Cellular and viral determinants of retroviral nuclear entry

Hamid, Faysal Bin; Kim, Jinsun; Shin, Cha‐Gyun

doi:10.1139/cjm-2015-0350

Cited by 31 publications

(26 citation statements)

References 150 publications

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“…Plant-based culture media provide the culturable microbiome with diverse nutrients at concentrations that mimic the root milieu. Additionally, plant materials in the form of plant-based culture media ( 51 , 62 ) or as a supplement to enrich standard artificial culture media ( 44 ) impaired the swarming motility of bacteria on agar plates, thereby halting their expansive progression and restricting the dominance of larger slimy colonies. In many cases, these slimy colonies masked the presence of some small colonies and/or μ-colonies.…”

Section: Discussionmentioning

confidence: 99%

G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla

et al. 2018

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The rapid development of high-throughput techniques and expansion of bacterial databases have accelerated efforts to bring plant microbiomes into cultivation. We introduced plant-only-based culture media as a successful candidate to mimic the nutritional matrices of plant roots. We herein employed a G3 PhyloChip microarray to meticulously characterize the culture-dependent and -independent bacterial communities of the maize root compartments, the endo- and ecto-rhizospheres. An emphasis was placed on the preference of the growth of unculturable candidate divisions/phyla on plant-only-based culture media over standard culture media (nutrient agar). A total of 1,818 different operational taxonomic units (OTUs) were resolved representing 67 bacterial phyla. Plant-only-based culture media displayed particular affinity towards recovering endophytic over ectophytic rhizobacteria. This was shown by the slightly higher recovery of CFUs for endophytes on plant-only-based culture media (26%) than on standard culture media (10%) as well as the higher taxa richness and numbers of exclusive families of unculturable divisions/phyla. Out of 30 bacterial phyla (comprising >95% of the whole population), 13 were of a significantly higher incidence on plant-only-based culture media, 6 phyla of which were not-yet-cultured (Atribacteria, OP9; Dependentiae, TM6; Latescibacteria, WS3; Marinimicrobia, SAR406; Omnitrophica, OP3; BRC1). Furthermore, plant-only-based culture media significantly enriched less abundant and/or hard-to-culture bacterial phyla (Acidobacteria, Gemmatimonadetes, and Tenericutes). These results present conclusive evidence of the ability of plant-only-based culture media to bring the plant-fed in situ microbiome into the status of plant-fed in vitro cultures, and to widen the scope of cultivation of heretofore-unculturable bacterial divisions/phyla.

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Section: Discussionmentioning

confidence: 99%

G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla

et al. 2018

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“…found that bacterial diversity (H’) significantly correlated with soil moisture in the Tibetan permafrost region. In a high Arctic polar oasis, Banerjee et al 42. found soil moisture was the key edaphic factor which drove the archaeal community structure.…”

Section: Discussionmentioning

confidence: 99%

The biogeography of soil archaeal communities on the eastern Tibetan Plateau

Shi

Adams

et al. 2016

Sci Rep

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The biogeographical distribution of soil bacterial communities has been widely investigated. However, there has been little study of the biogeography of soil archaeal communities on a regional scale. Here, using high-throughput sequencing, we characterized the archaeal communities of 94 soil samples across the eastern Tibetan Plateau. Thaumarchaeota was the predominant archael phylum in all the soils, and Halobacteria was dominant only in dry soils. Archaeal community composition was significantly correlated with soil moisture content and C:N ratio, and archaeal phylotype richness was negatively correlated with soil moisture content (r = −0.47, P < 0.01). Spatial distance, a potential measure of the legacy effect of evolutionary and dispersal factors, was less important than measured environmental factors in determining the broad scale archaeal community pattern. These results indicate that soil moisture and C:N ratio are the key factors structuring soil archaeal communities on the eastern Tibetan Plateau. Our findings suggest that archaeal communities have adjusted their distributions rapidly enough to reach range equilibrium in relation to past environmental changes e.g. in water availability and soil nutrient status. This responsiveness may allow better prediction of future responses of soil archaea to environmental change in these sensitive ecosystems.

