SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation

Given the relevance of the pig proteome in different studies, including human complex maladies, a statistical validation of the annotation is required for a better understanding of the role of specific genes and proteins in the complex networks underlying biological processes in the animal. Presently, approximately 80% of the pig proteome is still poorly annotated, and the existence of protein sequences is routinely inferred automatically by sequence alignment towards preexisting sequences. In this article, we introduce SUS-BAR, a database that derives information mainly from UniProt Knowledgebase and that includes 26 206 pig protein sequences. In SUS-BAR, 16 675 of the pig protein sequences are endowed with statistically validated functional and structural annotation. Our statistical validation is determined by adopting a cluster-centric annotation procedure that allows transfer of different types of annotation, including structure and function. Each sequence in the database can be associated with a set of statistically validated Gene Ontologies (GOs) of the three main sub-ontologies (Molecular Function, Biological Process and Cellular Component), with Pfam functional domains, and when possible, with a cluster Hidden Markov Model that allows modelling the 3D structure of the protein. A database search allows some statistics demonstrating the enrichment in both GO and Pfam annotations of the pig proteins as compared with UniProt Knowledgebase annotation. Searching in SUS-BAR allows retrieval of the pig protein annotation for further analysis. The search is also possible on the basis of specific GO terms and this allows retrieval of all the pig sequences participating into a given biological process, after annotation with our system. Alternatively, the search is possible on the basis of structural information, allowing retrieval of all the pig sequences with the same structural characteristics

The repetitive structure of DNA clamps: An overlooked protein tandem repeat

Structured tandem repeats proteins (STRPs) are a specific kind of tandem repeat proteins characterized by a modular and repetitive three-dimensional structure arrangement. The majority of STRPs adopt solenoid structures, but with the increasing availability of experimental structures and high-quality predicted structural models, more STRP folds can be characterized. Here, we describe “Box repeats”, an overlooked STRP fold present in the DNA sliding clamp processivity factors, which has eluded classification although structural data has been available since the late 1990s. Each Box repeat is a β⍺βββ module of about 60 residues, which forms a class V “beads-on-a-string” type STRP. The number of repeats present in processivity factors is organism dependent. Monomers of PCNA proteins in both Archaea and Eukarya have 4 repeats, while the monomers of bacterial beta-sliding clamps have 6 repeats. This new repeat fold has been added to the RepeatsDB database, which now provides structural annotation for 66 Box repeat proteins belonging to different organisms, including viruses

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences

We introduce BAR-PLUS (BAR+), a web server for functional and structural annotation of protein sequences. BAR+ is based on a large-scale genome cross comparison and a non-hierarchical clustering procedure characterized by a metric that ensures a reliable transfer of features within clusters. In this version, the method takes advantage of a large-scale pairwise sequence comparison of 13 495 736 protein chains also including 988 complete proteomes. Available sequence annotation is derived from UniProtKB, GO, Pfam and PDB. When PDB templates are present within a cluster (with or without their SCOP classification), profile Hidden Markov Models (HMMs) are computed on the basis of sequence to structure alignment and are cluster-associated (Cluster-HMM). Therefrom, a library of 10 858 HMMs is made available for aligning even distantly related sequences for structural modelling. The server also provides pairwise query sequence–structural target alignments computed from the correspondent Cluster-HMM. BAR+ in its present version allows three main categories of annotation: PDB [with or without SCOP (*)] and GO and/or Pfam; PDB (*) without GO and/or Pfam; GO and/or Pfam without PDB (*) and no annotation. Each category can further comprise clusters where GO and Pfam functional annotations are or are not statistically significant. BAR+ is available at http://bar.biocomp.unibo.it/bar2.0

Structural Characterization of the Highly Restricted Down Syndrome Critical Region on 21q22.13: New KCNJ6 and DSCR4 Transcript Isoforms

Down syndrome (DS) is caused by trisomy of chromosome 21 and it is the most common genetic cause of intellectual disability (ID) in humans. Subjects with DS show a typical phenotype marked by facial dysmorphisms and ID. Partial trisomy 21 (PT21) is a rare genotype characterized by the duplication of a delimited chromosome 21 (Hsa21) portion and it may or may not be associated with DS diagnosis. The highly restricted Down syndrome critical region (HR-DSCR) is a region of Hsa21 present in three copies in all individuals with PT21 and a diagnosis of DS. This region, located on distal 21q22.13, is 34 kbp long and does not include characterized genes. The HR-DSCR is annotated as an intergenic region between KCNJ6-201 transcript encoding for potassium inwardly rectifying channel subfamily J member 6 and DSCR4-201 transcript encoding Down syndrome critical region 4. Two transcripts recently identified by massive RNA-sequencing (RNA-Seq) and automatically annotated on Ensembl database reveal that the HR-DSCR seems to be partially crossed by KCNJ6-202 and DSCR4-202 isoforms. KCNJ6-202 shares the coding sequence with KCNJ6-201 which is involved in many physiological processes, including heart rate in cardiac cells and circuit activity in neuronal cells. DSCR4-202 transcript has the first two exons in common with DSCR4-201, the only experimentally verified gene uniquely present in Hominidae. In this study, we performed in silico and in vitro analyses of the HR-DSCR. Bioinformatic data, obtained using Sequence Read Archive (SRA) and SRA-BLAST software, were confirmed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and Sanger sequencing on a panel of human tissues. Our data demonstrate that the HR-DSCR cannot be defined as an intergenic region. Further studies are needed to investigate the functional role of the new transcripts, likely involved in DS phenotypes

