Characterization of a cDNA encoding a cytosolic peptidylprolyl cis-trans-isomerase from Blattella germanica

Molecular identification and expression analysis of a novel cyclophilin a gene in the red swamp crayfish, Procambarus clarkii

Cyclophilin A (Cyp A) is the main intracellular receptor of cyclosporin A (CsA) belonging to the immunophilin family, which is known as an effective immunosuppressive drug. This study aimed to gain insights into the structure and biological function of cyclophilin A in the red swamp crayfish, Procambarus clarkii (PcCypA). We cloned PcCypA by homology cloning and anchored polymerase chain reaction (PCR), and assessed its mRNA and protein expression levels in different tissues using quantitative real-time PCR and western blot analysis, respectively. The full-length DNA contained a 5' untranslated region (UTR) comprising 108 base pairs (bp), an open reading frame of 495 bp encoding a polypeptide of 164 amino acids with an estimated molecular mass of 17.3 kDa, and a 3' UTR of 281 bp including a significant poly(A) plus tail sequence. The predicted amino acid sequence of PcCypA shared high identity with CypA in other organisms. PcCypA transcripts were detected in the hepatopancreas, gill, heart, muscle, testis, and ovary of crayfish, with the highest expression levels in the heart. Western blot analysis found one 17-kDa band in all of the tissues examined, except for the ovary. Molecular identification and expression analysis of PcCypA will facilitate further studies of the immune defense mechanisms in red swamp crayfish, and provide new insights into freshwater invertebrate immunology.

Molecular cloning and functional characterization of cyclophilin A in yellow catfish (Pelteobagrus fulvidraco)

Cyclophilin A (CypA) is a ubiquitously expressed protein which involves in diverse pathological conditions including infection and inflammation. In this report, a CypA gene (designated as YC-CypA) was cloned from yellow catfish (Pelteobagrus fulvidraco) which is an important cultured fish species in Asian countries. The open reading frame (ORF) of YC-CypA encoded a polypeptide of 164 amino acids with calculated molecular weight of 17.70 kDa. The deduced amino acid sequences of the YC-CypA shared highly conserved structures with CypAs from the other species, indicating that YC-CypA should be a new member of the CypA family. Full-length YC-CypA protein was expressed in Escherichia coli and specific polyclonal antibody against YC-CypA was generated. The YC-CypA protein showed chemotactic activity by transwell migration assay. The mRNA and protein of YC-CypA could be detected in all examined tissues with relatively higher mRNA level in spleen and higher protein level in head kidney, respectively. The temporal expression patterns of YC-CypA, IL-1β and TNF-α mRNAs were analyzed in the liver, spleen and head kidney post of Edwardsiella ictaluri infection. By immunohistochemistry assay, slight enhancement of YC-CypA protein was observed in the liver, spleen, body kidney and head kidney of yellow catfish infected with E. ictaluri. In conclusion, YC-CypA of yellow catfish showed chemotactic activity in vitro and might have been involved in cytokines secretion in yellow catfish during the infection of E. ictaluri.

Validation of reference genes aiming accurate normalization of qPCR data in soybean upon nematode parasitism and insect attack

BACKGROUND

Soybean pathogens and pests reduce grain production worldwide. Biotic interaction cause extensive changes in plant gene expression profile and the data produced by functional genomics studies need validation, usually done by quantitative PCR. Nevertheless, this technique relies on accurate normalization which, in turn, depends upon the proper selection of stable reference genes for each experimental condition. To date, only a few studies were performed to validate reference genes in soybean subjected to biotic stress. Here, we report reference genes validation in soybean during root-knot nematode (Meloidogyne incognita) parasitism and velvetbean caterpillar (Anticarsia gemmatalis) attack.

