Endosymbiotic bacteria nodulating a new endemic lupine Lupinus mariae-josephi from alkaline soils in Eastern Spain represent a new lineage within the Bradyrhizobium genus

Lupinus mariae-josephi is a recently described endemic Lupinus species from a small area in Eastern Spain where it thrives in soils with active lime and high pH. The L. mariae-josephi root symbionts were shown to be very slow-growing bacteria with different phenotypic and symbiotic characteristics from those of Bradyrhizobium strains nodulating other Lupinus. Their phylogenetic status was examined by multilocus sequence analyses of four housekeeping genes (16S rRNA, glnII, recA, and atpD) and showed the existence of a distinct evolutionary lineage for L. mariae-josephi that also included Bradyrhizobium jicamae. Within this lineage, the tested isolates clustered in three different sub-groups that might correspond to novel sister Bradyrhizobium species. These core gene analyses consistently showed that all the endosymbiotic bacteria isolated from other Lupinus species of the Iberian Peninsula were related to strains of the B. canariense or B. japonicum lineages and were separate from the L. mariae-josephi isolates. Phylogenetic analysis based on nodC symbiotic gene sequences showed that L. mariae-josephi bacteria also constituted a new symbiotic lineage distant from those previously defined in the genus Bradyrhizobium. In contrast, the nodC genes of isolates from other Lupinus spp. from the Iberian Peninsula were again clearly related to the B. canariense and B. japonicum bv. genistearum lineages. Speciation of L. mariae-josephi bradyrhizobia may result from the colonization of a singular habitat by their unique legume host

Regulation of death receptor signaling by the autophagy protein TP53INP2

TP53INP2 positively regulates autophagy by binding to Atg8 proteins. Here, we uncover a novel role of TP53INP2 in death‐receptor signaling. TP53INP2 sensitizes cells to apoptosis induced by death receptor ligands. In keeping with this, TP53INP2 deficiency in cultured cells or mouse livers protects against death receptor‐induced apoptosis. TP53INP2 binds caspase‐8 and the ubiquitin ligase TRAF6, thereby promoting the ubiquitination and activation of caspase‐8 by TRAF6. We have defined a TRAF6‐interacting motif (TIM) and a ubiquitin‐interacting motif in TP53INP2, enabling it to function as a scaffold bridging already ubiquitinated caspase‐8 to TRAF6 for further polyubiquitination of caspase‐8. Mutations of key TIM residues in TP53INP2 abrogate its interaction with TRAF6 and caspase‐8, and subsequently reduce levels of death receptor‐induced apoptosis. A screen of cancer cell lines showed that those with higher protein levels of TP53INP2 are more prone to TRAIL‐induced apoptosis, making TP53INP2 a potential predictive marker of cancer cell responsiveness to TRAIL treatment. These findings uncover a novel mechanism for the regulation of caspase‐8 ubiquitination and reveal TP53INP2 as an important regulator of the death receptor pathway

The ubiquitin-conjugating enzyme UBE2QL1 coordinates lysophagy in response to endolysosomal damage

The autophagic clearance of damaged lysosomes by lysophagy involves extensive modification of the organelle with ubiquitin, but the underlying ubiquitination machinery is still poorly characterized. Here, we use an siRNA screening approach and identify human UBE2QL1 as a major regulator of lysosomal ubiquitination, lysophagy, and cell survival after lysosomal damage. UBE2QL1 translocates to permeabilized lysosomes where it associates with damage sensors, ubiquitination targets, and lysophagy effectors. UBE2QL1 knockdown reduces ubiquitination and accumulation of the critical autophagy receptor p62 and abrogates recruitment of the AAA-ATPase VCP/p97, which is essential for efficient lysophagy. Crucially, it affects association of LC3B with damaged lysosomes indicating that autophagosome formation was impaired. Already in unchallenged cells, depletion of UBE2QL1 leads to increased lysosomal damage, mTOR dissociation from lysosomes, and TFEB activation pointing to a role in lysosomal homeostasis. In line with this, mutation of the homologue ubc-25 in Caenorhabditis elegans exacerbates lysosome permeability in worms lacking the lysosome stabilizing protein SCAV-3/LIMP2. Thus, UBE2QL1 coordinates critical steps in the acute endolysosomal damage response and is essential for maintenance of lysosomal integrity

