CACAO Phage Hunters 2018
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| Status | Page | Date/Time | GO Term (Aspect) | Reference | Evidence | Notes | Links |
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| unacceptable | 9CAUD:Q9G097 | 2018-03-11 21:16:40 CDT | GO:0098003 viral tail assembly (P) | PMID:27824135 | ECO:0000315 mutant phenotype evidence used in manual assertion | The 29 repeats of the tape measure protein are essential to virion structure. Deletion mutants for repeat copies were constructed, then had tail length measured through electron microscopy. Authors found that, with increased deletion of repeat sequences, the phage tail shortened (Table 2). For example, normal phage tail length is 118nm, but repeat 1-29 deletion mutants had a tail of 65 nm.
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| acceptable | BPHK7:CAPSD | 2018-03-11 21:29:54 CDT | GO:0046797 viral procapsid maturation (P) | PMID:24889236 | ECO:0000315 mutant phenotype evidence used in manual assertion | HK97 delta domain is necessary for proper procapsid assembly. HK97 delta domain comprises the first 102 amino acids of the major capsid protein, is present during procapsid assembly, and is cleaved during capsid maturation. In Figure 2A, HK97 lacking the delta domain was found to have become insoluble. Figure 2B shows similar results, with delta-less HK97 present only in the pellet fraction (as marked by a circle). Figure 2C shows expression of a full-length HK97 protein plasmid (protease-) and delta-less HK97. Full-length HK97 is shown to properly form capsomers and proheads—signs of proper assembly— while the lack of bands for the delta-less HK97 show there is no formation of capsomers or proheads. From this, we can conclude that the delta-domain of HK97 is necessary for formation of a properly folded, soluble procapsid head.
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| acceptable | LAMBD:DECO | 2018-03-12 11:45:05 CDT | GO:0098021 viral capsid, decoration (C) | PMID:25053840 | ECO:0000314 direct assay evidence used in manual assertion | gpD serves as a decoration protein for the capsid and leads to stronger capsid formation. Procapsids were reconstituted in vitro and expanded through 2.5 M urea treatment. Biophysical properties were then assessed through atomic force microscopy. Figure 5 and Table 2 show that addition of gpD leads to an increase in breaking force (0.78 nN from 0.45nN without gpD), and a rescue of the spring constant (0.10 N/m, compared to 0.06 N/m without gpD and the 0.11 N/m of the procapsid). Addition of gpD also reinforces the capsid's stiffness, as shown by the further increase in Young's modulus (E): 0.88 GPa with gpD, 0.57 GPa without gpD, and 0.16 GPa for the procapsid. Based on these measurements, gpD reinforces the capsid, but is not necessary to its formation.
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| updatedbyinstructor | LAMBD:DECO | 2018-04-09 14:11:35 CDT | GO:0019073 viral DNA genome packaging (P) | PMID:18801370 | ECO:0000314 direct assay evidence used in manual assertion | Decoration protein gpD contributes to genome packaging in lambda phage. Here, it was evaluated whether gpD is necessary to genome packaging by acting as structural support for the capsid to withstand the high degree of pressure generated. In fig 3A it is shown that addition of gpD of 5uM and above results in a significant increase in the amount of genomic DNA packaged as indicated by the band. 3B is a dose-response curve, showing an increase in genome packaging with increased dose. Fig4 displays the effect of gpD on genome packaging as related to genome length, with no effect on DNA duplexes <37 kb and substantial effect on duplexes >43kb. These results then indicate that gpD reinforces the capsid head such that large DNA duplexes, like the 48kb of lambda phage, can be packaged effectively.
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