cDNA Cloning and Partial Characterization of the DJ-1 Gene from Tribolium castaneum

The DJ-1 gene is highly conserved across a wide variety of organisms and it plays a role in anti-oxidative stress mechanisms in cells. The red flour beetle, Tribolium castaneum, is widely used as a model insect species because it is easy to evaluate gene function in this species using RNA interference (RNAi). The T. castaneum DJ-1 (TcDJ-1) sequence is annotated in the T. castaneum genome database; however, the function and characteristics of the TcDJ-1 gene have not been elucidated. Here, we investigated the cDNA sequence of TcDJ-1 and partially characterized its function. First, we examined the TcDJ-1 amino acid sequence and found that it was highly conserved with sequences from other species. TcDJ-1 mRNA expression was higher in the early pupal and adult developmental stages. We evaluated oxidant tolerance in TcDJ-1 knockdown adults using paraquat and found that adults with TcDJ-1 knockdown exhibited increased sensitivity to paraquat. Our findings show that TcDJ-1 has an antioxidant function, as observed for DJ-1 from other insects. Therefore, these results suggest that TcDJ-1 protects against oxidative stress during metamorphosis.

The PsMYB12L/PsDFR Module is Involved in Double-Color Formation in Paeonia Suffruticosa ‘Shima Nishiki’

Background: Paeonia suffruticosa ‘Shima Nishiki’ is a extremely precious double-color cultivar in the world because of its unique and attractive flower color. However, the underlying molecular mechanisms of its double-color formation have not been completely unravelled until now. In the present study, firstly, the full-length cDNA sequence, genomic DNA sequence, promoter region sequence of the PsDFR gene in the red and pink petals of the ‘Shima Nishiki’ cultivar were cloned and analyzed, respectively. Meanwhile, the methylation level of CpG island and promoter region of this gene in the red and pink petals was also measured. Moreover, the identification of regulatory effect of PsMYB114L/PsMYB12L and PsDFR was performed. Results: Here, we found that the full-length cDNA sequence, genomic DNA sequence, promoter region sequence of PsDFR were identical in the red and pink petals, respectively. There were some differences for the methylation level of this gene in the red and pink petals, but these differences were little and didn’t show obvious regularity. In addition, the regulatory effect of PsMYB12L and PsDFR was successfully identified. Conclusions: Based on these above results, we concluded that PsMYB12L regulating the differential expression of PsDFR may be a key reason for the double-color formation. These results will advance our understanding of the molecular regulatory mechanisms of double-color formation in P. suffruticosa ‘Shima Nishiki’.

A SmelAAT Acyltransferase Variant Causes a Major Difference in Eggplant (Solanum melongena L.) Peel Anthocyanin Composition

Eggplant berries are rich in anthocyanins like delphinidin-3-rutinoside (D3R) and nasunin (NAS), which are accumulated at high amounts in the peel. NAS is derived by D3R through acylation and glycosylation steps. The presence of D3R or NAS is usually associated with black-purple or lilac fruit coloration of the most cultivated varieties, respectively. Building on QTL mapping position, a candidate gene approach was used to investigate the involvement of a BAHD anthocyanin acyltransferase (SmelAAT) in determining anthocyanin type. The cDNA sequence comparison revealed the presence of a single-base deletion in D3R-type line ‘305E40’ (305E40_aat) with respect to the NAS-type reference line ‘67/3’. This is predicted to cause a frame shift mutation, leading to a loss of SmelAAT function and, thus, D3R retention. RT-qPCR analyses confirmed SmelAAT and 305E40_aat expression during berry maturation. In D3R-type lines, ‘305E40’ and ‘DR2’ overexpressing the functional SmelAAT allele from ‘67/3’, the transcript levels of the transgene, correlated with the accumulation of NAS in fruit peel. Furthermore, it was also found a higher expression of the transcript for glucosyltransferase Smel5GT1, putatively involved with SmelAAT in the last steps of anthocyanin decoration. Finally, an indel marker matching with anthocyanin type in the ‘305E40’ × ’67/3’ segregating population was developed and validated in a wide number of accessions, proving its usefulness for breeding purposes.

Isolation, sequencing and expression of the gene encoding acetoacetyl-coa thiolase from Panax vietnamensis Ha et Grushv.