Regulation of death receptor signaling by the autophagy protein TP53INP2

TP53INP2 positively regulates autophagy by binding to Atg8 proteins. Here, we uncover a novel role of TP53INP2 in death‐receptor signaling. TP53INP2 sensitizes cells to apoptosis induced by death receptor ligands. In keeping with this, TP53INP2 deficiency in cultured cells or mouse livers protects against death receptor‐induced apoptosis. TP53INP2 binds caspase‐8 and the ubiquitin ligase TRAF6, thereby promoting the ubiquitination and activation of caspase‐8 by TRAF6. We have defined a TRAF6‐interacting motif (TIM) and a ubiquitin‐interacting motif in TP53INP2, enabling it to function as a scaffold bridging already ubiquitinated caspase‐8 to TRAF6 for further polyubiquitination of caspase‐8. Mutations of key TIM residues in TP53INP2 abrogate its interaction with TRAF6 and caspase‐8, and subsequently reduce levels of death receptor‐induced apoptosis. A screen of cancer cell lines showed that those with higher protein levels of TP53INP2 are more prone to TRAIL‐induced apoptosis, making TP53INP2 a potential predictive marker of cancer cell responsiveness to TRAIL treatment. These findings uncover a novel mechanism for the regulation of caspase‐8 ubiquitination and reveal TP53INP2 as an important regulator of the death receptor pathway

Human Stefin B Role in Cell's Response to Misfolded Proteins and Autophagy

<div><p>Alternative functions, apart from cathepsins inhibition, are being discovered for stefin B. Here, we investigate its role in vesicular trafficking and autophagy. Astrocytes isolated from stefin B knock-out (KO) mice exhibited an increased level of protein aggregates scattered throughout the cytoplasm. Addition of stefin B monomers or small oligomers to the cell medium reverted this phenotype, as imaged by confocal microscopy. To monitor the identity of proteins embedded within aggregates in wild type (wt) and KO cells, the insoluble cell lysate fractions were isolated and analyzed by mass spectrometry. Chaperones, tubulins, dyneins, and proteosomal components were detected in the insoluble fraction of wt cells but not in KO aggregates. In contrast, the insoluble fraction of KO cells exhibited increased levels of apolipoprotein E, fibronectin, clusterin, major prion protein, and serpins H1 and I2 and some proteins of lysosomal origin, such as cathepsin D and CD63, relative to wt astrocytes. Analysis of autophagy activity demonstrated that this pathway was less functional in KO astrocytes. In addition, synthetic dosage lethality (SDL) gene interactions analysis in <i>Saccharomyces cerevisiae</i> expressing human stefin B suggests a role in transport of vesicles and vacuoles These activities would contribute, directly or indirectly to completion of autophagy in wt astrocytes and would account for the accumulation of protein aggregates in KO cells, since autophagy is a key pathway for the clearance of intracellular protein aggregates.</p></div

Regulation of death receptor signaling by the autophagy protein TP53INP2

TP53INP2 positively regulates autophagy by binding to Atg8 proteins. Here, we uncover a novel role of TP53INP2 in death‐receptor signaling. TP53INP2 sensitizes cells to apoptosis induced by death receptor ligands. In keeping with this, TP53INP2 deficiency in cultured cells or mouse livers protects against death receptor‐induced apoptosis. TP53INP2 binds caspase‐8 and the ubiquitin ligase TRAF6, thereby promoting the ubiquitination and activation of caspase‐8 by TRAF6. We have defined a TRAF6‐interacting motif (TIM) and a ubiquitin‐interacting motif in TP53INP2, enabling it to function as a scaffold bridging already ubiquitinated caspase‐8 to TRAF6 for further polyubiquitination of caspase‐8. Mutations of key TIM residues in TP53INP2 abrogate its interaction with TRAF6 and caspase‐8, and subsequently reduce levels of death receptor‐induced apoptosis. A screen of cancer cell lines showed that those with higher protein levels of TP53INP2 are more prone to TRAIL‐induced apoptosis, making TP53INP2 a potential predictive marker of cancer cell responsiveness to TRAIL treatment. These findings uncover a novel mechanism for the regulation of caspase‐8 ubiquitination and reveal TP53INP2 as an important regulator of the death receptor pathway

Bimolecular fluorescence microscopy - dimerization of stefin B in HEK293 cells.

<p>Cells were transfected with different combinations of plasmids to follow dimerization of over expressed proteins. For each protein a yellow fluorescent N-terminal (NYFP) or C-terminal half (CYFP), respectively, was attached to the C-terminus of the desired protein. A: control: wild type (WT)-NYFP + SUMO-CYFP; B: WT-NYFP + WT-CYFP; C: G4R-NYFP + G4R-CYFP; D: G4R-NYFP + WT-CYFP. SUMO protein was selected as the control protein due to its high solubility and abundance. Scale bar: 10 µm.</p

Western blot analysis (A) of the protein expression of p62 and LC3-I and LC3-II in primary FVB +/+ (wild type) and StB −/− (knock out) astrocytes.

<p>(B) Western blot analysis of the protein expression of LC3-I and LC3-II in primary stefin B KO astrocytes after incubation with cathepsin inhibitor. 20 nM rapamycin and 5 µM E-64d were added to the medium for 24 hours. Cells were incubated with 80 nM bafilomycin for 30 minutes.</p