Shubo Jin

Constructing and random sequencing analysis of normalized cDNA library of testis tissue from oriental river prawn (Macrobrachium nipponense)

The oriental river prawn, Macrobrachium nipponense, is an important aquaculture species in China. Sexual precocity is a serious problem because of genetic retrogression, which has negative effects on product quality and dramatically affects price. Culture of all-male populations of this species would be economically advantageous, as the males grow faster and reach a much larger size than females. Developing such a culture scheme will require discovery of sex- or reproduction-related genes that affect sexual maturity and sex determination. In this study, a high-quality normalized testis cDNA library was constructed to identify novel transcripts. Of the 5280 successful sequencing reaction yields, 5202 expressed tagged sequences (ESTs) with an average length of 954 bp. Ultimately, 3677 unique sequences, including 891 contigs and 2786 singletons, were identified based on cluster and assembly analyses. Sixteen hundred (43.5%) genes were novel based on the NCBI protein database, thus these unidentified genes may improve basic molecular knowledge about M. nipponense. Of the novel unigenes, 34.4% (715/2077) were homologous to insects, such as Tribolium castaneum, Drosophila spp. and Apis mellifera. Fifty-two genes were identified as sex- or reproduction-related based on Gene Ontology classification and sequence comparison with data from other publications. These genes can be classified into groups based on different functions, including 10 sex-determination related genes, 8 male-reproductive genes, 5 cathepsin-related genes, 20 ubiquitin-related genes, 5 ferritin-related genes, and 4 LRR genes. The results of this study provide new sequence information about M. nipponense, which will be the basis for further genetic studies of this species and other decapods crustaceans.

Characterization, expression, and function analysis of gonad-inhibiting hormone in Oriental River prawn, Macrobrachium nipponense and its induced expression by temperature.

Gonad-inhibiting hormone (GIH) is a member of crustacean hyperglycemic hormone family and plays a major role in regulating reproduction in crustaceans. In this study, a full-length cDNA of GIH of Oriental River prawn, Macrobrachium nipponense (Mn-GIH) was cloned from the eyestalk. A 1350 bp full-length Mn-GIH cDNA harbored 336 bp of an open reading frame encoding signal peptide of 112 amino acid residues. Sequence analysis revealed that the overall cDNA sequence and specific functional sites of Mn-GIH were highly conserved with those in other crustacean species. Expression analysis by quantitative real-time PCR demonstrated its tissue-specific, larval developmental stage-specific, and ovary developmental stage-specific expression pattern, respectively. The RNAi by GIH-ds-RNA in vivo injection was effective in this study and resulted a 50% (day 1), 83% (day 5) and 63% (day 9) down-regulation compared to control. The obvious changes of gonad somatic index (GSI) rate also provided strong evidence to the inhibition effects of GIH on ovary maturation and spawning. Four temperature gradients (12 °C ± 1 °C, 17 °C ± 1 °C, 22 °C ± 1 °C, 27 °C ± 1 °C) were set to imitate the temperature in breeding and non-breeding seasons. The observed expression profiles suggest that Mn-GIH did not display a high level expression as supposed to maintain an immature ovary state under low temperature (12 °C). The results indicated that GIH was probably activated to concentrating and working by a proper temperature before reaching to breeding season.

Molecular characterization of insulin-like androgenic gland hormone-binding protein gene from the oriental river prawn Macrobrachium nipponense and investigation of its transcriptional relationship with the insulin-like androgenic gland hormone gene

Insulin-like androgenic gland hormone-binding protein (IAGBP) has been investigated in crustaceans in vitro. However, the relationship between IAGBP and its putative binding protein partner insulin-like androgenic gland hormone (IAG) has not been studied at the transcriptional level in vivo. In the current study, we cloned the full-length cDNA of IAGBP from the oriental river prawn Macrobrachium nipponense (Mn-IAGBP) and investigated the transcriptional patterns of Mn-IAGBP and the M. nipponense IAG gene (Mn-IAG) at different developmental stages and in different tissues. Mn-IAGBP mRNA was detected in all examined tissues from adult male prawns, with the highest transcriptional levels in the testis. Mn-IAG mRNA was detected in the androgenic gland and hepatopancreas. The genomic sequences of Mn-IAGBP and Mn-IAG were isolated by genome walking and two gene copies were found in both Mn-IAGBP and Mn-IAG. The relationship between Mn-IAGBP and Mn-IAG at the transcriptional level was studied by RNA interference. Injection of Mn-IAGBP double-stranded RNA (dsRNA) significantly reduced the transcription of Mn-IAG, while injection of Mn-IAG dsRNA significantly reduced the transcription of Mn-IAGBP in testis, muscle, androgenic gland, and hepatopancreas. These results demonstrate the involvement of the IAGBP gene in IAG signaling in M. nipponense.

