UniProt: the Universal Protein knowledgebase

Apweiler, Rolf; Bairoch, Amos Marc; Wu, Cathy; Barker, Winona C.; Boeckmann, Brigitte; Ferro, Serenella; Gasteiger, Elisabeth; Huang, Hongzhan; López, Rodrigo; Magrane, Michele; Martin, Maria Jesus; Natale, Darren A.; O′Donovan, Claire; Redaschi, Nicole; Yeh, Lai-Su L.

doi:10.1093/nar/gkh131

Cited by 3,358 publications

(2,393 citation statements)

References 24 publications

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“…The average interpair sequence identity among them is 75%. This result is comparable to the average inter-pair sequence identity, 79%, found for the other 22 aquaporin subfamilies for which representative sequences are available from the SwissProt database [17]. Despite the overall similarity between AQP0 sequences belonging to different vertebrate classes, a distinctive profile emerges for the residues lining the pore of each of the three groups: mammals, amphibians and fish.…”

Section: Resultssupporting

confidence: 74%

Mutations at key pore‐lining positions differentiate the water permeability of fish lens aquaporin from other vertebrates

Calvanese¹,

Pellegrini-Calace²,

Oliva³

2010

FEBS Letters

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a b s t r a c tAquaporin-0 (AQP0) is the major integral membrane protein of lens fiber cell and helps to maintain lens transparency by mediating inter-cell adhesion. To shed light on the unexpected higher water transport efficiency of killifish AQP0 as compared to mammalian orthologues, we performed a comparative analysis of all available AQP0 sequences and built 3D-models for representatives of different vertebrate classes. The analysis shows that air-living organisms evolved specific mutations at pore-lining positions to modulate the AQP0 water transport efficiency while maintaining the correct tertiary/quaternary arrangement to allow the formation of ''thin junctions'' between lens fiber cells. We conclude that the low permeability of mammalian AQP0 is required not to promote cell adhesion, but to modulate the water balance in a dry environment.

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Section: Resultssupporting

confidence: 74%

Mutations at key pore‐lining positions differentiate the water permeability of fish lens aquaporin from other vertebrates

Calvanese¹,

Pellegrini-Calace²,

Oliva³

2010

FEBS Letters

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“…The integrated gene set was translated into aminoacid sequences, which were used to search the InterPro database 48 by Iprscan (v 4.7) 49 . We used BLAST to search the metabolic pathway database 50 (release58) in KEGG and homologs in the SwissProt and TrEMBL databases in UniProt 51 (release 2011-01).…”

