Development of real-time PCR assays for discrimination and quantification of two Perkinsus spp. in the Manila clam Ruditapes philippinarum

The Manila clam Ruditapes philippinarum is infected with 2 Perkinsus species, Perkinsus olseni and P. honshuensis, in Japan. The latter was described as a new species in Mie Prefecture, Japan, in 2006. Ray's Fluid Thioglycollate Medium (RFTM) assay has been most commonly used to quantify Perkinsus infection. However, this assay cannot discriminate between species that resemble one another morphologically. We developed real-time PCR assays for the specific quantification of P. olseni and P. honshuensis. DNA was extracted using Chelex resin. Cultured P. olseni and P. honshuensis cells were counted and spiked into uninfected clam gill tissue prior to DNA extraction to generate standard curves, which allowed quantification based on the PCR cycle threshold values. We compared the RFTM assay with both real-time PCR assays by quantifying Perkinsus spp. in gill tissue samples from the same individual clams obtained from various localities in Japan. Infection intensities estimated by both assays were significantly correlated (r2 = 0.70). Our results suggest that the prevalence and infection intensity of P. honshuensis are much lower than for P. olseni in Manila clams.     

Leptin inhibits amyloid β‐protein fibrillogenesis by decreasing GM1 gangliosides on the neuronal cell surface through PI3K/Akt/mTOR pathway

Leptin is a centrally acting hormone that controls metabolic pathways. Recent epidemiological studies suggest that plasma leptin is protective against Alzheimer's disease. However, the mechanism that underlies this effect remains uncertain. To investigate whether leptin inhibits the assembly of amyloid β‐protein (Aβ) on the cell surface of neurons, we treated primary neurons with leptin. Leptin treatment decreased the GM1 ganglioside (GM1) levels in the detergent‐resistant membrane microdomains (DRMs) of neurons. The increase in GM1 expression induced by leptin was inhibited after pre‐treatment with inhibitors of phosphatidylinositol 3‐kinase (LY294002), Akt (triciribine) and the mammalian target of rapamycin (i.e. rapamycin), but not by an inhibitor of extracellular signal‐regulated kinase (PD98059). In addition, pre‐treatment with these reagents blocked the induction of GM1 in DRMs by leptin. Furthermore, Aβ assembly on the cell surface of neurons was inhibited greatly after treatment with leptin. This reduction was markedly inhibited after pre‐treatment with LY294002, triciribine, and rapamycin. These results suggest that leptin significantly inhibits Aβ assembly by decreasing GM1 expression in DRMs of the neuronal surface through the phosphatidylinositol 3‐kinase/Akt/mammalian target of rapamycin pathway.

     

Dopamine Receptor Genes and Evolutionary Differentiation in the Domestication of Fighting Cocks and Long-Crowing Chickens

The chicken domestication process represents a typical model of artificial selection, and gives significant insight into the general understanding of the influence of artificial selection on recognizable phenotypes. Two Japanese domesticated chicken varieties, the fighting cock (Shamo) and the long-crowing chicken (Naganakidori), have been selectively bred for dramatically different phenotypes. The former has been selected exclusively for aggressiveness and the latter for long crowing with an obedient sitting posture. To understand the particular mechanism behind these genetic changes during domestication, we investigated the degree of genetic differentiation in the aforementioned chickens, focusing on dopamine receptor D2, D3, and D4 genes. We studied other ornamental chickens such as Chabo chickens as a reference for comparison. When genetic differentiation was measured by an index of nucleotide differentiation (N _ST) newly devised in this study, we found that the N_ST value of DRD4 for Shamo (0.072) was distinctively larger than those of the other genes among the three populations, suggesting that aggressiveness has been selected for in Shamo by collecting a variety of single nucleotide polymorphisms. In addition, we found that in DRD4 in Naganakidori, there is a deletion variant of one proline at the 24^th residue in the repeat of nine prolines of exon 1. We thus conclude that artificial selection has operated on these different kinds of genetic variation in the DRD4 genes of Shamo and Naganakidori so strongly that the two domesticated varieties have differentiated to obtain their present opposite features in a relatively short period of time.     