Molecular characterization and mRNA expression of hypoxia inducible factor-1 and cognate inhibiting factor in Macrobrachium nipponense in response to hypoxia

Hypoxia inducible factors (HIFs) are considered to be the master switches of oxygen-dependent gene expression in mammalian species. Currently, very little is known about the function of this important pathway or the molecular structures of key players in the hypoxia-sensitive Oriental River Prawn Macrobrachium nipponense. In this study, HIFs-1α (HIF-1α), -1β (HIF-1β) and HIF 1-alpha inhibitor (FIH-1) from M. nipponense were cloned. The 4903-bp cDNA of M. nipponense HIF-1α (MnHIF-1α) encodes a protein of 1088 aa, M. nipponense HIF-1β (MnHIF-1β) spans 2042bp encoding 663 aa and the 1163bp M. nipponense FIH-1 (MnFIH-1) specifies a polypeptide of 345 aa. MnHIF-1 and MnFIH-1 homologs exhibit significant sequence similarity and share key functional domains with previously described vertebrate and invertebrate isoforms. Phylogenetic analysis identifies that genetic diversification of HIF-1 and FIH-1 occurred within the invertebrate lineage, indicating functional specialization of the oxygen sensing pathways in this group. Quantitative real-time RT-PCR demonstrated that MnHIF-1 and MnFIH-1 mRNA are expressed in different tissues and exhibit transcriptional responses to severe hypoxia in gill and muscle tissue, consistent with their putative role in oxygen sensing and the adaptive response to hypoxia. The role of HIF-1α in response to hypoxia was further investigated in the gills and muscles of prawns using in situ hybridization. These results suggested that HIF-1α plays an important role in oxygen sensing and homeostasis in M. nipponense.

Comparative proteomic study of the response to hypoxia in the muscle of oriental river prawn (Macrobrachium nipponense)

UNLABELLED Adaptation to hypoxia is a complex process involving up- or down-regulation of numerous different proteins. In order to understand the molecular responses to hypoxia in crustacean muscle tissue, flow cytometry and oxidative stress analysis were used to explore the (hypoxia) physiological response on Macrobrachium nipponense. A 2D-gel-based proteomic approach was performed to compare the muscle proteome of hypoxic and normoxic M. nipponense. MALDI-TOF/TOF identified 15 and five proteins were significantly up- and down-regulated, respectively, in M. nipponense muscle under hypoxic conditions for 24h. Five spots were confirmed as hemocyanin, indicating an important role in environmental regulation. Real-time quantitative PCR confirmed that hemocyanin, heat shock protein 70, glutathione S-transferases, metallothionein, phosphofructokinase, and pyruvate kinase 2 were all up-regulated by hypoxia stress. These results suggest that the cellular response to hypoxia involves regulating proteins that function in maintaining antioxidative capacity, energy levels and muscle structure. Western blotting confirmed that the well-known hypoxic stress markers hemocyanin and heat shock protein 70 were up-regulated. These results increase our understanding of hypoxia-induced proteomic and transcriptional changes in M. nipponense muscle tissue. BIOLOGICAL SIGNIFICANCE This 2-DE proteomic study investigated differentially expressed proteins in the muscle of prawns following hypoxia. Identified proteins may have roles in the response to hypoxia. These results improve our understanding of hypoxic stress in crustaceans and aquatic ecosystems.

Molecular insights into reproduction regulation of female Oriental River prawns Macrobrachium nipponense through comparative transcriptomic analysis

The oriental river prawn, Macrobrachium nipponense, is an important commercial aquaculture resource in China. During breeding season, short ovary maturation cycles of female prawns cause multi-generation reunions in ponds and affect the growth of females representing individual miniaturization (known as autumn -propagation). These reproductive characteristics pose problems for in large - scale farming. To date, the molecular mechanisms of reproduction regulation of M. nipponense remain unclear. To address this issue, we performed transcriptome sequencing and gene expression analyses of eyestalk and cerebral ganglia of female M. nipponense during breeding and non-breeding seasons. Differentially expressed gene enrichment analysis results revealed several important reproduction related terms and signaling pathways, such as “photoreceptor activity”, “structural constituent of cuticle” and “G-protein coupled receptor activity”. The following six key genes from the transcriptome were predicted to mediate environmental factors regulating reproduction of M. nipponense: neuroparsin, neuropeptide F II, orcokinin II, crustacean cardioactive peptide, pigment-dispersing hormone 3 and tachykinin. These results will contribute to a better understanding of the molecular mechanisms of reproduction of oriental river prawns. Further detailed functional analyses of the candidate reproduction regulation related neuropeptides are needed to shed light on the mechanisms of reproduction of crustacean.

Molecular cloning, characterization, and temporal expression of the clock genes period and timeless in the oriental river prawn Macrobrachium nipponense during female reproductive development

The circadian clock is crucial for sustaining rhythmic biochemical, physiological, and behavioral processes in living creatures. In this study, we isolated and characterized two circadian clock genes in Macrobrachium nipponense, period (Mnper) and timeless (Mntim). The complete Mnper cDNA measures 4283bp in length with an open reading frame encoding 1292 amino acids, including functional domains such as PER-ARNT-SIM (PAS), cytoplasmic localization domain (CLD), TIM interaction site (TIS), and nuclear localization signal (NLS). The deduced Mntim protein comprises1540 amino acids with functional domains such as PER interaction site (PIS), NLS, and CLD. Tissue distribution analyses showed that the two genes were highly expressed in the eyestalk and brain in both males and females, as well as being expressed in the ovary. The expression profiles of Mnper and Mntim were determined in the eyestalk, brain, and ovary under simulated breeding season and non-breeding season conditions. The expression profiles of both Mnper and Mntim appeared to be unaffected in the eyestalk. However, the expression of both genes exhibited significant seasonal variations in the brain, and thus we assumed the brain to be their functional location. The expression profiles under different simulated seasons and the variations during different ovarian stages indicate that both genes might be involved with female reproduction. Especially the mRNA levels in the brain varied greatly during these stages indicating that the clock function in the brain is closely related to ovarian development and female reproduction. And the reproductive roles of clock genes need to be elucidated.

