crops cabbage and tomatoes react to rising ambient temperatures. They increased the ambient temperature from 20 to 28°C (68 to 82.4 degrees Fahrenheit). "Until now, it was assumed that the plant shoot controlled the process for the entire plant and acted as a long-distance transmitter that signalled to the root that it should alter its growth," says Professor Marcel Quint from the Institute of Agricultural and Nutritional Sciences at MLU. His team has now been able to disprove this through extensive experiments in cooperation with researchers from the Leibniz Institute of Plant Biochemistry (IPB), ETH Zurich and the Max Planck Institute for Plant Breeding Research in Cologne. In one experiment, scientists cut off the shoot of the plants but allowed the roots to continue to grow. "We found that the roots were not affected by this and grew at elevated temperatures in the same way as on plants with intact shoots. The higher temperature stimulated cell division and the roots became significantly longer," says Quint. The team also used mutant plants whose shoots could no longer detect and respond to higher temperatures. Those were grafted onto roots without this defect. Here, too, the roots were able to react to the heat in the soil, even though the shoot did nothing.

The researchers found in all of their experiments that root cells increased the production of the growth hormone auxin, which was then transported to the root tips. There, it stimulated cell division and enabled the roots to reach further down into the soil. "As heat and drought usually occur in tandem, it makes sense for the plants to tap into deeper and cooler soil layers that contain water," Quint explains.

Scientists have understood how plant shoots react to higher temperatures for some time. Their cells also produce more auxin, but the plant reacts differently than its roots. The cells in the shoot stretch, the stalk grows taller, and the leaves become narrower and grow farther apart.

The study also provides new insights for plant breeding. "In view of climate change, root growth is becoming more and more important for breeding. Understanding the molecular basis for temperature-dependent root growth might help to effectively equip plants against drought stress and achieve stable yields in the long term," says Quint. Quint's team will continue its work in this field of research in the coming years. A few weeks ago, the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) granted him around 500,000 euros for a new research project on precisely this topic.

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Groundbreaking images of root chemicals offer new insights on plant growth

On a sunny springtime stroll through a park, it's easy to ignore the parts of plants that are hidden from view. Plant biologists see things differently. They look below the surface where plant roots are organized in elaborate systems that are critical to the organism's development. Intricately organized tree root systems, for example, can span as far underground as the tree grows high above the soil.

Applying an advanced imaging technology to plant roots, researchers at the University of California San Diego and Stanford University have developed a new understanding of essential root chemicals that are responsible for plant growth. Using a type of mass spectrometer, a study led by UC San Diego Biological Sciences Postdoctoral Scholar Tao Zhang and Assistant Professor Alexandra Dickinson produced a "roadmap" that profiles where key small molecules are distributed along stem cells of maize (corn) plant roots and how their placement factors into the plant's maturation. The findings were published in the journal Nature Communications.

"This chemical roadmap provides a resource that scientists can use to find new ways of regulating plant growth," said Dickinson, a faculty member in the Department of Cell and Developmental Biology. "Having more information about how roots grow could be useful in conservation as we think about protecting our plants in natural environments and making them more sustainable, especially in agriculture."

While working as a visiting scientist at Stanford University, Dickinson began collaborating with study co-first author Sarah Noll and Professor Richard Zare, who developed a mass spectrometry imaging system that helps surgeons distinguish between cancerous and benign tissue during tumor-removal operations.

Dickinson, Zare and Noll adapted the technology -- called "desorption electrospray ionization mass spectrometry imaging" or DESI-MSI -- to probe plant roots for the chemicals involved in growth and energy production. They initially focused on maize plants at the root tips, where stem cells play an active role in the plant's development. Their method involved cutting through the center of the root to get a clear image of the chemicals inside.

"To help understand plant roots from the biology side, we needed to find out which chemicals are there," said Zare. "Our imaging system sprays out droplets that strike different portions of the root and dissolve chemicals at that location. A mass spectrometer collects the droplet splash and tells us what those dissolved chemicals are. By systematically scanning the droplet target spot we make a spatial map of the root chemicals."