Convergence in Reflex Pathways from Multiple Cutaneous Nerves Innervating the Foot Depends upon the Number of Rhythmically Active Limbs during Locomotion

Neural output from the locomotor system for each arm and leg influences the spinal motoneuronal pools directly and indirectly through interneuronal (IN) reflex networks. While well documented in other species, less is known about the functions and features of convergence in common IN reflex system from cutaneous afferents innervating different foot regions during remote arm and leg movement in humans. The purpose of the present study was to use spatial facilitation to examine possible convergence in common reflex pathways during rhythmic locomotor limb movements. Cutaneous reflexes were evoked in ipsilateral tibialis anterior muscle by stimulating (in random order) the sural nerve (SUR), the distal tibial nerve (TIB), and combined simultaneous stimulation of both nerves (TIB&SUR). Reflexes were evoked while participants performed rhythmic stepping and arm swinging movement with both arms and the leg contralateral to stimulation (ARM&LEG), with just arm movement (ARM) and with just contralateral leg movement (LEG). Stimulation intensities were just below threshold for evoking early latency (<80 ms to peak) reflexes. For each stimulus condition, rectified EMG signals were averaged while participants held static contractions in the stationary (stimulated) leg. During ARM&LEG movement, amplitudes of cutaneous reflexes evoked by combined TIB&SUR stimulation were significantly larger than simple mathematical summation of the amplitudes evoked by SUR or TIB alone. Interestingly, this extra facilitation seen during combined nerve stimulation was significantly reduced when performing ARM or LEG compared to ARM&LEG. We conclude that locomotor rhythmic limb movement induces excitation of common IN reflex pathways from cutaneous afferents innervating different foot regions. Importantly, activity in this pathway is most facilitated during ARM&LEG movement. These results suggest that transmission in IN reflex pathways is weighted according to the number of limbs directly engaged in human locomotor activity and underscores the importance of arm swing to support neuronal excitability in leg muscles.     

Disturbed biopterin and folate metabolism in the Qdpr-deficient mouse

Quinonoid dihydropteridine reductase (QDPR) catalyzes the regeneration of tetrahydrobiopterin (BH4), a cofactor for monoamine synthesis, phenylalanine hydroxylation and nitric oxide production. Here, we produced and analyzed a transgenic Qdpr^−/− mouse model. Unexpectedly, the BH4 contents in the Qdpr^−/− mice were not decreased and even increased in some tissues, whereas those of the oxidized form dihydrobiopterin (BH2) were significantly increased. We demonstrated that unlike the wild-type mice, dihydrofolate reductase regenerated BH4 from BH2 in the mutants. Furthermore, we revealed wide alterations in folate-associated metabolism in the Qdpr^−/− mice, which suggests an interconnection between folate and biopterin metabolism in the transgenic mouse model.     

Metabolite Profiling Reveals YihU as a Novel Hydroxybutyrate Dehydrogenase for Alternative Succinic Semialdehyde Metabolism in Escherichia coli

