UniProt release 2015_07
Published June 24, 2015
Coding-non-coding RNAs: a game of hide-and-seek
It is well-established that microRNAs (miRNAs) are small eukaryotic non-coding RNA molecules that repress the expression of their target genes. miRNAs are transcribed by RNA polymerase II as large primary transcripts (pri-miRNA), that share the same characteristics as all other RNA polymerase II-transcribed RNAs, such as the presence of a 5’-cap and a 3’-poly(A) tail. pri-miRNAs are processed to smaller pre-miRNAs, which in turn are cleaved to produce mature miRNAs. In animals, this final maturation step occurs in the cytoplasm, while in plants it takes place in the nucleus. Cytosolic mature miRNAs guide the RNA-induced silencing complex (RISC) in repressing target genes through either cleavage or translational repression of their mRNAs.
A recent article published in Nature revealed that plant pri-miRNAs may not be as non-coding as previously assumed. Some do actually encode small regulatory peptides, called miPEPs, which enhance the accumulation of their corresponding mature miRNAs. This has been shown for Medicago truncatula pri-miR171b and Arabidopsis thaliana pri-miR165a which encode miPEP171b and miPEP165a, respectively. These two 20- and 18-amino acid-long peptides have been shown to be translated in vivo and to promote the transcription of their pri-miRNAs, resulting in the accumulation of mature miR171b and miR165a. This increase leads to the reduction of lateral root development in the case of miR171b and stimulation of main root growth for miR165a. The same effects were observed when synthetic peptides were applied to plants, suggesting that miPEPs might have agronomical applications.
Five other pri-miRNAs were experimentally shown to encode active miPEPs, suggesting that the presence of such small regulatory peptides may be widespread in plants. Computer analysis of the 5’-end of 50 pri-miRNAs in Arabidopsis thaliana revealed that all of them contained at least one ORF, which, if translated, could give rise to 3- to 59-amino acid-long peptides of unknown biological activity. No common signature was found among them, possibly due to the specificity of each putative miPEP for its own pri-miRNA.
Arabidopsis thaliana miPEP165a, miPEP160b, miPEP164a and miPEP319a and Medicago truncatula miPEP171b peptides have been manually annotated and are integrated into UniProtKB/Swiss-Prot as of this release. The sequences of the other 2 Medicago truncatula functionally characterized peptides, miPEP169d and miPEP171e, are unfortunately not available.
Cross-references to ESTHER
Cross-references have been added to ESTHER, a database of the Alpha/Beta-hydrolase fold superfamily of proteins.
ESTHER is available at http://bioweb.ensam.inra.fr/ESTHER/general?what=index.
The format of the explicit links is:
|Resource identifier||Gene locus.|
|Optional information 1||Family name.|
DR ESTHER; bacbr-grsb; Thioesterase.
<dbReference type="ESTHER" id="bacbr-grsb"> <property type="family name" value="Thioesterase"/> </dbReference>
Cross-references to Genevisible
Cross-references have been added to Genevisible, a search portal to normalized and curated expression data from GENEVESTIGATOR.
Genevisible is available at http://genevisible.com/search.
The format of the explicit links is:
|Resource identifier||Gene identifier.|
|Optional information 1||Organism code.|
DR Genevisible; P31946; HS.
<dbReference type="Genevisible" id="P31946"> <property type="organism ID" value="HS"/> </dbReference>
Removal of the cross-references to Genevestigator
Cross-references to Genevestigator have been removed.
Change of the cross-references to PomBase
Cross-references to PomBase may now optionally indicate a gene designation in order to align them with the format of other model organism databases.
DR PomBase; SPAC1565.08; cdc48.
DR PomBase; SPBC56F2.07c; -.
<dbReference type="PomBase" id="SPAC1565.08"> <property type="gene designation" value="cdc48"/> </dbReference>
<dbReference type="PomBase" id="SPBC56F2.07c"/>
This change did not affect the XSD, but may nevertheless require code changes.
Changes to the controlled vocabulary of human diseases
- 3-methylglutaconic aciduria with cataracts, neurologic involvement and neutropenia
- Amelogenesis imperfecta 1F
- Ataxia-oculomotor apraxia 4
- Cataract 43
- Cerebrocostomandibular syndrome
- Charcot-Marie-Tooth disease 2U
- Coenzyme Q10 deficiency, primary, 7
- Cole-Carpenter syndrome 1
- Cole-Carpenter syndrome 2
- Congenital bile acid synthesis defect 5
- Congenital contractures of the limbs and face, hypotonia, and developmental delay
- Diamond-Blackfan anemia 14, with mandibulofacial dysostosis
- Diamond-Blackfan anemia 15, with mandibulofacial dysostosis
- Dystonia 23
- Keppen-Lubinsky syndrome
- Laurence-Moon syndrome
- Lethal congenital contracture syndrome 7
- Lethal congenital contracture syndrome 8
- Lichtenstein-Knorr syndrome
- Lipoyltransferase 1 deficiency
- Meckel syndrome 12
- Mental retardation, autosomal dominant 32
- Mental retardation, autosomal dominant 33
- Mental retardation, autosomal recessive 48
- Mental retardation, autosomal recessive 49
- Metaphyseal dysplasia, Spahr type
- Mitochondrial short-chain enoyl-CoA hydratase 1 deficiency
- Neurologic, endocrine, and pancreatic disease, multisystem, infantile-onset
- Oliver-McFarlane syndrome
- Opitz GBBB syndrome 2
- Optic atrophy 8
- Osteogenesis imperfecta 16
- Peeling skin syndrome 3
- Peeling skin with leukonychia, acral punctate keratoses, cheilitis, and knuckle pads
- Premature ovarian failure 10
- Robinow syndrome, autosomal dominant 2
- Senior-Loken syndrome 8
- Short-rib thoracic dysplasia 13 with or without polydactyly
- Singleton-Merten syndrome 1
- Singleton-Merten syndrome 2
- Spastic paraplegia 73, autosomal dominant
- Spinocerebellar ataxia, autosomal recessive, 20
- Spondylometaphyseal dysplasia, Megarbane-Dagher-Melike type
- Tenorio syndrome
- Folate-sensitive neural tube defects -> Neural tube defects, folate-sensitive
- HIBCH deficiency -> 3-hydroxyisobutryl-CoA hydrolase deficiency
- Mental retardation, X-linked, syndromic 5 -> Pettigrew syndrome
- Spondyloepimetaphyseal dysplasia Pakistani type -> Brachyolmia type 4 with mild epiphyseal and metaphyseal changes
- Hypogonadism LHB-related
Changes to keywords