The resulting images, believed to be some of the first to reveal the transition between stem cells and mature root tissue, show the foundational role of metabolites -- molecules involved in the plant's energy production. Tricarboxylic acid (TCA) cycle metabolites became the focus of the research since they were found to be a key player in controlling root development.

Coming into the study, the researchers expected a relatively uniform distribution of chemicals. Instead, with their chemical roadmap in hand, they found that TCA metabolites are clustered in patches across the root.

"I was surprised by how many chemicals are featured in really distinct patterns," said Dickinson. "We can see that the plant is doing this on purpose -- it needs these molecules in specific regions to grow properly." The Dickinson lab showed that these TCA metabolites have predictable effects in development, not only in maize, but in another plant species as well (Arabidopsis). This is likely because TCA metabolites are highly conserved -- they are made in all plants as well as animals.

Also emerging from the new images were previously unidentified chemical compounds. Dickinson says the mystery compounds could be critical for plant growth since they also are grouped in patterns at specific locations, suggesting a prominent role in development. Dickinson and her colleagues are now investigating these compounds and comparing varieties of maize that have different levels of stress resistance for adverse threats such as severe climate conditions and drought. The new information will help them develop novel chemical and genetic strategies for improving plant growth and stress resilience.

"We're looking at different maize plants that have drought resistance to see if we've already found chemicals that are specific to that variety that we haven't seen in other varieties," said Dickinson. "We think that could be a way to find new compounds that can promote growth, especially in harsh conditions."

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Plant roots change shape and branch out for water

Researchers have discovered how plant roots adapt their shape to maximise their uptake of water, pausing branching when they lose contact with water and only resuming once they reconnect with moisture, ensuring they can survive even in the driest conditions.

Plant scientists from the University of Nottingham have discovered a novel water sensing mechanism that they have called 'Hydro-Signalling', which shows how hormone movement is linked with water fluxes. The findings have been published today in Science.

Water is the rate-limiting molecule for life on earth. The devastating impact of climate change is enhancing the effects of water stress on global agriculture. Climate change is causing rainfall patterns to become more erratic, impacting rain-fed crops in particular.

Roots play a critical role to reduce the impact of water stress on plants by adapting their shape (such as branching or growing deeper) to secure more water. Discovering how plant roots sense and adapt to water stress is vital importance for helping 'future proof' crops to enhance their climate resilience.

Using X-ray micro-CT imaging researchers were able to reveal that roots alter their shape in response to external moisture availability by linking the movement of water with plant hormone signals that control root branching.

The study provides critical information about the key genes and processes controlling root branching in response to limited water availability, helping scientists design novel approaches to manipulate root architecture to enhance water capture and yield in crops.

Dr. Poonam Mehra, postdoctoral fellow, from the School of Biosciences is one of the lead authors and explains: "When roots are in contact with moisture, a key hormone signal (auxin) moves inwards with water, triggering new root branches. However, when roots lose contact with moisture, they rely on internal water sources that mobilises another hormone signal (ABA) outwards, which acts to block the inwards movement of the branching signal. This simple, yet elegant mechanism enables plant roots to fine tune their shape to local conditions and optimize foraging."

Professor Malcolm Bennett, co-lead on the research adds: "Our plant research is vitally important for understanding how we can futureproof crops and find ways to ensure successful crop yields even in the most challenging climates. We are already experiencing a hotter climate and designing plants that can still access water in these conditions is vital and this research is an all important step in understanding how to do this." He continued: "These new discoveries were only possible because of the cutting-edge tools and collaborative approaches of the authors, which involved an international team of scientists based in the UK, Belgium, Sweden, USA and Israel.'"

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Fossil algae, dating from 541 million years ago, offer new insights into the plant kingdom's roots

Paleontologists have identified a new genus and species of algae called Protocodium sinense which predates the origin of land plants and modern animals and provides new insight into the early diversification of the plant kingdom.

