Three isoforms of the Atg16L1 protein contribute different autophagic properties

The mammalian Atg16L1 protein consists of a coiled-coil domain and a tryptophan-aspartic acid (WD) repeat domain and is involved in the process of autophagy. However, the mechanisms underlying the effect of the Atg16L1 isoforms on autophagy remain to be elucidated in humans. In the present study, we successfully cloned three isoforms: Atg16L1-1, which contains the complete sequence; Atg16L1-2, which lacks all of exon 8; and Atg16L1-3, which lacks the coiled-coil domain. Subsequent experiments showed that the three isoforms of Atg16L1 were colocalised with MDC within the cells. Quantitative analysis of fluorescence showed that the average number of dots of Atg16L1-1 that colocalised with MDC was higher than those of Atg16L1-2 and Atg16L1-3. The three isoforms of Atg16L1 also colocalised with the lysosome within the cells. The average number of dots of Atg16L1-1 that colocalised with the lysosome was higher than those of Atg16L1-2 and Atg16L1-3. However, although Atg16L1-1 and Atg16L1-3 colocalised with the mitochondria, Atg16L1-2 did not. Functional analysis showed that overexpression of the three isoforms of Atg16L1 had a stimulative effect on autophagy. Significant increase in the number of positive LC3-II dots per cell was observed in Atg16L1-1 (70.2 ± 2.39 dots); this number was greater than those of the other two isoforms. Atg16L1-2 appeared to have an average of 59.25 ± 2.22 LC3-II dots per cell. Atg16L1-3 appeared to have the least number of LC3-II dots per cell (48.25 ± 2.22 dots) (P < 0.001). Our results indicated that the degree of autophagy varied with different Atg16L1 isoforms. The different domains of Atg16L1 played different roles in the process of autophagy. The coiled-coil domain of Atg16L1 was involved in the process of autophagy.