Reconstruction and analysis of a genome-scale metabolic model for Eriocheir sinensis eyestalks

Reconstruction of Metabolic-Protein Interaction Integrated Network of Eriocheir sinensis and Analysis of Ecdysone Synthesis

Integrated networks have become a new interest in genome-scale network research due to their ability to comprehensively reflect and analyze the molecular processes in cells. Currently, none of the integrated networks have been reported for higher organisms. Eriocheir sinensis is a typical aquatic animal that grows through ecdysis. Ecdysone has been identified to be a crucial regulator of ecdysis, but the influence factors and regulatory mechanisms of ecdysone synthesis in E. sinensis are still unclear. In this work, the genome-scale metabolic network and protein-protein interaction network of E. sinensis were integrated to reconstruct a metabolic-protein interaction integrated network (MPIN). The MPIN was used to analyze the influence factors of ecdysone synthesis through flux variation analysis. In total, 236 integrated reactions (IRs) were found to influence the ecdysone synthesis of which 16 IRs had a significant impact. These IRs constitute three ecdysone synthesis routes. It is found that there might be alternative pathways to obtain cholesterol for ecdysone synthesis in E. sinensis instead of absorbing it directly from the feeds. The MPIN reconstructed in this work is the first integrated network for higher organisms. The analysis based on the MPIN supplies important information for the mechanism analysis of ecdysone synthesis in E. sinensis.

Molecular evidence for farnesoic acid O-methyltransferase (FAMeT) involved in the biosynthesis of vitellogenin in the Chinese mitten crab Eriocheir sinensis

Sesquiterpenoid methyl farnesoate (MF), a crustacean equivalent of insect juvenile hormone (JH III), has essential functions in regulating physiological processes in crustaceans, including reproduction and vitellogenesis. Farnesoic acid O-methyltransferase (FAMeT) is a key rate-limiting enzyme catalyzing the conversion of farnesoic acid (FA) to JH/MF in insects and crustaceans. In this study, a full-length cDNA of EsFAMeT from Eriocheir sinensis was isolated and characterized. The deduced EsFAMeT amino acid sequence indicated there were two conserved Methyltransf-FA domains characteristic of FAMeT family proteins. With use of sequence alignment analysis procedures, there was an indication that FAMeT proteins are highly conserved among crustaceans and FAMeT is more closely related to crustacean FAMeT than to insect FAMeT. Results from quantitative real-time PCR analysis revealed there was ubiquitous EsFAMeT in all tissues examined, with greater abundances of mRNA transcripts in the ovary. The transcription of EsFAMeT indicated there were stage-specific patterns in the hepatopancreas and ovary during ovarian development, with the greatest abundance during ovarian development Stages II and III, respectively. To investigate functions of EsFAMeT in vitellogenin biosynthesis in E. sinensis, RNA interference-mediated gene knockdown was used in vitro and in vivo. Injection of EsFAMeT dsRNA resulted in a marked decrease in EsVg (encoding vitellogenin) transcripts in the ovary and hepatopancreas both in vitro and in vivo. Results from the present study indicated EsFAMeT is involved in vitellogenin biosynthesis in the ovary and hepatopancreas of E. sinensis, providing a new resource to study modulatory effects of the FAMeT family of enzymes in crustacean reproduction.

RNAi silencing of the 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) gene inhibits vitellogenesis in Chinese mitten crab Eriocheir sinensis

The sesquiterpenoid methyl farnesoate (MF), a de-epoxide form of insect juvenile hormone III (JH III), plays an essential role in regulating many crucial physiological processes in crustaceans including vitellogenesis and reproduction. 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) is an important rate-limiting enzyme in the mevalonate pathway, which is critical for the synthesis of JH III and MF. In the present study, a full-length cDNA encoding HMGR (EsHMGR) in Eriocheir sinensis was isolated and characterised. Sequence analysis of EsHMGR revealed that it belongs to Class I HMGR family proteins with HMG-CoA-binding and NADPH-binding domains, both important for HMGR activity. In addition to its ubiquitous tissue expression, expression of EsHMGR was highly specific to the ovary, the main site of Vg synthesis. During ovarian development, EsHMGR expression in ovary displayed a stage-specific pattern, and was correlated with expression of vitellogenin (EsVg) in hepatopancreas, which suggests that EsHMGR possibly involved in vitellogenesis. To further investigate the functional role of EsHMGR in vitellogenin biosynthesis in E. sinensis, RNA interference-mediated gene silencing was carried out both in vitro and in vivo. Quantitative PCR results showed that injection of EsHMGR double-stranded RNA (dsRNA) led to a significant decrease in EsVg expression levels in ovary and hepatopancreas both in vitro and in vivo. Taken together, the results suggest that EsHMGR is involved in vitellogenin biosynthesis in female E. sinensis, which may provide a new resource for HMGR enzymes participating in reproduction in crustaceans.

