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1.  A Complex Comprising Phosphatidylinositol 4-Kinase IIIβ, ACBD3, and Aichi Virus Proteins Enhances Phosphatidylinositol 4-Phosphate Synthesis and Is Critical for Formation of the Viral Replication Complex 
Journal of Virology  2014;88(12):6586-6598.
Phosphatidylinositol 4-kinase IIIβ (PI4KB) is a host factor required for the replication of certain picornavirus genomes. We previously showed that nonstructural proteins 2B, 2BC, 2C, 3A, and 3AB of Aichi virus (AiV), a picornavirus, interact with the Golgi protein, acyl-coenzyme A binding domain containing 3 (ACBD3), which interacts with PI4KB. These five viral proteins, ACBD3, PI4KB, and the PI4KB product phosphatidylinositol 4-phosphate (PI4P) colocalize to the AiV RNA replication sites (J. Sasaki et al., EMBO J. 31:754–766, 2012). We here examined the roles of these viral and cellular molecules in the formation of AiV replication complexes. Immunofluorescence microscopy revealed that treatment of AiV polyprotein-expressing cells with a small interfering RNA targeting ACBD3 abolished colocalization of the viral 2B, 2C, and 3A proteins with PI4KB. A PI4KB-specific inhibitor also prevented their colocalization. Virus RNA replication increased the level of cellular PI4P without affecting that of PI4KB, and individual expression of 2B, 2BC, 2C, 3A, or 3AB stimulated PI4P generation. These results suggest that the viral protein/ACBD3/PI4KB complex plays an important role in forming the functional replication complex by enhancing PI4P synthesis. Of the viral proteins, 3A and 3AB were shown to stimulate the in vitro kinase activity of PI4KB through forming a 3A or 3AB/ACBD3/PI4KB complex, whereas the ACBD3-mediated PI4KB activation by 2B and 2C remains to be demonstrated.
IMPORTANCE The phosphatidylinositol 4-kinase PI4KB is a host factor required for the replication of certain picornavirus genomes. Aichi virus, a picornavirus belonging to the genus Kobuvirus, forms a complex comprising one of the viral nonstructural proteins 2B, 2BC, 2C, 3A, and 3AB, the Golgi protein ACBD3, and PI4KB to synthesize PI4P at the sites for viral RNA replication. However, the roles of this protein complex in forming the replication complex are unknown. This study showed that virus RNA replication and individual viral proteins enhance the level of cellular PI4P, and suggested that the viral protein/ACBD3/PI4KB complex plays an important role in forming a functional replication complex. Thus, the present study provides a new example of modulation of cellular lipid metabolism by viruses to support the replication of their genomes.
PMCID: PMC4054359  PMID: 24672044
2.  Isolation of Maedi/Visna Virus from a Sheep in Japan 
Maedi/visna (MV) is a lentiviral disease of sheep caused by the maedi/visna virus (MVV). Although MV is prevalent in many countries, it had not been reported in Japan. In 2011, however, three sheep in northern Japan were reported to be seropositive against the MVV antigen, indicating a persistent MVV infection. In the present study, we isolated MVV from one sheep to confirm MVV infection and conducted genomic classification of the virus. The co-culture of leukocytes from a seropositive sheep with fetal goat lung cells resulted in the formation of syncytial cells and the amplification of a long terminal repeat sequence of MVV by polymerase chain reaction. The isolate was confirmed as being MVV, rather than the caprine arthritis-encephalitis virus based on phylogenetic analysis of the gag gene sequence. Although the sheep was asymptomatic, nonpurulent meningitis and demyelination were found in the spinal cord. These were considered to be early lesions associated with pathogenic MVV infection. Therefore, the present study demonstrated that MVV is distributed in Japan.
PMCID: PMC3982815  PMID: 24141278
maedi/visna; PCR; retrovirus; sheep; virus disease
3.  Fine mapping of the major Soybean dwarf virus resistance gene Rsdv1 of the soybean cultivar ‘Wilis’ 
Breeding Science  2013;63(4):417-422.