The search for novel enzymes and enzymatic activities is important to map out all metabolic activities and reveal cellular metabolic processes in a more exhaustive manner. Here we present biochemical and physiological evidence for the function of the uncharacterized protein YihU in Escherichia coli using metabolite profiling by capillary electrophoresis time-of-flight mass spectrometry. To detect enzymatic activity and simultaneously identify possible substrates and products of the putative enzyme, we profiled a complex mixture of metabolites in the presence or absence of YihU. In this manner, succinic semialdehyde was identified as a substrate for YihU. The purified YihU protein catalyzed in vitro the NADH-dependent reduction of succinic semialdehyde to γ-hydroxybutyrate. Moreover, a yihU deletion mutant displayed reduced tolerance to the cytotoxic effects of exogenous addition of succinic semialdehyde. Profiling of intracellular metabolites following treatment of E. coli with succinic semialdehyde supports the existence of a YihU-catalyzed reduction of succinic semialdehyde to γ-hydroxybutyrate in addition to its known oxidation to succinate and through the tricarboxylic acid cycle. These findings suggest that YihU is a novel γ-hydroxybutyrate dehydrogenase involved in the metabolism of succinic semialdehyde, and other potentially toxic intermediates that may accumulate under stress conditions in E. coli.The search for novel enzymes is important to better our understanding of the metabolic systems of the cell. Although computational tools can be used to functionally annotate enzymes based on sequence homology, gene structure and expression, and prediction of enzyme-like domains, the identification of the exact physiological substrates remains difficult when sequence similarity to known enzymes is low (<60%) and requires experimental confirmation (1, 2). Consequently, many gaps remain in metabolic pathways even in the model microorganism Escherichia coli (3, 4). Moreover, the identification of dispensable enzymatic activities, such as metabolic bypass pathways or the characterization of enzymes that are expressed only under specific physiological conditions, is particularly challenging.The β-hydroxyacid dehydrogenase enzyme family is a structurally conserved group of enzymes that include β-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, and numerous uncharacterized homologs (5, 6). This enzyme family contains well conserved domains in its sequence that include a N-terminal Rossmann-fold characteristic of a dinucleotide binding site, a well defined sequence at the substrate binding site, and a conserved lysine residue proposed as a critical catalytic residue. This last specific structural feature has been proposed based on site-directed mutagenesis and x-ray crystal structures (6, 7). The E. coli K12 proteome appears to contain four β-hydroxyacid dehydrogenase paralogs. The product of the glxR gene has been identified as tartronate semialdehyde reductase, catalyzing the NAD⁺-dependent oxidation of d-glycerate and the NADH-dependent reduction of tartronate semialdehyde (8). This enzyme plays a role in allantoin utilization under anaerobic conditions in E. coli (9). However, the function of the other three representatives of the family remains unknown.Under aerobic conditions in E. coli, γ-aminobutyrate (GABA)² is metabolized via GABA transaminase (EC 2.6.1.19) (10) and oxidized to succinate by at least two different succinic semialdehyde dehydrogenases (EC 1.2.1.16 and EC 1.2.1.24) (11, 12), and then further metabolized in the tricarboxylic acid cycle. In some animals (13), plants (14), and bacterial species (15, 16), γ-hydroxybutyrate (GHB) can be produced during GABA catabolism through the reduction of succinic semialdehyde (SSA) under anaerobic conditions. A γ-hydroxybutyrate dehydrogenase (GHBDH) was recently identified in Arabidopsis thaliana (14). Interestingly, the Arabidopsis enzyme does not show significant homology with known GHBDHs, however, its sequence exhibits similarity to several dehydrogenases including β-hydroxyacid dehydrogenases and 6-phosphogluconate dehydrogenases. However, the existence of an equivalent of the GHBDH reaction and an alternative reductive pathway for GABA metabolism in E. coli is still unreported.We have previously developed a screening method, based on in vitro assays in combination with metabolite profiling by capillary electrophoresis-mass spectrometry (CE-MS), to discover novel enzymatic activities (17). We hereby refer to this method as Metabolic Enzyme and Reaction discovery by Metabolite profile Analysis and reactant IDentification (MERMAID). Using this method, the enzymatic activity of any uncharacterized protein can be tested in an unbiased way by monitoring changes in a complex metabolite mixture that are induced by the test protein. This can allow to directly determine the substrate(s) and/or product(s) of the reaction without designing specific assays. Compounds whose levels specifically decrease following incubation with a protein are likely substrates, whereas metabolites whose level increase during the incubation are likely products of the reaction. In this study, we screened the E. coli YihU protein using the MERMAID approach and observed that it displays reductase activity toward short chain aldehydes, predominantly toward SSA. This activity differs from that of the known β-hydroxyacid dehydrogenases. We further demonstrate the presence of an alternative reaction for SSA catabolism leading to the production of GHB in E. coli.     

