Cryo-EM structure of
            <i>Mycobacterium smegmatis</i>
            DyP-loaded encapsulin

Tang, Yanting; Mu, A.; Zhang, Yuying; Zhou, Shouli; Wang, Weiwei; Lai, Yuezheng; Zhou, Xinru; Liu, Fengjiang; Yang, Xiuna; Gong, Haiming; Wang, Quan; Rao, Zihe

doi:10.1073/pnas.2025658118

Cited by 46 publications

(57 citation statements)

References 65 publications

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“…DypB (class P) from R. jostii was shown to assemble with encapsulin in vitro [ 12 ], suggesting the potential of class P DyPs to act as cargo proteins of encapsulin. A recent high-resolution cryogenic electron microscopy study revealed that a DyP-type peroxidase from Mycobacterium smegmatis is a primary cargo protein of mycobacterial encapsulins [ 89 ]. Notably, this latter study noted that the encapsulin shell plays a role in stabilizing DyP in a dodecameric form, which is larger than any previously reported DyP oligomer.…”

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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“…Based on our finding, we speculate that the 3fold symmetry of the dye-decolorizing peroxidase (DyP) cargo mentioned briefly in the introduction and found in related encapsulins should bind the 3-fold axis of the shell. However, a concurrent structural study of the M. smegmatis DyP encapsulin appears to have the most defined cargo density positioned proximal to the 5-fold axis of the shell rather than the 3-fold axis (15). Without an abundance of structural data on diverse encapsulins, it remains unclear what role symmetry plays in the cargo-shell interaction.…”

Section: The Flp Cargo Protein Is Flexibly Bound Within the Encapsulin Shellmentioning

confidence: 99%

“…For the B. linens DyP encapsulin, only a single cargo protein was encapsulated despite additional space within the shell (13,14). However, a recent study of the M. smegmatis DyP encapsulin found both a minority species of the encapsulin contained a single hexameric DyP cargo while the majority of particles actually contained a dodecameric DyP complex from 2 DyP cargo interacting with one another (15). Furthermore, encapsulation of native and non-native cargo appears to cause significant destabilization of the nanocompartment (13,14), which may explain the absence of higher cargo loading ratios in many of these systems.…”

Section: Introductionmentioning

confidence: 99%

The encapsulin fromThermatoga maritimais a flavoprotein with a symmetry matched ferritin-like cargo protein

LaFrance

Cassidy-Amstutz

Nichols

et al. 2021

Preprint

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Bacterial nanocompartments, also known as encapsulins, are an emerging class of protein-based "organelles" found in bacteria and archaea. Encapsulins are virus-like icosahedral particles comprising a ~25-50 nm shell surrounding a specific cargo enzyme. Compartmentalization is thought to create a unique chemical environment to facilitate catalysis and isolate toxic intermediates. Many questions regarding nanocompartment structure-function remain unanswered, including how shell symmetry dictates cargo loading and to what extent the shell facilitates enzymatic activity. Here, we explore these questions using the model T. maritima nanocompartment known to encapsulate a redox-active ferritin-like protein. Biochemical analysis revealed the encapsulin shell to possess a flavin binding site located at the interface between capsomere subunits, suggesting the shell may play a direct and active role in the function of the encapsulated cargo. Furthermore, we used cryoEM to show that cargo proteins use a form of symmetry-matching to facilitate encapsulation and define stoichiometry. In the case of the T. maritima encapsulin, the decameric cargo protein with 5-fold symmetry preferentially binds to the pentameric-axis of the icosahedral shell. Taken together, these observations suggest the shell is not simply a passive barrier-it also plays a significant role in the structure and function of the cargo enzyme.

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“…At present, eight encapsulins have been resolved at near-atomic resolution by X-ray crystallography or three-dimensional cryo-electron microscopy (3D cryo-EM). These are the encapsulins from the archaeon P. furiosus (EncPf; PDB entry 2e0z) [29], and from the bacteria T. maritima (EncTm; PDB entry 3dkt) [6], Myxococcus xanthus (EncMx; PDB entry 4pt2) [30], Quasibacil-lus thermotolerans (EncQt; PDB entry 6nj8) [49], Synechococcus elongatus (EncSe; PDB entry 6 × 8 m) [31], Mycolicibacterium hassiacum (EncMh; PDB entry 6i9g) [50], Mycobacterium smegmatis (EncMs; PDB entry 7boj) [51], and Haliangium ochraceum (EncHo) [52]. All these encapsulins except EncSe are close relatives and are grouped in the classical family 1; EncSe belongs to family 2A and has distinctive structural and functional features.…”

Section: Nanocompartment Structurementioning

confidence: 99%

“…The TP-mediated, flexible interactions between the cargo and the encapsulin shell contribute to the low resolution observed for the encapsulated cargo. In the EncMs system, however, the dye-decolorizing peroxidase (DyP) cargo was clearly resolved in the cryo-EM structure [51]. DyP forms a dodecameric complex of two hexamers that stretches across the interior of the encapsulin, which contributes to DyP stability.…”

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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Cryo-EM structure of Mycobacterium smegmatis DyP-loaded encapsulin

Cited by 46 publications

References 65 publications

DyP-Type Peroxidases: Recent Advances and Perspectives

DyP-Type Peroxidases: Recent Advances and Perspectives

The encapsulin fromThermatoga maritimais a flavoprotein with a symmetry matched ferritin-like cargo protein

Nanotechnological Applications Based on Bacterial Encapsulins

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