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Abstract
Using a pan-neuronal GFP marker, a morphological screen was performed to detect Caenorhabditis elegans larval lethal mutants with severely disorganized major nerve cords. We recovered and characterized 21 mutants that displayed displacement or detachment of the ventral nerve cord from the body wall (Ven: ventral cord abnormal). Six mutations defined three novel genetic loci: ven-1, ven-2, and ven-3. Fifteen mutations proved to be alleles of previously identified muscle attachment/positioning genes, mup-4, mua-1, mua-5, and mua-6. All the mutants also displayed muscle attachment/positioning defects characteristic of mua/mup mutants. The pan-neuronal GFP marker also revealed that mutants of other mua/mup loci, such as mup-1, mup-2, and mua-2, exhibited the Ven defect. The hypodermis, the excretory canal, and the gonad were morphologically abnormal in some of the mutants. The pleiotropic nature of the defects indicates that ven and mua/mup genes are required generally for the maintenance of attachment of tissues to the body wall in C. elegans.
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Affiliation(s)
- G Shioi
- Division of Biological Science, Nagoya University Graduate School of Science, Chikusa-ku, Nagoya 464-8602, Japan
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2
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Asahina M, Ishihara T, Jindra M, Kohara Y, Katsura I, Hirose S. The conserved nuclear receptor Ftz-F1 is required for embryogenesis, moulting and reproduction in Caenorhabditis elegans. Genes Cells 2000; 5:711-23. [PMID: 10971653 DOI: 10.1046/j.1365-2443.2000.00361.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Nuclear receptors are essential players in the development of all metazoans. The nematode Caenorhabditis elegans possesses more than 200 putative nuclear receptor genes, several times more than the number known in any other organism. Very few of these transcription factors are conserved with components of the steroid response pathways in vertebrates and arthropods. Ftz-F1, one of the evolutionarily oldest nuclear receptor types, is required for steroidogenesis and sexual differentiation in mice and for segmentation and metamorphosis in Drosophila. RESULTS We employed two complementary approaches, direct mutagenesis and RNA interference, to explore the role of nhr-25, a C. elegans ortholog of Ftz-F1. Deletion mutants show that nhr-25 is essential for embryogenesis. RNA interference reveals additional requirements throughout the postembryonic life, namely in moulting and differentiation of the gonad and vulva. All these defects are consistent with the nhr-25 expression pattern, determined by in situ hybridization and GFP reporter activity. CONCLUSIONS Our data link the C. elegans Ftz-F1 ortholog with a number of developmental processes. Significantly, its role in the periodical replacement of cuticle (moulting) appears to be evolutionarily shared with insects and thus supports the monophyletic origin of moulting.
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Affiliation(s)
- M Asahina
- Department of Developmental Genetics, National Institute of Genetics, Mishima, Shizuoka-ken 411-8540, Japan
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3
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Aoki H, Sato S, Takanami T, Ishihara T, Katsura I, Takahashi H, Higashitani A. Characterization of Ce-atl-1, an ATM-like gene from Caenorhabditis elegans. Mol Gen Genet 2000; 264:119-26. [PMID: 11016841 DOI: 10.1007/s004380000291] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
An ATM-like gene was identified in the genome of Caenorhabditis elegans. The putative product of the gene, termed Ce-atl-1 (C. elegans ATM-like 1) consists of 2514 amino acid residues. The C-terminal sequence, which contains a PI-3 kinase-like domain, showed good homology with the products of the gene MEC1/ESR1 from budding yeast, the rad3+ gene of fission yeast and mammalian ATM (ataxia-telangiectasia and rad3+ related) genes. The results of RNA-mediated interference indicated that the major phenotype associated with repression of Ce-atl-1 was lethality (approximately 50-80%) during early embryogenesis. Among the surviving progeny, males (XO animals) arose at a high frequency (2-30%). In addition, 5% of oocyte chromosomes demonstrated aneuploidy due to a defect in pre-meiotic chromosomal segregation. Gene expression analyses indicated that Ce-atl-1 mRNA was expressed in all larval stages and that its level increased about fivefold in the adult stage. The adult expression level was decreased in the glp-4 mutant, which is defective in germ line proliferation. Ce-atl-1 was strongly expressed in both the mitotic and meiotic cells of adult gonads. In summary, Ce-atl-1 appears to be important for early embryogenesis, and loss of its function results in a defect in chromosome segregation, similar to what has been observed for AT-related proteins.
