Complete genome sequence of Anabaena variabilis ATCC 29413

Thiel, Teresa; Pratte, Brenda S.; Zhong, Jinshun; Goodwin, Lynne; Copeland, Alex; Lucas, Susan; Han, Cliff; Pitluck, Sam; Land, Miriam; Kyrpides, Nikos C.; Woyke, Tanja

doi:10.4056/sigs.3899418

Cited by 44 publications

(28 citation statements)

References 57 publications

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“…Incorrectly positioned species (or strains) can contribute to inaccurate ancestor assignment (e.g., genus or family) in abundance estimations. For example, a genome initially identified as Anabaena variabilis ATCC 29413 was reassigned to the genus Nostoc, not Anabaena (Thiel et al 2014). …”

Section: Discussionmentioning

confidence: 99%

Centrifuge: rapid and sensitive classification of metagenomic sequences

et al. 2016

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Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together, these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer-based indexing schemes, which require far more extensive space.

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Section: Discussionmentioning

confidence: 99%

Centrifuge: rapid and sensitive classification of metagenomic sequences

et al. 2016

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“…Cultures of vegetative filaments of Anabaena variabilis ATCC 29413 strain FD (obtained from Peter Wolk, MSU-DOE Plant Research Laboratory, East Lansing, MI, USA) (Currier & Wolk, 1979;Thiel et al, 2014) and N. punctiforme ATCC 29133 (obtained from Jack Meeks, University of California, Davis, CA, USA) were grown in Allen and Arnon liquid medium (Allen & Arnon, 1955) diluted fourfold with water (AA/4), and supplemented with 5 mM MOPS (pH 7.5), 2.5 mM NH 4 Cl, 2.5 mM NaNO 3 and 2.5 mM KNO 3 . Cultures were incubated under continuous illumination (17-22 mmol photons m 22 s 21 ) at 28 uC with shaking at 120 r.p.m.…”

Section: Methodsmentioning

confidence: 99%

“…According to the taxonomical studies by Rippka et al (1979), both species belong to subsection IV, which form unbranched filaments that are able to fix nitrogen by the formation of heterocysts. In the 16S phylogenetic tree as well as in the genome-based study, the species cluster in different groups (Shih et al, 2013;Thiel et al, 2014). Anabaena variabilis ATCC 29413 is closely related to Nostoc spp.…”

Section: Intracellular Storage Compounds Of Akinetesmentioning

confidence: 99%

“…The species are diverse with respect to the ecological niches they occupy. Anabaena variabilis ATCC 29413 is a planktonic freshwater organism isolated from the Mississippi and misinterpreted as Anabaena flos-aquae (Moore & Tischer, 1965;Thiel et al, 2014). For this lifestyle, the akinetes may require a lipid envelope layer to survive at the bottom of sediments.…”

Section: Intracellular Storage Compounds Of Akinetesmentioning

confidence: 99%

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Clear differences in metabolic and morphological adaptations of akinetes of two Nostocales living in different habitats

et al. 2016

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2 FIBA-INBIOTEC, Vieytes 3103, Mar del Plata, Buenos Aires, ArgentinaAkinetes are resting spore-like cells formed by some heterocyst-forming filamentous cyanobacteria for surviving long periods of unfavourable conditions. We studied the development of akinetes in two model strains of cyanobacterial cell differentiation, the planktonic freshwater Anabaena variabilis ATCC 29413 and the terrestrial or symbiotic Nostoc punctiforme ATCC 29133, in response to low light and phosphate starvation. The best trigger of akinete differentiation of Anabaena variabilis was low light; that of N. punctiforme was phosphate starvation. Light and electron microscopy revealed that akinetes of both species differed from vegetative cells by their larger size, different cell morphology and large number of intracellular granules. Anabaena variabilis akinetes had a multilayer envelope; those of N. punctiforme had a simpler envelope. During akinete development of Anabaena variabilis, the amount of the storage compounds cyanophycin and glycogen increased transiently, whereas in N. punctiforme, cyanophycin and lipid droplets increased transiently. Photosynthesis and respiration decreased during akinete differentiation in both species, and remained at a low level in mature akinetes. The clear differences in the metabolic and morphological adaptations of akinetes of the two species could be related to their different lifestyles. The results pave the way for genetic and functional studies of akinete differentiation in these species.

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“…Given that endosymbiotic theory suggests that the chloroplasts of plants were derived from the symbiosis of separate single bacterial cells38, we were interested in characterising the structure and function of DHDPS and DHDPR from the model cyanobacterial species, Anabaena variabilis (Av)39. Here, we present an in-depth characterisation of the structure and function of Av-DHDPS and Av-DHDPR in both solution and crystal states.…”

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confidence: 99%

Structure and Function of Cyanobacterial DHDPS and DHDPR

Christensen

Costa

Faou

et al. 2016

Sci Rep

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Lysine biosynthesis in bacteria and plants commences with a condensation reaction catalysed by dihydrodipicolinate synthase (DHDPS) followed by a reduction reaction catalysed by dihydrodipicolinate reductase (DHDPR). Interestingly, both DHDPS and DHDPR exist as different oligomeric forms in bacteria and plants. DHDPS is primarily a homotetramer in all species, but the architecture of the tetramer differs across kingdoms. DHDPR also exists as a tetramer in bacteria, but has recently been reported to be dimeric in plants. This study aimed to characterise for the first time the structure and function of DHDPS and DHDPR from cyanobacteria, which is an evolutionary important phylum that evolved at the divergence point between bacteria and plants. We cloned, expressed and purified DHDPS and DHDPR from the cyanobacterium Anabaena variabilis. The recombinant enzymes were shown to be folded by circular dichroism spectroscopy, enzymatically active employing the quantitative DHDPS-DHDPR coupled assay, and form tetramers in solution using analytical ultracentrifugation. Crystal structures of DHDPS and DHDPR from A. variabilis were determined at 1.92 Å and 2.83 Å, respectively, and show that both enzymes adopt the canonical bacterial tetrameric architecture. These studies indicate that the quaternary structure of bacterial and plant DHDPS and DHDPR diverged after cyanobacteria evolved.

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Complete genome sequence of Anabaena variabilis ATCC 29413

Cited by 44 publications

References 57 publications

Centrifuge: rapid and sensitive classification of metagenomic sequences

Centrifuge: rapid and sensitive classification of metagenomic sequences

Clear differences in metabolic and morphological adaptations of akinetes of two Nostocales living in different habitats

Structure and Function of Cyanobacterial DHDPS and DHDPR

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