Rapid detection of mecA and spa by the loop‐mediated isothermal amplification (LAMP) method

Aim: To develop a detection assay for staphylococcal mecA and spa by using loop‐mediated isothermal amplification (LAMP) method. Methods and Results: Staphylococcus aureus and other related species were subjected to the detection of mecA and spa by both PCR and LAMP methods. The LAMP successfully amplified the genes under isothermal conditions at 64°C within 60 min, and demonstrated identical results with the conventional PCR methods. The detection limits of the LAMP for mecA and spa, by gel electrophoresis, were 10² and 10 cells per tube, respectively. The naked‐eye inspections were possible with 10³ and 10 cells for detection of mecA and spa, respectively. The LAMP method was then applied to sputum and dental plaque samples. The LAMP and PCR demonstrated identical results for the plaque samples, although frequency in detection of mecA and spa by the LAMP was relatively lower for the sputum samples when compared to the PCR methods. Conclusion: Application of the LAMP enabled a rapid detection assay for mecA and spa. The assay may be applicable to clinical plaque samples. Significance and Impact of the Study: The LAMP offers an alternative detection assay for mecA and spa with a great advantage of the rapidity.     

ADP ribosylation of rat liver nucleosomal core histones.

When nucleosomal core histones were isolated from rat liver nuclei incubated with [14C]NAD+ and fractionated into the individual components (H2A, H2B, H3, and H4), [14C]adenosine diphosphate ribose (ADP-Rib) was found to be associated with all of them. However, while about 15% of the H2B molecules were modified, less than 2% of the other fractions contained radioactive ADP-Rib. The nucleotide attached to H2B was identified as a single monomer of ADP-Rib. On subjectint H2B to electrophoresis in polyacrylamide gels containing 2.5 M urea and 0.9 N acetic acid, one single band of H2B with 5% less mobility than the unomdified control was obtained. The linkage between H2B and ADP-Rib was rapidly hydrolyzed with 0.1 N NaOH or with 1 M neutral hydroxylamine. Hydrolysis of ADP-ribosylated H2B with trypsin generated a single peptide linked to ADP-Rib, which corresponded to the sequence Pro-Glu-Pro-Ala-Lys. We were able to dansylate the NH2-terminal proline, which proved that the imino group of this amino acid was not substituted. These findings, together with the chemical properties of the linkage, which were typical of those of an ester-like bond, strongly suggest that the ADP-Rib residue was linked to the gamma-COOH group of the glutamic acid in position 2 of H2B.     

Segregation of a QTL cluster for home-cage activity using a new mapping method based on regression analysis of congenic mouse strains

Recent genetic studies have shown that genetic loci with significant effects in whole-genome quantitative trait loci (QTL) analyses were lost or weakened in congenic strains. Characterisation of the genetic basis of this attenuated QTL effect is important to our understanding of the genetic mechanisms of complex traits. We previously found that a consomic strain, B6-Chr6C^MSM, which carries chromosome 6 of a wild-derived strain MSM/Ms on the genetic background of C57BL/6J, exhibited lower home-cage activity than C57BL/6J. In the present study, we conducted a composite interval QTL analysis using the F2 mice derived from a cross between C57BL/6J and B6-Chr6C^MSM. We found one QTL peak that spans 17.6 Mbp of chromosome 6. A subconsomic strain that covers the entire QTL region also showed lower home-cage activity at the same level as the consomic strain. We developed 15 congenic strains, each of which carries a shorter MSM/Ms-derived chromosomal segment from the subconsomic strain. Given that the results of home-cage activity tests on the congenic strains cannot be explained by a simple single-gene model, we applied regression analysis to segregate the multiple genetic loci. The results revealed three loci (loci 1–3) that have the effect of reducing home-cage activity and one locus (locus 4) that increases activity. We also found that the combination of loci 3 and 4 cancels out the effects of the congenic strains, which indicates the existence of a genetic mechanism related to the loss of QTLs.     

Raf Kinase Inhibitory Protein Function Is Regulated via a Flexible Pocket and Novel Phosphorylation-Dependent Mechanism

