Isolation and characterisation of a biotin-binding protein from the pregnant-rat serum and comparison with that from the chicken egg-yolk

A biotin-binding protein exhibiting partial immunological cross-reactivity with the purified chicken egg-yolk biotin-binding protein has been detected, for the first time, in the sera of pregnant/estrogenised female rats but not of the normal males. This protein, purified by affinity chromatography on a biotin-AH-Sepharose was homogeneous by electrophoretic and immunological criteria. It was a glycoprotein of Mr 66,000 without any detectable subunites, had a pI 4.1, and specifically bound [14C]biotin. Several structural and functional features of the biotin-binding protein of rat and chicken were found to be similar. These included immunological cross-reactivity, acidic and glycoprotein nature, ability to tightly bind [14C]biotin, estrogen stimulation for their appearance in circulation, and the pattern of distribution of radioiodinated peptides upon proteolysis with trypsin.     

A specificity map for the PDZ domain family

PDZ domains are protein-protein interaction modules that recognize specific C-terminal sequences to assemble protein complexes in multicellular organisms. By scanning billions of random peptides, we accurately map binding specificity for approximately half of the over 330 PDZ domains in the human and Caenorhabditis elegans proteomes. The domains recognize features of the last seven ligand positions, and we find 16 distinct specificity classes conserved from worm to human, significantly extending the canonical two-class system based on position -2. Thus, most PDZ domains are not promiscuous, but rather are fine-tuned for specific interactions. Specificity profiling of 91 point mutants of a model PDZ domain reveals that the binding site is highly robust, as all mutants were able to recognize C-terminal peptides. However, many mutations altered specificity for ligand positions both close and far from the mutated position, suggesting that binding specificity can evolve rapidly under mutational pressure. Our specificity map enables the prediction and prioritization of natural protein interactions, which can be used to guide PDZ domain cell biology experiments. Using this approach, we predicted and validated several viral ligands for the PDZ domains of the SCRIB polarity protein. These findings indicate that many viruses produce PDZ ligands that disrupt host protein complexes for their own benefit, and that highly pathogenic strains target PDZ domains involved in cell polarity and growth.     

Thraustochytrid Marine Protists: Production of PUFAs and Other Emerging Technologies

Thraustochytrids, the heterotrophic, marine, straminipilan protists, are now established candidates for commercial production of the omega-3 polyunsaturated fatty acid (ω-3 PUFA), docosahexaenoic acid (DHA), that is important in human health and aquaculture. Extensive screening of cultures from a variety of habitats has yielded strains that produce at least 50% of their biomass as lipids, and DHA comprising at least 25% of the total fatty acids, with a yield of at least 5 g L⁻¹. Most of the lipids occur as triacylglycerols and a lesser amount as phospholipids. Numerous studies have been carried out on salinity, pH, temperature, and media optimization for DHA production. Commercial production is based on a fed batch method, using high C/N ratio that favors lipid accumulation. Schizochytrium DHA is now commercially available as nutritional supplements for adults and as feeds to enhance DHA levels in larvae of aquaculture animals. Thraustochytrids are emerging as a potential source of other PUFAs such as arachidonic acid and oils with a suite of PUFA profiles that can have specific uses. They are potential sources of asataxanthin and carotenoid pigments, as well as other lipids. Genes of the conventional fatty acid synthesis and the polyketide-like PUFA synthesis pathways of thraustochytrids are attracting attention for production of recombinant PUFA-containing plant oils. Future studies on the basic biology of these organisms, including biodiversity, environmental adaptations, and genome research are likely to point out directions for biotechnology explorations. Potential areas include enzymes, polysaccharides, and secondary metabolites.     

