LMSD: LIPID MAPS structure database

Sud, Manish; Fahy, Eoin; Cotter, Dawn; Brown, Alex; Dennis, Edward A.; Glass, Christopher K.; Merrill, Alfred H.; Murphy, Robert C.; Raetz, Christian R. H.; Russell, David W.; Subramaniam, Shankar

doi:10.1093/nar/gkl838

Cited by 1,065 publications

(940 citation statements)

References 8 publications

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“…Accurate mass measurements for individual saponins and identified compounds were run using continuous accumulation of selected ions (CASI) using mass windows of 50-100 m/z and a transient of 4 megaword generating a transient of 2.93 s providing a mass resolving power of approximately 390,000 at 400 m/z. Lipids were putatively assigned by searching the LipidMaps database 74 (http://www.lipidmaps.org) and lipid class confirmed by collision-induced dissociation using a 10 m/z window centred around the monoisotopic peak with collision energy of between 15-20 V.…”

Section: Article Researchmentioning

confidence: 99%

The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

589

706

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Quinoa (Chenopodium quinoa Willd., 2n = 4x = 36) is a highly nutritious crop that is adapted to thrive in a wide range of agroecosystems. It was presumably first domesticated more than 7,000 years ago by pre-Columbian cultures and was known as the 'mother grain' of the Incan Empire 1 . Quinoa has adapted to the high plains of the Andean Altiplano (> 3,500 m above sea level), where it has developed tolerance to several abiotic stresses [2][3][4] . Quinoa has gained international attention because of the nutritional value of its seeds, which are gluten-free, have a low glycaemic index 5 , and contain an excellent balance of essential amino acids, fibre, lipids, carbohydrates, vitamins, and minerals 6 . Quinoa has the potential to provide a highly nutritious food source that can be grown on marginal lands not currently suitable for other major crops. This potential was recognized when the United Nations declared 2013 as the International Year of Quinoa, this being one of only three times a plant has received such a designation.Despite its agronomic potential, quinoa is still an underutilized crop 7 , with relatively few active breeding programs 8 . Breeding efforts to improve the crop for important agronomic traits are needed to expand quinoa production worldwide. To accelerate the improvement of quinoa, we present here the allotetraploid quinoa genome. We demonstrate the utility of the genome sequence by identifying a gene that probably regulates the presence of seed triterpenoid saponin content. Moreover, we sequenced the genomes of additional diploid and tetraploid Chenopodium species to characterize genetic diversity within the primary germplasm pool for quinoa and to understand sub-genome evolution in quinoa. Together, these resources provide the foundation for accelerating the genetic improvement of the crop, with the objective of enhancing global food security for a growing world population. Sequencing, assembly and annotationWe sequenced and assembled the genome of the coastal Chilean quinoa accession PI 614886 (BioSample accession code SAMN04338310) using single-molecule real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) and optical and chromosome-contact maps from BioNano Genomics 9 and Dovetail Genomics 10 . The assembly contains 3,486 scaffolds, with a scaffold N50 of 3.84 Mb and 90% of the assembled genome contained in 439 scaffolds (Table 1). The total assembly size of 1.39 gigabases (Gb) is similar to the reported size estimates of the quinoa genome (1.45-1.50 Gb (refs 11,12)). To combine scaffolds into pseudomolecules, an existing linkage map from quinoa 13 was integrated with two new linkage maps. The resulting map (Extended Data Fig. 1) of 6,403 unique markers spans a total length of 2,034 centimorgans (cM) and consists of 18 linkage groups (Supplementary Table 7), corresponding to the haploid chromosome number of quinoa. Pseudomolecules (hereafter referred to as chromosomes, which are numbered according to a previously published single-nucleotide polymorphism (SNP) linkage ...

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Section: Article Researchmentioning

confidence: 99%

The genome of Chenopodium quinoa

Jarvis

Lightfoot

et al. 2017

Nature

589

706

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“…Cyclic fatty acids accumulate in root tissues of cotton seedlings during the early growth stages and include malvalic acid (8,9-methylene-8Z-heptadecenoic acid, 32.6% of total fatty acid), sterculic acid (9,10-methylene-9-octadecenoic acid, 11.0%), and dihydrosterculic acid (9S,10R-methyleneoctadecanoic acid, 0.6%) (22,35). These cyclic fatty acids are enriched in the TAG fractions and presumed to be packaged into LDs in root cells.…”

