Autophagy controls the quality and quantity of the eukaryotic cytoplasm while performing two evolutionarily highly conserved functions: cell-autonomous provision of energy and nutrients by cytosol autodigestion during starvation, and removal of defunct organelles and large aggregates exceeding the capacity of other cellular degradative systems. In contrast to these autodigestive processes, autophagy in yeast has additional, biogenesis functions. However, no equivalent biosynthetic roles have been described for autophagy in mammals. Here, we show that in mammalian cells, autophagy has a hitherto unappreciated positive contribution to the biogenesis and secretion of the proinflammatory cytokine IL-1b via an export pathway that depends on Atg5, inflammasome, at least one of the two mammalian Golgi reassembly stacking protein (GRASP) paralogues, GRASP55 (GORASP2) and Rab8a. This process, which is a type of unconventional secretion, expands the functional manifestations of autophagy beyond autodigestive and quality control roles in mammals. It enables a subset of cytosolic proteins devoid of signal peptide sequences, and thus unable to access the conventional pathway through the ER, to enter an autophagy-based secretory pathway facilitating their exit from the cytoplasm.

Autophagy is a cell biological pathway affecting immune responses. In vitro, autophagy acts as a cell-autonomous defense against Mycobacterium tuberculosis, but its role in vivo is unknown. Here we show that autophagy plays a dual role against tuberculosis: antibacterial and anti-inflammatory. M. tuberculosis infection of Atg5 fl/fl LysM-Cre + mice relative to autophagy-proficient littermates resulted in increased bacillary burden and excessive pulmonary inflammation characterized by neutrophil infiltration and IL-17 response with increased IL-1α levels. Macrophages from uninfected Atg5 fl/fl LysM-Cre + mice displayed a cell-autonomous IL-1α hypersecretion phenotype, whereas T cells showed propensity toward IL-17 polarization during nonspecific activation or upon restimulation with mycobacterial antigens. Thus, autophagy acts in vivo by suppressing both M. tuberculosis growth and damaging inflammation.utophagy is a fundamental cell biological process (1) with impact on aging, development, cancer, neurodegeneration, myodegeneration, metabolic disorders (2), idiopathic inflammatory diseases, and infection and immunity (3). Much of the physiological effects of autophagy are the result of degradative activities of autophagy (1), although biogenesis and secretory roles (4-6) of autophagy are beginning to be recognized (7). The execution of autophagy depends on factors collectively termed "Atg proteins," such as Atg5 (1) and Beclin 1 (Atg6) (8), whereas regulation of autophagy responds to various inputs via mammalian target of rapamycin (mTOR), including the presence of microbes (9), the TAB2/3-TAK1-IKK signaling axis (10), and processes downstream of pattern-recognition receptors and immune cytokine activation (3,(11)(12)(13).In the context of its immunological functions, autophagy acts in four principal ways (14). (i) Autophagy cooperates with conventional pattern-recognition receptors (PRRs), such as Toll-like receptors, RIG-I-like receptors (RLRs), and NOD-like receptors, and acts as both a regulator (11,12,15,16) and an effector of PRR signaling (17-19). (ii) Autophagy affects the presentation of cytosolic antigens in the context of MHC II molecules (20) in T-cell development, differentiation, polarization, and homeostasis (21,22). (iii) Most recently, autophagy has been shown to contribute to both the negative (6,7,(23)(24)(25) and positive (6, 7) regulation of unconventional secretion of the leaderless cytosolic proteins known as "alarmins," such as IL-1β and HMGB1. (iv) Autophagy can capture and eliminate intracellular microbes, including Mycobacterium tuberculosis (17, 26-29), which was one of the first two bacterial species (26, 30) to be recognized as targets for autophagic removal. This activity recently has been shown to depend on the recognition and capture of microbes by adaptors that represent a specialized subset of PRRs termed "sequestosome-like receptors" (SLRs) (31).M. tuberculosis is one of the first microbes recognized as being subject to elimination by immunological autophagy by murine and human...

Background: Both autophagy and the heat stress response represent protein management alternatives for the stressed cell. Their inter-relationship is not known. Results: Heat shock factor-1 knockdown increases and HSP70 overexpression inhibits autophagy in cell culture model. Preactivation of heat shock inhibits exercise-induced autophagy in humans. Conclusion: Heat shock response plays a negative role in autophagy regulation. Significance: Heat shock response regulates autophagy.