Raf kinase inhibitory protein (RKIP/PEBP1), a member of the phosphatidylethanolamine binding protein family that possesses a conserved ligand-binding pocket, negatively regulates the mammalian mitogen-activated protein kinase (MAPK) signaling cascade. Mutation of a conserved site (P74L) within the pocket leads to a loss or switch in the function of yeast or plant RKIP homologues. However, the mechanism by which the pocket influences RKIP function is unknown. Here we show that the pocket integrates two regulatory signals, phosphorylation and ligand binding, to control RKIP inhibition of Raf-1. RKIP association with Raf-1 is prevented by RKIP phosphorylation at S153. The P74L mutation increases kinase interaction and RKIP phosphorylation, enhancing Raf-1/MAPK signaling. Conversely, ligand binding to the RKIP pocket inhibits kinase interaction and RKIP phosphorylation by a noncompetitive mechanism. Additionally, ligand binding blocks RKIP association with Raf-1. Nuclear magnetic resonance studies reveal that the pocket is highly dynamic, rationalizing its capacity to interact with distinct partners and be involved in allosteric regulation. Our results show that RKIP uses a flexible pocket to integrate ligand binding- and phosphorylation-dependent interactions and to modulate the MAPK signaling pathway. This mechanism is an example of an emerging theme involving the regulation of signaling proteins and their interaction with effectors at the level of protein dynamics.Raf kinase inhibitory protein (RKIP/PEBP1) is a signaling modulator that regulates key signal transduction cascades in mammalian cells (reviewed in reference 16). A negative regulator of mitogen-activated protein kinase (MAPK) signaling (42), RKIP inhibits Raf kinase by binding directly to Raf-1, thereby preventing the phosphorylation and activation of Raf-1 (8, 38). RKIP functions as a regulator of the spindle checkpoint and promotes genomic stability by preventing MAPK from inhibiting Aurora B kinase (10). Consistent with this role, RKIP suppresses lung metastasis by prostate tumor cells in an orthotopic murine model (15). RKIP may be a general metastasis suppressor for solid tumors, since RKIP expression is low or undetectable in prostate and breast tumors, melanoma, hepatocellular carcinoma, and colorectal tumors (1, 2, 14, 15, 19, 34). Finally, RKIP suppresses NF-κB activation (43), inhibits G protein-coupled receptor (GPCR) kinase 2 (GRK2)-mediated downregulation of GPCRs (28), and potentiates the efficacy of chemotherapeutic agents (5). Thus, RKIP regulates three key mammalian signaling pathways involving MAPK, GPCR, and NF-κB signaling.RKIP is a member of the phosphatidylethanolamine binding protein (PEBP) family, which extends from bacteria to humans and consists of more than 400 proteins (16, 33). X-ray crystallographic studies have demonstrated that highly conserved sequences cluster around a pocket capable of binding anions, including o-phosphorylethanolamine (PE), acetate, and cacodylate (3, 35). This pocket is the only clearly identifiable feature for potential ligand binding within the RKIP architecture. Although the ligand-binding pocket shares homology with phospholipid binding domains, PEBP associates with phospholipid membranes primarily via peripheral, ionic interactions rather than more integrally inserting itself into the membrane (reference 39 and data not shown). The fact that RKIP interacts with protein targets such as Raf-1 and is phosphorylated by other protein kinases raises the possibility that the pocket mediates protein-protein interactions.The physiological role of the ligand-binding pocket is illustrated by studies of plant and yeast PEBPs. In the plant homologue of RKIP, mutation of the conserved DPDxP motif within the pocket (the equivalent of P74L) causes tomato plants to switch developmentally from shoot growth to flowering (32). The Saccharomyces cerevisiae RKIP/PEBP homologue, Tfs1p, functions as a negative regulator of RasGAP (Ira2), leading to upregulation of yeast Ras, activation of adenylyl cyclase, and increased cyclic AMP activation of protein kinase A (6). Yeast Ras signaling is inhibited by the corresponding P74L mutation in the pocket of Tfs1p, blocking Tfs1p interaction with Ira2. These results highlight the functional importance of the pocket among eukaryotic RKIP/PEBP family members. However, the molecular mechanism by which the pocket influences RKIP function and the significance of ligand binding to the pocket are unknown.Previous work has established the phosphorylation-mediated control of RKIP function. RKIP binds Raf-1, inhibiting Raf-1 activation and consequent signaling to MAPK (38, 42). When RKIP residue S153 is phosphorylated by protein kinase C (PKC), which occurs following cell stimulation with growth factors such as epidermal growth factor (EGF) or serum, RKIP can no longer bind to Raf-1, and thus it is inactivated as a Raf-1 inhibitor (8). Phosphorylation at S153 promotes the association of RKIP with, and inhibition of, GRK2, a kinase that phosphorylates and downregulates GPCRs such as the β-adrenergic receptor (28). Thus, S153 phosphorylation of RKIP is a key regulatory element of its association with and inhibition of different targets. The importance of the pocket and that of S153 phosphorylation have been independently established, but it is not clear whether these regulatory elements are functionally linked. Addressing this question is important for advancing our understanding of the molecular mechanism of RKIP function, which is likely to be pertinent to many RKIP/PEBP family members.In the present study, using cellular, biochemical, and structural approaches, we demonstrate that the highly conserved ligand-binding pocket integrates two regulatory signals, phosphorylation and ligand binding, to control RKIP function. Our results suggest that, in contrast to the mechanisms for other pocket-containing single-domain proteins, the structure and/or dynamics of the pocket influences RKIP interaction with and phosphorylation by kinases. This mechanism is likely conserved among RKIP homologues in eukaryotes.     

GC-1 mRHBDD1 knockdown spermatogonia cells lose their spermatogenic capacity in mouse seminiferous tubules

Background  

Apoptosis is important for regulating spermatogenesis. The protein mRHBDD1 (mouse homolog of human RHBDD1)/rRHBDD1 (rat homolog of human RHBDD1) is highly expressed in the testis and is involved in apoptosis of spermatogonia. GC-1, a spermatogonia cell line, has the capacity to differentiate into spermatids within the seminiferous tubules. We constructed mRHBDD1 knockdown GC-1 cells and evaluated their capacity to differentiate into spermatids in mouse seminiferous tubules.