Discovered at a site in China, this 541-million-year-old fossil is the first and oldest green alga from this era to be preserved in three dimensions, enabling the researchers to investigate its internal structure and identify the new specimen with unprecedented accuracy. The study is published today in BMC Biology, opening a window into a world of evolutionary puzzles that scientists are just beginning to unravel.

"Protocodium belongs to a known lineage of green algae and has a surprisingly modern architecture, showing that these algae were already well diversified before the end of the Ediacaran period," says co-author Cédric Aria, postdoctoral fellow in the Department of Ecology & Evolutionary Biology in the Faculty of Arts & Science at the University of Toronto and based at the Royal Ontario Museum (ROM). "Its discovery touches the origin of the entire plant kingdom and puts a familiar name on the organisms that preceded the Cambrian explosion over half a billion years ago, when the world's first modern ecosystems emerged."

The newly discovered Protocodium fossils were found by a team led by Hong Hua, professor of geology, and including Shu Chai, postdoctoral researcher, both of Northwest University, Xi'an, China. It is part of the Gaojiashan biota, the name given to a significant group of exceptionally well-preserved fossils, at the Dengying Formation in the southern Shaanxi Province. In the past 20 years, this geological formation has yielded important fossil species documenting the end of the Ediacaran Period 541-million-years ago.

Organisms and their parts that do not originally absorb minerals -- unlike shells or bones -- require exceptional conditions to be preserved. In this case, the whole fossils and their fine cellular details were preserved in three dimensions due to the replacement of the original organic material by phosphate. This mode of preservation allowed the researchers to use various electron and X-ray microscopy techniques to virtually slice the fossil, unveil its internal structure with precision and ultimately identify it as a close relative of the modern Codium alga, a type of seaweed.

Protocodium fossils are small spheres half a millimetre wide, like large grains of pollen, covered by a multitude of smaller domes. Thanks to the 3D examination, the researchers determined the domed surface to be part of a complex, single cell that contains thin strands called siphons. This morphology is typical of certain modern single-celled seaweeds that contain many nuclei.

The discovery of Protocodium would call for caution when identifying generic spherical Ediacaran fossils and may imply that organisms like Codium are in fact much older and widespread. The famous Doushantuo fossil embryos, also from China and preserved in 3D, have

been at the heart of debates about the deep origin of certain animal groups. Specific stages of some of these animal-like embryos resemble the unicellular Protocodium on the outside, but 3D slicing reveals how they are comprised of many cells. On the other hand, numerous 2D, round fossils of uncertain algal or other affinity are also known from the Ediacaran and older periods, but in less detail.

"We know that seaweed-like fossils are at least one billion-years-old," says Chai, the study's first author. "But until now, flat, grainy two-dimensional preservation has made it challenging to recognize more than general morphological structures."

Green algae are photosynthetic organisms, which means they convert light and carbon dioxide into sugars and oxygen. They were therefore likely important foundations of Earth's early ecosystems, and the study suggests green algae were already established in the world's shallow waters as carbon dioxide recyclers and oxygen producers before the Cambrian explosion.

Apart from its smaller size, Protocodium appears surprisingly identical to the modern Codium, a type of green algae found in many seas worldwide. Certain types of this seaweed are notoriously invasive -- such as Codium fragile subspecies tomentosoides, dubbed "dead man's fingers" for its appearance, and spread along with commercially farmed shellfish. From an evolutionary perspective, green algae like the ancient Protocodium and land plants share a common ancestor that was thought to be about one billion to one billion and a half years old, but now likely older -- the assignment of Protocodium so close to a modern group pushes back in time the history of the entire plant kingdom.

"It's very telling that such an organism has remained practically unchanged over at least 540 million years," says Aria. "By the Ediacaran, evolution had driven it towards a stable adaptive zone -- it's been comfortable there since, and more than that, quite successful. So much so, in fact, that nowadays Codium takes advantage of global trade to easily outcompete other algal species."

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Blueprint reveals how plants build a sugar transport lane

A tiny region at the root tip has been found to be responsible for orchestrating the growth and development of the complex network of vascular tissues that transport sugars through plant roots.