Prevention of skipping of exon 7 during pre-mRNA splicing of Survival Motor Neuron 2 (SMN2) holds the promise for cure of spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. Here, we report T-cell-restricted intracellular antigen 1 (TIA1) and TIA1-related (TIAR) proteins as intron-associated positive regulators of SMN2 exon 7 splicing. We show that TIA1/TIAR stimulate exon recognition in an entirely novel context in which intronic U-rich motifs are separated from the 5 splice site by overlapping inhibitory elements. TIA1 and TIAR are modular proteins with three N-terminal RNA recognition motifs (RRMs) and a C-terminal glutamine-rich (Q-rich) domain. Our results reveal that any one RRM in combination with a Q domain is necessary and sufficient for TIA1-associated regulation of SMN2 exon 7 splicing in vivo. We also show that increased expression of TIA1 counteracts the inhibitory effect of polypyrimidine tract binding protein, a ubiquitously expressed factor recently implicated in regulation of SMN exon 7 splicing. Our findings expand the scope of TIA1/TIAR in genome-wide regulation of alternative splicing under normal and pathological conditions.Current estimates suggest that 95 to 100% of human genes with two or more exons are alternatively spliced, affecting all major aspects of cellular metabolism under normal and pathological conditions (12, 42). The mechanism of alternative splicing involves a complex combinatorial control in which exonic and intronic splicing enhancers (ESEs and ISEs, respectively), and silencers (ESSs and ISSs, respectively) play significant roles. In general, serine-and arginine-rich (SR) proteins promote exon inclusion through interactions with ESEs, whereas heteronuclear ribonucleoproteins (hnRNPs) promote exon exclusion through interactions with ESSs and ISSs (13, 34). Most of these proteins contain at least one RNA recognition motif (RRM) that is responsible for providing target specificity (11). Depending on the site of binding, SR proteins can also promote exon skipping, and hnRNPs can promote exon inclusion (17,26). Alternative splicing is also regulated by several other factors not related to SR proteins and hnRNPs. In addition, RNA structures that directly or indirectly affect spliceosome assembly and catalytic core formation could modulate the outcome of splicing (42, 47).The splicing reaction calls for the highest degree of precision since a shift in splicing position by 1 nucleotide could have devastating consequences (12). The biggest challenge in our understanding of alternative splicing emanates from our inability to fully comprehend the combinatorial control exerted by cis elements. Using functional or genomic approaches, a vast majority of studies have concentrated on deciphering the nature of cis elements located within exons (6,27,61,63,66). Very few studies have been dedicated to intronic cis elements, mostly focusing on the regions that flank exonic sequences (59,65,66,69). Recent genome-wide analyses of intronic sequences revealed significant ...

Here we report a novel finding of an antisense oligonucleotide (ASO) microwalk in which we examined the position-specific role of intronic residues downstream from the 59 splice site (59 ss) of SMN2 exon 7, skipping of which is associated with spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. Our results revealed the inhibitory role of a cytosine residue at the 10th intronic position ( 10 C), which is neither conserved nor associated with any known splicing motif. Significance of 10 C emerged from the splicing pattern of SMN2 exon 7 in presence of a 14-mer ASO (L14) that sequestered two adjacent hnRNP A1 motifs downstream from 10 C and yet promoted SMN2 exon 7 skipping. Another 14-mer ASO (F14) that sequestered both, 10 C and adjacent hnRNP A1 motifs, led to a strong stimulation of SMN2 exon 7 inclusion. The inhibitory role of 10 C was found to be tightly linked to its unpaired status and specific positioning immediately upstream of a RNA:RNA helix formed between the targeting ASO and its intronic target. Employing a heterologous context as well as changed contexts of SMN2 intron 7, we show that the inhibitory effect of unpaired 10 C is dependent upon a long-distance interaction involving downstream intronic sequences. Our report furnishes one of the rare examples in which an ASO-based approach could be applied to unravel the critical role of an intronic position that may not belong to a linear motif and yet play significant role through long-distance interactions.