Structure and assembly pattern of a freshwater short-tailed cyanophage Pam1

Zhang, Juntao; Yang, Feng; Du, Kang; Li, Weifang; Chen, Yuxing; Jiang, Yong-Liang; Li, Qiong; Zhou, Cong‐Zhao

doi:10.1016/j.str.2021.10.004

Cited by 13 publications

(8 citation statements)

References 74 publications

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“…Similar to the previously reported portal proteins 12 , 13 , the portal of A-1(L) also consists of five typical domains: barrel, crown, wing, stem, and clip, of which the barrel domain is absent in some phages (Supplementary Fig. 1a ).…”

Section: Resultssupporting

confidence: 83%

Structure of the intact tail machine of Anabaena myophage A-1(L)

Yu,

Yang,

Zhang

et al. 2024

Nat Commun

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The Myoviridae cyanophage A-1(L) specifically infects the model cyanobacteria Anabaena sp. PCC 7120. Following our recent report on the capsid structure of A-1(L), here we present the high-resolution cryo-EM structure of its intact tail machine including the neck, tail and attached fibers. Besides the dodecameric portal, the neck contains a canonical hexamer connected to a unique pentadecamer that anchors five extended bead-chain-like neck fibers. The 1045-Å-long contractile tail is composed of a helical bundle of tape measure proteins surrounded by a layer of tube proteins and a layer of sheath proteins, ended with a five-component baseplate. The six long and six short tail fibers are folded back pairwise, each with one end anchoring to the baseplate and the distal end pointing to the capsid. Structural analysis combined with biochemical assays further enable us to identify the dual hydrolytic activities of the baseplate hub, in addition to two host receptor binding domains in the tail fibers. Moreover, the structure of the intact A-1(L) also helps us to reannotate its genome. These findings will facilitate the application of A-1(L) as a chassis cyanophage in synthetic biology.

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Section: Resultssupporting

confidence: 83%

Structure of the intact tail machine of Anabaena myophage A-1(L)

Yu,

Yang,

Zhang

et al. 2024

Nat Commun

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“…The Pam3 virions were amplified by infecting the host Pseudoanabaena 1,806 isolated from Lake Chaohu. The Pam3 virion particles were purified by the methods described previously ( 32 – 34 ). Briefly, the crude lysate after phage infection was harvested by PEG-NaCl precipitation and differential centrifugation.…”

Section: Methodsmentioning

confidence: 99%

“…The structures of the portal vertex and neck were solved by the sequential localized classification and symmetry relaxation, as reported previously ( 34 , 37 ). The brief protocols are as follows ( SI Appendix , Fig.…”

Section: Methodsmentioning

confidence: 99%

Fine structure and assembly pattern of a minimal myophage Pam3

Yang

Jiang

Zhang

et al. 2023

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

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The myophage possesses a contractile tail that penetrates its host cell envelope. Except for investigations on the bacteriophage T4 with a rather complicated structure, the assembly pattern and tail contraction mechanism of myophage remain largely unknown. Here, we present the fine structure of a freshwater Myoviridae cyanophage Pam3, which has an icosahedral capsid of ~680 Å in diameter, connected via a three-section neck to an 840-Å-long contractile tail, ending with a three-module baseplate composed of only six protein components. This simplified baseplate consists of a central hub-spike surrounded by six wedge heterotriplexes, to which twelve tail fibers are covalently attached via disulfide bonds in alternating upward and downward configurations. In vitro reduction assays revealed a putative redox-dependent mechanism of baseplate assembly and tail sheath contraction. These findings establish a minimal myophage that might become a user-friendly chassis phage in synthetic biology.

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“…S 3 ). Thanks to our recently reported structure of Pam1 [ 62 ], the structural proteins for Pam1 and Pam5 could be better annotated, such as head proteins: portal, scaffolding, capsid, and cement protein, followed by tail proteins: adaptor, needle head, spike, needle, etc. (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…A couple of ORFs in Pam1, 2, 3, and 5 genomes have been annotated as the putative receptor-binding proteins (RBPs), which possess a primary sequence similarity less than 20% to each other (Table S 4 ). Structural analysis of Pam1 tailspike gp17 (PDB code of 7eea) revealed a C-terminal receptor-binding domain that contains a right-handed parallel β-helix and a distal β-sandwich, both of which are proposed to be responsible for the recognition of host extracellular polysaccharides [ 62 ]. Moreover, we predicted the 3-D structures of putative RBPs of Pam2, 3, and 5 via AlphaFold 2.0 [ 68 ].…”

Section: Resultsmentioning

confidence: 99%

Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining

Yang

Zhang

et al. 2022

Microbiome

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Background As important producers using photosynthesis on Earth, cyanobacteria contribute to the oxygenation of atmosphere and the primary production of biosphere. However, due to the eutrophication of urban waterbodies and global warming, uncontrollable growth of cyanobacteria usually leads to the seasonal outbreak of cyanobacterial blooms. Cyanophages, a group of viruses that specifically infect and lyse cyanobacteria, are considered as potential environment-friendly agents to control the harmful blooms. Compared to the marine counterparts, only a few freshwater cyanophages have been isolated and genome sequenced to date, largely limiting their characterizations and applications. Results Here, we isolated five freshwater cyanophages varying in tail morphology, termed Pam1~Pam5, all of which infect the cyanobacterium Pseudanabaena mucicola Chao 1806 that was isolated from the bloom-suffering Lake Chaohu in Anhui, China. The whole-genome sequencing showed that cyanophages Pam1~Pam5 all contain a dsDNA genome, varying in size from 36 to 142 Kb. Phylogenetic analyses suggested that Pam1~Pam5 possess different DNA packaging mechanisms and are evolutionarily distinct from each other. Notably, Pam1 and Pam5 have lysogeny-associated gene clusters, whereas Pam2 possesses 9 punctuated DNA segments identical to the CRISPR spacers in the host genome. Metagenomic data-based calculation of the relative abundance of Pam1~Pam5 at the Nanfei estuary towards the Lake Chaohu revealed that the short-tailed Pam1 and Pam5 account for the majority of the five cyanophages. Moreover, comparative analyses of the reference genomes of Pam1~Pam5 and previously reported cyanophages enabled us to identify three circular and seven linear contigs of virtual freshwater cyanophages from the metagenomic data of the Lake Chaohu. Conclusions We propose a high-throughput strategy to systematically identify cyanophages based on the currently available metagenomic data and the very limited reference genomes of experimentally isolated cyanophages. This strategy could be applied to mine the complete or partial genomes of unculturable bacteriophages and viruses. Transformation of the synthesized whole genomes of these virtual phages/viruses to proper hosts will enable the rescue of bona fide viral particles and eventually enrich the library of microorganisms that exist on Earth.

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Structure and assembly pattern of a freshwater short-tailed cyanophage Pam1

Cited by 13 publications

References 74 publications

Structure of the intact tail machine of Anabaena myophage A-1(L)

Structure of the intact tail machine of Anabaena myophage A-1(L)

Fine structure and assembly pattern of a minimal myophage Pam3

Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining

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