Panax vietnamensis Ha et Grushv., naturally distributed in Ngoc Linh Mountain, is an endemic Panax species of Vietnam. For centuries, P. vietnamensis has been used in traditional folk medicine to treat many serious diseases or enhance physical strength. Ginsenosides are responsible for most of the medicinal effects of the Panax species. Acetoacetyl-CoA thiolase (AACT) is considered as an important enzyme involved in the biosynthesis of ginsenoside. In this study, a full-length cDNA of the gene encoding AACT protein (GeneBank accession number MZ272018) was obtained from P. vietnamensis using reverse transcription PCR. The gene open reading frame (1224 bp) encodes 408 amino acids. This cDNA sequence is 99.08% similar to the cDNA sequence of Panax notoginseng (KJ804173.1). The functional analysis of its protein by InterPro showed that the structure of AACT monomer consists of three domains, including thiolase-like domain (17-285), N-terminal (18-276), and C-terminal (286-406). Although there were some differences in the nucleotide sequence of the AACT cDNA gene between P. vietnamensis and the reference species, all important domains and sites related to the thiolase activity were observed. Phylogenetic analysis using AACT cDNA gene sequence revealed a close relationship of P. vietnamensis with P. notoginseng and Trachyspemum ammi. The quantitative real-time PCR results indicated the expression of AACT gene of P. vietnamensis depended on types of tissue and plant developmental stages (1, 4, 6 and 11 years old). The gene was expressed at higher levels in roots than in leaves and the highest expression of AACT gene was detected in the 11-year-old roots. The results provided valuable information for further studies on the biosynthesis of ginsenoside in P. vietnamensis in particular and Panax species in general.

Cloning and expression analysis of GATA1 gene in Carassius auratus red var

BackgroundGATA1 is a key transcription factor in the GATA family, and promotes the differentiation and maturation of red blood cell, which is essential for normal hematopoiesis.ResultsOur results showed that the cDNA sequence ofGATA1 was 2730 bp long encoding 443 amino acids. qRT-PCR analysis demonstrated thatGATA1 had the highest expression in testis (T), followed by pituitary (P) and spleen (S).GATA1 gene expression inC. auratusred var. embryo from the neuroblast stage (N) to the embryo hatching (H) changes continuously; and the gene expression levels of nonylphenol (NP)-treated and those of control embryos were significantly different. Moreover, Methylation levels ofGATA1gene in NP-treated embryos were higher than those in control embryos, indicating that NP affectedGATA1methylation.ConclusionsOur study provides cues for further studying the roles ofGATA1 gene in fish development, and suggested a potential molecular mechanism by which NP leads to abnormal development of fish embryos.

Expression, structure and function analysis of the sperm-oocyte fusion genes Juno and Izumo1 in sheep (Ovis aries)

Background JUNO and IZUMO1 are the first receptor-ligand protein pairs discovered to be essential for sperm-oocyte fusion; their interaction is indispensable for fertilization. Methods PCR was used to clone the full-length DNA sequence of the Juno gene in sheep. The single nucleotide polymorphism (SNP) loci of Juno were genotyped by Sequenom MassARRAY®. PCR combined with rapid amplification of cDNA Ends were used to clone the full-length cDNA sequence of Juno and Izumo1. Reverse transcriptase-PCR (RT-PCR) and real time-quantitative-PCR (RT-qPCR) were used to analyze the genes’ expression in tissues of sheep, and single cell RNA-seq was used to analyze the genes’ expression in oocytes, granulosa cells and follicular theca of polytocous and monotocous Small Tail Han ewes. Bioinformatics was used to analyze advanced structure and phylogeny of JUNO and IZUMO1 proteins. Results The full-length DNA sequence of the Juno gene in sheep was cloned and nine SNPs were screened. We found a significant association between the g.848253 C > A locus of Juno and litter size of Small Tail Han sheep (P < 0.05). The full-length cDNA sequence of Juno and Izumo1 genes from Small Tail Han sheep were obtained. We found a new segment of the Izumo1 CDS consisting of 35 bp, and we confirmed the Izumo1 gene has 9 exons, not 8. RT-qPCR showed that Juno and Izumo1 genes were highly expressed in ovarian and testicular tissues, respectively (P < 0.01). Single cell RNA-seq showed Juno was specifically expressed in oocytes, but not in granulosa cells or follicular theca, while Izumo1 displayed little to no expression in all three cell types. There was no difference in expression of the Juno gene in oocyte and ovarian tissue in sheep with different litter sizes, indicating expression of Juno is not related to litter size traits. Bioinformatic analysis revealed the g.848253 C > A locus of Juno results in a nonconservative missense point mutation leading to a change from Phe to Leu at position 219 in the amino acid sequence. Conclusions For the first time, this study systematically analyzed the expression, structure and function of Juno and Izumo1 genes and their encoded proteins in Small Tail Han sheep, providing the basis for future studies of the regulatory mechanisms of Juno and Izumo1 genes.

