PaperBLAST

Full List of Papers Linked to VIMSS243098

SCO2776 acetyl/propionyl CoA carboxylase, beta subunit from Streptomyces coelicolor A3(2)

• Origin of the 3-methylglutaryl moiety in caprazamycin biosynthesis
  Bär, Microbial cell factories 2022
  • “...analysis of S. coelicolor M1154 revealed genes homologue to liuA ( sco2779 ), liuB ( sco2776 ), liuD ( sco2777 ) and liuE ( sco2778 ) (Additional file 1 : Fig. S6). No homologue was found for liuC in this cluster though, raising the question if...”
  • “...: Fig. S7A). To investigate if the Liu-pathway is connected to caprazamycin biosynthesis, we deleted sco2776 to sco2779 in the heterologous host S. coelicolor M1154 resulting in S. coelicolor M1154 sco2776 - sco2779 . Successful deletion and absence of wildtype genes was verified by PCR and...”
• Comparative Proteomic Analysis of Transcriptional and Regulatory Proteins Abundances in S. lividans and S. coelicolor Suggests a Link between Various Stresses and Antibiotic Production
  Clara, International journal of molecular sciences 2022
  • “...of malonyl or methyl-malonylCoA, possibly used for fatty acids and/or polyketide (ACT) biosynthesis. SCO2777 and SCO2776 were highly abundant in SC but poorly abundant in SL , in both Pi conditions (Figure S2A of [ 9 ]), suggesting that SCO2775 represses the expression of the corresponding...”
• AccR, a TetR Family Transcriptional Repressor, Coordinates Short-Chain Acyl Coenzyme A Homeostasis in Streptomyces avermitilis
  Lyu, Applied and environmental microbiology 2020 (secret)
• Iron competition triggers antibiotic biosynthesis in Streptomyces coelicolor during coculture with Myxococcus xanthus
  Lee, The ISME journal 2020
  • “...accumulated acetyl-CoA; (ii) the acetyl-CoA synthetase (SCO6195) converted acetate to acetyl-CoA; and (iii) acetyl-CoA carboxylases (SCO2776, SCO2777, and SCO4921) converted acetyl-CoA to malonyl-CoA (Fig. 1e ). Considering that the transcription levels of genes involved in other acetyl-CoA-associated pathways, such as glycolysis and the citrate cycle, showed...”
• A Novel Two-Component System, Encoded by the sco5282/sco5283 Genes, Affects Streptomyces coelicolor Morphology in Liquid Culture
  Arroyo-Pérez, Frontiers in microbiology 2019
  • “...G 1.45E-45 1.41E-03 1.44E-15 SCO2774 Acyl-CoA dehydrogenase 1.56 Amino acid degradation I 8.90E-09 1.41E-04 4.44E-16 SCO2776 Carboxylase 2.11 Amino acid degradation I 3.14E-15 1.33E-01 3.77E-15 SCO2777 Carboxylase 2.12 Amino acid degradation I 1.85E-15 1.16E-01 0.00E+00 SCO2778 Hydroxymethylglutaryl-CoA lyase 1.96 Amino acid degradation I 2.54E-13 2.75E-01 1.06E-03...”
• Role of Wax Ester Synthase/Acyl Coenzyme A:Diacylglycerol Acyltransferase in Oleaginous Streptomyces sp. Strain G25
  Röttig, Applied and environmental microbiology 2016
  • “...AccA2, PccA, and SCO4381), four subunits (AccB, PccB, SCO2776, and SCO4380), and two subunits (AccE, PccE) from S. coelicolor (49) AcpP from S. coelicolor...”
• The ROK family regulator Rok7B7 pleiotropically affects xylose utilization, carbon catabolite repression, and antibiotic production in streptomyces coelicolor
  Świątek, Journal of bacteriology 2013
  • “...of branched-chain amino acids (SCO2008 to SCO2012 and SCO2776 to SCO2779) and an enolase (SCO7638) were 2- to 3-fold enhanced in the mutant. Furthermore,...”
• Crp is a global regulator of antibiotic production in streptomyces
  Gao, mBio 2012
  • “...SCO5877 , SCO5878 , SCO6271 , SCO6275 , and SCO5222 ) and primary metabolism ( SCO2776 , SCO4921 , SCO5144 , and SCO5535 ). All displayed at least a 2-fold change in their transcriptional levels following Crp induction. Asterisks indicate changes in expression that are statistically...”
• Fatty acid biosynthesis in actinomycetes
  Gago, FEMS microbiology reviews 2011
  • “...putative subunits ( accA1, accA2, pccA, SCO4381 ), four genes encoding subunits ( accB, pccB, SCO2776, SCO4380 ) and two genes encoding subunits ( accE, pccE ) ( Bramwell et al. , 1996 ; Diacovich et al. , 2004 ; Rodriguez and Gramajo, 1999 ; Rodriguez...”
  • “...form a discrete enzyme complex. This is the case for the and subunits pccA and SCO2776 and for SCO4381 and SCO4380 , respectively. An enzymatic PCC complex was partially characterized in S. coelicolor ( Bramwell et al. , 1996 ) consisting of a biotinylated protein, PccA,...”
• Genome-wide dynamics of a bacterial response to antibiotics that target the cell envelope
  Hesketh, BMC genomics 2011
  • “...amino acids as an energy source in the moenomycin treated cells. Indeed, expression of accD1 (SCO2776) encoding the biotin-dependent acetyl-CoA carboxylase enzyme, a key enzyme in branched chain amino acid degradation, was 5-fold up-regulated 90 min after moenomycin addition (see Additional file 3 ). Genes encoding...”

