̽��ֱ�� of Cambridge - James Locke

Opinion: Plants can tell time even without a brain

Anonymous — Wed, 21 Aug 2019 09:35:07 +0000

Anyone who has travelled across multiple time zones and suffered jet lag will understand just how powerful our biological clocks are. In fact, every cell in the human body has its own molecular clock, which is capable of generating a daily rise and fall in the number of many proteins the body produces over a 24-hour cycle. ̽��ֱ��brain contains a master clock that keeps the rest of the body in sync, using light signals from the eyes to keep in time with environment.

Plants have similar circadian rhythms that help them tell the time of day, preparing plants for photosynthesis prior to dawn, turning on heat-protection mechanisms before the hottest part of the day, and producing nectar when pollinators are most likely to visit. And just like in humans, every cell in the plant appears to have its own clock.

Our eyes and brain rely on sunlight to coordinate activity in the body according to the time of day. Yomogi1/Shutterstock

But unlike humans, plants don’t have a brain to keep their clocks synchronised. So how do plants coordinate their cellular rhythms? Our new research shows that all the cells in the plant coordinate partly through something called local self-organisation. This is effectively the plant cells communicating their timing with neighbouring cells, in a similar way to how schools of fish and flocks of birds coordinate their movements by interacting with their neighbours.

Previous research found that the time of the clock is different in different parts of a plant. These differences can be detected by measuring the timing of the daily peaks in clock protein production in the different organs. These clock proteins generate the 24-hour oscillations in biological processes.

For instance, clock proteins activate the production of other proteins that are responsible for photosynthesis in leaves just before dawn. We decided to examine the clock across all the major organs of the plant to help us understand how plants coordinate their timing to keep the entire plant ticking in harmony.

What makes plants tick

We found that in thale cress (Arabidopsis thaliana) seedlings, the number of clock proteins peaks at different times in each organ. Organs, such as leaves, roots and stems, receive different signals from their local micro-environment, such as light and temperature, and use this information to independently set their own pace.

If rhythms in different organs are out of sync, do plants suffer from a kind of internal jet lag? While the individual clocks in different organs peak at different times, this didn’t result in complete chaos. Surprisingly, cells began to form spatial wave patterns, where neighbour cells lag in time slightly behind one another. It’s a bit like a stadium or “Mexican” wave of sports fans standing up after the people next to them to create a wave-like motion through the crowd.

Plant cells communicate between their neighbours to coordinate the time. James Locke, Author provided

Our work shows that these waves arise from the differences between organs as cells begin to communicate. When the number of clock proteins in one cell peaks, the cell communicates this to its slower neighbours, which follow the first cell’s lead and produce more clock proteins too. These cells then do the same to their neighbours, and so on. Such patterns can be observed elsewhere in nature. Some firefly species form spatial wave patterns as they synchronise their flashes with their neighbours.

Local decision-making by cells, combined with signalling between them, might be how plants make decisions without a brain. It allows cells in different parts of the plant to make different decisions about how to grow. Cells in the shoot and root can separately optimise growth to their local conditions. ̽��ֱ��shoot can bend towards where light is unobstructed and the roots can grow towards water or more nutrient-rich soil. It could also allow plants to survive the loss of organs through damage or being eaten by a herbivore.

This might explain how plants are able to continuously adapt their growth and development to cope with changes in their environment, which scientists call “plasticity”. Understanding how plants make decisions isn’t just interesting, it will help scientists breed new plant varieties that can respond to their increasingly changeable environment with climate change.

This article is republished from ̽��ֱ��Conversation under a Creative Commons license. Read the original article.

Mark Greenwood and James Locke from the ̽��ֱ��'s Sainsbury Laboratory reveal how plants tell the time and coordinate their cellular rhythms. This article was originally published on ̽��ֱ��Conversation.

Understanding how plants make decisions isn’t just interesting, it will help scientists breed new plant varieties

Mark Greenwood & James Locke

Alexander Steinhof

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'Noisy' gene atlas to help explain how plants survive environmental change

ta385 — Fri, 25 Jan 2019 13:04:40 +0000

Plant scientists at the Sainsbury Laboratory Cambridge ̽��ֱ�� (SLCU) have built a gene expression atlas that maps the ‘noisy genes’ of genetically identical plants. ̽��ֱ��research, published today in Molecular Systems Biology, found that around 9% of the genes in otherwise identical plants are highly variable in the way that they behave. Interestingly, many of these highly variable (noisiest) genes help a plant respond to its environment, including genes involved in reacting to light, temperature, pathogens and nutrients.

