The human immune system includes a billion-year-old family of proteins used by bacteria to defend themselves against viruses

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The human immune system, that marvel of complexity, subtlety, and sophistication, includes a billion-year-old family of proteins used by bacteria to defend themselves against viruses, scientists at Dana-Farber Cancer Institute and in Israel have discovered.

The findings, published online today by the journal Science, are the latest in a growing body of evidence that components of our immune system – as advanced a shield against disease as exists on the planet – evolved early in ancient forms of life.

The study shows that the immune system absorbed already existing elements, and over eons of evolution, put them to use in novel ways to meet the requirements of creatures as biologically complicated as human beings.

“There has been a tremendous amount of work by researchers around the world to understand how the human immune system functions,” says the study’s senior author, Philip Kranzusch, Ph.D., of Dana-Farber. “The discovery that key parts of human immunity are shared in bacteria provides a new blueprint for research in this area.”

The proteins at the center of the study are known as gasdermins. When a cell becomes infected or turns cancerous, gasdermins form pores that punch holes in its membrane, causing it to die. Substances known as inflammatory cytokines leak from the holes, signaling the presence of infection or cancer and prompting the immune system to rally to the body’s defense.

This process, called pyroptosis, is one facet of the immune system’s repertoire for killing diseased or infected cells. It complements the better-known process of apoptosis, in which crippled or infected cells self-destruct after being damaged.

“Pyroptosis represents one of the fastest ways that the innate immune system [the body’s first line of defense against pathogens] responds to potential threats,” says the new study’s co-first author, Alex Johnson, Ph.D., of Dana-Farber.

The human genome holds the code for six gasdermin proteins, which are expressed at varying levels in different cell types. For the current study, Johnson and his colleagues explored whether the ancestors of any of these proteins existed in bacteria.

They had good reason for thinking they might. In 2019, Kranzusch and his colleagues found that a human immune signaling pathway called cGAS-STING, which senses abnormalities linked to cancer and infection, originated in bacteria. “This and other discoveries motivated us to look for additional connections between immune-related proteins in human and bacterial cells,” Kranzusch notes.

Co-first author Tanita Wein, Ph.D., co-senior author Rotem Sorek, Ph.D., and colleagues at the Weizmann Institute of Science, in Israel, analyzed sections of bacterial DNA known as “antiphage defense islands” because they contain clusters of genes that protect bacteria from infection by viruses known as phages.

They identified 50 bacterial genes predicted to give rise to proteins whose structure was similar to that of gasdermin proteins in mammals.

“I determined a series of structures of these proteins using X-ray crystallography, which confirmed at atomic detail their architectural similarity with mammalian gasdermins,” Johnson relates. The types of bacteria that harbor these proteins are widespread, living in soil, leaves, and other natural habitats. (The particular bacterium most studied in Johnson’s research was first identified on a corn plant in Wisconsin.)

Johnson’s structural work showed that while human and bacterial gasdermins are structurally alike, the bacterial versions tend to be about half as big, yet serve as building blocks for membrane pores larger than those seen in humans. All these gasdermins are activated by a similar mechanism, but the chain of events they set in motion is far more extensive in human cells.

In bacterial cells, viral infection may trigger cells to die from punctured membranes, stopping viruses in their tracks. In human cells, the death of an infected cell triggers a cascade of events that brings other elements of the immune system to bear on the infection.

“This is an example of a very primitive form of defense, which in humans has been adapted and expanded with regulatory systems that enable our bodies to respond to infection or cancer,” Kranzusch says.

The discovery of traces of a primitive form of immunity within the staggering complexity of the human immune system can help researchers better understand how the system came to be. “Seeing the simplest version of a machine can give you a new level of understanding of the machine as a whole,” Kranzusch remarks.  “The same principle can apply to research into the immune system.”

Co-authors of the study are: Brianna Duncan-Lowey, Ph.D., of Dana-Farber; Megan Mayer, MS, of the Harvard Center for Cryo-Electron Microscopy; and Erez Yimiya, Yaara Oppenheimer-Shaanan, Ph.D., and Gil Amitai, Ph.D., of the Weizmann Institute.


Gasdermin, the executioner of pyroptosis

Pyroptosis was defined as gasdermin-mediated programmed death in 2015.29 The gasdermin superfamily is composed of gasdermin A/B/C/D (GSDMA/B/C/D), gasdermin E (GSDME, also referred to as DFNA5) and DFNB59 (Pejvakin, PJVK) in human (Gsdma1-3, Gsdmc1-4, Gsdmd, Dfna5, and Dfnb59 in mice).30,31,32,33,34 Among these conserved proteins, GSDMD and DFNA5 are most deeply studied in pyroptotic death. Except for Pejvakin, all these members consist of two conserved domains, the N-terminal pore-forming domain and the C-terminal repressor domain (PFD and RD).35,36,37,38

The PFD of most gasdermins could induce pyroptosis, which has not yet been detected for Pejvakin.17,30,39 In general, gasdermins maintain oligomerization through the interaction between PFD and RD, and the cytotoxic effects of PFD could be inhibited by RD.37,38 When the host is stimulated by a variety of exogenous or endogenous factors, gasdermins are cleaved by some caspases or granzymes, and the N-terminal PFD is dissociated from the C-terminal RD, and then the N-terminal PFD oligomerizes and forms pores in the cell membrane, causing the release of inflammatory molecules and cell pyroptotic death.30,40,41 Although a number of gasdermin family proteins have been reported to be linked to human diseases,20,29,39,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63 the specific mechanism and function remain to be studied.

