Comparative analysis of Saccharomyces cerevisiaeWW domains and their interacting proteins

Hesselberth, Jay R.; Miller, John P.; Golob, Anna L.; Stajich, Jason E.; Michaud, Gregory A.; Fields, Stanley

doi:10.1186/gb-2006-7-4-r30

Cited by 54 publications

(36 citation statements)

References 66 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…2A), contains a PPxY sequence in its C-terminal region that fits the PY motif recognized by WW domain-containing proteins, such as the E3 ubiquitin ligase Rsp5p/Npi1p (14,37). We introduced mutations in the PPPY motif of Sna4p or removed the PPPY sequence and examined the localization of these Sna4p variants fused to GFP expressed in WT cells.…”

Section: Resultsmentioning

confidence: 99%

Dual Sorting of the Saccharomyces cerevisiae Vacuolar Protein Sna4p

et al. 2009

View full text Add to dashboard Cite

Sna4p, a vacuolar membrane protein, belongs to a small family of proteins conserved in plants and fungi. It is transported to the vacuolar membrane via the alkaline phosphatase (ALP) pathway, which bypasses the multivesicular bodies (MVBs). Here, we show that transfer of Sna4p by the ALP route involves the AP-3 adaptor protein complex, which binds to an acidic dileucine sorting signal in the cytoplasmic region of Sna4p. In addition, Sna4p can use the MVB pathway by using a PPPY motif, which is involved in the interaction with ubiquitin ligase Rsp5p. Deletion or mutation of the Sna4p PPPY motif or a low level of Rsp5p inhibits the entrance of Sna4p into MVBs. Sna4p is polyubiquitylated on its only lysine, and Sna4p lacking this lysine shows defective MVB sorting. These data indicate that Sna4p has two functional motifs, one for interaction with the AP-3 complex, followed by entry into the ALP pathway, and one for binding Rsp5p, which directs the protein to the MVB pathway. The presence of these two motifs allows Sna4p to localize to both the vacuolar membrane and the lumen.

show abstract

Section: Resultsmentioning

confidence: 99%

Dual Sorting of the Saccharomyces cerevisiae Vacuolar Protein Sna4p

et al. 2009

View full text Add to dashboard Cite

show abstract

“…We propose that the WW-domain proteins are very suitable for these functions, since they are present in the cytosol of all eukaryotic cells, and they also represent an ancient, very simple motif selected for protein-protein interactions (66,72,85). Indeed, we were able to identify several WWdomain proteins in both yeasts and plants (65), which could be used by tombusviruses for such regulatory roles.…”

Section: Rsp5p and Ww-domain Proteins Act As Cirfs Against Tombusvirumentioning

confidence: 68%

“…Accordingly, binding of Rsp5p and other WW-domain proteins to the p92 pol replication protein leads to the degradation of p92 pol (64,65). The WW domain is a simple and highly conserved protein domain involved in protein-protein interactions (66,67). The sequences of WW domains are highly variable (except from the conserved residues), which likely affect substrate specificity (66).…”

mentioning

confidence: 99%

“…The WW domain is a simple and highly conserved protein domain involved in protein-protein interactions (66,67). The sequences of WW domains are highly variable (except from the conserved residues), which likely affect substrate specificity (66). The canonical WW domain contains two signature tryptophan residues and a conserved proline residue, which are part of a globular fold with three beta-sheets.…”

mentioning

confidence: 99%

“…The canonical WW domain contains two signature tryptophan residues and a conserved proline residue, which are part of a globular fold with three beta-sheets. WW-domain proteins, which are represented by multiple proteins in various organisms, including humans, bind to ligands usually carrying proline-rich sequences (66).…”

mentioning

confidence: 99%

See 2 more Smart Citations

Novel Mechanism of Regulation of Tomato Bushy Stunt Virus Replication by Cellular WW-Domain Proteins