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How It Works

PaperBLAST builds a database of protein sequences that are linked to scientific articles. These links come from automated text searches against the articles in EuropePMC and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot, BRENDA, CAZy (as made available by dbCAN), BioLiP, CharProtDB, MetaCyc, EcoCyc, TCDB, REBASE, the Fitness Browser, and a subset of the European Nucleotide Archive with the /experiment tag. Given this database and a protein sequence query, PaperBLAST uses protein-protein BLAST to find similar sequences with E < 0.001.

To build the database, we query EuropePMC with locus tags, with RefSeq protein identifiers, and with UniProt accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use queries of the form "locus_tag AND genus_name" to try to ensure that the paper is actually discussing that gene. Because EuropePMC indexes most recent biomedical papers, even if they are not open access, some of the links may be to papers that you cannot read or that our computers cannot read. We query each of these identifiers that appears in the open access part of EuropePMC, as well as every locus tag that appears in the 500 most-referenced genomes, so that a gene may appear in the PaperBLAST results even though none of the papers that mention it are open access. We also incorporate text-mined links from EuropePMC that link open access articles to UniProt or RefSeq identifiers. (This yields some additional links because EuropePMC uses different heuristics for their text mining than we do.)

For every article that mentions a locus tag, a RefSeq protein identifier, or a UniProt accession, we try to select one or two snippets of text that refer to the protein. If we cannot get access to the full text, we try to select a snippet from the abstract, but unfortunately, unique identifiers such as locus tags are rarely provided in abstracts.

PaperBLAST also incorporates manually-curated protein functions:

• Proteins from NCBI's RefSeq are included if a GeneRIF entry links the gene to an article in PubMed^®. GeneRIF also provides a short summary of the article's claim about the protein, which is shown instead of a snippet.
• Proteins from Swiss-Prot (the curated part of UniProt) are included if the curators identified experimental evidence for the protein's function (evidence code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that describe the protein's function are shown (with bold headings).
• Proteins from BRENDA, a curated database of enzymes, are included if they are linked to a paper in PubMed and their full sequence is known.
• Every protein from the non-redundant subset of BioLiP, a database of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself does not include descriptions of the proteins, those are taken from the Protein Data Bank. Descriptions from PDB rely on the original submitter of the structure and cannot be updated by others, so they may be less reliable. (For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every ligand is represented among a group of structures with similar sequences, but for PaperBLAST, we use the non-redundant set provided by BioLiP.)
• Every protein from EcoCyc, a curated database of the proteins in Escherichia coli K-12, is included, regardless of whether they are characterized or not.
• Proteins from the MetaCyc metabolic pathway database are included if they are linked to a paper in PubMed and their full sequence is known.
• Proteins from the Transport Classification Database (TCDB) are included if they have known substrate(s), have reference(s), and are not described as uncharacterized or putative. (Some of the references are not visible on the PaperBLAST web site.)
• Every protein from CharProtDB, a database of experimentally characterized protein annotations, is included.
• Proteins from the CAZy database of carbohydrate-active enzymes are included if they are associated with an Enzyme Classification number. Even though CAZy does not provide links from individual protein sequences to papers, these should all be experimentally-characterized proteins.
• Proteins from the REBASE database of restriction enzymes are included if they have known specificity.
• Every protein with an evidence-based reannotation (based on mutant phenotypes) in the Fitness Browser is included.
• Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators) with experimentally-determined DNA binding sites from the PRODORIC database of gene regulation in prokaryotes.
• Putative transcription factors from RegPrecise that have manually-curated predictions for their binding sites. These predictions are based on conserved putative regulatory sites across genomes that contain similar transcription factors, so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
• Coding sequence (CDS) features from the European Nucleotide Archive (ENA) are included if the /experiment tag is set (implying that there is experimental evidence for the annotation), the nucleotide entry links to paper(s) in PubMed, and the nucleotide entry is from the STD data class (implying that these are targeted annotated sequences, not from shotgun sequencing). Also, to filter out genes whose transcription or translation was detected, but whose function was not studied, nucleotide entries or papers with more than 25 such proteins are excluded. Descriptions from ENA rely on the original submitter of the sequence and cannot be updated by others, so they may be less reliable.

Except for GeneRIF and ENA, the curated entries include a short curated description of the protein's function. For entries from BioLiP, the protein's function may not be known beyond binding to the ligand. Many of these entries also link to articles in PubMed.

For more information see the PaperBLAST paper (mSystems 2017) or the code. You can download PaperBLAST's database here.

Changes to PaperBLAST since the paper was written:

• November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
• February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
• June 2022: incorporated some coding sequences from ENA with the /experiment tag.
• March 2022: incorporated BioLiP.
• April 2020: incorporated TCDB.
• April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
• February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
• January 2018: incorporated BRENDA.
• December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
• September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.

Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.

Secrets

PaperBLAST cannot provide snippets for many of the papers that are published in non-open-access journals. This limitation applies even if the paper is marked as "free" on the publisher's web site and is available in PubmedCentral or EuropePMC. If a journal that you publish in is marked as "secret," please consider publishing elsewhere.

Omissions from the PaperBLAST Database

Many important articles are missing from PaperBLAST, either because the article's full text is not in EuropePMC (as for many older articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an article that characterizes a protein's function but is missing from PaperBLAST, please notify the curators at UniProt or add an entry to GeneRIF. Entries in either of these databases will eventually be incorporated into PaperBLAST. Note that to add an entry to UniProt, you will need to find the UniProt identifier for the protein. If the protein is not already in UniProt, you can ask them to create an entry. To add an entry to GeneRIF, you will need an NCBI Gene identifier, but unfortunately many prokaryotic proteins in RefSeq do not have corresponding Gene identifers.

References

PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.

Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.

Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.

UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.

BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.

The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.

CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.

The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.

The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.

REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.

Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.