In a paper published in Science today, an international team of scientists present a detailed blueprint of how plants construct phloem cells -- the tissue responsible for transporting and accumulating sugars and starch in the parts of the plant that we harvest (seeds, fruits and storage tubers) to feed much of the world.

This pivotal research reveals how global signals in root meristems coordinate distinct maturation phases of the phloem tissue.

Phloem is a highly specialised vascular tissue that forms an interconnected network of continuous strands throughout a plant's body. It transports sugars, nutrients and a range of signalling molecules between leaves, roots, flowers and fruits.

As a result, phloem is central to plant function. Understanding how the phloem network is initiated and develops is important for future applications in agriculture, forestry and biotechnology as it could reveal how to better transport this sugar energy to where it is needed.

How do plants build a sugar lane in a multi-lane highway?

Plant roots continue to grow throughout a plant's life. This phenomenon, known as indeterminate growth, means roots continually elongate as they add new tissues to the tip of the root -- like constructing a never-ending highway. A continuous file of specialised phloem cells running the length of roots (analogous to a lane on a highway) delivers the primary nutrient, sucrose, to the parts of the plant where it is needed for growth. To fulfil this vital role, phloem tissue must develop and mature rapidly so it can supply sugars to surrounding tissues -- akin to building a service lane that needs to be completed in the first stage of constructing a multi-lane highway.

The problem that has long puzzled plant scientists is how a single instructive gradient of proteins are able to stage the construction phases across all the different specialised cell files (highway lanes) that are present in roots. How does one cell type read the same gradient as its neighbours, but interprets it differently to stage its own specialised development is a question that plant scientists have been working to resolve.

Over the past 15 years, researchers in Yrjö Helariutta's teams at the University of Cambridge and University of Helsinkihave uncovered the central role of cell-to-cell communication and complex feedback-mechanisms involved in vascular patterning. This new research, undertaken with collaborators at New York University and North Carolina State University, reveals how this single lane of phloem cells is constructed independently of surrounding cells.

The Sainsbury/Helsinki group dissected each step in the construction of the phloem cell file (the sugar transport lane) in the model plant Arabidopsis thaliana using single-cell RNA-seq and live imaging. Their work showed how the proteins that control the broad maturation gradient of the root interact with the genetic machinery that specifically controls phloem development.

This is one mechanism that appears to help the phloem cell file to fast-track maturation using its own machinery to interpret the maturation cues. Dr Pawel Roszak, co-first-author of the study and researcher at the Sainsbury Laboratory Cambridge University (SLCU), explains: "We have shown how global signals in the root meristem interact with the cell type specific factors to determine distinct phases of phloem development at the cellular resolution. Using cell sorting followed by deep, high-resolution single-cell sequencing of the underlying gene regulatory network revealed a "seesaw" mechanism of reciprocal genetic repression that triggers rapid developmental transitions."

The group also showed how phloem development is staged over time, with early genetic programs inhibiting late genetic programs and vice versa -- just as the road asphalt-laying work crews' hand over construction to lane painters in the latter stages of highway construction. In addition, they showed how early phloem regulators instructed specific genes to split the phloem cells into two different subtypes -- like the construction of a fork in the road leading to two separate destinations.

Co-leader of the work, Professor Yrjö Helariutta, said his teams' reconstruction of the steps from birth to terminal differentiation of protophloem in the Arabidopsis root exposed the steps. Helariutta said: "Broad maturation gradients interfacing with cell-type specific transcriptional regulators to stage cellular differentiation is required for phloem development."

"By combining single-cell transcriptomics with live imaging, here we have mapped the cellular events from the birth of the phloem cell to its terminal differentiation into phloem sieve element cells. This allowed us to uncover genetic mechanisms that coordinate cellular maturation and connect the timing of the genetic cascade to broadly expressed master regulators of meristem maturation. The precise timing of developmental mechanisms was critical for proper phloem development, with apparent "fail safe" mechanisms to ensure transitions."

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