Identification of genes in the hypothalamus-pituitary-gonad axis in the brain of Amur sturgeons (Acipenser schrenckii) by comparative transcriptome analysis in relation to kisspeptin treatment

Kisspeptin plays an important role in the reproduction and onset of puberty in vertebrates through stimulation of gonadotropin-releasing hormone (GnRH). However, the mechanisms whereby kisspeptin-related genes regulate sexual differentiation in teleosts are poorly understood. We aimed to study the relationship between the hypothalamus-pituitary-gonad (HPG) axis and sexual differentiation in relation to kisspeptin in the sturgeon Acipenser schrenckii. We performed comparative transcriptomic analysis of the brains of sturgeons treated with KISS1-10 during the gonadal sex-differentiation-sensitive period (170-210days post-hatching (dph)) using an Illumina sequencing platform. We also analyzed mRNA expression levels of genes in the HPG axis using real-time quantitative polymerase chain reaction, and measured estradiol-17β (E2) and testosterone (T) levels in the brain and gonads using radioimmunological methods. A total of 75,960 and 74,907 unigenes were produced from Kisspeptin-treated and physiological saline-treated fish, respectively, among which 47,891 genes were matched to the non-redundant nr database. Potential genes and their functions were identified by GO (32,435), KEGG (37,619), and COG analyses (18,502). A total of 3169 unigenes were differentially expressed between transcriptomes in KISS1-10- and saline-injected fish, including 300 up-regulated and 2869 down-regulated unigenes. Gene expression levels of KISS1, G protein-coupled receptor-54, GnRH, androgen receptor, estrogen receptor, and Cyp19a in the brain and gonad were significantly affected by KISS1-10 treatment. KISS1-10 injection also significantly increased brain levels of E2 and T, compared with controls. These results support important roles for KISS1 in the regulation of the HPG axis, and in sex differentiation and reproduction in the Amur sturgeon.

Dietary cholesterol-induced transcriptome differences in the intestine, hepatopancreas, and muscle of Oriental River prawn Macrobrachium nipponense

Cholesterol is an important nutrient for crustaceans. In this study, we performed comparative transcriptome analyses to explore the transcriptome differences in the intestine, hepatopancreas, and muscle of Macrobrachium nipponense fed either a low cholesterol (LC) or high cholesterol (HC) diet (2.8 or 17.1g cholesterol per kg diet). High-throughput RNA-Seq was conducted, resulting in 7.65, 5.88, and 7.59G clean bases from the intestine, hepatopancreas, and muscle of the LC group, respectively, and 7.59, 6.73, and 6.70G clean bases from the same tissues of the HC group. Assembly of clean reads resulted in 230,946 unigenes. The following enriched pathways were identified: xenobiotic and drug metabolism by cytochrome P450; chloroalkane and chloroalkene degradation; metabolic and biosynthetic pathways; fatty acid metabolism and biosynthesis; and immune-related pathways. To the best of our knowledge, this is the first study to describe how functional unigenes and biosynthetic and metabolic pathways are affected by dietary cholesterol in aquatic crustaceans. Thus, these results contribute to our understanding of the molecular mechanisms underlying the cholesterol requirement of crustaceans.

iTRAQ-based quantitative proteomic analysis of embryonic developmental stages in Amur sturgeon, Acipenser schrenckii

The Amur sturgeon, Acipenser schrenckii, is an important aquaculture species in China with annual production of about 150 thousand tons in 2015. In this study, we investigated the regulatory proteins and pathways affecting embryonic development of Amur sturgeon, by analyzing of the differential proteomes among four embryonic developmental stages using isobaric tags for relative and absolute quantitation (iTRAQ), combined with the analysis of effects of microelements and antioxidants on embryonic development. Seventy-four, 77, and 76 proteins were differentially expressed according to iTRAQ analysis between the fertilized egg and blastula, blastula and neurula, and neurula and heart-beat stages, respectively. GO and KEGG enrichment analyses indicated that Gluconeogenesis, Ribosome and Proteasome were the most enriched pathways, which may promote energy formation, immune system protection and protein synthesis process in A. schrenckii. The measurement of microelements indicated that Mn, Cu and Fe were obtained from their parents or water environment in A. schrenckii, while Zn plays vital roles throughout embryonic development. The dramatically high level of malondialdehyde (MDA) across the embryonic development may be the main reason leading to a low hatching rate in A. schrenckii. This study provides the basis for further proteome analysis of embryonic development in A. schrenckii.