Soybean dwarf virus (SbDV), a Luteoviridae family member, causes dwarfing, yellowing and sterility of soybean (Glycine max), leading to one of the most serious problems in soybean production in northern Japan. Previous studies revealed that the Indonesian soybean cultivar ‘Wilis’ is resistant to SbDV and that the resistance can be introduced into Japanese cultivars. A major QTL for SbDV resistance has been reported between SSR markers Sat_217 and Satt211 on chromosome 5. In this study, we named this QTL Rsdv1 (resistance to SbDV) and developed near-isogenic lines incorporating Rsdv1 (Rsdv1-NILs) using Sat_217 and Satt211 markers. The Rsdv1-NILs were resistant to SbDV in greenhouse inoculation and field tests, indicating that Rsdv1 alone is sufficient for the resistance phenotype. We fine-mapped Rsdv1 within the 44-kb region between Sat_11 and Sct_13. None of the six genes predicted in this region was closely related to known virus resistance genes in plants. Thus, Rsdv1 may confer resistance by a previously unknown mechanism. We suggest that Rsdv1 may be a useful source for the Japanese soybean breeding program to introduce SbDV resistance.
PMCID: PMC3859353  PMID: 24399914
disease resistance; Glycine max; near-isogenic lines; SSR markers
4.  Understanding egorrhea from cultural-clinical psychology 
Based on his observations in Japanese clinical settings, Fujinawa (1972) conceptualized egorrhea syndrome, which includes symptoms such as erythrophobia, fear of eye-to-eye confrontation, olfactory reference syndrome, delusions of soliloquy, delusions of sleep talking, and thought broadcasting. The key feature of this syndrome is self-leakage, a perceived sense that one's personal internal information, such as feelings and thoughts, are leaking out. To reach a more comprehensive understanding of egorrhea, this paper aims to present general overview and reconsider the phenomenon of self-leakage using cultural-clinical psychology as a framework. First, the symptoms of egorrhea are reviewed in relation to other related psychopathologies such as social anxiety disorder (SAD) and taijin kyofusho (TKS), as well as schizophrenia. Second, a series of empirical studies conducted using Japanese non-clinical samples are summarized. The results of these studies form the basis for subsequent discussions, which incorporates the cultural-clinical psychology perspective proposed by Ryder et al. (2011). This paper ends with a general discussion regarding implications for research and clinical practice.
PMCID: PMC3842623  PMID: 24348445
egorrhea symptoms; cognitive model; taijin-kyofusho; schizophrenia; social anxiety disorder; culture
5.  Presumptive acute lung injury following multiple surgeries in a cat 
The Canadian Veterinary Journal  2013;54(4):381-386.
A 12-year-old, 3.5-kg spayed female domestic shorthair cat had a tracheal mass identified as malignant B-cell lymphoma. The cat had tracheal resection and subsequently developed laryngeal paralysis. Due to multiple episodes of respiratory distress the cat subsequently had tracheal surgeries. Finally, the cat had a sudden onset of severe respiratory distress and collapsed. Computed tomography imaging and arterial blood gas analysis supported a diagnosis of acute lung injury.
PMCID: PMC3595944  PMID: 24082167
6.  Herniation of Duodenum into the Right Ventral Hepatic Peritoneal Cavity with Groove Formation at the Ventral Hepatic Surface in a 2-Week-Old Chicken 
Internal hernia in avian species is very rare. A necropsy of a 2-week-old SPF White Leghorn chicken revealed that a loop of the duodenum and part of the pancreas (4 × 2 × 1 cm) was protruding through the abnormal foramen (2.5 cm in diameter) in the right posthepatic septum into the right ventral hepatic peritoneal cavity. The herniated loop was located underneath the ventral hepatic surface, leaving a groove on the right hepatic lobe (2 × 1.5 × 0.4 cm). The part of the pancreas involved in the hernia was grossly enlarged. Microscopically, a zone of pressure atrophy of hepatic tissue was characterized by crowdedness of hepatocytes with pyknotic nuclei and faint eosinophilic cytoplasm and indistinct narrow sinusoids. The pancreas revealed hypertrophy of the acinar cells with an increase in the secretory granules and basophilic cytoplasm. This is the first report of duodenum herniation into the right ventral hepatic peritoneal cavity resulting in groove formation on the ventral hepatic surface in a 2-week-old chicken.
