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Study

Study Name: Marine cyanobacterial communities from the University of California, Santa Cruz, USA, analyzing cyanobacterial DNA methylation

Projects

Biosamples

Organisms

Biosamples: 3 Seq. Projects: 7
STUDY INFORMATION
GOLD Study ID Gs0111415
Study Name Marine cyanobacterial communities from the University of California, Santa Cruz, USA, analyzing cyanobacterial DNA methylation
Other Names DNA Methylation in Marine Cyanobacteria
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject Accession
SRA Studies
SRA Study Id SRP112340  (Link to NCBI )
Study Title Synechococcus sp. OG1 Genome sequencing
Study Abstract
  
SRA Study Id SRP103261  (Link to NCBI )
Study Title Marine cyanobacteria communities from the University of California, Santa Cruz, USA, analyzing cyanobacterial DNA methylation - Crocosphaera watsoni WH8501 Co-Culture metagenome
Study Abstract
  
SRA Study Id SRP103262  (Link to NCBI )
Study Title Marine cyanobacteria communities from the University of California, Santa Cruz, USA, analyzing cyanobacterial DNA methylation - Crocosphaera watsoni WH8502 Co-Culture metagenome
Study Abstract
  
SRA Study Id SRP112337  (Link to NCBI )
Study Title Synechococcus sp. 7002 Genome sequencing
Study Abstract
  
SRA Study Id SRP103257  (Link to NCBI )
Study Title Marine cyanobacteria communities from the University of California, Santa Cruz, USA, analyzing cyanobacterial DNA methylation - Trichodesmium erythraeum IMS101 Co-Culture metagenome
Study Abstract
  
Legacy ER Study ID 77996
Legacy GOLD ID Gm0077996
Added By Michelle Isbandi on 2014-09-15
Last Modified By JGI automated process on 2019-09-06
PI Jonathan Zehr
Description Cyanobacteria are important microorganisms from multidisciplinary perspectives: ecology (carbon and nitrogen fixation), basic biology (circadian rhythms and photosynthesis), and biotechnological applications (production of hydrogen, hydrocarbons and other compounds). Marine nitrogen-fixing cyanobacteria are a particularly important group, since they are key to the nitrogen balance of the oceans, but also are metabolically diverse and can be used for production of compounds without the need for fixed inorganic nitrogen. Filamentous non-heterocystous Trichodesmium and unicellular Crocosphaera inhabit tropical and subtropical open ocean waters (Zehr, 2011). Cyanothece or Cyanothece-like strains inhabit niches that range from coastal seawaters to tropical rice fields (Rippka, 1988). Crocosphaera and Cyanothece fix nitrogen during the night (Colon-Lopez et al 1997; Shi et al., 2010), whereas Trichodesmium fixes N2 during the day (Chen et al., 1996). A small unicellular Synechococcus PCC7002 has been intensely used as a model cyanobacterium (e.g. Zhang and Bryant, 2011) because it can be genetically transformed (Stevens and Porter, 1980). Little is known about DNA methylation in cyanobacteria (Lambert and Carr, 1984; Jager and Pott, 1988; Padhy et al., 1988) and almost nothing about methylation in marine cyanobacteria. Some years ago, a novel nucleotide modification (Zehr et al., 1991) was identified in a Trichodesmium NIBB 1067 by one of us (Figure 1). This suggested that methylation may be important in marine cyanobacteria, and more recently, genome analysis by our group showed that the genomes from our research organisms contain a number of genes encoding DNA methyltransferases. Genome restriction analysis showed that the genome of Crocosphaera WH8501 is fully methylated at GATC site (dA methylation by Dam), while genome of Trichodesmium IMS101 was semi-methylated (Figure 2). Together with earlier studies in other cyanobacteria (Lambert and Carr, 1984), these evidences suggest that DNA methylation is widespread among cyanobacteria, and the extent of DNA methylation is different among different species. DNA methylation could play several roles in growth and activity of these cyanobacteria besides post-replication DNA repair. DNA methylation in prokaryotes, in general, plays a critical role in protection against viral invasions (Bertani and Weigle, 1953), thus characterizing DNA methylation may help to explain the resistance of marine microorganisms to viral lysis (Waterbury and Valois, 1993; Wilson et al., 1993). Furthermore, methylation is likely to be responsible for differences in the physiology and ecology among closely related strains. For example, comparison of genome sequences did not reveal any substantial differences between the wild type of Synechococcus PCC7002 and a variant that grew 25% faster. The high rates of transposition displayed by Crocosphaera watsonii strain WH8501 (20% of genes are transposases), but not WH8502 strain and four other closely related Crocosphaera strains (less than 5% of genes are transposases, Bench et al., 2013) may be due to differences in DNA methylation (Casadeus and Low, 2006; Dowen et al., 2012). Demethylation and increased transcription of corresponding genes in response to nitrogen-limiting condition has been observed recently in a diatom (Veluchamy et al., 2013). Whether and how DNA methylation is involved in regulation of DNA expression in cyanobacteria leading to a different metabolic state remains to be determined.
Relevance
Study Information Visibility Public
Metagenomic Study Yes
Publication
Is GEBA No
Is HMP No
ECOSYSTEM CLASSIFICATION
Ecosystem Host-associated
Ecosystem Category Microbial
Ecosystem Type Bacteria
Ecosystem Subtype Unclassified
Specific Ecosystem Unclassified
STUDY COMPOSITION
Number of Biosamples 3
Number of Organisms 4
Number of Seq Projects 7
Number of Analysis Projects 8
Number of Related Studies 0

 

 

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