The characteristics of pyroptosis

Pyroptosis is composed of “pyro” and “ptosis”. “Pyro” means fire, indicating the properties of inflammation of pyroptosis, but “ptosis” means falling, which is consistent with other forms of programmed cell death.7 There are some similarities between pyroptosis and apoptosis, such as DNA damage and chromatin condensation.64,65 Interestingly, pyroptotic cells emerged swelling and a lot of bubble-like protrusions appear on the surface of the cellular membrane before its rupture.66 Similarly, membrane blebbing also occurs during apoptosis, and caspase-3 is necessary for this process.67,68,69,70,71,72,73,74,75,76

However, the unique morphological characteristics of pyroptosis are obviously different from those of apoptosis. It is generally believed that apoptosis is a safe form of death, but pyroptosis can cause inflammation, activated by extracellular or intracellular stimulation, such as bacterial, viral, toxin, and chemotherapy drugs.77 In fact, unlike the explosive rupture associated with necrosis, pyroptosis causes flattening of the cytoplasm due to plasma membrane leakage.66

In addition, caspases activation or release of granzymes results in the N-terminal of gasdermin oligomerization and pore formation (1–2 μm in diameter) in the plasma membrane, which allows mature IL-1β/IL-18 with a diameter of 4.5 nm and caspase-1 with a diameter of 7.5 nm to pass through, respectively.30 In the meantime, the water entering through the pores causes cell swelling and osmotic lysis, thus resulting in rupture of the plasma membrane and the release of IL-1β and IL-18.78,79

Thus, the pyroptotic cells are permeable to 7-aminoactinomycin (7-AAD), propidium iodide (PI), and ethidium bromide (EtBr) because of the low molecular weight of these dyes.79 On the contrary, in comparison with pyroptotic cells, apoptotic cells maintain membrane integrity,80 so that these dyes can’t stain them.81,82,83,84 Intriguingly, similar to apoptotic cells, Annexin V also stains pyroptotic cells and the dye binds to phosphatidyl serine (PS).85

Therefore, Annexin V cannot differentiate apoptotic cells from pyroptotic cells. In addition, apoptotic bodies are formed in the process of apoptosis, while pyroptotic bodies are formed in the process of pyroptosis.80 Interestingly, the diameter of pyroptotic bodies is similar to that of apoptotic bodies, and thier size are both 1–5 µm.66

Besides, there is a very special form of DNA damage with dUTP nick-end labeling (TUNEL) staining positive in the early stage of pyroptosis,79,86,87,88,89,90,91,92,93 which is different from that of apoptosis. Compared with apoptosis, the intensity of DNA damage is lower in pyroptotic cells.

The DNA fragmentation of pyroptosis is random and the nucleus remains intact,94,95,96,97 while the apoptotic DNA fragment is ordered and the nucleus is fragmented.23,98,99,100 Interestingly, caspase activation is associated with both pyroptosis and apoptosis. Initially, pyroptosis was considered to be caspase-1-related cell death.5,23,101,102

It is worth mentioning that recent studies have shown that other caspases, including caspase-3/4/5/6/8/9/11, also cause pyroptosis in other different cells,16,17,29,39,94,103,104,105 and play major roles in innate immunity and tumorigenesis.106,107,108,109,110,111 Caspase-3 was previously thought to be the executor of apoptosis, but it was suggested that caspase-3 can also induce pyroptosis by cleaving GSDME.16,17,71 More surprisingly, the apoptosis-related protein caspase-8 can also directly cleave GSDMD to induce pyroptosis.103

In addition, the activation of caspase-9 is also involved in pyroptosis by cleaving and activating caspase-3,112 and caspase-6 mediates the cleavage of GSDMC.21 Although current studies have found that caspase-1 and caspase-4/5/11 are only associated with pyroptosis, while caspase-2, caspase-7, and caspase-10 are only related to apoptosis,36,113,114,115,116,117 the connections between caspases and pyroptosis as well as caspases and apoptosis may be reported one after another in the future with the deepening of studies. Apoptosis is affected by the level of ATP, and apoptosis is accompanied by the activation of PARP, causing ATP depletion.118 However, the effector proteins of pyroptosis belong to the gasdermin family23 (Tables 1 and 2).

Table 1 Similarities between pyroptosis and apoptosis

From: Pyroptosis: mechanisms and diseases

CharacteristicsPyroptosisApoptosis
Programmed cell deathYesYes
PS exposureYesYes
Annexin V stainingYesYes
TUNEL stainingYesYes
DNA damageYesYes
Chromatin condensationYesYes
Membrane blebbingYesYes
The diameters of pyroptotic bodies and apoptotic bodies (1–5 µm)YesYes
Caspase-3 activationYesYes
Caspase-6 activationYesYes
Caspase-8 activationYesYes
Caspase-9 activationYesYes

Table 2 Differences between pyroptosis and apoptosis

From: Pyroptosis: mechanisms and diseases

CharacteristicsPyroptosisApoptosis
InflammationYesNo
Apoptotic bodiesNoYes
Pyroptotic bodiesYesNo
Intact nucleusYesNo
Pore formationYesNo
Cell swellingYesNo
Cell shrinkNoYes
Osmotic lysisYesNo
Membrane integrityNoYes
7-AAD stainingYesNo
PI stainingYesNo
EtBr stainingYesNo
Caspase-1 activationYesNo
Caspase-4 activationYesNo
Caspase-5 activationYesNo
Caspase-11 activationYesNo
Caspase-2 activationNoYes
Caspase-7 activationNoYes
Caspase-10 activationNoYes
PARP cleavageNoYes
Gasdermin cleavageYesNo

reference link: https://www.nature.com/articles/s41392-021-00507-5/tables/2


More information: Alex G. Johnson et al, Bacterial gasdermins reveal an ancient mechanism of cell death, Science (2022). DOI: 10.1126/science.abj8432.

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