PMCID: PMC3942940  PMID: 23759688
chicken; groove; hernia; posthepatic; septum
7.  Intrasynovial Tendon Graft for Chronic Flexor Tendon Laceration of the Finger: A Case Report 
We present the case of a patient with flexor digitorum profundus tendon laceration at the A2 pulley level caused by an injury to the base of the right ring finger by a knife. The patient was treated by flexor tendon reconstruction from the palm to the fingertip by using the left second toe flexor tendon as a graft, which improved the active range of motion. Further improvement was achieved by subsequent tenolysis, which eventually restored nearly normal function. Our experience with this case indicates that the intrasynovial tendon is a reasonable graft source for the synovial space in fingers and may enable restoration of excellent postoperative function.
PMCID: PMC3763753  PMID: 24015158
Flexor tendon graft; intrasynovial tendon; friction; tenolysis.
8.  Transient dissociation of the transducer protein from Anabaena sensory rhodopsin concomitant with formation of the M state produced upon photoactivation 
Journal of the American Chemical Society  2011;133(34):13406-13412.
Anabaena sensory rhodopsin (ASR), a microbial rhodopsin in the cyanobacterium sp. PCC7120, has been suggested to regulate cell processes in a light-quality-dependent manner (color-discrimination) through interaction with a water-soluble transducer protein (Tr). However, light-dependent ASR-Tr interaction changes have yet to be demonstrated. We applied the transient grating (TG) method to investigate protein–protein interaction between ASR with Tr. The molecular diffusion component of the TG signal upon photostimulation of ASRAT (ASR with an all-trans retinylidene chromophore) revealed that Tr dissociates from ASR upon formation of the M-intermediate and rebinds to ASR during the decay of M; i.e. light induces transient dissociation of ASR and Tr during the photocycle. Further correlating the dissociation of the ASR-Tr pair with the M-intermediate, no transient dissociation was observed after the photoexcitation of the blue-shifted ASR13C (ASR with 13-cis, 15-syn chromophore), which does not produce M. This distinction between ASRAT and ASR13C, the two isomeric forms in a color-sensitive equilibrium in ASR, provides a potential mechanism for color-sensitive signaling by ASR.
PMCID: PMC3161138  PMID: 21774544
microbial rhodopsins; proteinn–protein interaction; diffusion; retinal; transient grating
9.  A necrotic lung ball caused by co-infection with Candida and Streptococcus pneumoniae 
A necrotic lung ball is a rare radiological feature that is sometimes seen in cases of pulmonary aspergillosis. This paper reports a rare occurrence of a necrotic lung ball in a young male caused by Candida and Streptococcus pneumoniae.
Case report
A 28-year-old male with pulmonary candidiasis was found to have a lung ball on computed tomography (CT) of the chest. The patient was treated with β-lactams and itraconazole and then fluconazole, which improved his condition (as found on a following chest CT scan) and serum β-D-glucan level. The necrotic lung ball was suspected to have been caused by coinfection with Candida and S. pneumoniae.
A necrotic lung ball can result from infection by Candida and/or S. pneumoniae, indicating that physicians should be aware that patients may still have a fungal infection of the lungs that could result in a lung ball, even when they do not have either Aspergillus antibodies or antigens.
PMCID: PMC3259690  PMID: 22259251
lung ball; necrotic lung ball; Candida; Streptococcus pneumoniae
10.  Porcine Rotavirus Closely Related to Novel Group of Human Rotaviruses 
Emerging Infectious Diseases  2011;17(8):1491-1493.
We determined nucleotide sequences and inferred amino acid sequences of viral protein (VP) 4, VP6, VP7, and nonstructural protein 4 genes of a porcine rotavirus strain (SKA-1) from Japan. The strain was closely related to a novel group of human rotavirus strains (B219 and J19).