Barajas

Kovalev

Qin

et al. 2015

J Virol

View full text Add to dashboard Cite

Replication of (؉)RNA viruses depends on several co-opted host proteins but is also under the control of cell-intrinsic restriction factors (CIRFs). By using tombusviruses, small model viruses of plants, we dissect the mechanism of inhibition of viral replication by cellular WW-domain-containing proteins, which act as CIRFs. By using fusion proteins between the WW domain and the p33 replication protein, we show that the WW domain inhibits the ability of p33 to bind to the viral RNA and to other p33 and p92 replication proteins leading to inhibition of viral replication in yeast and in a cell extract. Overexpression of WWdomain protein in yeast also leads to reduction of several co-opted host factors in the viral replicase complex (VRC). These host proteins, such as eEF1A, Cdc34 E2 ubiquitin-conjugating enzyme, and ESCRT proteins (Bro1p and Vps4p), are known to be involved in VRC assembly. Simultaneous coexpression of proviral cellular factors with WW-domain protein partly neutralizes the inhibitory effect of the WW-domain protein. We propose that cellular WW-domain proteins act as CIRFs and also as regulators of tombusvirus replication by inhibiting the assembly of new membrane-bound VRCs at the late stage of infection. We suggest that tombusviruses could sense the status of the infected cells via the availability of cellular susceptibility factors versus WWdomain proteins for binding to p33 replication protein that ultimately controls the formation of new VRCs. This regulatory mechanism might explain how tombusviruses could adjust the efficiency of RNA replication to the limiting resources of the host cells during infections. IMPORTANCEReplication of positive-stranded RNA viruses, which are major pathogens of plants, animals, and humans, is inhibited by several cell-intrinsic restriction factors (CIRFs) in infected cells. We define here the inhibitory roles of the cellular Rsp5 ubiquitin ligase and its WW domain in plant-infecting tombusvirus replication in yeast cells and in vitro using purified components. The WW domain of Rsp5 binds to the viral RNA-binding sites of p33 and p92 replication proteins and blocks the ability of these viral proteins to use the viral RNA for replication. The WW domain also interferes with the interaction (oligomerization) of p33 and p92 that is needed for the assembly of the viral replicase. Moreover, WW domain also inhibits the subversion of several cellular proteins into the viral replicase, which otherwise play proviral roles in replication. Altogether, Rsp5 is a CIRF against a tombusvirus, and it possibly has a regulatory function during viral replication in infected cells. P lus-stranded (ϩ)RNA viruses, which are widespread and emerging pathogens, replicate in the cytosol of infected cells by assembling membrane-bound viral replicase complexes (VRCs). The VRCs consist of the viral RNA and viral proteins, as well as co-opted host-coded proteins (1-8). Rapid progress has recently been made in understanding the functions of the viral replication proteins, including the v...

show abstract

Binding by calmodulin is coupled to transient unfolding of the third FF domain of Prp40A

et al. 2023

View full text Add to dashboard Cite

Human pre‐mRNA processing protein 40 homolog A (hPrp40A) is a splicing factor that interacts with the Huntington's disease protein huntingtin (Htt). Evidence has accumulated that both Htt and hPrp40A are modulated by the intracellular Ca2+ sensor calmodulin (CaM). Here we report characterization of the interaction of human CM with the third FF domain (FF3) of hPrp40A using calorimetric, fluorescence and structural approaches. Homology modeling, differential scanning calorimetry and small angle X‐ray scattering (SAXS) data show FF3 forms a folded globular domain. CaM was found to bind FF3 in a Ca2+‐dependent manner with a 1:1 stoichiometry and a dissociation constant (Kd) of 25 ± 3 μM at 25°C. NMR studies showed that both domains of CaM are engaged in binding and SAXS analysis of the FF3‐CaM complex revealed CaM occupies an extended configuration. Analysis of the FF3 sequence showed that the anchors for CaM binding must be buried in its hydrophobic core, suggesting that binding to CaM requires unfolding of FF3. Trp anchors were proposed based on sequence analysis and confirmed by intrinsic Trp fluorescence of FF3 upon binding of CaM and substantial reductions in affinity for Trp‐Ala FF3 mutants. The consensus model of the complex showed that binding to CaM binding occurs to an extended, non‐globular state of the FF3, consistent with coupling to transient unfolding of the domain. The implications of these results are discussed in the context of the complex interplay of Ca2+ signaling and Ca2+ sensor proteins in modulating Prp40A‐Htt function.

show abstract

Comparative analysis of Saccharomyces cerevisiaeWW domains and their interacting proteins

Cited by 54 publications

References 66 publications

Dual Sorting of the Saccharomyces cerevisiae Vacuolar Protein Sna4p

Dual Sorting of the Saccharomyces cerevisiae Vacuolar Protein Sna4p

Novel Mechanism of Regulation of Tomato Bushy Stunt Virus Replication by Cellular WW-Domain Proteins

Binding by calmodulin is coupled to transient unfolding of the third FF domain of Prp40A

Contact Info

Product

Resources

About