This variation in gene behaviour could be useful in nature for populations of genetically similar plants to hedge against environmental stress such as drought, high salinity or extreme temperatures. This means that there will always a few plants in the population that are prepared to survive different stresses due to their variable gene behaviours (hedging their bets). But this variability can also be a problem, such as in agriculture where environments are more controlled and farmers want uniform crops that germinate and flower at the same time and respond equally to applications of fertilisers and water.

This is the first time that global levels of noise in gene expression has been measured in plants. ̽��ֱ��online open-access atlas (AraNoisy) will provide a resource for plant scientists around the world to study how gene expression variability influences plant survival and diversity within clonal populations. This important stepping-stone will help us to better understand how plants survive in fluctuating environments, and could eventually lead to further research in both plant conservation efforts and future crop development.

What is gene expression?

Looking at the full genetic code (called the genome) of an individual plant or animal is not enough to fully understand the individual’s characteristics. ̽��ֱ��way genes behave (gene expression) can differ markedly between individuals with the same genome. A gene is expressed when the genetic code of the gene is used to direct a set of reactions that synthesise a protein or other functional molecule within a cell. Copying a segment of DNA to RNA is the first step in this sequence and is called transcription. In this study, ‘noise’ in gene expression refers to the measured level of variation in RNA between individual plants. Measuring the variability in gene expression reveals which genes are noisier than others.

Dr Sandra Cortijo, from the Locke Group at SLCU, is researching how gene expression is regulated and what causes some genes to be expressed in unpredictable ways. To examine this, Cortijo took on the mammoth task of measuring global levels of noise in gene expression in a single plant species. Using genetically identical plants, she measured the expression of all their individual genes over a 24-hour period.

'For our model plant, we used seedlings of a small wild brassica relative, called thale cress (Arabidopsis thaliana), which is most commonly seen growing as a weed in the cracks of pavements,' Cortijo said. 'We performed RNA-sequencing on individual seedlings every two hours over a 24-hour period and analysed the variability for 15,646 individual genes in the plant’s genome.

'We identified that 9% (1,358 individual genes) of the genes were highly variable for at least one time point during the 24-hour period. We found that these highly variable genes fell into two sets influenced by the diurnal cycle – genes with more variable activity at night or genes that have more variable activity during the day.'

As part of the study, Cortijo also identified factors that might increase gene expression variability. Highly variable genes tend to be shorter, to be targeted by a higher number of other genes (transcription factors) and to be characterised by a ‘closed’ chromatin environment (which is an environment that allows gene expression to be altered by attaching additional molecules during the gene reading process (transcription) without actually changing a cell’s DNA).

'These results shed new light on the impact of transcriptional variability in gene expression regulation in plants and can be used as a foundation for further studies into how noisy genes are connected with how plants respond to their environment,' Cortijo said. 'Plants are a wonderful system to work with when looking at how genes are regulated in response to environmental changes as they cannot move and thus have to continually sense and respond to environmental changes.

̽��ֱ��evolution of variable gene expression could increase the robustness of a plant population against varying environments without changing their genes. Understanding how plants produce and regulate this noise in gene expression will be important for the future development of more uniform performing crops and to understand how populations of wild plants can survive more frequent weather extremes due to climate change.'

SLCU Research Group Leader, Dr James Locke, said the data was a significant new resource for further research: 'This is an important resource for scientists studying how genetically identical plants survive fluctuating environments and provides a basis for future work looking at how genetic and epigenetic factors regulate variability for individual genes.'

This research was supported by a fellowship from the Gatsby Charitable Foundation. ̽��ֱ��Locke Group is also further supported by the European Research Council.

Reference

Cortijo, S, Aydin, Z, et al. Widespread inter-individual gene expression variability in Arabidopsis thaliana. Molecular Systems Biology. 24 Jan 2019. DOI: 10.15252/msb.20188591

As parents of identical twins will tell you, they are never actually identical, even though they have the same genes. This is also true in the plant world. Now, new research by the ̽��ֱ�� of Cambridge is helping to explain why ‘twin’ plants, with identical genes, grown in identical environments continue to display unique characteristics all of their own.

This is an important resource for studying how genetically identical plants survive fluctuating environments

James Locke

Spot the difference: Genetically identical thale cress plants grown under the exact same environmental conditions show significant visible differences. Could this be due to variable gene expression?

Further information

AraNoisy noisy gene atlas

AraNoisy is a web-based tool for accessing inter-individual transcriptional variability in Arabidopsis thaliana, throughout a 24-hour diurnal cycle. Gene expression variability for individual genes of interest can be viewed here.

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