PMCID: PMC3381553  PMID: 21801631
pigs; rotavirus; viruses; phylogeny; sequences; Japan; viral protein; nonstructural protein; dispatch
11.  Pitavastatin approved for treatment of primary hypercholesterolemia and combined dyslipidemia 
Pitavastatin was first developed in Japan and is expanding the regions in which it is clinically available. A considerable number of clinical studies have been conducted and published to date on the usefulness of pitavastatin for patients with primary hypercholesterolemia or combined dyslipidemia. Pitavastatin demonstrates potent low-density lipoprotein cholesterol reduction at low doses of 1–4 mg/day. It also affects the regression of coronary plaques, as observed in intravascular ultrasound-guided percutaneous coronary intervention studies. Moreover, the persistent, long-term high-density lipoprotein cholesterol elevation observed in the populations treated with pitavastatin is worthy of further attention. The reported improvements in lipid profiles are consistent among the studies conducted in Japan, Korea, Thailand, and Europe. In light of accumulating clinical experience worldwide, pitavastatin is now expected to establish its position for preventing and treating cardiovascular disease.
PMCID: PMC2988623  PMID: 21127702
randomized clinical trial; Japan; Korea; Thailand; Europe
12.  Effect of a Large Dose of Di (2-ethylhexyl) phthalate (DEHP) on Hepatic Peroxisome in Cynomolgus Monkeys (Macaca Fascicularis) 
To elucidate the effect of a large dose of di (2-ethylhexyl) phthalate (DEHP), a plasticizer and peroxisome proliferator-activated receptor-α (PPARα) agonist, on hepatic peroxisomes, we orally administered 1,000 mg/kg/day, once daily, to 3 male and 4 female cynomolgus monkeys for 28 days consecutively. Light-microscopic and electron microscopic examinations of the liver were carried out in conjunction with measurement of the hepatic fatty acid β-oxidation system (FAOS), carnitine acetyltransferase (CAT) and carnitine palmitoyltransferase (CPT) activities, which are peroxisomal and/or mitochondrial enzyme activities. Electron microscopically, enlargement of the mitochondria was observed with lamellar orientation of the cristae along the major axis. Although the number of peroxisomes showed a tendency to increase when compared with those in a biopsied specimen before treatment, no abnormality in morphology was observed. A slight increase in CPT activity was noted at termination. No changes were noted in hepatic FAOS or CAT activity. In conclusion, although repeated oral treatment of cynomolgus monkeys with a large dose of DEHP induced a subtle increase in the numbers of peroxisomes with slight enlargements of the mitochondria, this low-sensitivity response to peroxisome proliferators in cynomolgus monkeys was considered to be closer to the response in humans than that in rodents.
PMCID: PMC3234641  PMID: 22272015
cynomolgus monkey; Di (2-ethylhexyl) phthalate (DEHP); hepatocyte; mitochondria; peroxisome
13.  Aichi Virus 2A Protein Is Involved in Viral RNA Replication ▿  
Journal of Virology  2008;82(19):9765-9769.
The Aichi virus 2A protein is not a protease, unlike many other picornavirus 2A proteins, and it is related to a cellular protein, H-rev107. Here, we examined the replication properties of two 2A mutants in Vero cells and a cell-free translation/replication system. In one mutant, amino acids 36 to 126 were replaced with an unrelated amino acid sequence. In the other mutant, the NC motif conserved in the H-rev107 family of proteins was changed to alanine residues. The two mutations abolished virus replication in cells. The mutations affected both negative- and positive-strand synthesis, the defect in positive-strand synthesis being more severe than that in negative-strand synthesis.
PMCID: PMC2546980  PMID: 18653460
14.  Interaction between Polypeptide 3ABC and the 5′-Terminal Structural Elements of the Genome of Aichi Virus: Implication for Negative-Strand RNA Synthesis▿  
Journal of Virology  2008;82(13):6161-6171.
Secondary structural elements at the 5′ end of picornavirus genomic RNA function as cis-acting replication elements and are known to interact specifically with viral P3 proteins in several picornaviruses. In poliovirus, ribonucleoprotein complex formation at the 5′ end of the genome is required for negative-strand synthesis. We have previously shown that the 5′-end 115 nucleotides of the Aichi virus genome, which are predicted to fold into two stem-loops (SL-A and SL-C) and one pseudoknot (PK-B), act as a cis-acting replication element and that correct folding of these structures is required for negative-strand synthesis. In this study, we investigated the interaction between the 5′-terminal 120 nucleotides of the genome and the P3 proteins, 3AB, 3ABC, 3C, and 3CD, by gel shift assay and Northwestern analysis. The results showed that 3ABC and 3CD bound to the 5′-terminal region specifically. The binding of 3ABC was observed on both assays, while that of 3CD was detected only on Northwestern analysis. No binding of 3AB or 3C was observed. Binding assays using mutant RNAs demonstrated that disruption of the base pairings of the stem of SL-A and one of the two stem segments of PK-B (stem-B1) abolished the 3ABC binding. In addition, the specific nucleotide sequence of stem-B1 was responsible for the efficient 3ABC binding. These results suggest that the interaction of 3ABC with the 5′-terminal region of the genome is involved in negative-strand synthesis. On the other hand, the ability of 3CD to interact with the 5′-terminal region did not correlate with the RNA replication ability.
