Computational prediction of Pho regulons in cyanobacteria

Su, Zhengchang; Olman, Victor; Xu, Ying

doi:10.1186/1471-2164-8-156

Cited by 82 publications

(122 citation statements)

References 29 publications

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“…Furthermore, the CYA_1475 and CYA_2058 transcripts also increased in abundance in cells grown in medium containing Pi and either EtPhn or AePhn, indicating that transcription from the putative Phnase genes is controlled by the presence of the substrate, and is not strongly impacted by the Pi concentration of the medium. Consistent with this result, none of the putative Phnases has a predicted upstream consensus Pho box sequence that has recently been characterized for many cyanobacteria including Syn OS-B 0 and Syn OS-A (Su et al, 2007). None of the Syn OS-B 0 transcripts encoding putative Phnases showed a marked increase in cells grown in medium devoid of P or supplemented with MePhn, EtPhn or AePhn as sole sources of P (Figure 4).…”

Section: Putative Phnasessupporting

confidence: 71%

Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats

et al. 2010

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Synechococcus sp. represents an ecologically diverse group of cyanobacteria found in numerous environments, including hot-spring microbial mats, where they are spatially distributed along thermal, light and oxygen gradients. These thermophiles engage in photosynthesis and aerobic respiration during the day, but switch to fermentative metabolism and nitrogen fixation at night. The genome of Synechococcus OS-B 0 , isolated from Octopus Spring (Yellowstone National Park) contains a phn gene cluster encoding a phosphonate (Phn) transporter and a C-P lyase. A closely related isolate, Synechococcus OS-A, lacks this cluster, but contains genes encoding putative phosphonatases (Phnases) that appear to be active only in the presence of the Phn substrate. Both isolates grow well on several different Phns as a sole phosphorus (P) source. Interestingly, Synechococcus OS-B 0 can use the organic carbon backbones of Phns for heterotrophic growth in the dark, whereas in the light this strain releases organic carbon from Phn as ethane or methane (depending on the specific Phn available); Synechococcus OS-A has neither of these capabilities. These differences in metabolic strategies for assimilating the P and C of Phn by two closely related Synechococcus spp. are suggestive of niche-specific constraints in the evolution of nutrient assimilation pathways and syntrophic relationships among the microbial populations of the hotspring mats. Thus, it is critical to evaluate levels of various P sources, including Phn, in thermally active habitats and the potential importance of these compounds in the biogeochemical cycling of P and C (some Phn compounds also contain N) in diverse terrestrial environments.

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Section: Putative Phnasessupporting

confidence: 71%

Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats

et al. 2010

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“…PhoB can regulate non-phosphate-related genes in bacteria, such as virulence genes in Vibrio cholerae (Pratt et al, 2010), antibiotic-regulating genes in Streptomyces (Santos-Beneit et al, 2011) and acid-stress genes in Escherichia coli (Suziedeliene et al, 1999). Although there is no direct evidence that PhoBR regulates other genes in cyanophage hosts, some predicted that pho boxes in marine Synechococcus (Su et al, 2007) are upstream of hli genes. There is no such evidence for Prochlorococcus thus far.…”

Section: Pho Box Motifs In Cultured Cyanomyovirus Genomesmentioning

confidence: 99%

“…To improve on analyses in our previous work -while recognizing that computational predictions ultimately require experimental confirmation-we used a position weight matrix based on predicted Prochlorococcus and Synechococcus pho box motifs (Su et al, 2007), tailoring our search to capture host-like pho boxes.…”

Section: Pho Box Motifs In Cultured Cyanomyovirus Genomesmentioning

confidence: 99%

“…Here, we used 129 pho box motifs computationally predicted upstream of genes in four Prochlorococcus and two marine Synechococcus genomes (Su et al, 2007) to generate a position weight matrix of the pho box motif with the Bio.Motif module from the Biopython software package (Cock et al, 2009). The position weight matrix was used to search upstream intergenic regions in the cyanomyovirus genomes for putative binding sites for the response regulator phoB.…”

