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Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.

Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, Krastins B, Chase M, Sarracino D, Osburne MS, Henn MR, Chisholm SW - Environ. Microbiol. (2010)

Bottom Line: Patterns among non-core genes that may drive niche diversification revealed that phosphorus-related gene content reflects source waters rather than host strain used for isolation, and that carbon metabolism genes appear associated with putative mobile elements.However, no clear diagnostic genes emerged to distinguish these phage groups, suggesting blurred boundaries possibly due to cross-infection.Finally, genome-wide comparisons of both diverse and closely related, co-isolated genomes provide a locus-to-locus variability metric that will prove valuable for interpreting metagenomic data sets.

View Article: PubMed Central - PubMed

Affiliation: Massachusetts Institute of Technology, Cambridge, MA, USA. mbsulli@email.arizona.edu

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Proposed role of 2-oxoglutarate (2OG) during cyanophage infection.A. In uninfected cyanobacteria, nitrogen limitation causes 2OG to accumulate, leading to 2OG-dependent binding of NtcA to promoters of nitrogen-stress genes, resulting in their expression.B. Phage infection draws down cellular nitrogen causing N-stress and likely leading to 2OG accumulation. Several cyanophage-encoded enzymes (in bold) suggest that increased 2OG may facilitate phage infection. First, a putative phytanoyl-CoA dioxygenase may convert 2OG to succinate, a major electron donor to respiratory electron transport in cyanobacteria (Cooley and Vermaas, 2001) thus potentially generating energy for the infection process. Second, 2OG-dependent dioxygenase [2OG-Fe(II)] superfamily proteins may function in cyanophage DNA repair (Weigele et al., 2007). Third, cyanophage genomes have multiple NtcA promoters driving genes encoding diverse functions – possibly exploiting the host NtcA-driven N-stress response system.
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fig06: Proposed role of 2-oxoglutarate (2OG) during cyanophage infection.A. In uninfected cyanobacteria, nitrogen limitation causes 2OG to accumulate, leading to 2OG-dependent binding of NtcA to promoters of nitrogen-stress genes, resulting in their expression.B. Phage infection draws down cellular nitrogen causing N-stress and likely leading to 2OG accumulation. Several cyanophage-encoded enzymes (in bold) suggest that increased 2OG may facilitate phage infection. First, a putative phytanoyl-CoA dioxygenase may convert 2OG to succinate, a major electron donor to respiratory electron transport in cyanobacteria (Cooley and Vermaas, 2001) thus potentially generating energy for the infection process. Second, 2OG-dependent dioxygenase [2OG-Fe(II)] superfamily proteins may function in cyanophage DNA repair (Weigele et al., 2007). Third, cyanophage genomes have multiple NtcA promoters driving genes encoding diverse functions – possibly exploiting the host NtcA-driven N-stress response system.

Mentions: Three features of the cyanophage genomes suggest that they modulate 2OG levels to stimulate NtcA activity as needed to promote phage gene expression (Fig. 6). First, all 16 genomes contain numerous NtcA binding sites (1–16 per genome; average = 8.9), which apparently promote a diversity of both T4 phage and cyanophage functions (Fig. 1). Second, 14 of the 16 genomes contain numerous 2OG-FeII oxygenase superfamily proteins (Table 3). Third, all 16 cyanophages contain at least one and often numerous hypothetical proteins with possible phytanoyl-CoA-dioxygenase domains, (Table S4), which may act on 2OG, in this case as oxidoreductases.


Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from diverse hosts and environments.

Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, Krastins B, Chase M, Sarracino D, Osburne MS, Henn MR, Chisholm SW - Environ. Microbiol. (2010)

Proposed role of 2-oxoglutarate (2OG) during cyanophage infection.A. In uninfected cyanobacteria, nitrogen limitation causes 2OG to accumulate, leading to 2OG-dependent binding of NtcA to promoters of nitrogen-stress genes, resulting in their expression.B. Phage infection draws down cellular nitrogen causing N-stress and likely leading to 2OG accumulation. Several cyanophage-encoded enzymes (in bold) suggest that increased 2OG may facilitate phage infection. First, a putative phytanoyl-CoA dioxygenase may convert 2OG to succinate, a major electron donor to respiratory electron transport in cyanobacteria (Cooley and Vermaas, 2001) thus potentially generating energy for the infection process. Second, 2OG-dependent dioxygenase [2OG-Fe(II)] superfamily proteins may function in cyanophage DNA repair (Weigele et al., 2007). Third, cyanophage genomes have multiple NtcA promoters driving genes encoding diverse functions – possibly exploiting the host NtcA-driven N-stress response system.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3037559&req=5

fig06: Proposed role of 2-oxoglutarate (2OG) during cyanophage infection.A. In uninfected cyanobacteria, nitrogen limitation causes 2OG to accumulate, leading to 2OG-dependent binding of NtcA to promoters of nitrogen-stress genes, resulting in their expression.B. Phage infection draws down cellular nitrogen causing N-stress and likely leading to 2OG accumulation. Several cyanophage-encoded enzymes (in bold) suggest that increased 2OG may facilitate phage infection. First, a putative phytanoyl-CoA dioxygenase may convert 2OG to succinate, a major electron donor to respiratory electron transport in cyanobacteria (Cooley and Vermaas, 2001) thus potentially generating energy for the infection process. Second, 2OG-dependent dioxygenase [2OG-Fe(II)] superfamily proteins may function in cyanophage DNA repair (Weigele et al., 2007). Third, cyanophage genomes have multiple NtcA promoters driving genes encoding diverse functions – possibly exploiting the host NtcA-driven N-stress response system.
Mentions: Three features of the cyanophage genomes suggest that they modulate 2OG levels to stimulate NtcA activity as needed to promote phage gene expression (Fig. 6). First, all 16 genomes contain numerous NtcA binding sites (1–16 per genome; average = 8.9), which apparently promote a diversity of both T4 phage and cyanophage functions (Fig. 1). Second, 14 of the 16 genomes contain numerous 2OG-FeII oxygenase superfamily proteins (Table 3). Third, all 16 cyanophages contain at least one and often numerous hypothetical proteins with possible phytanoyl-CoA-dioxygenase domains, (Table S4), which may act on 2OG, in this case as oxidoreductases.

Bottom Line: Patterns among non-core genes that may drive niche diversification revealed that phosphorus-related gene content reflects source waters rather than host strain used for isolation, and that carbon metabolism genes appear associated with putative mobile elements.However, no clear diagnostic genes emerged to distinguish these phage groups, suggesting blurred boundaries possibly due to cross-infection.Finally, genome-wide comparisons of both diverse and closely related, co-isolated genomes provide a locus-to-locus variability metric that will prove valuable for interpreting metagenomic data sets.

View Article: PubMed Central - PubMed

Affiliation: Massachusetts Institute of Technology, Cambridge, MA, USA. mbsulli@email.arizona.edu

Show MeSH
Related in: MedlinePlus