Section: Resultsmentioning

confidence: 99%

“…Many studies have now detailed the complex fragmentation patterns for the complete structural elucidation and quantification of TAGs (19 -21). Supported by advances in bioinformatics (LIPID MAPS) (22), improvements in mass spectrometry, and availability of unique purified standards, it is now feasible to achieve comprehensive lipid identification and quantification directly from complex mixtures. For lipidomics applications, lipids most often are extracted from tissues or cell lines in organic solvents, losing the spatial information of lipid organization within the original sample.…”

mentioning

confidence: 99%

Visualization of Lipid Droplet Composition by Direct Organelle Mass Spectrometry

Horn

Ledbetter

James

et al. 2011

Journal of Biological Chemistry

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An expanding appreciation for the varied functions of neutral lipids in cellular organisms relies on a more detailed understanding of the mechanisms of lipid production and packaging into cytosolic lipid droplets (LDs). Conventional lipid profiling procedures involve the analysis of tissue extracts and consequently lack cellular or subcellular resolution. Here, we report an approach that combines the visualization of individual LDs, microphase extraction of lipid components from droplets, and the direct identification of lipid composition by nanospray mass spectrometry, even to the level of a single LD. The triacylglycerol (TAG) composition of LDs from several plant sources (mature cotton (Gossypium hirsutum) embryos, roots of cotton seedlings, and Arabidopsis thaliana seeds and leaves) were examined by direct organelle mass spectrometry and revealed the heterogeneity of LDs derived from different plant tissue sources. The analysis of individual LDs makes possible organellar resolution of molecular compositions and will facilitate new studies of LD biogenesis and functions, especially in combination with analysis of morphological and metabolic mutants. Furthermore, direct organelle mass spectrometry could be applied to the molecular analysis of other subcellular compartments and macromolecules. LDs4 are organelles that are specialized for the storage of neutral lipids and as such provide energy-rich reserves in all cellular organisms (1). Understanding LD ontogeny is of major importance to human physiology; on the one hand, seed oils, packaged in LDs, make up a growing proportion of daily caloric intake in most diets around the world, and on the other hand, the regulation of lipid storage and mobilization underlies significant human health issues: obesity, diabetes and cardiovascular disease.Although storage is considered the principal role of neutral lipids, LDs in nonfat storing tissues recently have become more appreciated for their dynamic nature and functional roles independent of storage. These roles include acyl reserves for phospholipid recycling (2), lipid signaling (3), membrane trafficking (2, 4), inflammation and cancer (5), and hostpathogen interactions (6, 7). These various functions attributed to LDs vary with cell type and likely are manifested by differences in droplet composition. The basic structural model of LDs in plant seeds provides a thermodynamically stable organization that is thought to be conserved throughout eukaryotes, although the nature of the lipids and proteins associated with droplets varies with cell/tissue type. The structure describes a neutral lipid core (triacylglycerols in plant seeds and/or steryl esters in other organisms or cell types) surrounded by a phospholipid monolayer with specific proteins associated with the LD surface (8). Although the endoplasmic reticulum is considered by most to be the major cellular location for LD biogenesis, droplets associate frequently with other subcellular compartments, presumably to carry out unique functions (9).The recent emphasis...

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“…Phosphotidylcholines also have readily identifiable mass-to-charge ratios, most of which are even numbered. The structures of several phosphotidylcholines were determined by using MS/MS to obtain fragmentation profiles and comparing the results to an online database (43). Typical fragmentation patterns of phosphotidylcholines were obtained by consulting the scientific literature (44).…”

Section: Methodsmentioning

confidence: 99%

Structure of faustovirus, a large dsDNA virus

Klose

Reteno

Benamar

et al. 2016

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

117

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International audienceMany viruses protect their genome with a combination of a protein shell with or without a membrane layer. Here we describe the structure of faustovirus, the first DNA virus (to our knowledge) that has been found to use two protein shells to encapsidate and protect its genome. The crystal structure of the major capsid protein, in combination with cryo-electron microscopy structures of two different maturation stages of the virus, shows that the outer virus shell is composed of a double jelly-roll protein that can be found in many double-stranded DNA viruses. The structure of the repeating hexameric unit of the inner shell is different from all other known capsid proteins. In addition to the unique architecture, the region of the genome that encodes the major capsid protein stretches over 17,000 bp and contains a large number of introns and exons. This complexity might help the virus to rapidly adapt to new environments or hosts

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LMSD: LIPID MAPS structure database

Cited by 1,065 publications

References 8 publications

The genome of Chenopodium quinoa

The genome of Chenopodium quinoa

Visualization of Lipid Droplet Composition by Direct Organelle Mass Spectrometry

Structure of faustovirus, a large dsDNA virus

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