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Affiliation(s)
- H Aoki
- Institute of Genetic Ecology, Tohoku University, Sendai, Japan
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4
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Abstract
In cholinergic neurons, high-affinity choline uptake in presynaptic terminals is the rate-limiting step in acetylcholine synthesis. Using information provided by the Caenorhabditis elegans Genome Project, we cloned a cDNA encoding the high-affinity choline transporter from C. elegans (cho-1). We subsequently used this clone to isolate the corresponding cDNA from rat (CHT1). CHT1 is not homologous to neurotransmitter transporters, but is homologous to members of the Na+-dependent glucose transporter family. Expression of CHT1 mRNA is restricted to cholinergic neurons. The characteristics of CHT1-mediated choline uptake essentially match those of high-affinity choline uptake in rat brain synaptosomes.
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Affiliation(s)
- T Okuda
- Department of Neurochemistry, Faculty of Medicine, University of Tokyo and CREST of Japan Science and Technology Corporation, Bunkyo-ku, Tokyo 113-0033, Japan.
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5
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Winnier AR, Meir JY, Ross JM, Tavernarakis N, Driscoll M, Ishihara T, Katsura I, Miller DM. UNC-4/UNC-37-dependent repression of motor neuron-specific genes controls synaptic choice in Caenorhabditis elegans. Genes Dev 1999; 13:2774-86. [PMID: 10557206 PMCID: PMC317130 DOI: 10.1101/gad.13.21.2774] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The UNC-4 homeoprotein and the Groucho-like corepressor UNC-37 specify synaptic choice in the Caenorhabditis elegans motor neuron circuit. In unc-4 mutants, VA motor neurons are miswired with inputs from interneurons normally reserved for their lineal sisters, the VB motor neurons. Here we show that UNC-4 and UNC-37 function together in VA motor neurons to repress VB-specific genes and that this activity depends on physical contact between UNC-37 and a conserved Engrailed-like repressor domain (eh1) in UNC-4. Missense mutations in the UNC-4 eh1 domain disrupt interactions between UNC-4 and UNC-37 and result in the loss of UNC-4-dependent repressor activity in vivo. A compensatory amino acid substitution in UNC-37 suppresses specific unc-4 alleles by restoring physical interactions with UNC-4 as well as UNC-4-dependent repression of VB-specific genes. We propose that repression of VB-specific genes by UNC-4 and UNC-37 is necessary for the creation of wild-type inputs to VA motor neurons. The existence of mammalian homologs of UNC-4 and UNC-37 indicates that a similar mechanism could regulate synaptic choice in the vertebrate spinal cord.
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Affiliation(s)
- A R Winnier
- Department of Cell Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
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6
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Abstract
To elucidate the mechanism of sensory cilium formation, we analyzed mutants in the Caenorhabditis elegans che-2 gene. These mutants have extremely short cilia with an abnormal posterior projection, and show defects in behaviors that are mediated by ciliated sensory neurons. The che-2 gene encodes a new member of the WD40 protein family, suggesting that it acts in protein-protein interaction. Analysis of mutation sites showed that both the amino-terminal WD40 repeats and the carboxyl-terminal non-WD40 domain are necessary for the CHE-2 function. CHE-2-tagged green fluorescent protein is localized at the cilia of almost all the ciliated sensory neurons. Expression of che-2 in a subset of sensory neurons of a che-2 mutant by using a heterologous promoter resulted in restoration of the functions and cilium morphology of only the che-2-expressing neurons. Thus, che-2 acts cell-autonomously. This technique can be used in the future for determining the function of each type of che-2-expressing sensory neuron. Using green fluorescent protein, we found that the extension of cilia in wild-type animals took place at the late embryonic stage, whereas the cilia of che-2 mutant animals remained always short during development. Hence, the abnormal posterior projection is due to the inability of cilia to extend, rather than degeneration of cilia once correctly formed. Expression of che-2 in a che-2 mutant under a heat shock promoter showed that the extension of cilia, surprisingly, can occur even at the adult stage, and that such cilia can function apparently normally in behavior.
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Affiliation(s)
- M Fujiwara
- Structural Biology Center, National Institute of Genetics, Mishima 411-8540, Japan and Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima 411-8540, Japan.
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7
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Takanami T, Sato S, Ishihara T, Katsura I, Takahashi H, Higashitani A. Characterization of a Caenorhabditis elegans recA-like gene Ce-rdh-1 involved in meiotic recombination. DNA Res 1998; 5:373-7. [PMID: 10048487 DOI: 10.1093/dnares/5.6.373] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A recA-like gene was identified in the Caenorhabditis elegans genome project database. The putative product of the gene, termed Ce-rdh-1 (C. elegans RAD51 and DMC1/LIM15 homolog 1), consists of 357 amino acid residues. The predicted amino acid sequence of Ce-rdh-1 showed 46-60% identity to both RAD51 type and DMC1/LIM15 type genes in several eukaryote species. The results of RNAi (RNA-mediated interference) indicated that repression of Ce-rdh-1 blocked chromosome condensation of six bivalents and dissociation of chiasmata in oocytes of F1 progeny. Oogenesis did not proceed to the diakinesis stage. Accordingly, all the eggs produced (F2) died in early stages. These results suggest that Ce-rdh-1 participates in meiotic recombination.