Glucose and phosphate inhibit respiration and oxidative metabolism in cultured hamster eight-cell embryos: evidence for the "crabtree effect"

The development of hamster eight-cell embryos is inhibited by glucose in culture medium containing inorganic phosphate (Pi). This is hypothetically attributed to the "Crabtree effect," in which enhanced glycolysis inhibits respiratory activity and oxidative metabolism. To examine this hypothesis, oxygen consumption of hamster eight-cell embryos was measured using a microelectrode. A two- to three-fold decrease in oxygen consumption was observed in embryos cultured with glucose and Pi. Oxidizable substrates and intermediates of the Krebs cycle supported embryo development only in the absence of glucose and Pi; Krebs cycle inhibitors (fluoroacetate and arsenite) arrested embryo development. Under anaerobic conditions, pyruvate and lactate did not support embryo development. Inhibition of both respiration and oxidative activity in cultured hamster embryos by glucose and Pi is consistent with the existence of a Crabtree effect and indicates that the metabolic properties of preimplantation embryonic cells differ markedly from those of most somatic cells and resemble some cancer cells.     

Thraustochytrium gaertnerium sp. nov.: a new thraustochytrid stramenopilan protist from mangroves of Goa, India

Thraustochytrids are ubiquitous, chemo-organotrophic, marine stramenipilan protists belonging to the class Labyrinthulomycetes. Their taxonomy is largely based on life cycle development stages. We describe here a new species of thraustochytrid isolated from mangroves of Goa, India. The organism is characterized by large zoosporangia with two distinct development cycles. In one, typical thalli with ectoplasmic net elements mature into zoosporangia that divide to form heterokont biflagellate zoospores, leaving behind a proliferation body. In the second type, the thalli develop into amoeboid cells, reminiscent of the genus Ulkenia Gaertner. Unlike Ulkenia, however, the 'amoebae' do not immediately produce zoospores, but round up prior to division into zoospores. The two types of development occur simultaneously in single cell-derived in- vitro cultures. Molecular characterization of the new isolate involving 18S rRNA gene typing and comparative phylogenetic analysis further establish it to be a new and distinct thraustochytrid species with Schizochytrium aggregatum Goldstein and Belsky and Thraustochytrium kinnei Gaertner as the closest forms. We have named this new species as Thraustochytrium gaertnerium, deriving its species name in honour of Dr Alwin Gaertner, a pioneer in the studies of taxonomy and ecology of thraustochytrids.     

Successful recovery of preimplantation embryos by nonsurgical uterine flushing in the bonnet monkey

A major limitation to progress in primate embryology is the lack of an adequate supply of preimplantation embryos. We describe a method for recovering preimplantation-embryos in bonnet monkeys (Macaca radiata ) using a nonsurgical uterine flushing technique similar to the one previously employed in rhesus monkeys. Forty cyclic females were screened for cervical cannulation, and 10% of these had an impassable cervix. Eleven females suitable for cannulation were selected, and 27 menstrual cycles were monitored over a 5-mo period. Seventy-one percent of the cycles showed estrogen peaks, which were observed between Days 9 and 14 of the cycle. Following natural mating, uterine flushings were performed on Days 5 to 8 of pregnancy (Day 0 = the day following the estrogen peak). Of the 27 recovery attempts, 9 (33.3%) resulted in the recovery of ovulation products, including those of an unfertilized oocyte and empty zona (2 cases), retarded cleavage-stage (4 to 8-cell) embryos (4 cases), morula (1 case) and blastocysts (2 cases). These results show, for the first time, that the nonsurgical uterine flushing technique can be successfully performed to recover uterine-stage preimplantation embryos from bonnet monkeys.     

