LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs)

Wei, Tian‐Ran; Gong, Jing; Jamitzky, Ferdinand; Heckl, Wolfgang M.; Stark, Robert W.; Rössle, Shaila C.

doi:10.1186/1472-6807-8-47

Cited by 31 publications

(37 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We first compiled a list of 375 human proteins annotated as containing LRRs in InterPro (18), the Swiss-Prot section of UniProt (19), and LRRML (a conformational database and an extensible markup language description of LRRs) (17). As shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…We identified the positions of individual LRR sequences within each LRR domain, and classified each repeat based upon consensus sequences and lengths of their VSs. Identified repeats were assigned into classes: bacterial (S), ribonuclease inhibitor-like (RI), cysteine-containing (CC), SDS22, plant-specific (PS), typical (T), and Treponema pallidum (Tp) (13,17). By using this approach, we reasoned that functionally related LRR-only proteins would be placed together by virtue of their similar LRR domains.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

Eisenberg

Heath

et al. 2010

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

182

185

View full text Add to dashboard Cite

In innate immune sensing, the detection of pathogen-associated molecular patterns by recognition receptors typically involve leucine-rich repeats (LRRs). We provide a categorization of 375 human LRR-containing proteins, almost half of which lack other identifiable functional domains. We clustered human LRR proteins by first assigning LRRs to LRR classes and then grouping the proteins based on these class assignments, revealing several of the resulting protein groups containing a large number of proteins with certain non-LRR functional domains. In particular, a statistically significantnumber of LRR proteins in the typical (T) and bacterial + typical (S+T) categories have transmembrane domains, whereas most of the LRR proteins in the cysteine-containing (CC) category contain an F-box domain (which mediates interactions with the E3 ubiquitin ligase complex). Furthermore, by examining the evolutionary profiles of the LRR proteins, we identified a subset of LRR proteins exhibiting strong conservation in fungi and an enrichment for "nucleic acid-binding" function. Expression analysis of LRR genes identifies a subset of pathogen-responsive genes in human primary macrophages infected with pathogenic bacteria. Using functional RNAi, we show that MFHAS1 regulates Toll-like receptor (TLR)-dependent signaling. By using protein interaction network analysis followed by functional RNAi, we identified LRSAM1 as a component of the antibacterial autophagic response.pathogen-response | anti-bacterial | inflammation | pathogen sensors | autophagy

show abstract

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

Eisenberg

Heath

et al. 2010

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

182

185

View full text Add to dashboard Cite

show abstract

“…This method can be extended to predict LRR motifs in other LRR containing proteins besides TLRs, since all LRR types possess the same HCS pattern. TLR1 TLR2 TLR3 TLR4 TLR5 TLR6 TLR7 TLR8 TLR9 TLR10 InterPro 4 4 8 7 7 3 9 10 6 4 Pfam 4 4 7 7 8 3 8 9 6 4 SMART 6 9 19 12 10 7 16 17 19 7 Swiss-Prot 8 14 22 21 15 13 27 24 26 15 TollML 21 21 25 23 23 21 28 28 28 21 [8] can further provide suitable LRR structural templates. This LRR template assembling approach was proven to be both feasible and significant by recent structure modeling research into human TLR7-9 [33].…”

Section: Database Comparisonmentioning

confidence: 99%

“…(1) Data management information: TollML ID and access/ modification date; (2) Primary information extracted from the NCBI and related literature: FASTA sequence, biological definition, cell information, glycosylation sites and ligands; (3) Protein family classification; (4) Database cross links: NCBI, Swiss-Prot [23], PDB [24], LRRML [8] and PubMed [25]; (5) Three-level motif information.…”

Section: Database Contentmentioning

confidence: 99%

See 1 more Smart Citation

TollML: a database of toll-like receptor structural motifs

et al. 2010

Self Cite

View full text Add to dashboard Cite

Toll-like receptors (TLRs) play a key role in the innate immune system. TLRs recognize pathogenassociated molecular patterns and initiate an intracellular kinase cascade to induce an immediate defensive response. During recent years TLRs have become the focus of tremendous research interest. A central repository for the growing amount of relevant TLR sequence information has been created. Nevertheless, structural motifs of most sequenced TLR proteins, such as leucine-rich repeats (LRRs), are poorly annotated in the established databases. A database that organizes the structural motifs of TLRs could be useful for developing pattern recognition programs, structural modeling and understanding functional mechanisms of TLRs. We describe TollML, a database that integrates all of the TLR sequencing data from the NCBI protein database. Entries were first divided into TLR families (TLR1-23) and then semi-automatically subdivided into three levels of structural motif categories: (1) signal peptide (SP), ectodomain (ECD), transmembrane domain (TD) and Toll/IL-1 receptor (TIR) domain of each TLR; (2) LRRs of each ECD; (3) highly conserved segment (HCS), variable segment (VS) and insertions of each LRR. These categories can be searched quickly using an easy-to-use web interface and dynamically displayed by graphics. Additionally, all entries have hyperlinks to various sources including NCBI, Swiss-Prot, PDB, LRRML and PubMed in order to provide broad external information for users. The TollML database is available at http://tollml.lrz.de.

show abstract

IDENTIFICATION OF MYCOSIS‐RELATED GENES IN THEEASTERN SUBTERRANEAN TERMITE BY SUPPRESSION SUBTRACTIVE HYBRIDIZATION

Gao¹,

Tancredi²,

Thompson

2012

Arch Insect Biochem Physiol

View full text Add to dashboard Cite

The Eastern subterranean termite Reticulitermes flavipes (Isoptera, Rhinotermitidae) is a cosmopolitan, structural pest that is the target of research into termite innate immunity. In this study, we use suppression subtractive hybridization to construct a normalized cDNA library of genes excessively expressed upon fungal infection. At 24 h postinfection with Metarhizium anisopliae, the library revealed 182 expressed sequence tag (EST) clones that potentially represent immune responsive genes. The nucleotide sequence from a majority (97%) of ESTs assembled into a small number (n = 13) of contiguous sequences, with the remainder (n = 6) representing singletons. Our screen therefore captured as many as 19 different mRNAs highly expressed in response to the fungal pathogen at this time. Primary sequencing of all loci revealed that approximately half (n = 10) contained open reading frames with significant similarity to known proteins. These clones represent nuclear and mitochondrial coding genes, as well as putative long noncoding RNA genes. Quantitative polymerase chain reaction analysis of coding genes on independently infected groups of worker termites confirms in each case that the transcripts identified from the library are up-regulated postfungal infection. The genes identified here are relevant to future studies on termite biocontrol and social insect immunity.

show abstract

LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs)

Cited by 31 publications

References 26 publications

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity

TollML: a database of toll-like receptor structural motifs

IDENTIFICATION OF MYCOSIS‐RELATED GENES IN THEEASTERN SUBTERRANEAN TERMITE BY SUPPRESSION SUBTRACTIVE HYBRIDIZATION

Contact Info

Product

Resources

About