FINDINGS

The expression stability of nine classical reference genes (GmCYP2, GmELF1A, GmELF1B, GmACT11, GmTUB, GmTUA5, GmG6PD, GmUBC2 and GmUBC4) was evaluated using twenty-four experimental samples including different organs, developmental stages, roots infected with M. incognita and leaves attacked by A. gemmatalis. Two different algorithms (geNorm and NormFinder) were used to determine expression stability. GmCYP2 and GmUBC4 are the most stable in different organs. Considering the developmental stages, GmELF1A and GmELF1B genes are the most stable. For spatial and temporal gene expression studies, normalization may be performed using GmUBC4, GmUBC2, GmCYP2 and GmACT11 as reference genes. Our data indicate that both GmELF1A and GmTUA5 are the most stable reference genes for data normalization obtained from soybean roots infected with M. incognita, and GmCYP2 and GmELF1A are the most stable in soybean leaves infested with A. gemmatalis.

CONCLUSIONS

Future expression studies using nematode infection and caterpilar infestation in soybean plant may utilize the reference gene sets reported here.

A cyclophilin A inducible expressed in gonad of zhikong scallop Chlamys farreri

Cyclophilin A (CypA), a receptor for the immunosuppressive agent cyclosporin A (CsA), is a cis-trans peptidyl-prolyl isomerase (PPIase) which accelerates the cis-trans isomerization of prolyl-peptide bonds, interacts with a variety of proteins and therefore regulates their activities. One CypA (designated CfCypA) cDNA was cloned from Chlamys farreri by expressed sequence tag (EST) and rapid amplification of cDNA ends (RACE) techniques. The full-length cDNA of CfCypA consisted of 1,248 nucleotides with a canonical polyadenylation signal sequence AATAAA, a poly (A) tail, and an open reading frame (ORF) of 495 nucleotides encoding a polypeptide of 164 amino acids. The deduced amino acid sequence shared high similarity with CypA from the other species, indicating that CfCypA should be a new member of the CypA family. Quantitative real-time (RT) PCR was employed to assess the mRNA expression of CfCypA in various tissues and its temporal expression in haemocytes and gonad of scallops challenged with Vibrio anguillarum. The mRNA transcripts of CfCypA could be detected in all the examined tissues with highest expression level in gonad. After bacterial challenge, the expression level of CfCypA was almost unchanged in haemocytes, but up-regulated in gonad and increased to the peak (22.59-fold; P < 0.05) at 4 h post-injection, and then dropped to the original level at 8 h post-injection. These results indicated that CfCypA was constitutive expressed in haemocytes, but could be induced in gonad, and perhaps played a critical role in response to the bacterial challenge in gonad.

Molecular coordinated regulation of gene expression during ovarian development in the penaeid shrimp

To understand the molecular events of ovarian development in penaeid shrimp, RNA arbitrarily primed polymerase chain reaction (RAP-PCR) was used to identify differentially expressed genes during ovarian maturation in Metapenaeus ensis. From a screening of 700 clones in a cDNA library of the shrimp ovary by the products of RAP-PCR of different maturation stages, 91 fragments with differentially expressed pattern as revealed by dot-blot hybridization were isolated and sequenced. Forty-two of these fragments show significant sequence similarity to known gene products and the differentially expressed pattern of 10 putative genes were further characterized via Northern hybridization. Putative glyceraldehyde-3-phosphate dehydrogenase and arginine kinase are related to provision of energy for active cellular function in oocyte development. Translationally controlled tumor protein, actin, and keratin are related to the organization of cytoskeleton to accomplish growth and development of oocytes. High mobility group protein DSP1, heat shock protein 70, and nucleoside diphosphate kinase may act as repressors before the onset of ovarian maturation. Peptidyl-prolyl cis-trans isomerase and glutathione peroxidase are related to the stabilization of proteins and oocytes. This study provides new insights on the molecular events in the ovarian development in the shrimp.

Cloning and characterisation of the immunophilin X-CypA in Xenopus laevis

This paper reports the cloning of Xenopus laevis, cyclophilin A gene, X-CypA. This study is the first developmental and functional characterisation in vivo of cyclophilin A in a vertebrate. X-CypA belongs to the superfamily of the immunophilin/PPIase proteins that can bind the immunosuppressant drug Cyclosporin A. Sequence analysis showed that X-CypA is highly conserved during evolution. RT-PCR and in situ hybridisation analysis showed that X-CypA expression is regulated during development and its transcripts are found in three major expression domains: nervous system, sensory organs and pronephros. Over-expression of X-CypA in embryos, analysed by in situ hybridisation and RT-PCR, leads to an expansion and disorganisation of the neural crest domain.