Comparison of biotin binding protein of pregnant rat serum with rat serum albumin

The purified biotin binding protein of pregnant rat serum was shown to be immunologically similar to rat serum albumin as assessed by a sensitive radioimmunoassay. In radioimmunoassay for rat biotin binding protein, the binding of [¹²⁵I] rat biotin binding protein to anti-chicken egg yolk biotin binding protein antibodies was displaced by both rat serum (10–100 nl) and purified rat serum albumin (0.1–10 ng). Similarly, in radioimmunoassay for rat serum albumin the binding of [¹²⁵I] rat serum albumin to either anti-rat serum albumin antibodies or anti-chicken egg yolk biotin binding protein antibodies was displaced by unlabelled rat biotin binding protein at comparable concentration range (0·5–10 ng). Significant fractions of radioiodinated rat biotin binding protein and rat serum albumin bound to antibodies to chicken egg yolk biotin binding protein. In immature rats, the circulating half-lives of rat biotin binding protein and rat serum albumin were determined to be 12 and 17 h respectively. The rat biotin binding protein and rat serum albumin were analysed by techniques that exploit their physicochemical properties. They displayed similar electrophoretic mobilities in alkaline as well as denaturing sodium dodecyl sulphate-polyacrylamide gels. However, in nonequilibrium pH gradient polyacrylamide gel electrophoresis, they resolved clearly. In two-dimensional tryptic peptide map analysis, the two proteins showed similarities as well as significant differences in the relative distribution patterns of their iodopeptides. These results showed that the primary structure of rat biotin binding protein and rat serum albumin were different in finer details despite the fact that they shared significant immunological cross-reactivity.     

The protein phosphatase 2A regulatory subunit B55α is a modulator of signaling and microRNA expression in acute myeloid leukemia cells

We recently discovered that the protein phosphatase 2A (PP2A) B55α subunit (PPP2R2A) is under-expressed in primary blast cells and is unfavorable for remission duration in AML patients. In this study, reverse phase protein analysis (RPPA) of 230 proteins in 511 AML patient samples revealed a strong correlation of B55α with a number of proteins including MYC, PKC α, and SRC. B55α suppression in OCI-AML3 cells by shRNA demonstrated that the B subunit is a PKCα phosphatase. B55α does not target SRC, but rather the kinase suppresses protein expression of the B subunit. Finally, the correlation between B55α and MYC levels reflected a complex stoichiometric competition between B subunits. Loss of B55α in OCI-AML3 cells did not change global PP2A activity and the only isoform that is induced is the one containing B56α. In cells containing B55α shRNA, MYC was suppressed with concomitant induction of the competing B subunit B56α (PPP2R5A). A recent study determined that FTY-720, a drug whose action involves the activation of PP2A, resulted in the induction of B55α In AML cells, and a reduction of the B subunit rendered these cells resistant to FTY-720. Finally, reduction of the B subunit resulted in an increase in the expression of miR-191-5p and a suppression of miR-142-3p. B55α regulation of these miRs was intriguing as high levels of miR-191 portend poor survival in AML, and miR-142-3p is mutated in 2% of AML patient samples. In summary, the suppression of B55α activates signaling pathways that could support leukemia cell survival.     

Molecular evidence of fungal signatures in the marine protist Corallochytrium limacisporum and its implications in the evolution of animals and fungi

Fungi, animals, and single-celled organisms belonging to the choanozoans together constitute the supergroup Opisthokonta. The latter are considered crucial in understanding the evolutionary origin of animals and fungi. The choanozoan Corallochytrium limacisporum is an enigmatic marine protist of considerable interest in opisthokontan evolution. Several isolates of the organism were obtained from a coral reef lagoon in the Lakshadweep group of islands of the Arabian Sea. The capability of these cultures to grow on media containing inorganic nitrogen sources prompted us to examine the possible presence of fungal signatures, namely the enzyme alpha-aminoadipate reductase (alpha-AAR) involved in the alpha-aminoadipate (AAA) pathway for synthesizing lysine and ergosterol, in one of the isolates. These features, as well as the sterol C-14 reductase gene involved in the sterol pathway of animals and fungi, were detected in the organism. Phylogenetic trees based on the alpha-AAR gene suggested that Corallochytrium limacisporum is a sister clade to fungi, while those based on the C-14 reductase gene did not adequately resolve whether the organism was more closely related to fungi or animals. While many studies indicate that Corallochytrium is a sister clade to animals, we suggest that further studies are required to examine whether this protist is in fact more closely related to fungi rather than to animals.