The
processes that govern the formation of symbiotic structures between
nitrogen-fixing bacteria and legumes in the latter's roots remain
largely a mystery to science, but researchers have recently discovered
that a duplication of the genes is playing a key role.
A paper describing the researchers’ findings was published in the journal Nature Plants.
Nitrogen is one of the most important ingredients of life. It is an
integral component of amino acids, proteins, and the nucleic acids that
make up DNA and RNA—the very building blocks of living organisms. If
plants, animals, fungi, bacteria or any other organisms suffer from
nitrogen deficiency, they will almost certainly die.
Some 80 percent of the atmosphere is made up of nitrogen gas, so one
might think that nitrogen deficiency is unlikely. But nitrogen in this
form—molecules composed of two nitrogen atoms bonded together, or N2–cannot be used by almost all organisms.
Nitrogen-fixing bacteria are the only bacteria in all of nature that can break the incredibly strong triple bond of N2 and attach the nitrogen atoms to hydrogen to make ammonia (NH3)—a
species of nitrogen-based molecule that organisms can actually take up
and use. This process is called biological nitrogen fixation. Many
plants are able to take up the ammonia synthesized by the
nitrogen-fixing bacteria, and other organisms, including animals, can
eat those plants or eat animals that have eaten those plants, and in
this way gain their nitrogen "fix".
There are also a small number of plants, in particular legumes such as
peas, beans and lentils, that enjoy a symbiotic relationship with
rhizobia in which the bacteria are incorporated into some of the cells
in the roots of the plants, forming small nodule-like growths. The
symbiotic bargain between bacteria and plant involves the rhizobia
trading some of their ammonia for other types of nutrients needed for
development.
But lots of crops do not enjoy this symbiotic relationship with
rhizobia. And in these cases, farmers need to spread manure or synthetic
fertiliser on their fields so that these crops can access life-giving
nitrogen from ammonia.
For sustainable agriculture, this poses two major problems. Synthetic
fertilizer is produced via the Haber-Bosch process, one of the most
important chemical reactions in the modern world. It uses high
temperatures and pressures to combine atmospheric nitrogen to hydrogen
to artificially produce ammonia.
But the easiest, cheapest way to source the hydrogen ingredient
necessary for this ammonia recipe is by breaking apart the methane
molecules that make up natural gas, in turn producing carbon dioxide as a
byproduct. This makes fertilizer production one of the leading causes
of global warming within agriculture.
In addition, application of both manure and synthetic fertilizer to
fields results in ammonia agricultural runoff into rivers and streams.
This "nitrogen pollution" causes deadly algal blooms that suck out
oxygen offshore, resulting in vast underwater dead zones.
"So, if scientists can learn more about how the rhizobia-legume
symbiosis happens, maybe we can engineer other types of plants than just
legumes that can form such a symbiosis, or even fix nitrogen directly,"
said a co-author of the paper.
"This could radically reduce our dependence on manure and synthetic
fertilizer, or even eliminate their need entirely. This has long been
the Holy Grail of sustainable agriculture.”
While a lot is known about this symbiosis, a great deal remains
mysterious, in particular the biochemical process that governs
endosymbiosis—how the bacteria incorporates itself into the plant's root
nodule cells. In most legume species, the rhizobia become entrapped in
the host through curly hairs on the outside of the roots.
The bacteria then "infect" plant cells, proliferating inside them, via
tubular infection threads. These threads are in turn enveloped by a
membrane produced by the host plant, forming a structure akin to
organelles (the "organs" that perform different functions inside a
cell). This nitrogen-fixing organelle-like structure is called the
symbiosome, which has in effect radically reorganized the cell to
accommodate the rhizobia bacterium.
It was known that the plant-derived symbiosome membrane provides an
interface for exchange of nutrients and "signals"—chemical
directives—between the two symbionts, plant and bacterium, and that the
plant-cell cytoskeleton (the filament-like internal scaffolding within
cells) plays a key role in this interface.
In addition, researchers suspected that as the central vacuole—the
large, water-storage organelle in plant cells—exerts force on the cell
and cell wall to maintain pressure equilibrium, thus helping to
coordinate the internal organisation of the cell, it likely plays some
role in the symbiosome.
But the underlying mechanisms of how all of this might work remained largely unknown.
In the common liverwort, Marchantia polymorpha—one of the earliest plants to conquer land some 400 million years ago, there is a protein, the kinesin-like calmodulin-binding protein,
or KCBP. Kinesins are "motor" proteins that work to transport molecules
throughout the cells of many different types of organisms by "walking"
along internal microtubule structures. KCBP however is unique to plants
and in liverworts is essential to the growth of their rhizoids,
root-like structures of these early plants. The protein is thought to be
one of the key evolutionary developments that allowed plants to adapt
to land.
Tantalizingly, in the barrelclover plant (a type of legume), the genes
that are responsible for production of this KCBP are activated just
about everywhere in root hairs at the infection-thread stage.
So the researchers focused on the KCBP-encoding genes, using BLAST
(Basic Local Alignment Search Tool) analysis, a program that compares
genetic or protein sequences of specific organisms to databases of such
sequences to find similar regions.
They found that in the barrelclover's genome, there is a duplication of
them. And where this duplication of KCBP-encoding genes occurs, their
activity appears solely related to interactions between the barrelclover
and the rhizobia bacteria that enable the formation of the symbiosome.
A separate phylogenetic analysis—an evolutionary history of genetic
changes in ancestral species over time—found that this duplication of
KCBP-encoding genes only occurs in the legumes that form symbiosomes.
The researchers believe that the rhizobia are hijacking the plant's
duplicate KCBP to direct a cross linking of microtubules within the cell
to control how the central vacuole in symbiotic cells forms. In this
way, it governs symbiosome development.
There remain many unresolved questions. The team now aim to identify
what is driving the activation (expression) of the duplicate KCBP genes,
to find the genès that act in concert with those governing the
duplicate Genest to regulate rhizobia accommodation in the cell, and to
explore how chemical signalling works across these two very different
kingdoms of life, plant and bacteria, to govern the symbiosis.
https://www.nature.com/articles/s41477-022-01261-4