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Decoding the secret language of photosynthesis

For decades, scientists have been stumped by the signals plants send themselves to initiate photosynthesis, the process of turning sunlight into sugars. UC Riverside researchers have now decoded those previously opaque signals.

For half a century botanists have known that the command center of a plant cell, the nucleus, sends instructions to other parts of the cell, compelling them to move forward with photosynthesis. These instructions come in the form of proteins, and without them, plants won't turn green or grow.

"Our challenge was that the nucleus encodes hundreds of proteins containing building blocks for the smaller organelles. Determining which ones are the signal to them to trigger photosynthesis was like finding needles in a haystack," said UCR botany professor Meng Chen.

The process the scientists in Chen's laboratory used to find four of these proteins is now documented in a Nature Communications paper.

Previously, Chen's team demonstrated that certain proteins in plant nuclei are activated by light, kicking off photosynthesis. These four newly identified proteins are part of that reaction, sending a signal that transforms small organs into chloroplasts, which generate growth-fueling sugars.

Chen compares the whole photosynthesis process to a symphony.

"The conductors of the symphony are proteins in the nucleus called photoreceptors that respond to light. We showed in this paper that both red and blue light-sensitive photoreceptors initiate the symphony. They activate genes that encode the building blocks of photosynthesis."

The unique situation, in this case, is that the symphony is performed in two "rooms" in the cell, by both local (nucleus) and remote musicians. As such, the conductors (photoreceptors), who are present only in the nucleus, must send the remotely located musicians some messages over distance. This last step is controlled by the four newly discovered proteins that travel from the nucleus to the chloroplasts.

This work was funded by the National Institutes of Health, in the hopes that it will help with a cure for cancer. This hope is based on similarities between chloroplasts in plant cells and mitochondria in human cells. Both organelles generate fuel for growth, and both harbor genetic material.

Currently, a lot of research describes communication from organelles back to the nucleus. If something is wrong with the organelles, they'll send signals to the nucleus "headquarters." Much less is known about the activity-regulating signals sent from the nucleus to the organelles.

"The nucleus may control the expression of mitochondrial and chloroplast genes in a similar fashion," said Chen. "So, the principles we learn from the nucleus-to-chloroplast communication pathway might further our understanding of how the nucleus regulates mitochondrial genes, and their dysfunction in cancer," Chen said.

The significance of understanding how photosynthesis is controlled has applications beyond disease research. Human settlements on another planet would likely require indoor farming and creating a light scheme to increase yields in that environment. Even more immediately, climate change is posing challenges for crop growers on this planet.

"The reason we can survive on this planet is because organisms like plants can do photosynthesis. Without them there are no animals, including humans," Chen said. "A full understanding of and ability to manipulate plant growth is vital for food security."

Youra Hwang, Soeun Han, Chan Yul Yoo, Liu Hong, Chenjiang You, Brandon H. Le, Hui Shi, Shangwei Zhong, Ute Hoecker, Xuemei Chen, Meng Chen. Anterograde signaling controls plastid transcription via sigma factors separately from nuclear photosynthesis genes. Nature Communications, 2022; 13 (1) DOI: 10.1038/s41467-022-35080-0

Flowers critical link to bacteria transmission in wild bees

Summary:
Flowers are a hot spot of transmission of bacteria that end up in the microbiome of wild bees, new research has found. The work shows for the first time that multiple flower and wild bee species share several of the same types of bacteria. Bees therefore obtain both food and bacteria from flowers. These bacteria may play important roles in bee health.

The research, which was just published in the journal Microbial Ecology, shows for the first time that multiple flower and wild bee species share several of the same types of bacteria. Bees therefore obtain both food and bacteria from flowers. These bacteria may play important roles in bee health.

The research on the wild bee microbiome, or the community of microorganisms that live in the bee, follows similar work on the human microbiome that has surged in popularity in the past decade. There has been research on the microbiome of honeybees and bumblebees, but very little on wild bees.

While wild bees don't get the same amount of attention as honey bees or bumblebees, they are a critical piece of the pollination puzzle. Wild bees could become more important because of the decline in numbers of honey bees due to colony collapse disorder, which has resulted in the loss of more than 10 million hives in the past decade.

Currently, honey bees are relied on for almost all commercial pollination needs.

"We are putting all our pollination needs in one basket," said Quinn McFrederick, an assistant professor of entomology at UC Riverside who is the lead author of the paper. "What if this collapses?

Like honey bees, wild bees pollinate crops, but there is no way to effectively manage them so they can be shipped to a site, like honeybees are, to pollinate a specific crop, such as almond trees in central California.

"People have said that wild bees are like an insurance policy," McFrederick said. If we can't meet our pollination needs with honey bees, we need to better understand wild bees."