Section: Digital Gene Expression (Dge)mentioning

confidence: 99%

A heterozygous moth genome provides insights into herbivory and detoxification

et al. 2013

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l e t t e r sHow an insect evolves to become a successful herbivore is of profound biological and practical importance. Herbivores are often adapted to feed on a specific group of evolutionarily and biochemically related host plants 1 , but the genetic and molecular bases for adaptation to plant defense compounds remain poorly understood 2 . We report the first whole-genome sequence of a basal lepidopteran species, Plutella xylostella, which contains 18,071 protein-coding and 1,412 unique genes with an expansion of gene families associated with perception and the detoxification of plant defense compounds. A recent expansion of retrotransposons near detoxification-related genes and a wider system used in the metabolism of plant defense compounds are shown to also be involved in the development of insecticide resistance. This work shows the genetic and molecular bases for the evolutionary success of this worldwide herbivore and offers wider insights into insect adaptation to plant feeding, as well as opening avenues for more sustainable pest management.The global pest P. xylostella (Lepidoptera: Yponomeutidae) is thought to have coevolved with the crucifer plant family 3 ( Supplementary Fig. 1) and has become the most destructive pest of economically important food crops, including rapeseed, cauliflower and cabbage 4 . Recently, the total cost of damage and management worldwide was estimated at $4-5 billion per annum 5,6 . This insect is the first species to have evolved resistance to dichlorodiphenyltrichloroethane (DDT) in the 1950s 7 and to Bacillus thuringiensis (Bt) toxins in the 1990s 8 and has developed resistance to all classes of insecticide, making it increasingly difficult to control 9,10 . P. xylostella provides an exceptional system for understanding the genetic and molecular bases of how insect herbivores cope with the broad range of plant defenses and chemicals encountered in the environment (Supplementary Fig. 2).We used a P. xylostella strain (Fuzhou-S) collected from a field in Fuzhou in southeastern China (26.08 °N, 119.28 °E) for sequencing ( Supplementary Fig. 1). Whole-genome shotgun-based Illumina sequencing of single individuals (Supplementary Table 1), even after ten generations of laboratory inbreeding, resulted in a poor initial assembly (N50 = 2.4 kb, representing the size above which 50% of the total length of the sequences is included), owing to high levels of heterozygosity ( Supplementary Figs. 3 and 4 and Supplementary Table 2). Subsequently, we sequenced 100,800 fosmid clones (comprising ~10× the genome length) to a depth of 200× ( Supplementary Fig. 5 and Supplementary Tables 3-5), assembling the resulting sequence data into 1,819 scaffolds, with an N50 of 737 kb, spanning ~394 Mb of the genome sequence (version 1; Supplementary Fig. 6 and Supplementary Table 6). The assembly covered 85.5% of a set of protein-coding ESTs (Supplementary Tables 7 and 8) generated by transcriptome sequencing 11 . Alignment of a subject scaffold against a 126-kb BAC (GenBank GU058050) from an altern...

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“…The sequence between 18 kb upstream and 4 kb downstream Y2R was searched using BLASTX 21 towards the Uniprot/Swissprot database. 22 We also translated the nucleotide sequence into all six reading frames using sixpack from the EMBOSS suite. 23 Detected open reading frames encoding peptides longer than 100 amino-acid residues were analyzed for homology with proteins in the UniProt/Swissprot database.…”

Section: Bioinformaticsmentioning

confidence: 99%

Common neuropeptide Y2 receptor gene variant is protective against obesity among Swedish men

et al. 2005

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Background: Gut hormones and their receptors are considered important in the control of feeding behavior. The gut hormone peptide-YY (PYY) has anorexic effects via the inhibitory neuropeptide Y2 receptor (Y2R) highly expressed in orexigenic NPY/ AGRP neurons within the arcuate nucleus, a major integrator of appetite control in the hypothalamus. Design: Genetic case-control association study of single nucleotide polymorphisms (SNPs) in Y2R and PYY. Subjects: Swedish Caucasians comprising 148 lean, 129 overweight/obese and 226 morbidly obese men. Measurements: Genotypes of the common, silent and conserved SNP Y2R 585T4C and the common SNP PYY Arg72Thr, as well as various obesity-related clinical parameters. Results: Obese men had a lower allele and homozygosity frequency of the common allele 585T4C:T which was particularly evident comparing morbidly obese with lean men (P ¼ 0.002), and analyzing dependence between continuous body mass index (BMI) and genotype (P ¼ 0.002). In agreement, systolic blood pressure tended to be lower in those homozygous for allele T, which was not explained by the BMI -genotype dependence. We found no association to obesity for the PYY Arg72Thr polymorphism, which is located nearby the essential carboxy terminal. Conclusion: A common and conserved variant of the PYY and NPY receptor Y2R is less prevalent among obese compared to among lean Swedish men. This suggests that the common Y2R variant is protective against obesity. Our findings further implicate Y2R in food intake regulation.

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UniProt: the Universal Protein knowledgebase

Cited by 3,358 publications

References 24 publications

Mutations at key pore‐lining positions differentiate the water permeability of fish lens aquaporin from other vertebrates

Mutations at key pore‐lining positions differentiate the water permeability of fish lens aquaporin from other vertebrates

A heterozygous moth genome provides insights into herbivory and detoxification

Common neuropeptide Y2 receptor gene variant is protective against obesity among Swedish men

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