PMCID: PMC2447086  PMID: 18448525
15.  Generation of Recombinant Rotavirus with an Antigenic Mosaic of Cross-Reactive Neutralization Epitopes on VP4▿  
Journal of Virology  2008;82(13):6753-6757.
Recombinant rotavirus (RV) with cDNA-derived chimeric VP4 was generated using recently developed reverse genetics for RV. The rescued virus, KU//rVP4(SA11)-II(DS-1), contains SA11 (simian RV strain, G3P[2])-based VP4, in which a cross-reactive neutralization epitope (amino acids 381 to 401) on VP5* is replaced by the corresponding sequence of a different P-type DS-1 (human RV strain, G2P[4]). Serological analyses with a panel of anti-VP4- and -VP7-neutralizing monoclonal antibodies revealed that the rescued virus carries a novel antigenic mosaic of cross-reactive neutralization epitopes on its VP4 surface. This is the first report of the generation of a recombinant RV with artificial amino acid substitutions.
PMCID: PMC2447055  PMID: 18434390
16.  Three-Dimensional Cell and Tissue Patterning in a Strained Fibrin Gel System 
PLoS ONE  2007;2(11):e1211.
Techniques developed for the in vitro reproduction of three-dimensional (3D) biomimetic tissue will be valuable for investigating changes in cell function in tissues and for fabricating cell/matrix composites for applications in tissue engineering techniques. In this study, we show that the simple application of a continuous strain to a fibrin gel facilitates the development of fibril alignment and bundle-like structures in the fibrin gel in the direction of the applied strain. Myoblasts cultured in this gel also exhibited well-aligned cell patterning in a direction parallel to the direction of the strain. Interestingly, the direction of cell proliferation was identical to that of cell alignment. Finally, the oriented cells formed linear groups that were aligned parallel to the direction of the strain and replicated the native skeletal muscle cell patterning. In addition, vein endothelial cells formed a linear, aligned vessel-like structure in this system. Thus, the system enables the in vitro reproduction of 3D aligned cell sets replicating biological tissue patterns.
PMCID: PMC2077807  PMID: 18030345
17.  Osteopontin Participates in Th1-Mediated Host Resistance against Nonlethal Malaria Parasite Plasmodium chabaudi chabaudi Infection in Mice  
Infection and Immunity  2006;74(4):2423-2427.
Osteopontin (OPN) knockout mice (OPN-KO mice) died of Plasmodium chabaudi chabaudi infection, although wild-type (WT) mice had self-limiting infections. OPN was detected in the WT mice at 2 days postinfection. OPN-KO mice produced significantly smaller amounts of interleukin-12 and gamma interferon than WT mice produced. These results suggested that OPN is involved in Th1-mediated immunity against malaria infection.
PMCID: PMC1418913  PMID: 16552072
18.  The 5′-Terminal Region of the Aichi Virus Genome Encodes cis-Acting Replication Elements Required for Positive- and Negative-Strand RNA Synthesis 
Journal of Virology  2005;79(11):6918-6931.