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Affiliation(s)
- T Takanami
- Institute of Genetic Ecology, Tohoku University, Sendai, Japan
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8
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Take-Uchi M, Kawakami M, Ishihara T, Amano T, Kondo K, Katsura I. An ion channel of the degenerin/epithelial sodium channel superfamily controls the defecation rhythm in Caenorhabditis elegans. Proc Natl Acad Sci U S A 1998; 95:11775-80. [PMID: 9751741 PMCID: PMC21716 DOI: 10.1073/pnas.95.20.11775] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ultradian rhythms are widespread phenomena found in various biological organisms. A typical example is the defecation behavior of the nematode Caenorhabditis elegans, which repeats at about 45-sec intervals. To elucidate the mechanism, we studied flr-1 mutants, which show very short defecation cycle periods. The mutations also affect some food-related functions, including growth rate, the expulsion step of defecation behavior, and the regulation of the dauer larva (a nonfeeding, special third-stage larva) formation in the unc-3 (Olf-1/EBF homolog) background. The flr-1 gene encodes a novel ion channel belonging to the DEG/ENaC (C. elegans degenerin and mammalian epithelial sodium channel) superfamily. A flr-1::GFP (green fluorescent protein) fusion gene that can rescue the flr-1 mutant phenotypes is expressed only in the intestine from embryos to adults. These results suggest that FLR-1 may be a component of an intestinal regulatory system that controls the defecation rhythm as well as other functions.
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Affiliation(s)
- M Take-Uchi
- Structural Biology Center, National Institute of Genetics, Mishima 411-8540, Japan
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9
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Katsura I. [Cell-lineage and cell-differentiation of the nematode Caenorhabditis elegans]. Tanpakushitsu Kakusan Koso 1996; 41:1936-43. [PMID: 8890658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- I Katsura
- Structural Biology Center, National Institute of Genetics, Shizuoka, Japan
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10
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Hishida R, Ishihara T, Kondo K, Katsura I. hch-1, a gene required for normal hatching and normal migration of a neuroblast in C. elegans, encodes a protein related to TOLLOID and BMP-1. EMBO J 1996; 15:4111-22. [PMID: 8861940 PMCID: PMC452133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Proteins of the tolloid/bone morphogenetic protein (BMP)-1 family play important roles in the differentiation of cell fates. Among those proteins are BMP-1, which plays a role in cartilage and bone formation in mammals, the TOLLOID protein, which is required for the establishment of the dorsoventral axis of Drosophila embryos and BP10/SpAN, which are thought to act in the morphogenesis of sea urchins. These proteins have some properties in common. First, they contain the astacin metalloprotease domain, the CUB domain and the epidermal growth factor-like domain. Second, they are expressed in embryos at stages expected for their role in cell differentiation. Third, at least BMP-1 and TOLLOID are thought to interact with proteins of the transforming growth factor-beta family. We report that the hch-1 gene of the nematode Caenorhabditis elegans encodes a tolloid/BMP-1 family protein. The protein has the characteristic domains common to the tolloid/ BMP-1 family. Like other members of the family, it is expressed in embryos. However, the phenotype of hch-1 mutants shows that it is required for normal hatching and normal migration of a post-embryonic neuroblast. Furthermore, in spite of its expression in embryogenesis, it is not required for the viability of embryos. These results show new functions of the tolloid/BMP-1 family proteins and give insight into their evolution.