Control genes in quantitative molecular biological techniques: the variability of invariance

The measurement of transcript levels constitutes the foundation of today's molecular genetics. Independent of the techniques used, quantifications are generally normalised using invariant control genes to account for sample handling, loading and experimental variation. All of the widely used control genes are evaluated, dissecting different methodological approaches and issues regarding the experimental context (e.g. development and tissue type). Furthermore, the major sources of error are highlighted when applying these techniques. Finally, different approaches undertaken to assess the invariance of control genes are critically analysed to generate a procedure that will help to discern the best control for novel experiments.

Fast folding of Escherichia coli cyclophilin A: a hypothesis of a unique hydrophobic core with a phenylalanine cluster

Escherichia coli cyclophilin A, a 164 residue globular protein, shows fast and slow phases of refolding kinetics from the urea-induced unfolded state at pH 7.0. Given that the slow phases are independent of the denaturant concentration and may be rate-limited by cis/trans isomerizations of prolyl peptide bonds, the fast phase represents the true folding reaction. The extrapolation of the fast-phase rate constant to 0 M urea indicates that the folding reaction of cyclophilin A is extraordinarily fast and has about 700 s(-1) of the rate constant. Interrupted refolding experiments showed that the protein molecules formed in the fast phase had already been fully folded to the native state. This finding overthrows the accepted view that the fast folding is observed only in small proteins of fewer than 100 amino acid residues. Examination of the X-ray structure of cyclophilin A has shown that this protein has only one unique hydrophobic core (phenylalanine cluster) formed by evolutionarily conserved phenylalanine residues, and suggests that this architecture of the molecule may be responsible for the fast folding behavior.

Oxygen stress increases prolyl cis/trans isomerase activity and expression of cyclophilin 18 in rabbit blastocysts

The peptidyl-prolyl cis/trans isomerase (PPIase) activity and the expression of cyclophilins were studied in 6-day-old rabbit preimplantation embryos cultured under physiological and increased oxygen concentrations of 5% and 20% O(2), respectively. The PPIase activity was completely inhibited by cyclosporin A (CsA). The inhibitor of FK506-binding proteins, rapamycin, had no effect on the PPIase activity, indicating that the PPIase activity in rabbit blastocysts originates from cyclophilins. Using CsA affinity chromatography, only one cyclophilin with a molecular mass of about 17.8 kDa was separated. The cDNA of rabbit cyclophilin was cloned and sequenced. Analysis of the 682-base pair cDNA revealed an open reading frame coding for a polypeptide of 164 amino acid residues with a molecular weight of 17.83 kDa. Homologies of 90% and 96% for the cDNA and amino acid sequence, respectively, to the human CyP18 were found, suggesting that the novel rabbit cyclophilin is a member of the CyP18 family (rabCyP18). The transcription level of rabCyP18 mRNA was 8.3 +/- 0.6 pg in 100 ng total RNA in noncultured blastocysts. In vitro culture with moderate oxygen stress (20% O(2)) resulted in a 1.5-fold increase in rabCyP18 transcription and an increased PPIase activity compared to that of blastocysts cultured with 5% O(2). Increase in transcription rate and PPIase activity by oxygen stress suggests an involvement of CyP18 in oxygen defense in rabbit preimplantation embryos.

Characterisation and quantification of earthworm cyclophilins: identification of invariant and heavy metal responsive isoforms

We report the identification of two earthworm cyclophilin genes, which resemble the cytosolic cyclophilin-A and the signal sequence containing cyclophilin-B. Using fully quantitative PCR we were able to assess the transcript regulation of both cyclophilin isoforms, as well as a further independent control gene (actin), during exposure to heavy metals. Whilst the expression of cyclophilin-B and actin remained exceptionally constant, cyclophilin-A was up-regulated 38-fold. This intriguing observation has profound implications regarding cyclophilin's use as an invariant control and highlights the fact that it is essential to treat cyclophilin isoforms as separate entities, rather than one functional unit.