For this research, McFrederick and co-authors collected bees and flowers at two sites in Texas and one on the UC Riverside campus. He simulated bee nests by drilling holes into wood and placing these nests in fields with wildflowers. (The wild bees naturally nest in abandoned holes in trees created by beetles.)

The bees established nests in wood and McFrederick collected them and analyzed the microbiomes of their guts and the pollen they were carrying.

At the same sites, he also collected flowers that the bees visited and flowers that they didn't visit. To ensure flowers had not been visited by bees, he placed bags over them before they bloomed and then picked them once they matured and opened.

He found that the bacteria were present on the flowers whether they were bagged or not. The presence of bee-associated bacteria in bagged flowers suggests the bacteria may be transmitted to flowers via plant surfaces, the air or small insects, he said.

The UC Riverside researchers believe the bacteria shared by flowers and wild bees may be beneficial. Their current research is studying that more closely.

One reason McFrederick believes the bacteria is beneficial is because of the presence of Lactobacillus bacteria, which were found on all the flower and bee samples.

Lactobacillus is a group of bacteria that includes many species used by humans to preserve everything from kimchi and pickles to sourdough bread and sauerkraut. McFrederick believes that the bacteria might help preserve the nectar and pollen the wild bee stores in her nest as a food source for her soon-to-be born larvae.

Researcher just served a world first CRISPR meal

Summary:
For (probably) the first time ever, plants modified with the "genetic scissors" CRISPR-Cas9 has been cultivated, harvested and cooked. D professor in Plant Cell and Molecular Biology served pasta with "CRISPRy" vegetable fry to a radio reporter. Although the meal only fed two people, it was still the first step towards a future where science can better provide farmers and consumers across the world with healthy, beautiful and hardy plants.

CRISPR (Clustered regularly interspaced short palindromic repeats)-Cas9 is a complicated name for an easy, but targeted, way of changing the genes of an organism. The decisive discovery was published in 2012 by researchers at Umeå University, and the "Swiss army knife of genetic engineering" has been predicted to change the world. With CRISPR-Cas9, researchers can either replace one of the billions of "letters" present in an organism's genome (i.e. the entire gene pool consisting of DNA) or remove short segments, similar to when you edit a written text in a word processor. The technology is called "gene editing" or "genome editing."

The first clinical applications are underway; maybe we can soon cure hereditary disease using this technology. However, the situation differs somewhat in the agricultural field. There, the issue is not IF researchers can create plants leading to a more sustainable land management, but rather if these will be allowed in farming. Will plants whose genome has been edited using CRISPR-Cas9 fall under GMO legislation or not? If they do, it makes them illegal to plant in great parts of the world. If not, they will -- just like other plants -- be allowed to be grown at the farmers own discretion.

The EU has avoided answering the question, but in November 2015 the Swedish Board of Agriculture interpreted the law as if only a segment of DNA has been removed and no "foreign DNA" has been inserted, it is not to be regarded as a genetically modified organism -- a GMO. That also means that the plant can be cultivated without prior permission. In spring 2016, American authorities stated that they agreed. The organism in question there was a mushroom who had lost the part of its DNA that made it go brown. This opens up for using the technology to develop plants of the future.

This summer has been the first time that plants that have been gene-edited using CRISPR-Cas9 -- in a way that does not classify the plant as GMO -- have been allowed to be cultivated outside of the lab. This is definitely the first time in Europe, and even if it been done before in other parts of the world, it has been kept secret. This time, it was a cabbage plant and the Radio Sweden gardening show "Odla med P1" took part in the harvest leading to the probably first-ever meal of CRISPR-Cas9 genome-edited plants. The first CRISPR meal to have been enjoyed was "Tagliatelle with CRISPRy fried vegetables."

"The CRISPR-plants in question grew in a pallet collar in a garden outside of Umeå in the north of Sweden and were neither particularly different nor nicer looking than anything else," says plant scientist Stefan Jansson. But they represent both a new phase of agriculture where scientific advances will be implemented in new plant species and that to a small or large extent will be made available to farmers across the world. In other words: a meal for the future. ScienceDaily, 5 September 2016.

Fluid mosaic model of plasma membrane

Sustainable alternative to methyl bromide for tomato production

Summary:
Field studies in two Florida locations evaluated and compared anaerobic soil disinfestations (ASD) and chemical soil fumigation (CSF) performance on w**d and nematodes control, and on fruit yield and quality of fresh-market tomato. Results indicated that ASD (applied using a mixture of composted poultry litter and molasses as carbon source) may be a potentially sustainable alternative to conventional CSF for controlling plant-parasitic nematodes and w**ds without causing negative effects on fruit yield and quality.

