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Molecular Characterization , 3 D Modeling of Grass Carp Autophagy Related 16 Protein Like 1 ( ATG 16 L 1 )

Autophagy is a highly conserved homoeostatic mechanism, which plays a pivotal role in both metabolism and immune systems. Among autophagy related (ATG) proteins, ATG16L1 assists the formation of the phagophore and participates in the resistant of bacterial invasion in mammals. However, in grass carp (ctenopharyngodon idellus), one of the four major Chinese carps, the characterization of ATG16L1 remains to be defined. This paper described the cloning and characterization of grass carp ATG16L1 (gcATG16L1) and the 3D structure of its WD40-repeat domain was predicted. The CDS of gcATG16L1 consists of 1872 base pairs and encodes 624 amino acids with three conserved domains, a ATG5-binding domain, a coiled-coil domain (CCD), and a WD40-repeat domain. The phylogenetic analysis clusters gcATG16L1 with common carp but independently of the zebrafish homolog, since zebrafish ATG16L1 lacks WD40-repeat domain. The 3D structure of gcATG16L1 WD40-repeat domain was the first homology model of fish ATG16L1 and revealed a high similarity with the mammalian counterparts, which has been deduced to be involved in mediating interaction with several factors, such as ubiquitin and NOD-CARD, and regulating inflammatory response. Introduction Autophagy is a phenomenon firstly observed in yeast that cells ‘eat themselves’ in deprived conditions [1]. It’s a highly conserved homoeostatic mechanism in eukaryotes [2], which is initially activated by nutrient depletion or stress, then formatting a double-membrane autophagosome, sequestrating and degrading cytoplasmic constituents. Apart from its classic role in bulk-degradation, autophagy also plays a crucial role in fundamental biological process such as intracellular clearance, differentiation, development, programmed cell death, and antigen representation [3]. At least 18 ATG proteins are required in the autophagosome formatting process, and ATG5-ATG12-ATG16L1 conjugate complex is essential for the autophagosome formation [4]. Under physiological conditions, these three proteins are predominately diffusely distributed in the cytoplasm. Upon the induction of autophagy, the quantity of ATG5-ATG12-ATG16L1 punctate remarkably increased. The inhibition of autophagy in the upstream results in the disappearance of such punctate. However, downstream inhibition of autophagy at the level of autophagosome elongation leads to the punctate further accumulation [5].