Sites of Intra- and Intermolecular Cross-linking of the N-terminal Extension of Troponin I in Human Cardiac Whole Troponin Complex

Our previous studies (Howarth, J. W., Meller, J., Solaro, R. J., Trewhella, J., and Rosevear, P. R. (2007) J. Mol. Biol. 373, 706–722) of the unique N-terminal region of human cardiac troponin I (hcTnI), predicted a possible intramolecular interaction near the basic inhibitory peptide. To explore this possibility, we generated single cysteine mutants (hcTnI-S5C and hcTnI-I19C), which were labeled with the hetero-bifunctional cross-linker benzophenone-4-maleimide. The labeled hcTnI was reconstituted to whole troponin and exposed to UV light to form cross-linked proteins. Reversed-phase high-performance liquid chromatography and SDS-PAGE indicated intra- and intermolecular cross-linking with hcTnC and hcTnT. Moreover, using tandem mass spectrometry and Edman sequencing, specific intramolecular sites of interaction were determined at position Met-154 (I19C mutant) and Met-155 (S5C mutant) of hcTnI and intermolecular interactions at positions Met-47 and Met-80 of hcTnC in all conditions. Even though specific intermolecular cross-linked sites did not differ, the relative abundance of cross-linking was altered. We also measured the Ca²⁺-dependent ATPase rate of reconstituted thin filament-myosin-S1 preparation regulated by either cross-linked or non-labeled troponin. Ca²⁺ regulation of the ATPase rate was lost when the Cys-5 hcTnI mutant was cross-linked in the absence of Ca²⁺, but only partially inhibited with Cys-19 cross-linking in either the presence or absence of Ca²⁺. This result indicates different functional effects of cross-linking to Met-154 and Met-155, which are located on different sides of the hcTnI switch peptide. Our data provide novel evidence identifying interactions of the hcTnI-N terminus with specific intra- and intermolecular sites.The human cardiac variant of troponin I (hcTnI)² has structural and functional specializations that are related to its critical role in control of cardiac dynamics. These specializations include variations in amino acids that are significant factors in the response of the heart to: adrenergic stimulation (1), sarcomere length (2, 3), and pH (4, 5). An especially significant region of specialization is a unique N-terminal extension of 30–32 amino acids, which contains serial serines at positions 23/24 that are substrates for kinases that control cardiac dynamics (6–8). Despite its significance in control of cardiac function, molecular mechanisms of how the N-terminal human cardiac troponin I (N-hcTnI) region controls sarcomeric and cardiac function remain poorly understood. There is evidence that upon phosphorylation the interaction between the N-hcTnI and the N-lobe of N-hcTnC is weakened (9, 10). The structure of the N-hcTnI was missing in the crystal structure of cardiac troponin (11). However, we recently reported (12) the structure of the N-terminal peptide using NMR. Docking of this structure into the core troponin structure indicated the potential for a previously unappreciated intramolecular interactions of the N terminus with the regions at or near the highly basic inhibitory peptide region of cardiac troponin (12, 13). This interaction appeared plausible not only on the basis of the structure of hcTnI, but also on the basis of the preponderance of basic amino acids in the inhibitory peptide and the presence of acidic residues in the N terminus.In experiments reported here, we tested the hypothesis that the unique N-terminal region of hcTnI engages in both intra- and intermolecular interactions. We introduced Cys residues into the N-hcTnI at positions 5 and 19 and labeled the Cys residue with the hetero-bifunctional cross-linker, BP-MAL, which upon UV irradiation cross-links to residues within ∼10 Å of the modified Cys (14). We analyzed the cross-linked peptides by Edman sequencing and mass spectrometry to determine specific sites of interaction. The intramolecular sites of interaction were Met-154 and Met-155 in the hcTnI switch peptide for labeled positions 19 and 5, respectively. The intermolecular cross-linking sites on N-hcTnC were 47 and 80 for hcTnI labeled at either position 5 or 19. Measurement of Ca²⁺-dependent ATPase rate in reconstituted preparations indicated that allosteric effects of the different specific intramolecular cross-links (position Met-154 versus Met-155) to different hydrophobic positions on the switch peptide may affect hcTnC interaction with the switch peptide.     

