iLIR

Abstract

Macroautophagy was initially considered to be a nonselective process for bulk breakdown of cytosolic material. However, recent evidence points toward a selective mode of autophagy mediated by the so-called selective autophagy receptors (SARs). SARs act by recognizing and sorting diverse cargo substrates (e.g., proteins, organelles, pathogens) to the autophagic machinery. Known SARs are characterized by a short linear sequence motif (LIR-, LRS-, or AIM-motif) responsible for the interaction between SARs and proteins of the Atg8 family. Interestingly, many LIR-containing proteins (LIRCPs) are also involved in autophagosome formation and maturation and a few of them in regulating signaling pathways. Despite recent research efforts to experimentally identify LIRCPs, only a few dozen of this class of—often unrelated—proteins have been characterized so far using tedious cell biological, biochemical, and crystallographic approaches. The availability of an ever-increasing number of complete eukaryotic genomes provides a grand challenge for characterizing novel LIRCPs throughout the eukaryotes. Along these lines, we developed iLIR, a freely available web resource, which provides in silico tools for assisting the identification of novel LIRCPs. Given an amino acid sequence as input, iLIR searches for instances of short sequences compliant with a refined sensitive regular expression pattern of the extended LIR motif (xLIR-motif) and retrieves characterized protein domains from the SMART database for the query. Additionally, iLIR scores xLIRs against a custom position-specific scoring matrix (PSSM) and identifies potentially disordered subsequences with protein interaction potential overlapping with detected xLIR-motifs. Here we demonstrate that proteins satisfying these criteria make good LIRCP candidates for further experimental verification. Domain architecture is displayed in an informative graphic, and detailed results are also available in tabular form. We anticipate that iLIR will assist with elucidating the full complement of LIRCPs in eukaryotes.

Selective Autophagy of BES1 Mediated by DSK2 Balances Plant Growth and Survival

“…DSK2 physically interacted with all ATG8 members tested in GST pull-down assays, including ATG8e (Figure 4A). To further characterize the role of DSK2 as a possible autophagy receptor, we examined the DSK2 protein sequence for predicted AIMs using iLIR prediction software (Kalvari et al, 2014). AIMs are typified by the consensus sequence W/F/Y-X-X-L/I/V, which is often adjacent to acidic or phosphorylated residues (Kalvari et al, 2014).…”

“…To further characterize the role of DSK2 as a possible autophagy receptor, we examined the DSK2 protein sequence for predicted AIMs using iLIR prediction software (Kalvari et al, 2014). AIMs are typified by the consensus sequence W/F/Y-X-X-L/I/V, which is often adjacent to acidic or phosphorylated residues (Kalvari et al, 2014). DSK2A has two regions with high-scoring AIMs, each of which is surrounded by multiple BIN2 consensus phosphorylation sites (S/T-X-X-X-S/T) (Figure 4B) (Zhao et al, 2002).…”

Mechanisms of Selective Autophagy in Normal Physiology and Cancer

“…Our understanding of how the seven mammalian ATG8 proteins control selective autophagy is limited, and the extent to which the two ATG8 subfamilies - LC3 and GABARAP - play unique or redundant roles in selective autophagy is not entirely clear. Many ATG8-associated proteins, including selective autophagy receptors, contain short linear peptide sequences that bind directly to ATG8s – the so-called LIR motif (LC3 interacting region)[39–41]. LIR motifs typically contain a W/F/Y-X-X-ψ sequence (ψ, hydrophobic residue: L/I/V, X is any residue), and often are preceded by acidic residues or by phosphorylation sites (as discussed in the section below), which modulate ATG8 binding.…”

“…Non-canonical LIR sequences also exist suggesting further molecular determinants of ATG8 interacting proteins may yet be uncovered[42]. In-depth reviews of the importance of the LIR motif in selective autophagy and autophagosome machinery are presented elsewhere[39,41]. …”

Autophagosomes take the Klp98-A train

“…To strengthen and extend this model, it will be important to characterize mutations in the motor domain and to precisely define the Atg8/LC3-and Rab14-interacting regions of Klp98A. A number of putative LC3 interacting regions (LIRs) can be identified in the Klp98A peptide sequence using prediction software, 14 and mutation of these motifs should help to define the role of this interaction. In mammalian cells, the interaction between KIF16B and Rab14 is influenced by GTP/GDP binding, providing a means to regulate cargo-motor association.…”