A study in the June 2016 issue of HortScience focused on the effects of ASD in an open-field, fresh-market tomato production system. Field studies were conducted to evaluate and compare ASD with chemical soil fumigation (CSF) treatments for controlling w**ds and nematodes, as well as for influence on tomato fruit yield and quality. In experiments conducted in southwestern (Immokalee) and northern Florida (Citra), conventional CSF was compared with two ASD treatments, which consisted of amending the soil with 22 Mg·ha-1 of composted poultry litter and two rates of molasses (13.9 and 27.7 m3·ha-1) as a carbon source.

Analyses showed that the application of ASD did not negatively affect commercial tomato fruit quality, and that quality and the mineral content of fruit produced with ASD was comparable or higher than that of fruit produced in CSF plots.

In both locations, the application of ASD provided a level of root-knot nematode control equivalent to, or more effective, than the CSF. Additional results showed that, in Immokalee, the CSF provided the most significant w**d control, "but ASD treatments also suppressed w**ds enough to prevent an impact on yield," the authors said. In Citra, all treatments, including the CSF, provided poor w**d control relative to the Immokalee site.

"Overall, the results of the two locations demonstrate that the ASD technique may be a valid and sustainable alternative to the conventional CSF, and could be transferred at commercial level," the authors said. "Molasses rates showed similar performance in terms of root-knot nematode and w**d control, yield, and fruit quality; therefore, the lower molasses rate could be suggested to reduce the cost of the ASD treatment."

On-going research is focused on substitutions for composted broiler litter and minimizing nutrient inputs in an ASD system.

Francesco Di Gioia et al. The Effects of Anaerobic Soil Disinfestation on W**d and Nematode Control, Fruit Yield, and Quality of Florida Fresh-market Tomato. HortScience, June 2016

Climate change has less impact on drought than previously expected

A new study from the University of California, Irvine and the University of Washington shows that water conserved by plants under high CO2 conditions compensates for much of the effect of warmer temperatures, retaining more water on land than predicted in commonly used drought assessments.

According to the study published this week in the Proceedings of the National Academy of Sciences, the implications of plants needing less water with more CO2 in the environment changes assumptions of climate change impacts on agriculture, water resources, wildfire risk, and plant growth.

The study compares current drought indices with ones that take into account changes in plant water use. Reduced precipitation will increase droughts across southern North America, southern Europe and northeastern South America. But the results show that in Central Africa and temperate Asia -- including China, the Middle East, East Asia and most of Russia -- water conservation by plants will largely counteract the parching due to climate change.

"This study confirms that drought will intensify in many regions in the future," said coauthor James Randerson, UCI professor of Earth system science. "It also shows that plant water needs will have an important influence on water availability, and this part of the equation has been neglected in many drought and hydrology studies."

Recent studies have estimated that more than 70 percent of our planet will experience more drought as carbon dioxide levels quadruple from pre-industrial levels over about the next 100 years. But when researchers account for changes in plants' water needs, this falls to 37 percent, with bigger differences concentrated in certain regions.

The reason is that when Earth's atmosphere holds more carbon dioxide, plants actually benefit from having more of the molecules they need to build their carbon-rich bodies. Plants take in carbon dioxide through tiny openings called stomata that cover their leaves. But as they draw in carbon dioxide, moisture escapes. When carbon dioxide is more plentiful, the stomata don't need to be open for as long, and so the plants lose less water. The plants thus draw less water from the soil through their roots.

Global climate models already account for these changes in plant growth. But many estimates of future drought use today's standard indices, like the Palmer Drought Severity Index, which only consider atmospheric variables such as future temperature, humidity and precipitation.

"New satellite observations and improvements in our understanding hydrological cycle have led to significant advances in our ability to model changes in soil moisture," said Randerson. "Unfortunately, using proxy estimates of drought stress can give us misleading results because they ignore well-established principles from plant physiology."

Planners will need accurate long-term drought predictions to design future water supplies, anticipate ecosystem stresses, project wildfire risks and decide where to locate agricultural fields.

"In some sense there's an easy solution to this problem, which is we just have to create new metrics that take into account what the plants are doing," said lead author Abigail Swann, a University of Washington assistant professor of atmospheric sciences. "We already have the information to do that; we just have to be more careful about ensuring that we're considering the role of the plants."

Is this good news for climate change? Although the drying may be less extreme than in some current estimates, droughts will certainly increase, researchers said, and other aspects of climate change could have severe effects on vegetation.

"There's a lot we don't know, especially about hot droughts," Swann said. The same drought at a higher temperature might have more severe impacts, she noted, or might make plants more stressed and susceptible to pests.

"Even if droughts are not extremely more prevalent or frequent, they may be more deadly when they do happen," she said.