Chromobacterium pathogenicity island 1 type III secretion system is a major virulence determinant for Chromobacterium violaceum‐induced cell death in hepatocytes

Chromobacterium violaceum is a Gram‐negative bacterium that causes fatal septicaemia in humans and animals. C. violaceum ATCC 12472 possesses genes associated with two distinct type III secretion systems (T3SSs). One of these systems is encoded by Chromobacterium pathogenicity islands 1 and 1a (Cpi‐1/‐1a), another is encoded by Chromobacterium pathogenicity island 2 (Cpi‐2). Here we show that C. violaceum causes fulminant hepatitis in a mouse infection model, and Cpi‐1/‐1a‐encoded T3SS is required for its virulence. In addition, using C. violaceum strains with defined mutations in the genes that encode the Cpi‐1/‐1a or Cpi‐2 locus in combination with cultured mammalian cell lines, we found that C. violaceum is able to induce cytotoxicity in a Cpi‐1/‐1a‐dependent manner. Characterization of Chromobacterium‐induced cytotoxicity revealed that cell lysis by C. violaceum infection involves the formation of pore structures on the host cell membrane, as demonstrated by protection by cytotoxicity in the presence of osmoprotectants. Finally, we demonstrated that CipB, a Cpi‐1/‐1a effector, is implicated in translocator‐mediated pore formation and the ability of CipB to form a pore is essential for Chromobacterium‐induced cytotoxicity. These results strongly suggest that Cpi‐1/‐1a‐encoded T3SS is a virulence determinant that causes fatal infection by the induction of cell death in hepatocytes.     

Horizontal transfer of non-conjugative plasmid in colony biofilm of Escherichia coli on food-based media

We previously showed that non-conjugative, non-viral lateral plasmid transfer occurs in a colony biofilm of mixed Escherichia coli strains cultured on common laboratory media, such as LB agar. In this report, to investigate the possibility of this plasmid transfer under conditions possible outside the laboratory, we examined the activities of foodstuffs and mixed food extracts, which are possible nutrients for bacteria in human environments, for supporting lateral plasmid transfer. Lateral plasmid transfer occurred in colony biofilms grown on several foodstuffs (roasted meats) and on agar media containing mixed food extracts, which consisted of sugar, milk, and extracts of several foodstuffs (vegetables, fruits, and meats). Lateral plasmid transfer did not occur in liquid culture consisting of the same mixed food extracts, suggesting the importance of colony-biofilm formation. These results suggest the possibility that lateral transfer of non-conjugative plasmid between bacterial cells occurs in biofilms grown with foods or food-like nutrients in the environment.     

A systematic survey of in vivo obligate chaperonin‐dependent substrates

Chaperonins are absolutely required for the folding of a subset of proteins in the cell. An earlier proteome‐wide analysis of Escherichia coli chaperonin GroEL/GroES (GroE) interactors predicted obligate chaperonin substrates, which were termed Class III substrates. However, the requirement of chaperonins for in vivo folding has not been fully examined. Here, we comprehensively assessed the chaperonin requirement using a conditional GroE expression strain, and concluded that only ～60% of Class III substrates are bona fide obligate GroE substrates in vivo. The in vivo obligate substrates, combined with the newly identified obligate substrates, were termed Class IV substrates. Class IV substrates are restricted to proteins with molecular weights that could be encapsulated in the chaperonin cavity, are enriched in alanine/glycine residues, and have a strong structural preference for aggregation‐prone folds. Notably, ～70% of the Class IV substrates appear to be metabolic enzymes, supporting a hypothetical role of GroE in enzyme evolution.