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Affiliation(s)
- R Hishida
- Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka-ken, Japan
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11
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Hishida R, Ishihara T, Kondo K, Katsura I. hch-1, a gene required for normal hatching and normal migration of a neuroblast in C. elegans, encodes a protein related to TOLLOID and BMP-1. EMBO J 1996. [DOI: 10.1002/j.1460-2075.1996.tb00786.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Katsura I, Kondo K, Amano T, Ishihara T, Kawakami M. Isolation, characterization and epistasis of fluoride-resistant mutants of Caenorhabditis elegans. Genetics 1994; 136:145-54. [PMID: 8138152 PMCID: PMC1205766 DOI: 10.1093/genetics/136.1.145] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
We have isolated 13 fluoride-resistant mutants of the nematode Caenorhabditis elegans. All the mutations are recessive and mapped to five genes. Mutants in three of the genes (class 1 genes: flr-1 X, flr-3 IV, and flr-4 X) are resistant to 400 micrograms/ml NaF. Furthermore, they grow twice as slowly as and have smaller brood size than wild-type worms even in the absence of fluoride ion. In contrast, mutants in the other two genes (class 2 genes: flr-2 V and flr-5 V) are only partially resistant to 400 micrograms/ml NaF, and they have almost normal growth rates and brood sizes in the absence of fluoride ion. Studies on the phenotypes of double mutants showed that class 2 mutations are epistatic to class 1 mutations concerning growth rate and brood size but hypostatic with respect to fluoride resistance. We propose two models that can explain the epistasis. Since fluoride ion depletes calcium ion, inhibits some protein phosphatases and activates trimeric G-proteins, studies on these mutants may lead to discovery of a new signal transduction system that controls the growth of C. elegans.
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Affiliation(s)
- I Katsura
- DNA Research Center, National Institute of Genetics, Mishima, Japan
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13
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Abstract
Development of multicellular organisms is controlled mainly by cell-signaling systems. In this review I first discuss methods of genetic analysis and properties of mutants of cell-signaling systems in general and in the nematode C. elegans. Then, I describe two of our approaches to isolating new mutants in cell-signaling of C. elegans. The first approach is to select for mutants that have the same visible phenotype as those in known cell-signaling genes. In a survey of larval lethal mutations we found that there are quite a few mutants in which the inner surface of the body wall is detached from the outer surface of the intestine. Some of them map in genes that are known to act in cell-signaling systems in vulval induction or sex myoblast migration, which are not essential to the growth and survival of C. elegans. Therefore, we think many of the mutations of the above phenotype disrupt cell-signaling in an unidentified essential function, and also cell-signaling in the non-essential functions. The second approach is to isolate mutants resistant to a drug expected to disturb cell-signaling. As the drug we have chosen sodium fluoride, which depletes calcium ion, activates G-proteins and inactivates some phosphatases. The mutants are grouped into two classes (three and two genes, respectively) according to degree of fluoride-resistance and growth rate of larvae. Although there is so far no direct evidence that these mutants are related to cell-signaling, they show complex epistasis that can be explained by a model consisting of a cell-signaling pathway.
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Affiliation(s)
- I Katsura
- DNA Research Center, National Institute of Genetics, Shizuoka-ken, Japan
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14
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Katsura I. [Replication and gene expression of lambda phage]. Tanpakushitsu Kakusan Koso 1992; 37:2580-8. [PMID: 1438832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- I Katsura
- DNA Research Center, National Institute of Genetics, Shizuoka, Japan
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15
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Katsura I, Kobayashi H. Structure and inherent properties of the bacteriophage lambda head shell. VII. Molecular design of the form-determining major capsid protein. J Mol Biol 1990; 213:503-11. [PMID: 2141087 DOI: 10.1016/s0022-2836(05)80211-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Some mutations in the major capsid protein (gpE) of lambda phage can alter the size and shape of the head shell or block the pathway of head maturation. Previous studies on the classification of such mutants showed that there are at least five functional sites on the gpE molecule. In this study, we determined the amino acid exchanges by DNA sequencing to elucidate the molecular design of the form-determining multifunctional protein gpE. In addition, we characterized the mutated gpE molecules by two-dimensional gel electrophoresis and studied suppression patterns of amber mutants at 43 amino acid residues. Those mutations map at 19 amino acid residues at 22 bases, which are located in three regions, 40 to 91, 222 to 246, and 284 to 324 of the 341 amino acid residues of gpE. These regions seem to be important in the activity of gpE, since amber mutations in these regions are suppressed on the average by less species of suppressors than those outside these regions. The mutations having different phenotypes are not segregated from each other, while some mutations having the same phenotype are separated far apart in the primary structure. This suggests that the functional sites were formed during evolution after the folding pattern of the ancestral gpE polypeptide chain had been established. Many of the mutations are located at serine, glycine and proline residues in predicted beta-turns.
