Transcriptomic analysis of the autophagy machinery in crustaceans

Abstract

BackgroundThe giant freshwater prawn, Macrobrachium rosenbergii, is a decapod crustacean that is commercially important as a food source. Farming of commercial crustaceans requires an efficient management strategy because the animals are easily subjected to stress and diseases during the culture. Autophagy, a stress response process, is well-documented and conserved in most animals, yet it is poorly studied in crustaceans.ResultsIn this study, we have performed an in silico search for transcripts encoding autophagy-related (Atg) proteins within various tissue transcriptomes of M. rosenbergii. Basic Local Alignment Search Tool (BLAST) search using previously known Atg proteins as queries revealed 41 transcripts encoding homologous M. rosenbergii Atg proteins. Among these Atg proteins, we selected commonly used autophagy markers, including Beclin 1, vacuolar protein sorting (Vps) 34, microtubule-associated proteins 1A/1B light chain 3B (MAP1LC3B), p62/sequestosome 1 (SQSTM1), and lysosomal-associated membrane protein 1 (Lamp-1) for further sequence analyses using comparative alignment and protein structural prediction. We found that crustacean autophagy marker proteins contain conserved motifs typical of other animal Atg proteins. Western blotting using commercial antibodies raised against human Atg marker proteins indicated their presence in various M. rosenbergii tissues, while immunohistochemistry localized Atg marker proteins within ovarian tissue, specifically late stage oocytes.ConclusionsThis study demonstrates that the molecular components of autophagic process are conserved in crustaceans, which is comparable to autophagic process in mammals. Furthermore, it provides a foundation for further studies of autophagy in crustaceans that may lead to more understanding of the reproduction- and stress-related autophagy, which will enable the efficient aquaculture practices.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2996-4) contains supplementary material, which is available to authorized users.

Identification of the autophagy pathway in a mollusk bivalve, Crassostrea gigas

“…Similar results were obtained for the abalone Haliotis diversicolor for saGABARAP [11]. The presence of the MAP1LC3, SQSTM1, and BECN1 proteins was also detected by western blot in various tissues of the giant freshwater prawn M. rosenbergii including the hepatopancreas, ovary, muscle, brain, eyestalk, and thoracic glands [10]. More generally it is know that autophagy occurs at a basal level in mammalian systems [37].…”

“…The sequences of several proteins implicated in the core molecular machinery of autophagy were incomplete. However, these proteins that are conserved in other invertebrates like the crustacean Macrobrachium rosenbergii [10], play important roles in the mechanism of autophagy. In our study, we obtained the complete sequences for ATG7, ATG12, and ATG9 by RACE-PCR.…”

“…Homologs of ATG genes have been found in Homo sapiens, worms, flies, and mammals [1], and many have similar roles as in yeast [5]. The core molecular machinery of the autophagy pathway, which corresponds to ATG proteins essential for autophagosome formation [6,7], is highly conserved in eukaryotic cells including plants, yeast, and mammals [6,[8][9][10]. In yeast, this core mechanism consists of 18 Atg proteins, classified into several functional groups: the Atg1/ULK (unc-51 like autophagy activating kinase) complex, class III phosphatidylinositol 3-kinase (PtdIns3K) complex, Atg12/ATG12 (autophagy related 12) and Atg8/LC3 (autophagy related 8/microtubule associated protein 1 light chain 3) conjugation systems, and Atg9/ATG9 (autophagy related 9) and its cycling system [5].…”

Autophagy-Associated Shrinkage of the Hepatopancreas in Fasting Male Macrobrachium rosenbergii Is Rescued by Neuropeptide F

“…The autophagy machinery is ubiquitous in all living species, and it has been recently well characterized at genome level in crustaceans as well ( Suwansa-Ard et al, 2016 ). We have recently described the autophagy response to starvation in the ovary of the female giant freshwater prawn M. rosenbergii ( Kankuan et al, 2017 ).…”

“…Moreover, autophagy has been observed in the intestine and hepatopancreas of the freshwater shrimp, Neocaridina heteropoda , during cell death processes ( Rost-Roszkowska et al, 2012 ; Sonakowska et al, 2016 ). Recently, our group reported the presence of several autophagy gene mRNAs in the transcriptome and the expression of the corresponding proteins in various tissues of the giant freshwater prawn M. rosenbergii ( Suwansa-Ard et al, 2016 ). More recently, we showed that starvation could induce oocyte maturation in association with up-regulation of autophagy markers in the ovary tissue of the female prawns ( Kankuan et al, 2017 ).…”