Corrigendum: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

In the above-mentioned article, one result reported in the third paragraph of the Results subsection “ceRNAts of individual lnceRNAs tend to be functionally related” was in error. This paragraph should now read: “On average, mESC-expressed lnceRNAs have 20.2 predicted MREs per kb of transcript that are specific to 12 different mESC-expressed miRNAs. This MRE density is similar to the density within 3′ UTRs of ceRNAts (20.4 MREs predicted per kb; P = 0.34, two-tailed Mann-Whitney U test) (Supplemental Fig. S9; Supplemental Table S8). A single lnceRNA might, therefore, be as likely as an mRNA to regulate post-transcriptionally the transcript abundance of many mRNAs via crosstalk with many miRNAs.” Corrected versions of Supplemental Figure S9 and Supplemental Table S8 are also now provided online. This correction does not affect any of the conclusions of the paper. The authors apologize for any confusion caused by this error

Análise do acúmulo de transcritos de ?-3-dessaturases em genótipos de soja contrastantes para o teor de ácido linolênico.

Os ácidos graxos poliinsaturados, como linoléico e linolênico, são os principais responsáveis pela alta instabilidade oxidativa a altas temperaturas do óleo destinado a frituras e à fabricação de biodiesel. A biossíntese de ácidos graxos poliinsaturados é catalisada pelas dessaturases. A -6-dessaturase converte ácido oléico (18:19) a linoléico (18:29,12) e a -3-dessaturase produz ácido linolênico (18:39,12,15) a partir de 18:29,12. Três genes principais (GmFAD3A, GmFAD3B e GmFAD3C) foram caracterizados como responsáveis pela produção de -3-dessaturase em soja. Os mecanismos precisos de regulação da produção de ácido linolênico ainda não são muito claros, o que dificulta o processo de obtenção de genótipos com baixo conteúdo desse ácido graxo. A análise molecular de mutantes de soja com baixo conteúdo de ácido linolênico poderá ajudar a elucidar tais mecanismos. Os objetivos principais deste trabalho foram determinar os níveis de mRNAs das principais -3-dessaturases, correlacionando-os com as concentrações relativas de ácidos linolênico durante a ontogenia da semente de soja em genótipos normais e mutantes. Para isso, foram utilizados três genótipos contrastantes para essa característica: A29, (~1% 18:315,12,9); N85-2176 (~3% 18:315,12,9) e Tucunaré (Variedade comercial, ~8% 18:315,12,9). As plantas foram cultivadas em casa de vegetação e suas sementes foram coletadas separadamente em 5 estádios de desenvolvimento de acordo com o peso úmido da semente: 1º estádio: 0 a 125 mg; 2º estádio: 126 a 250 mg; 3º estádio: 251 a 375 mg; 4º estádio: superior a 376 mg; 5 º estádio: semente madura. Os teores de ácidos graxos na fração óleo das sementes nos cinco estádios de desenvolvimento foram determinados por cromatografia gasosa e a expressão gênica, por PCR quantitativo, utilizando como o controle endógeno o gene da GAPDH (gliceraldeído-3-fosfato desidrogenase). De modo geral, o conteúdo de 18:39,12,15 decresceu drasticamente nos estádios iniciais em todos os genótipos. No entanto, não foi observada expressão diferencial entre os genes GmFAD3A, GmFAD3B e GmFAD3C, que pudessem explicar tais alterações. O genótipo A29, seguido de N85-2176, apresentou a menor concentração de 18:39,12,15 durante todo o desenvolvimento da semente. Estes genótipos apresentaram expressão praticamente nula do gene GmFAD3A. Além disso, A29 apresentou expressão reduzida do gene GmFAD3B. Assim, pelo menos em parte, os níveis de transcritos dos genes GmFAD3A e GmFAD3B explicam as diferenças na concentração de ácidos graxos da fração óleo em A29 e N85-2176. Apoio financeiro: CNPq e CAPES

Identifying the 993-994 CE Miyake event in the oldest dated living tree in Europe

Combined dendrochronology and accelerator mass spectrometry radiocarbon (AMS 14C) dating analyses were used in order to date an old living tree named Italus, growing in the Pollino massif in Southern Italy. Wiggle match AMS 14C dating analysis was performed on a 320-yr-long floating chronology obtained by cross-dating four wood cores extracted from the exposed roots of the tree. Following this approach, an age for the tree of ≈1230 yr was estimated. This age makes Italus the oldest living tree in Europe. High-resolution 14C dating analyses performed on single rings extracted from the tree stem allowed us to identify the 993.994 CE large excursion in atmospheric 14C concentration (Miyake event) revealing for the first time its presence in the Mediterranean basin