Plant Science

Researchers in Japan have edited plant mitochondrial DNA for the first time, which could lead to a more secure food supply.

Nuclear DNA was first edited in the early 1970s, chloroplast DNA was first edited in 1988, and animal mitochondrial DNA was edited in 2008. However, no tool previously successfully edited plant mitochondrial DNA.

Researchers used their technique to create four new lines of rice and three new lines of rapeseed (canola).

“We knew we were successful when we saw that the rice plant was more polite – it had a deep bow,” said Associate Professor Shin-ichi Arimura, joking about how a fertile rice plant bends under the weight of heavy seeds.

Arimura is an expert in plant molecular genetics at the University of Tokyo and led the research team, whose results were published in Nature Plants. Collaborators at Tohoku University and Tamagawa University also contributed to the research.

Genetic diversity for the food supply

Researchers hope to use the technique to address the current lack of mitochondrial genetic diversity in crops, a potentially devastating weak point in our food supply.

In 1970, a fungal infection arrived on Texas corn farms and was exacerbated by a gene in the corn’s mitochondria. All corn on the farms had the same gene, so none were resistant to the infection. Fifteen percent of the entire American corn crop was killed that year. Corn with that specific mitochondrial gene has not been planted since.

“We still have a big risk now because there are so few plant mitochondrial genomes used in the world. I would like to use our ability to manipulate plant mitochondrial DNA to add diversity,” said Arimura.

Plants without pollen

Most farmers do not save seeds from their harvest to replant next year. Hybrid plants, the first-generation offspring of two genetically different parent subspecies, are usually hardier and more productive.

To ensure farmers have fresh, first-generation hybrid seeds each season, agricultural supply companies produce seeds through a separate breeding process using two different parent subspecies. One of those parents is male infertile – it cannot make pollen.

Researchers refer to a common type of plant male infertility as cytoplasmic male sterility (CMS). CMS is a rare but naturally occurring phenomenon caused primarily by genes not in the nucleus of the cells, but rather the mitochondria.

Green beans, beets, carrots, corn, onions, petunia, rapeseed (canola) oil, rice, rye, sorghum, and sunflowers can be grown commercially using parent subspecies with CMS-type male infertility.

Beyond green

Plants use sunlight to produce most of their energy, through photosynthesis in green-pigmented chloroplasts. However, chloroplasts’ fame is overrated, according to Arimura.

“Most of a plant isn’t green, only the leaves above the ground. And many plants don’t have leaves for half the year,” said Arimura.

Plants get a significant portion of their energy through the same “powerhouse of the cell” that produces energy in animal cells: the mitochondria.

“No plant mitochondria, no life,” said Arimura.

Mitochondria contain DNA completely separate from the cell’s main DNA, which is stored in the nucleus. Nuclear DNA is the long double-helix genetic material inherited from both parents. The mitochondrial genome is circular, contains far fewer genes, and is primarily inherited only from mothers.

The animal mitochondrial genome is a relatively small molecule contained in a single circular structure with remarkable conservation between species.

“Even a fish’s mitochondrial genome is similar to a human’s,” said Arimura.

Plant mitochondrial genomes are a different story.

“The plant mitochondrial genome is huge in comparison, the structure is much more complicated, the genes are sometimes duplicated, the gene expression mechanisms are not well-understood, and some mitochondria have no genomes at all – in our previous studies, we observed that they fuse with other mitochondria to exchange protein products and then separate again,” said Arimura.

Manipulating plant mitochondrial DNA

To find a way to manipulate the complex plant mitochondrial genome, Arimura turned to collaborators familiar with the CMS systems in rice and rapeseed (canola). Prior research strongly suggested that in both plants, the cause of CMS was a single, evolutionarily unrelated mitochondrial gene in rice and in rapeseed (canola): clear targets in the perplexing maze of plant mitochondrial genomes.

Arimura‘s team adapted a technique that had previously edited mitochondrial genomes of animal cells growing in a dish. The technique, called mitoTALENs, uses a single protein to locate the mitochondrial genome, cut the DNA at the desired gene, and delete it.

