Most disease causing bacteria, including Escherichia coli (pictured here) need iron to proliferate. Photo: NIAID.
Editor’s note, December 30, 2020: The paper discussed in the following article has come under scrutiny following concerns about some of its images. The discussion on PubPeer is available to view here. The journal that published the paper added the following note on December 11: “Readers are alerted that the reliability of data presented in this manuscript is currently in question. Appropriate editorial action will be taken once this matter is resolved.”
The cells that make up different forms of life on the planet contain lots of iron. Atoms of this element help transfer energy molecules, participate in metabolic pathways and contribute to repairing damaged DNA.
Clearly, iron is important – which is why it’s curious that we don’t know a lot about the cellular mechanisms that ferry iron around, transporting it between different subcellular sites.
Scientists used to think this job was performed exclusively by regulatory proteins, and have studied these proteins well. But more recent discoveries suggest that a different cellular mechanism may be at work as well.
A team of scientists from the National Centre for Biological Sciences, Bengaluru, has discovered a new type of riboswitch in bacteria. This one can bind to iron – presenting an entirely different cellular mechanism.
Riboswitches are RNA entities that detect and respond to the levels of different substances inside our cells.
Ailong Ke, a structural biologist at Cornell University, told c&en magazine that Ramesh & co.’s study is “very neat” and their discovery “adds to our fundamental understanding of what RNA can do”.
Arati Ramesh and her team combined bioinformatics and biochemical methods to find this ‘sense iron’ riboswitch – which the group is calling ‘Sensei’.
“Iron-binding proteins have been the best-studied iron sensors so far. With the discovery of Sensei RNAs, the responsibility of iron sensing and modulation is now extended to RNAs,” Ramesh, a biochemist, told Chemistry World.
Riboswitches are parts of messenger RNA (mRNA) – which is a type of RNA that plays a critical role in a cell’s ability to make proteins using the DNA as a manual.
(High-school flashback: DNA and RNA are nucleic acids. Carbohydrates, lipids, nucleic acids and proteins are the four macromolecules essential for life).
Riboswitches are part of this process. They instruct the cell by sending ‘on’ and ‘off’ commands that regulate the production of certain proteins.
Supratim Sengupta, a professor at IISER Kolkata who has previously studied riboswitches that bind to other molecules, said the analogy of a ‘fuse’ might be more apt than that of a ‘switch’.
“Like a fuse that stops the flow of current in a circuit when the current exceeds a certain threshold,” he said, “riboswitches can also stop the production of certain proteins when the chemical signal – [the presence or quantity of] a small molecule or metal ion – in the environment exceeds a certain threshold.”
For example, fluoride riboswitches in many bacteria ‘sense’ the presence of elevated levels of fluoride ions. They then respond in a way that increases the expression of other genes in the bacteria’s DNA that help the bacteria better survive these conditions.
The simple logic is that the higher the concentration of a certain molecule, the more likely it is that it will bind to the riboswitch.
Ramesh and her colleagues were studying riboswitches sensitive to nickel and cobalt, or NiCo. That’s when they found a type of NiCo riboswitches that lacked the features required to bind to cobalt.
When they took a closer look, they noticed that the riboswitches were associated with parts of the DNA related iron transporters and enzymes.
In Ramesh’s words to Chemistry World: “These variants were found near genes encoding for iron-related proteins, raising the possibility that they could bind iron.”
To make sure, her team ‘fed’ iron ions into two chambers, one with the mRNA that had the Sensei riboswitches and one without. After some tests, they concluded that the chamber with the mRNA had sequestered a greater quantity of iron ions.
Earlier this year, Joseph Cotruvo, Jr., an assistant professor at Pennsylvania State University, and a colleague had reported in a different study that “the riboswitch initially proposed to respond to [NiCo] also responds to iron.” Subsequently, “we presented data suggesting that iron may actually be the most likely metal for [this switch] to sense within a cell,” he told The Wire Science.
Cotruvo, Jr. explained that the Sensei riboswitch is closely related to the NiCo riboswitch but that it is found in different bacteria. These switches also seem to bind iron in different ways – with the effect that the Sensei switch binds selectively to iron.
Scientists have discovered more than 30 types of riboswitches so far, distinguished by the molecule each switch senses. They are primarily found in bacteria. Only a couple types are known in higher organisms and none are found in humans.
In addition, not all bacteria possess the same riboswitches – and the details of their function differ between different classes of switches.
“It is possible that riboswitches are holdovers from an early ‘RNA world’ in which RNA was the primary carrier of genetic information [instead of DNA today], and RNA carried out a cell’s chemical reactions, most of which are now catalysed by proteins,” Cotruvo, Jr. said.
Riboswitches offer one window through which scientists can get a glimpse of how RNA-based organisms, including many pathogenic bacteria, work.
Indeed, the specificity of riboswitches for the molecules that they bind, and the importance of those molecules for the survival of the bacterium, has motivated researchers to explore riboswitches as novel antibiotic targets as well.
“Because iron is an essential nutrient, understanding how iron-sensing riboswitches work and what their specific roles are in the cell are the first steps toward exploring these riboswitches as potential drug-targets,” he added.
The way to do this is to create molecules that mimic riboswitch. According to Sengupta, there could be two ways to do this.
One is to design synthetic riboswitches that respond to known chemical signals and incorporate them into the genetic material of the pathogen.
The other way is to create small, artificial molecules that mimic the chemical signal that the riboswitch senses, and then trick the riboswitch into getting activated when it should not – making it respond by turning off the production of proteins responsible for antibiotic resistance.
Some researchers are also exploring the possibility of building biosensors based on riboswitches. But right now, there is still much to learn.
“There is also a lot of effort in learning the molecular details behind how these riboswitches work, and how the riboswitches fit into the cellular pathways that they regulate – learning the ‘grammar’,” Cotruvo, Jr. said.
For example, Ramesh et al found that when the Sensei riboswitch binds to iron (specifically, Fe2+), its shape changes to resemble a four-leaf clover. This transformation then affects how the mRNA is decoded, which in turn affects the final protein. Ramesh told c&en that her team’s next step is to figure out the biochemical reactions in this pathway.
“We propose that there is a portion of the RNA which can recruit ribosomes, and that portion is opened up when iron binds,” Ramesh told the magazine.
This won’t be easy. Studying RNA and all its mechanisms, in Cotruvo, Jr.’s telling, has unique challenges compared to other biological molecules like DNA and proteins due to RNA’s intrinsic instability and structural plasticity.
Sengupta agreed. “Even the SARS-CoV-2 virus is an RNA virus about which we still don’t know much. On the other hand, we know a fair bit about RNA. … Whether we know enough to effectively manipulate them is a different question altogether.”
Renuka Kulkarni is a science writer based in Pune, India, and is currently pursuing a PhD in political ecology.