Section: Identification Of Pho Box Motifs In Cultured Cyanomyovirus Gmentioning

confidence: 99%

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Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent

et al. 2013

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Viruses that infect marine cyanobacteria-cyanophages-often carry genes with orthologs in their cyanobacterial hosts, and the frequency of these genes can vary with habitat. To explore habitatinfluenced genomic diversity more deeply, we used the genomes of 28 cultured cyanomyoviruses as references to identify phage genes in three ocean habitats. Only about 6-11% of genes were consistently observed in the wild, revealing high gene-content variability in these populations. Numerous shared phage/host genes differed in relative frequency between environments, including genes related to phosphorous acquisition, photorespiration, photosynthesis and the pentose phosphate pathway, possibly reflecting environmental selection for these genes in cyanomyovirus genomes. The strongest emergent signal was related to phosphorous availability; a higher fraction of genomes from relatively low-phosphorus environments-the Sargasso and Mediterranean Sea-contained host-like phosphorus assimilation genes compared with those from the N. Pacific Gyre. These genes are known to be upregulated when the host is phosphorous starved, a response mediated by pho box motifs in phage genomes that bind a host regulatory protein. Eleven cyanomyoviruses have predicted pho boxes upstream of the phosphate-acquisition genes pstS and phoA; eight of these have a conserved cyanophage-specific gene (PhCOG173) between the pho box and pstS. PhCOG173 is also found upstream of other shared phage/host genes, suggesting a unique regulatory role. Pho boxes are found upstream of high light-inducible (hli) genes in cyanomyoviruses, suggesting that this motif may have a broader role than regulating phosphorous-stress responses in infected hosts or that these hlis are involved in the phosphorous-stress response.

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“…Finally, since four PhoP homologues are involved in the Pho regulon of M. xanthus, we attempted to find Pho boxes (PhoP binding sites), as defined by similarity to the consensus Pho box sequences of E. coli, B. subtilis, and cyanobacteria (11,12,21), in Pho gene promoter regions. No sequences that significantly resembled known Pho boxes could be identified in these regions.…”

Section: Discussionmentioning

confidence: 99%

Phosphate Acquisition Components of the Myxococcus xanthus Pho Regulon Are Regulated by both Phosphate Availability and Development

et al. 2008

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In many organisms, phosphatase expression and phosphate (P) uptake are coordinately regulated by the Pho regulon. In Myxococcus xanthus P limitation initiates multicellular development, a process associated with changes in phosphatase expression. We sought here to characterize the link between P acquisition and development in this bacterium, an organism capable of preying upon other microorganisms as a sole nutrient source. M. xanthus seems to possess no significant internal P stores, as reducing the P concentration to less than 10 M retarded growth within one doubling time. Pyrophosphate, polyphosphate, and glyceraldehyde-3-phosphate could support growth as sole P sources, although many other P-containing biomolecules could not (including nucleic acids and phospholipids). Several Pho regulon promoters were found to be highly active during vegetative growth, and P limitation specifically induced pstSCAB, AcPA1, and pho3 promoter activity and repressed pit expression. Enhanced pstSCAB and pho3 promoter activities in a phoP4 mutant (in the presence of high and low concentrations of P) suggested that PhoP4 acts as a repressor of these genes. However, in a phoP4 background, the activities of pstSCAB remained P regulated, suggesting that there is additional regulation by a P-sensitive factor. Initiation of multicellular development caused immediate downregulation of Pho regulon genes and caused pstSCAB and pho3 promoter activities to become P insensitive. Hence, P acquisition components of the M. xanthus Pho regulon are regulated by both P availability and development, with developmental down-regulation overriding up-regulation by P limitation. These observations suggest that when development is initiated, subsequent changes in P availability become irrelevant to the population, which presumably has sufficient intrinsic P to ensure completion of the developmental program.

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Computational prediction of Pho regulons in cyanobacteria

Cited by 82 publications

References 29 publications

Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats

Alternative pathways for phosphonate metabolism in thermophilic cyanobacteria from microbial mats

Genetic diversity in cultured and wild marine cyanomyoviruses reveals phosphorus stress as a strong selective agent

Phosphate Acquisition Components of the Myxococcus xanthus Pho Regulon Are Regulated by both Phosphate Availability and Development

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