Abigail L. S. Swann, Forrest M. Hoffman, Charles D. Koven, James T. Randerson. Plant responses to increasing CO2 reduce estimates of climate impacts on drought severity. Proceedings of the National Academy of Sciences, 2016; 201604581 DOI: 10.1073/pnas.1604581113

More tomatoes, faster: Accelerating tomato engineering
Summary:
While looking for ways to make tomatoes and other crop plants more productive, researchers developed a way to cut the time required to modify a tomato's genes by six weeks. The improvement will save on money and resources while accelerating tomato research.

While looking for ways to make tomatoes and other crop plants more productive, BTI Assistant Professor Joyce Van Eck and former postdoctoral scientist Sarika Gupta developed a better method for "transforming" a tomato -- a process that involves inserting DNA into the tomato genome and growing a new plant. By adding the plant hormone auxin to the medium that supports growth of tomato cells, they can speed up the plant's growth, ultimately accelerating the pace of their research. They describe this advance in a study published in Plant Cell, Tissue and Organ Culture.

Typically, transformation works by using a soil bacterium called Agrobacterium tumefaciens to insert a new segment of DNA into the cells of tomato seedling tissues. The transformed cells are transplanted onto plant regeneration medium, which contains nutrients and hormones that cause the tissue to grow into a tiny new plant. These plantlets are then transferred to root induction medium where they grow roots, before being planted in soil and hardened in the greenhouse. In the new method, the Van Eck lab adds auxin to the regeneration and rooting media. The addition reduces the length of the procedure from 17 weeks to just 11.

"If you can speed up the plant development, which is what the auxin is doing, you can decrease the time it takes to get genetically engineered lines," said Van Eck.

Researchers in the Van Eck lab perform tomato transformations routinely, as a research method to understand how individual genes affect tomato growth and development. Their new protocol not only saves time, but uses fewer materials, and saves money. The researchers can then finish experiments sooner and potentially run more projects at once.

The project came out of a collaboration with Cold Spring Harbor Laboratory to identify gene pathways that could be used to breed crops with higher yields.

"We're looking at the genes and gene networks involved in stem cell proliferation, meristem development and flowering and branching," said Van Eck, "with the end goal being that maybe genes that we identify in tomato, which is strictly being used as a model, might help us understand what can be done to increase yield in other crops."

Sarika Gupta, Joyce Van Eck. Modification of plant regeneration medium decreases the time for recovery of Solanum lycopersicum cultivar M82 stable transgenic lines. Plant Cell, Tissue and Organ Culture (PCTOC), 2016; DOI: 10.1007/s11240-016-1063-9

Miracle fruit's flowering, fruiting behaviors revealed
Summary:
Researchers studied flower morphology and development of miracle fruit using microscopic techniques. Analyses showed that miracle fruit flowers require 100 days to develop from reproductive meristem to full anthesis. Heavy fruit drop was observed at 40 to 60 days after anthesis, and fruit with persistent style developed and ripened 90 days after anthesis. Miracle fruit was determined to be strongly insect-pollinated and that it has features to prevent self-fertilization. Further research was recommended to identify the pollinator.

Miracle berry (Synsepalum dulcificum), also known as miracle fruit, is a valuable horticultural species indigenous to West Africa. The authors of a study in the June 2016 issue of HortScience say that miracle fruit is "a very promising species" that has not been adequately studied. "Miracle fruit is a rare fruit crop with high economical value in the medical and food industry," they explained. The fleshy pulp of the miracle fruit contains miraculin, a glycoprotein that has an extraordinary effect on taste buds in the tongue: it makes sour or acidic food taste sweet. The authors said that miraculin could "possibly help diabetics to eat sweet food without taking in sugar," and they noted that the fruit has already been investigated as for its potential as a natural food sweetener. Surprisingly, very little is known about the species in terms of how miracle fruit's flowers grow and develop. Researchers Chen Xingway, Thohirah Lee Abdullah, Sima Taheri, Nur Ashikin Psyquay Abdullah, and Siti Aishah Hassan used microscopic techniques to identify flower morphology and development of miracle fruit. Their report contains in-depth descriptions of flower and fruit developmental stages. "Our results could improve understanding of pollination ecology and methods to manipulate flowering and fruit development," they explained.

Analyses indicated that a miracle fruit flower took 100 days to develop from reproductive meristem to full anthesis. The scientists found that the flower development could be divided into six distinct stages based on size and appearance of the flower bud.

Heavy fruit dropping was observed at 40 to 60 days after anthesis, which contributed to low fruiting percentage. The fruit with persistent style developed and ripened 90 days after anthesis. "Successful pollination coupled with proper nutrient and water management could decrease premature fruit drop and obtain greater miracle fruit yield," the authors said.

"From the observations on the flowering behavior and flower architecture in this study, miracle fruit is suggested to be insect-pollinated and has features that prevent self-fertilization," the scientists noted. They recommended further research on pollination ecology be performed to identify the pollinator for miracle fruit.

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