Identification, characterization and mRNA transcript abundance profiles of the carboxylesterase (CXE5) gene in Eriocheir sinensis suggest that it may play a role in methyl farnesoate degradation

The sesquiterpenoid methyl farnesoate (MF) is a de-epoxidized form of insect juvenile hormone (JH) III in crustaceans, and its precise titer plays important roles in regulating many critical physiological processes, including reproduction and ovarian maturation. Understanding the synthetic and degradation pathways of MF is equally important for determining how to maintain MF titers at appropriate levels and thus for potential applications in crab aquaculture. Although the synthetic pathway of MF has been well established, little is known about MF degradation. Previous research proposed that specific carboxylesterases (CXEs) that degrade MF in crustaceans are conserved from those of JH III. In this study, we identified a novel Es-CXE5 gene from Eriocheir sinensis. The Es-CXE5 protein contains some conserved motifs, including catalytic triad and oxyanion hole, which are characteristics of the biologically active CXE family. The phylogenetic analysis showed that Es-CXE5 belongs to the hormone/semiochemical processing group of the CXE family. Moreover, Tissue and stage-specific expression results suggested that Es-CXE5 expression in hepatopancreas was highest and associated with the hemolymph MF titer. Furthermore, Es-CXE5 mRNA transcripts were detected in both in vitro and in vivo experiments and ESA experiment in the hepatopancreas and ovary. The results of this study showed that Es-CXE5 mRNA abundance in the hepatopancreas was notably induced by MF addition but had no effect on the ovary. Taken together, our results suggest that Es-CXE5 may degrade MF in the hepatopancreas and may thus be involved in ovarian development in E. sinensis.

Potential role of Methoprene-tolerant (Met) in methyl farnesoate-mediated vitellogenesis in the Chinese mitten crab (Eriocheir sinensis)

Methoprene-tolerant (Met) belongs to the basic helix-loop-helix (bHLH)-Per-Arnt-Sim (PAS) family of nuclear transcriptional regulators and is a leading candidate receptor for juvenile hormone (JH III) in insects. Methyl farnesoate (MF) is a de-epoxide form of JH III that regulates many developmental processes in crustaceans, including reproduction, molting, and morphogenesis, much like JH III in insects. In this study, the full-length cDNA for Met was cloned from the Chinese mitten crab (Eriocheir sinensis) (EsMet). The amino acid sequence of EsMet contains three conserved domains (bHLH, PAS-A, and PASB) characteristic of the bHLH-PAS family, having six conserved amino acid residues specifically responsible for JH or MF binding. Tissue distribution analysis revealed that EsMet mRNA is highly expressed in the hepatopancreas. In addition, EsMet and EsVg expression in the hepatopancreas were found to be significantly increased in early endogenous vitellogenic oocytes (stage II) during ovarian development, and the hemolymph MF titer was significantly increased in late exogenous vitellogenic oocytes (stage III), indicating that EsMet is involved in vitellogenesis regulation. In vitro, MF addition markedly upregulated EsMet and EsVg expression in hepatopancreatic tissue, but only EsVg was induced in ovarian tissue. In vivo, EsMet and EsVg expression in the hepatopancreas were both significantly and synchronously increased after MF injection, but not in the ovaries. In addition, EsMet and EsVg expression were upregulated in the hepatopancreas after eyestalk ablation, while only EsVg expression was induced in the ovaries. Thus, our results indicate that Met may act as a receptor for MF in MF-mediated vitellogenesis in crustaceans.

