Characterization of two circular plasmids from the marine diatomCylindrotheca fusiformis: plasmids hybridize to chloroplast and nuclear DNA

Jacobs, Jerry D.; Ludwig, J R; Hildebrand, Mark; Kukel, A.; Feng, Tao; Ord, Robin W.; Volcani, Benjamin E.

doi:10.1007/bf00587592

Cited by 27 publications

(32 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…S9). We also tested whether regions of plasmids previously isolated from the diatom Cylindrotheca fusiformis (45,46) could support episomes in P. tricornutum. Two plasmids, pCF1 and pCF2, containing low-GC, 560-bp regions (28.9% and 28.4% GC, respectively) were constructed (see SI Appendix, Materials and Methods), and each yielded 7-12-fold more P. tricornutum ex-conjugant colonies than the pPtPBR2 negative control (SI Appendix, Fig.…”

Section: Identification Of Diatom Centromeres Using Chip-sequencing Andmentioning

confidence: 99%

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

Diner

Noddings

Lian

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Centromeres are essential for cell division and growth in all eukaryotes, and knowledge of their sequence and structure guides the development of artificial chromosomes for functional cellular biology studies. Centromeric proteins are conserved among eukaryotes; however, centromeric DNA sequences are highly variable. We combined forward and reverse genetic approaches with chromatin immunoprecipitation to identify centromeres of the model diatom Phaeodactylum tricornutum. We observed 25 unique centromere sequences typically occurring once per chromosome, a finding that helps to resolve nuclear genome organization and indicates monocentric regional centromeres. Diatom centromere sequences contain low-GC content regions but lack repeats or other conserved sequence features. Native and foreign sequences with similar GC content to P. tricornutum centromeres can maintain episomes and recruit the diatom centromeric histone protein CENH3, suggesting nonnative sequences can also function as diatom centromeres. Thus, simple sequence requirements may enable DNA from foreign sources to persist in the nucleus as extrachromosomal episomes, revealing a potential mechanism for organellar and foreign DNA acquisition.diatom | Phaeodactylum tricornutum | episome | centromere | CENH3

show abstract

Section: Identification Of Diatom Centromeres Using Chip-sequencing Andmentioning

confidence: 99%

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

Diner

Noddings

Lian

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

show abstract

“…Two plasmids, pCfl and pCf2, from the marine diatom Cylindrotheca fusiformis have been characterized in detail. These are small circular DNA molecules, 4.27 kb for pCfl and 4.08 kb for pCf2 [22]. They co-band with chloroplast and mitochondrial DNA in CsC1-Hoechst 33258 gradients [22].…”

Section: Introductionmentioning

confidence: 99%

“…These are small circular DNA molecules, 4.27 kb for pCfl and 4.08 kb for pCf2 [22]. They co-band with chloroplast and mitochondrial DNA in CsC1-Hoechst 33258 gradients [22]. We have cloned them, and shown by hybridization analyses that the plasmids share regions of similarity, but not identity [22].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Nucleotide sequence of diatom plasmids: identification of open reading frames with similarity to site-specific recombinases

Hildebrand

Hasegawa

et al. 1992

Plant Mol Biol

Self Cite

View full text Add to dashboard Cite

We have determined the nucleotide sequence of two small circular DNA plasmids, pCf1 and pCf2 [22], from the marine diatom Cylindrotheca fusiformis. pCf1 is 4273 bp, and pCf2 is 4079 bp in size. In each plasmid, all of the major open reading frames (ORFs) are encoded on the same DNA strand. Two ORFs are similar, comparing the two plasmids. ORF218 (pCf1) and ORF217 (pCf2) share 80% amino acid identity and ORF482 (pCf1) and ORF484 (pCf2) share 54% amino acid identity. ORF218/217 shows significant similarity (28-31% amino acid identity) to the Tn3 class of resolvases. Resolvases are most commonly found in bacterial transposons. However, two other features found in the Tn3 class of transposon are missing in the plasmids; an ORF encoding a transposase and terminal inverted repeat sequences. This, and data mapping the portions of the plasmids that hybridize to genomic chloroplast DNA, suggest that the plasmids do not contain active transposons. By analogy with the R46 plasmid from Enterobacter [5, 6], another potential role for the resolvases encoded by pCf1 and pCf2 is the conversion of multimeric forms of the plasmid to monomers. The similarity of ORF218/217 to resolvases documents the first identification of a potential coding function in an algal plasmid.