“While deleting most genes creates problems, deleting a CMS gene solves a problem for plants. Without the CMS gene, plants are fertile again,” said Arimura.

The fully fertile four new lines of rice and three new lines of rapeseed (canola) that researchers created are a proof of concept that the mitoTALENs system can successfully manipulate even the complex plant mitochondrial genome.

“This is an important first step for plant mitochondrial research,” said Arimura.

Researchers will study the mitochondrial genes responsible for plant male infertility in more detail and identify potential mutations that could add much-needed diversity.

Read the paper: Nature Plants

Article source: University of Tokyo

Image: Tomohiko Kazama

High in the Andes Mountains, dagger-shaped ice spires house thriving microbial communities, offering an oasis for life in one of Earth’s harshest environments as well as a possible analogue for life on other planets.

The distinctive icy blade formations known as nieves penitentes (or, “penitent ones”) are named for their resemblance to praying monks in white robes and form in cold, dry conditions at elevations above 13,000 feet. The penitentes, which can range from a few inches to 15 feet high, are found in some of the most hostile conditions on Earth, with extreme winds, temperature fluctuations and high UV radiation exposure due to the thin atmosphere.

And yet, as a recently published study led by CU Boulder student researchers finds, these spires offer shelter for microbes by providing a water source in an otherwise arid, nutrient-poor environment.

In March 2016, CU Boulder students and faculty members traveled to Volcán Llullaillaco in Chile, the world’s second-highest volcano. The two-week expedition into the arid landscape, planned in collaboration with their Chilean colleagues, was no easy feat.

“This is a very remote area that’s difficult to access,” said Steve Schmidt, a professor in CU Boulder’s Department of Ecology and Evolutionary Biology (EBIO) and a co-author of the study. “The entire back of one of our pickup trucks had to be filled with barrels of drinking water. It’s no trivial thing to go out there, and that’s one of the reasons these formations haven’t been studied much.”

After reaching the penitente fields at 16,000 feet above sea level, the scientists noticed patches of red coloration, a telltale sign of microbial activity that has been previously observed in other snow and ice formations around the world.

Upon bringing back samples for analysis, the researchers confirmed the presence of algal species Chlamydomonas and Chloromonas in the ice, the first documentation of snow algae or any other life forms in the penitentes.

“Snow algae have been commonly found throughout the cryosphere on both ice and snow patches, but our finding demonstrated their presence for the first time at the extreme elevation of a hyper-arid site,” said Lara Vimercati, lead author of the study and a doctoral researcher in EBIO. “Interestingly, most of the snow algae found at this site are closely related to other known snow algae from alpine and polar environments.”

The new findings add to scientists’ understanding of the limits of life on Earth, says Alexandra Krinsky, a co-author of the study and an undergraduate in the Department of Molecular, Cellular and Developmental Biology who helped analyze the samples.

“From looking at the extreme environments of the dry Andes to the aquatic life roaming the sea floor, we have broken the original ideas of where life can and has been found,” she said.

The study may also have implications for the search for alien life. Penitente-like formations have recently been discovered on Pluto and are speculated to exist on Europa, one of Jupiter’s moons. The Atacama region in Chile is also considered to be the best Earth analogue for the soils of Mars.

“We’re generally interested in the adaptations of organisms to extreme environments,” Schmidt said. “This could be a good place to look for upper limits of life.”

“Our study shows how no matter how challenging the environmental conditions, life finds a way when there is availability of liquid water,” Vimercati said.

Additional co-authors of the research include Adam Solon of CU Boulder; John Darcy of the University of Colorado Denver; Dorota Porazinska of the University of Florida; and Pablo Arán and Cristina Dorador of the Universidad de Antofagasta (Chile).

Read the paper: Arctic, Antarctic, and Alpine Research

Article source: University of Colorado at Boulder

Image: Steve Schmidt/CU Boulder