Aichi virus is a member of the family Picornaviridae. It has already been shown that three stem-loop structures (SL-A, SL-B, and SL-C, from the 5′ end) formed at the 5′ end of the genome are critical elements for viral RNA replication. In this study, we further characterized the 5′-terminal cis-acting replication elements. We found that an additional structural element, a pseudoknot structure, is formed through base-pairing interaction between the loop segment of SL-B (nucleotides [nt] 57 to 60) and a sequence downstream of SL-C (nt 112 to 115) and showed that the formation of this pseudoknot is critical for viral RNA replication. Mapping of the 5′-terminal sequence of the Aichi virus genome required for RNA replication using a series of Aichi virus-encephalomyocarditis virus chimera replicons indicated that the 5′-end 115 nucleotides including the pseudoknot structure are the minimum requirement for RNA replication. Using the cell-free translation-replication system, we examined the abilities of viral RNAs with a lethal mutation in the 5′-terminal structural elements to synthesize negative- and positive-strand RNAs. The results showed that the formation of three stem-loops and the pseudoknot structure at the 5′ end of the genome is required for negative-strand RNA synthesis. In addition, specific nucleotide sequences in the stem of SL-A or its complementary sequences at the 3′ end of the negative-strand were shown to be critical for the initiation of positive-strand RNA synthesis but not for that of negative-strand synthesis. Thus, the 5′ end of the Aichi virus genome encodes elements important for not only negative-strand synthesis but also positive-strand synthesis.
PMCID: PMC1112095  PMID: 15890931
20.  Aichi Virus Leader Protein Is Involved in Viral RNA Replication and Encapsidation 
Journal of Virology  2003;77(20):10799-10807.
Aichi virus, a member of the family Picornaviridae, encodes a leader (L) protein of 170 amino acids (aa). The Aichi virus L protein exhibits no significant sequence homology to those of other picornaviruses. In this study, we investigated the function of the Aichi virus L protein in virus growth. In vitro translation and cleavage assays indicated that the L protein has no autocatalytic activity and is not involved in polyprotein cleavage. The L-VP0 junction was cleaved by 3C proteinase. Immunoblot analysis showed that the L protein is stably present in infected cells. Characterization of various L mutants derived from an infectious cDNA clone revealed that deletion of 93 aa of the center part (aa 43 to 135), 50 aa of the N-terminal part (aa 4 to 53), or 90 aa of the C-terminal part (aa 74 to 163) abolished viral RNA replication. A mutant (Δ114-163) in which 50 aa of the C-terminal part (aa 114 to 163) were deleted exhibited efficient RNA replication and translation abilities, but the virus yield was 4 log orders lower than that of the wild type. Sedimentation analysis of viral particles generated in mutant Δ114-163 RNA-transfected cells showed that the mutant has a severe defect in the formation of mature virions, but not in that of empty capsids. Thus, the data obtained in this study indicate that the Aichi virus L protein is involved in both viral RNA replication and encapsidation.
PMCID: PMC224959  PMID: 14512530
21.  The 5′-End Sequence of the Genome of Aichi Virus, a Picornavirus, Contains an Element Critical for Viral RNA Encapsidation 
Journal of Virology  2003;77(6):3542-3548.
Picornavirus positive-strand RNAs are selectively encapsidated despite the coexistence of viral negative-strand RNAs and cellular RNAs in infected cells. However, the precise mechanism of the RNA encapsidation process in picornaviruses remains unclear. Here we report the first identification of an RNA element critical for encapsidation in picornaviruses. The 5′ end of the genome of Aichi virus, a member of the family Picornaviridae, folds into three stem-loop structures (SL-A, SL-B, and SL-C, from the most 5′ end). In the previous study, we constructed a mutant, termed mut6, by exchanging the seven-nucleotide stretches of the middle part of the stem in SL-A with each other to maintain the base pairings of the stem. mut6 exhibited efficient RNA replication and translation but formed no plaques. The present study showed that in cells transfected with mut6 RNA, empty capsids were accumulated, but few virions containing RNA were formed. This means that mut6 has a severe defect in RNA encapsidation. Site-directed mutational analysis indicated that as the mutated region was narrowed, the encapsidation was improved. As a result, the mutation of the 7 bp of the middle part of the stem in SL-A was required for abolishing the plaque-forming ability. Thus, the 5′-end sequence of the Aichi virus genome was shown to play an important role in encapsidation.
PMCID: PMC149490  PMID: 12610129
22.  Construction of an Infectious cDNA Clone of Aichi Virus (a New Member of the Family Picornaviridae) and Mutational Analysis of a Stem-Loop Structure at the 5′ End of the Genome 
Journal of Virology  2001;75(17):8021-8030.