show abstract

“…Culturing temperature was 20 "C and illumination was DNA and RNA isolation from diatom cells. Genomic DNA was extracted from 1 g wet cells by the SDSIproteinase K method according to Jacobs et al (1992). The DNA-containing extract was purified by CsCl density gradient centrifugation at 20°C, 100000 g for 20 h. The DNA fraction was repeatedly extracted with n-butanol and dialyzed for 18 h against 2 1 10 mM Tris/HCI pH 8.0, 1 mM EDTA.…”

mentioning

confidence: 99%

Frustulins: Domain Conservation in a Protein Family Associated with Diatom Cell Walls

Kröger

Bergsdorf

Sumper

1996

European Journal of Biochemistry

137

117

View full text Add to dashboard Cite

The outstanding feature of a diatom is the species-specific design and ornamentation of the silicabased cell wall, termed frustulum. A new frustulum is shaped in a specialized organelle (silica deposition vesicle) and secreted. Proteins in the lumen of this organelle may control the biomineralization process and are likely to remain associated with the mature cell wall. Therefore a study of the structures of proteins associated with the diatom cell wall was initiated. The complete primary structures of three cell wall proteins (denoted as frustulins) have been determined. In addition, partial amino acid sequences from two more cell wall components were obtained. From these data, a highly conserved domain has been identified as a common building block of diatom cell wall proteins that is repeated several time; per polypeptide chain together with polyproline/hydroxyproline or polyglycine spacers. All frustulins characterized so far, are synthesized as preproteins with a novel type of N-terminal presequence.Keywords: diatom ; cell wall; hydroxyproline-rich glycoprotein ; presequence; Cylindrotheca fusiformis.The cell wall of diatoms is composed of amorphous, hydrated silica and organic components (Volcani, 1981). The species-specific design and ornamentation of the cell wall's silica skeleton is the most fascinating aspect of diatom biology and the basis for diatom systematics. It was estimated that there are more than 10 000 recent diatom species each displaying a different cell wall structure (Pickett-Heaps et al., 1990). The diatom cell wall (also termed frustulum or frustle) consists of two parts, the epitheca and the hypotheca. Each theca is composed of a valve and several silica strips (girdle bands). It is the girdle band region in which epitheca and hypotheca overlap (see Fig. 1).New valves are produced after cell division and cytokinesis of the mother protoplast. The resulting daughter protoplasts are trapped within the mother cell wall. Each daughter protoplast produces a new valve in a specialized intracellular organelle, the silica deposition vesicle (Volcani, 1981). In this organelle the polymerization of silicate takes place. The vesicle develops closely beneath the plasma membrane and extends during the process of silica deposition. Finally, it spans the whole area beneath the plasma membrane, containing a new valve. The latter is exocytosed and the daughter cells separate, each possessing a maternal epitheca and a newly formed hypotheca. It is suggested that cytoskeleton and cytoplasmic organells take part in shaping the silica deposition vesicle and thus are determinants of cell wall morphology . In addition it is assumed that an organic matrix within the vesicle may exert influence on the fine patterning of the cell wall (Pickett-Heaps et al., 1990). This is an attractive hypothesis, since certain organic macromolecules are known to function as templates and regulators for inorganic crystal growth in vitro (Weiner and Addadi, 1991).The species-specific structure of a diatom cell wall demands genet...

show abstract

Characterization of two circular plasmids from the marine diatomCylindrotheca fusiformis: plasmids hybridize to chloroplast and nuclear DNA

Cited by 27 publications

References 39 publications

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

Diatom centromeres suggest a mechanism for nuclear DNA acquisition

Nucleotide sequence of diatom plasmids: identification of open reading frames with similarity to site-specific recombinases

Frustulins: Domain Conservation in a Protein Family Associated with Diatom Cell Walls

Contact Info

Product

Resources

About