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“…Both the p12 N-and C-terminal domains are required to be in cis (5), suggesting that p12 acts as a bridge between the CA within the PIC and the host chromatin. As MLV requires cells to proceed through mitosis for integration (12) and lacks the interactions with host proteins involved in active nuclear transport of HIV (13,14), p12 is proposed to function in retaining the PIC in the nucleus postmitosis (5,8,9). Alternate chromatin tethers functionally replacing the C-terminal function did not alter the MLV integration profile, ruling out the possibility that the p12 chromatin tether is the driving determinant for integration site selection (8).…”

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confidence: 99%

Phosphorylation Requirement of Murine Leukemia Virus p12

Brzezinski

Felkner

Modi

et al. 2016

J Virol

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The p12 protein of murine leukemia virus (MLV) Gag is associated with the preintegration complex (PIC), and mutants of p12 (PM14) exhibit defects in nuclear entry/retention. Mutants of the phosphorylated serine 61 also have been reported to have defects in the early life cycle. Here we show that a phosphorylated peptide motif derived from human papillomavirus 8 (HPV-8), the E2 hinge region including residues 240 to 255, can functionally replace the main phosphorylated motif of MLV p12 and can rescue the viral titer of a strain with the lethal p12-PM14 mutation. Complementation with the HPV-8 E2 hinge motif generated multiple second-site mutations in live viral passage assays. Additional p12 phosphorylation sites were detected, including the late domain of p12 (PPPY) as well as the late domain/protease cleavage site of matrix (LYPAL), by mass spectrometry and Western blotting. Chromatin binding of p12-green fluorescent protein (GFP) fusion protein and functional complementation of p12-PM14 occurred in a manner independent of the E2 hinge region phosphorylation. Replacement of serine 61 by alanine within the minimal tethering domain ( 61 SPMASRLRGRR 71 ) maintained tethering, but in the context of the full-length p12, mutants with substitutions in S61 remained untethered and lost infectivity, indicating phosphorylation of p12 serine 61 functions to temporally regulate early and late p12 functions. IMPORTANCE The p12 protein, required for both early and late viral functions, is the predominant phosphorylated viral protein of Moloney MLV and is required for virus viability. Our studies indicate that the N terminus of p12 represses the early function of the chromatin binding domain and that deletion of the N terminus activates chromatin binding in the wild-type Moloney MLV p12 protein. Mass spectrometry and mutagenesis studies suggest that phosphorylation of both the repression domain and the chromatin binding domain acts to temporally regulate this process at the appropriate stages during infection.T he murine leukemia virus (MLV) (genus Gammaretrovirus, family Retroviridae) Gag protein p12 is a multifunctional protein required in both early and late stages of viral replication. During the late stages of viral assembly, new virions must bud off their host cells, requiring membrane scission. The MLV p12 encodes a late-assembly (L) domain ( 31 PPPY 34 ) (1, 2), reported to interact with the host vesicular trafficking machinery, specifically the E3 ubiquitin ligases in the NEDD4 family, to facilitate Gag ubiquitylation and subsequent budding (3). In addition, the 25 DLL 27 motif in p12 has been reported to recruit clathrin to budding virions, which is required for correct particle morphogenesis and infectivity (4).In infected cells, two domains required for early replication were identified by mutational analysis: within the p12 N terminus at residues 10 to 24 (mutants PM5 to PM8) and within the p12 C terminus at residues 60 to 74 (mutants PM13 to PM15) (1, 5). The N terminus of p12 interacts with capsid (CA), ...

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Cellular and viral determinants of retroviral nuclear entry

Cited by 31 publications

References 150 publications

G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla

G3 PhyloChip Analysis Confirms the Promise of Plant-Based Culture Media for Unlocking the Composition and Diversity of the Maize Root Microbiome and for Recovering Unculturable Candidate Divisions/Phyla

The biogeography of soil archaeal communities on the eastern Tibetan Plateau

Phosphorylation Requirement of Murine Leukemia Virus p12

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