Reconstruction of Eriocheir sinensis Y-organ Genome-Scale Metabolic Network and Differential Analysis After Eyestalk Ablation

Genome-scale metabolic network (GSMN) has been proven to be a useful tool for the system analysis of organism metabolism and applied to deeply explore the metabolic functions or mechanisms in many organisms, including model or non-model organisms. However, the systematic studies on the metabolisms of aquatic animals are seldom reported, especially the aquatic crustaceans. In this work, we reconstructed an Eriocheir sinensis Y-organ GSMN based on the transcriptome sequencing of Y-organ, which includes 1,645 reactions, 1,885 unigenes, and 1,524 metabolites distributed in 100 pathways and 11 subsystems. Functional module and centrality analysis of the GSMN show the main metabolic functions of Y-organ. Further analysis of the differentially expressed unigenes in Y-organ after eyestalk ablation reveals that 191 genes in the network were up-regulated and 283 were down-regulated. The unigenes associated with the ecdysone synthetic pathway were all up-regulated, which is consistent with the report on the increasing secretion of ecdysone after eyestalk ablation. Besides, we compared the Y-organ GSMN with that of E. sinensis eyestalk and hepatopancreas, and we analyzed the specific metabolisms in each organ. The specific metabolisms and pathways of these three networks are closely related to their corresponding metabolic functions. The GSMN reconstructed in this work provides a new method and many novel clues for further understanding the physiological function of Y-organ. It also supplies a new platform for the investigation of the interactions among different organs in the growth process of E. sinensis.

Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production

In this study, we reconstructed for the first time a genome-scale metabolic model (GSMM) of Ganoderma lucidum strain CGMCC5.26, termed model iZBM1060, containing 1060 genes, 1202 metabolites, and 1404 reactions. Important findings based on model iZBM1060 and its predictions are as follows: (i) The extracellular polysaccharide (EPS) biosynthetic pathway was elucidated completely. (ii) A new fermentation strategy is proposed: addition of phenylalanine increased EPS production by 32.80% in simulations and by 38.00% in experiments. (iii) Eight genes for key enzymes were proposed for EPS overproduction. Model iZBM1060 provides a useful platform for regulating EPS production in terms of system metabolic engineering for G. lucidum, as well as a guide for future metabolic pathway construction of other high value-added edible/ medicinal mushroom species.

Similarities between decapod and insect neuropeptidomes

Background. Neuropeptides are important regulators of physiological processes and behavior. Although they tend to be generally well conserved, recent results using trancriptome sequencing on decapod crustaceans give the impression of significant differences between species, raising the question whether such differences are real or artefacts. Methods. The BLAST+ program was used to find short reads coding neuropeptides and neurohormons in publicly available short read archives. Such reads were then used to find similar reads in the same archives, and the DNA assembly program Trinity was employed to construct contigs encoding the neuropeptide precursors as completely as possible. Results. The seven decapod species analyzed in this fashion, the crabs Eriocheir sinensis, Carcinus maenas and Scylla paramamosain, the shrimp Litopenaeus vannamei, the lobster Homarus americanus, the fresh water prawn Macrobrachium rosenbergii and the crayfish Procambarus clarkii had remarkably similar neuropeptidomes. Although some neuropeptide precursors could not be assembled, in many cases individual reads pertaining to the missing precursors show unambiguously that these neuropeptides are present in these species. In other cases, the tissues that express those neuropeptides were not used in the construction of the cDNA libraries. One novel neuropeptide was identified: elongated PDH (pigment dispersing hormone), a variation on PDH that has a two-amino-acid insertion in its core sequence. Hyrg is another peptide that is ubiquitously present in decapods and is likely a novel neuropeptide precursor. Discussion. Many insect species have lost one or more neuropeptide genes, but apart from elongated PDH and hyrg all other decapod neuropeptides are present in at least some insect species, and allatotropin is the only insect neuropeptide missing from decapods. This strong similarity between insect and decapod neuropeptidomes makes it possible to predict the receptors for decapod neuropeptides that have been deorphanized in insects. This includes the androgenic insulin-like peptide that seems to be homologous to drosophila insulin-like peptide 8.