Shotgun EM of mycobacterial protein complexes during stationary phase stress

Kirykowicz, Angela Mary; Woodward, Jeremy D.

doi:10.1016/j.crstbi.2020.09.002

Cited by 11 publications

(8 citation statements)

References 52 publications

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“…An additional unique characteristic of several DyPs is their function as a cargo protein for encapsulin, a bacterial nanocompartment protein. One of the best-studied of these DyPs is MtDyP (class P) from Mycobacterium tuberculosis [ 13 , 26 ], a bacterium that slips through defenses generated by the host immune response and induces tuberculosis. MtDyP, which is shielded from oxidative stress in the nanocompartment through association with encapsulin, appears to play an important role in defending against the immune assault by virtue of its peroxidase activity.…”

Section: Physiological Role Of Dyp-type Peroxidasesmentioning

confidence: 99%

DyP-Type Peroxidases: Recent Advances and Perspectives

Sugano

Yoshida

2021

IJMS

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In this review, we chart the major milestones in the research progress on the DyP-type peroxidase family over the past decade. Though mainly distributed among bacteria and fungi, this family actually exhibits more widespread diversity. Advanced tertiary structural analyses have revealed common and different features among members of this family. Notably, the catalytic cycle for the peroxidase activity of DyP-type peroxidases appears to be different from that of other ubiquitous heme peroxidases. DyP-type peroxidases have also been reported to possess activities in addition to peroxidase function, including hydrolase or oxidase activity. They also show various cellular distributions, functioning not only inside cells but also outside of cells. Some are also cargo proteins of encapsulin. Unique, noteworthy functions include a key role in life-cycle switching in Streptomyces and the operation of an iron transport system in Staphylococcus aureus, Bacillus subtilis and Escherichia coli. We also present several probable physiological roles of DyP-type peroxidases that reflect the widespread distribution and function of these enzymes. Lignin degradation is the most common function attributed to DyP-type peroxidases, but their activity is not high compared with that of standard lignin-degrading enzymes. From an environmental standpoint, degradation of natural antifungal anthraquinone compounds is a specific focus of DyP-type peroxidase research. Considered in its totality, the DyP-type peroxidase family offers a rich source of diverse and attractive materials for research scientists.

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Section: Physiological Role Of Dyp-type Peroxidasesmentioning

confidence: 99%

DyP-Type Peroxidases: Recent Advances and Perspectives

Sugano

Yoshida

2021

IJMS

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“…Moreover, it has been shown that some encapsulin systems may possess multiple cargo proteins, which are made up of one core cargo protein and up to three secondary cargo proteins according to the TPs (6). Notably, a large proportion of native cargo proteins are DyP-type peroxidases, conferring the resistance of the cell to oxidative stress (6,7,11,(15)(16)(17)(18). However, to date, the structural information on the cargo-encapsulated encapsulins is not yet available (SI Appendix, Table S1), and thus, little is known about the structural arrangement and mechanistic features of the cargo proteins loaded in the encapsulins.…”

mentioning

confidence: 99%

“…Actinobacteria harbors the largest number of encapsulin or encapsulin-like systems (6). DyP-containing encapsulins have already been reported from mycobacteria, including Mycobacterium smegmatis (15) and Mycobacterium tuberculosis (19). These have been considered as potential biomarkers to detect active tuberculosis (TB) (20).…”

mentioning

confidence: 99%

Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin

Tang

Zhang

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Encapsulins containing dye-decolorizing peroxidase (DyP)-type peroxidases are ubiquitous among prokaryotes, protecting cells against oxidative stress. However, little is known about how they interact and function. Here, we have isolated a native cargo-packaging encapsulin from Mycobacterium smegmatis and determined its complete high-resolution structure by cryogenic electron microscopy (cryo-EM). This encapsulin comprises an icosahedral shell and a dodecameric DyP cargo. The dodecameric DyP consists of two hexamers with a twofold axis of symmetry and stretches across the interior of the encapsulin. Our results reveal that the encapsulin shell plays a role in stabilizing the dodecameric DyP. Furthermore, we have proposed a potential mechanism for removing the hydrogen peroxide based on the structural features. Our study also suggests that the DyP is the primary cargo protein of mycobacterial encapsulins and is a potential target for antituberculosis drug discovery.

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“…Each of these three cargos has independent antioxidant activity and is encapsulated in the nanocompartment when coexpressed with the encapsulin gene in E. coli [76]. In M. tuberculosis cells grown in standard laboratory conditions, however, only nanocompartments with the core cargo Mt-DyP have been identified [77]; results are similar for M. smegmatis [54].…”

Section: Cargo Loadingmentioning

confidence: 89%

“…EMD-3608) [53]. An adapted shotgun electron microscopy method identified numerous protein complexes in M. smegmatis and were used efficiently to find new encapsulin nanocages [54].…”

Section: Nanocompartment Structurementioning

confidence: 99%

Nanotechnological Applications Based on Bacterial Encapsulins

et al. 2021

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Encapsulins are proteinaceous nanocontainers, constructed by a single species of shell protein that self-assemble into 20–40 nm icosahedral particles. Encapsulins are structurally similar to the capsids of viruses of the HK97-like lineage, to which they are evolutionarily related. Nearly all these nanocontainers encase a single oligomeric protein that defines the physiological role of the complex, although a few encapsulate several activities within a single particle. Encapsulins are abundant in bacteria and archaea, in which they participate in regulation of oxidative stress, detoxification, and homeostasis of key chemical elements. These nanocontainers are physically robust, contain numerous pores that permit metabolite flux through the shell, and are very tolerant of genetic manipulation. There are natural mechanisms for efficient functionalization of the outer and inner shell surfaces, and for the in vivo and in vitro internalization of heterologous proteins. These characteristics render encapsulin an excellent platform for the development of biotechnological applications. Here we provide an overview of current knowledge of encapsulin systems, summarize the remarkable toolbox developed by researchers in this field, and discuss recent advances in the biomedical and bioengineering applications of encapsulins.

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Shotgun EM of mycobacterial protein complexes during stationary phase stress

Cited by 11 publications

References 52 publications

DyP-Type Peroxidases: Recent Advances and Perspectives

DyP-Type Peroxidases: Recent Advances and Perspectives

Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin

Nanotechnological Applications Based on Bacterial Encapsulins

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