Identification of a Glycerophosphocholine Phosphodiesterase, GDE5, in chicken

Glycerophosphodiester phosphodiesterase (GDPD/GDE) catalyzes the hydrolysis of glycerophosphodiesters to glycerol 3-phosphate and alcohol. It was discovered that the glycerophosphodiesterase family plays a role in lipid metabolism and signal pathway in recent years, but little has been known about the characteristics of chicken GDEs. Here, chicken GDE5 (cGDE5) was identified and characterized for the first time. The full length coding cDNA sequence of cGDE5 was cloned, which encoded a polypeptide with 678 amino acids containing a carbohydrate-binding module 20 (CBM20) and a GDPD domain. Tissue expression profiles showed that cGDE5 mRNA was high in various tissues. such as heart, brain, skeletal muscle and testis. Moreover, cGDE5 was demonstrated to exhibit glycerophosphocholine phosphodiesterase activity. These results together suggested that cGDE5, as a unique member of GDE family, may play multiple roles as a cytoplasmic glycerophosphocholine phosphodiesterase.

Cloning and Expression Analysis of GATA1 gene in Carassius auratus red var.

Background: GATA1 is a key transcription factor in the GATA family, and promotes the differentiation and maturation of red blood cell, which is essential for normal hematopoiesis.Results: Our results showed that the cDNA sequence of GATA1 was 2730 bp long encoding 443 amino acids. qRT-PCR analysis demonstrated that GATA1 had the highest expression in testis(T), followed by pituitary(P) and spleen(S). GATA1 gene expression in C. auratus red var. embryo from the neuroblast stage (N) to the embryo hatching(H) changes continuously; and the gene expression levels of nonylphenol (NP)-treated and those of control embryos were significantly different. Moreover, Methylation levels of GATA1 gene in NP-treated embryos were higher than those in control embryos, indicating that NP affected GATA1 methylation.Conclusions: Our study provides cues for further studying the roles of GATA1 gene in fish development, and suggested a potential molecular mechanism by which NP leads to abnormal development of fish embryos.

A Cassava CPRF-2-like bZIP Transcription Factor Showed Increased Transcript Levels during Light Treatment

Background: bZIP proteins participate in the regulation of gene expression, playing crucial roles in various biological processes in plants, including response to environmental changes. Luminosity is an environmental factor of extreme importance for plant metabolism, acting as a regulator of its growth and development. Despite advances in the identification of bZIP proteins in several plant species, studies on these transcription factors in cassava are lacking. Cassava (Manihot esculenta Crantz) is one of the most important food crops in tropical and subtropical regions, mainly in developing countries, where its storage root is a major source of calories for low-income people. Objectives: Our main aim was the isolation of a cDNA sequence encoding a bZIP protein from cassava (MebZIP) as well as the in silico characterization of its nucleotide and deduced amino acid sequences. In addition, we evaluated the expression pattern of the MebZIP gene in response to light, and its possible relationship with regulation of the chalcone synthase (MeCHS) gene. Method: RT-PCR and 3’ and 5’ RACE assays were used to isolate the full-length cDNA sequence of MebZIP. Bioinformatics tools were used to characterize the nucleotide and amino acid sequences of MebZIP. Semiquantitative RT-PCR assays were used to evaluate the expression levels of MebZIP and MeCHS genes. Results: We isolated the full-length cDNA sequence of MebZIP with a 1320-bp ORF encoding a deduced protein with a predicted molecular weight and isoelectric point of 47 kDa and 5.85, respectively. Comparative analyses with GenBank sequences showed high identity of MebZIP with bZIP CPRF-2 of Hevea brasiliensis (XP_021650934) and Petroselinum crispum (Q99090.2). Besides the basic region and leucine zipper domains, MebZIP contains putative conserved domains (D1- D4), found in parsley CPRF-2 and bZIP proteins closely related to this protein. Since CPRF proteins are known for their function in regulation of the CHS gene by light, we evaluated the expression levels of the MebZIP gene and the possible target gene to be regulated by MebZIP (the MeCHS gene) in cassava under light conditions. Semi-quantitative RT-PCR assays revealed that MebZIP transcription increased in response to white light, with maximum expression levels at 6 h of light exposure. On the other hand, the expression levels of the MeCHS gene were statistically constant in all samples, indicating that they were not influenced by the experimental conditions used here. Conclusion: The putative MebZIP protein identified in this work contains the conserved domains (bZIP, D1-D4) that indicate its functionality, thus allowing it to be considered a new member of the bZIP transcription factor CPRF-2 family. The expression levels of the MebZIP gene increased during white light exposure, indicating a potential function in light-response in cassava.