Aichi virus is the type species of a new genus, Kobuvirus, of the family Picornaviridae. In this study, we constructed a full-length cDNA clone of Aichi virus whose in vitro transcripts were infectious to Vero cells. During construction of the infectious cDNA clone, a novel sequence of 32 nucleotides was identified at the 5′ end of the genome. Computer-assisted prediction of the secondary structure of the 5′ end of the genome, including the novel sequence, suggested the formation of a stable stem-loop structure consisting of 42 nucleotides. The function of this stem-loop in virus replication was investigated using various site-directed mutants derived from the infectious cDNA clone. Our data indicated that correct folding of the stem-loop at the 5′ end of the positive strand, but not at the 3′ end of the negative strand, is critical for viral RNA replication. The primary sequence in the lower part of the stem was also suggested to be crucial for RNA replication. In contrast, nucleotide changes in the loop segment did not so severely reduce the efficiency of virus replication. A double mutant, in which both nucleotide stretches of the middle part of the stem were replaced by their complementary nucleotides, had efficient RNA replication and translation abilities but was unable to produce viruses. These results indicate that the stem-loop at the 5′ end of the Aichi virus genome is an element involved in both viral RNA replication and production of infectious virus particles.
PMCID: PMC115046  PMID: 11483747
23.  Translation Initiation at the CUU Codon Is Mediated by the Internal Ribosome Entry Site of an Insect Picorna-Like Virus In Vitro 
Journal of Virology  1999;73(2):1219-1226.
AUG-unrelated translation initiation was found in an insect picorna-like virus, Plautia stali intestine virus (PSIV). The positive-strand RNA genome of the virus contains two nonoverlapping open reading frames (ORFs). The capsid protein gene is located in the 3′-proximal ORF and lacks an AUG initiation codon. We examined the translation mechanism and the initiation codon of the capsid protein gene by using various dicistronic and monocistronic RNAs in vitro. The capsid protein gene was translated cap independently in the presence of the upstream cistron, indicating that the gene is translated by internal ribosome entry. Deletion analysis showed that the internal ribosome entry site (IRES) consisted of approximately 250 bases and that its 3′ boundary extended slightly into the capsid-coding region. The initiation codon for the IRES-mediated translation was identified as the CUU codon, which is located just upstream of the 5′ terminus of the capsid-coding region by site-directed mutagenesis. In vitro translation assays of monocistronic RNAs lacking the 5′ part of the IRES showed that this CUU codon was not recognized by scanning ribosomes. This suggests that the PSIV IRES can effectively direct translation initiation without stable codon-anticodon pairing between the initiation codon and the initiator methionyl-tRNA.
PMCID: PMC103943  PMID: 9882324
24.  Attractant and Repellent Signaling Conformers of Sensory Rhodopsin−Transducer Complexes† 
Biochemistry  2010;49(31):6696-6704.
Attractant and repellent signaling conformers of the dual-signaling phototaxis receptor sensory rhodopsin I and its transducer subunit (SRI−HtrI) have recently been distinguished experimentally by the opposite connection of their retinylidene protonated Schiff bases to the outwardly located periplasmic side and inwardly located cytoplasmic side. Here we show that the pKa of the outwardly located Asp76 counterion in the outwardly connected conformer is lowered by ∼1.5 units from that of the inwardly connected conformer. The pKa difference enables quantitative determination of the relative amounts of the two conformers in wild-type cells and behavioral mutants prior to photoexcitation, comparison of their absorption spectra, and determination of their relative signaling efficiency. We have shown that the one-photon excitation of the SRI−HtrI attractant conformer causes a Schiff base connectivity switch from inwardly connected to outwardly connected states in the attractant signaling photoreaction. Conversely, a second near-UV photon drives the complex back to the inwardly connected conformer in the repellent signaling photoreaction. The results suggest a model of the color-discriminating dual-signaling mechanism in which phototaxis responses (his-kinase modulation) result from the photointerconversion of the two oppositely connected SRI−HtrI conformers by one-photon and two-photon activation. Furthermore, we find that the related repellent phototaxis SRII−HtrII receptor complex has an outwardly connected retinylidene Schiff base like the repellent signaling forms of the SRI−HtrI complex, indicating the general applicability of macro conformational changes, which can be detected by the connectivity switch, to phototaxis signaling by sensory rhodopsin−transducer complexes.
PMCID: PMC2914491  PMID: 20590098

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