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Affiliation(s)
- I Katsura
- Department of Biology, College of Arts and Sciences, University of Tokyo, Japan
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16
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Abstract
The mechanism of length determination in bacteriophage lambda tails is discussed as a model for regulation in protein assembly systems. The lambda tail is a long flexible tube ending in a conical part and a single tail fiber. Its length is exactly determined in the sense that the number of major tail protein (gpV) molecules, which comprise more than 80% of the mass of the tail, is exactly the same in all tails. Assembly of gpV is regulated by the initiator complex, which contains the tail fiber and the conical part, and by the terminator protein gpU. There are two key points in the assembly of gpV with respect to length determination. (1) Assembly of gpV on the initiator pauses at the correct tail length. Binding of gpU to the tail only fixes the pause firmly. (2) When the tail length is too short, binding of gpU to tails is inhibited. Deletions and a duplication (both in frame) in gene H, which codes for one of the proteins in the initiator, result in production of phage particles with altered tail length. Moreover, the tail length is roughly proportional to the length of the mutated versions of gene H. This shows that the tail length is measured by the length of gene H protein (gpH), which seems to be approximately as long as the tail tube, if extended like a thread, according to secondary structure prediction (alpha-helices connected by other structures). Various pieces of evidence show that about six molecules of gpH are attached to the remaining portion of the initiator by the C-terminal part and folded into a somewhat compact form, while they are elongated as they are enclosed in the tail tube during assembly of gpV. Unlike interaction between the length-measuring genome RNA and the coat protein of tobacco mosaic virus, the major tail protein gpV does not bind specifically to the ruler protein gpH. Rather, gpH determines the tail length by inhibiting the binding of gpU to short tails and by signalling the pause when the correct tail length is attained.
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Affiliation(s)
- I Katsura
- Department of Biology, College of Arts and Sciences, University of Tokyo, Japan
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17
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Ishihara T, Ichihara Y, Hayano T, Katsura I, Sogawa K, Fujii-Kuriyama Y, Takahashi K. Primary structure and transcriptional regulation of rat pepsinogen C gene. J Biol Chem 1989; 264:10193-9. [PMID: 2722863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The entire rat pepsinogen C gene has been isolated from a rat genomic library, using the rat pepsinogen C cDNA as a probe. Southern blot analysis showed that there exists at least two rat pepsinogen C genes. The nucleotide sequences of the coding regions and the 5'- and 3'-flanking regions of one of the rat pepsinogen C genes have been determined. This gene is split into 9 exons interrupted by eight intervening sequences. The 5'-flanking region is similar to that of the human pepsinogen C gene, but only the former has the core sequence of the Sp1 binding site. The amount of transcripts of the rat pepsinogen C genes was found to increase during development, and a similar increase was shown to be induced by injection of hydrocortisone. As a candidate of a factor which regulates the transcription, we found a 25-kDa protein by Southwestern blotting. It binds to a specific site in the 5'-flanking region of the gene only in the presence of Mg2+ ion, and it is present in the nuclear fraction of the gastric mucosa but not of the liver.
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Affiliation(s)
- T Ishihara
- Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Japan
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18
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Ishihara T, Ichihara Y, Hayano T, Katsura I, Sogawa K, Fujii-Kuriyama Y, Takahashi K. Primary structure and transcriptional regulation of rat pepsinogen C gene. J Biol Chem 1989. [DOI: 10.1016/s0021-9258(18)81784-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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19
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Abstract
Some amino acid substitutions in the major capsid protein (gene E product) of lambda phage are found to cause a defect in DNA packaging. These substitutions permit initiation of DNA packaging and expansion of the prohead. However, cleavage of the concatemer DNA at the cos site takes place only to a very small extent, and the capsid eventually becomes empty. Interestingly, the mutations are suppressed by a decrease of the DNA length between the cos sites by 8000 to 10,000 bases. These properties are similar to those of amber mutants in gene D, which codes for the capsid outer-surface protein. Studies on the E missense.D amber double mutant show that the E protein and the D protein contribute additively to the stabilization of the condensed form of the DNA molecule in phage heads.
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Affiliation(s)
- I Katsura
- Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Japan
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20
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Ichinose M, Miki K, Furihata C, Tatematsu M, Ichihara Y, Ishihara T, Katsura I, Sogawa K, Fujii-Kuriyama Y, Tanji M. DNA methylation and expression of the rat pepsinogen gene in embryonic, adult, and neoplastic tissues. Cancer Res 1988; 48:1603-9. [PMID: 3345531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The relationship between methylation and expression of rat pepsinogen 1 (Pg1) genes was investigated in various tissues. On Northern blotting with a Pg1 complementary DNA probe, Pg1 mRNA was detected only in the glandular stomach of normal rats. Methylation analysis with Msp1/HpaII and Hha1 revealed tissue specific methylation patterns of Pg1 genes with less methylated in the stomach than in other normal tissues not expressing the genes. During stomach development, there was a progressive increase in the Pg1 mRNA level that almost coincided with change in the mucosal pepsinogen level and progressive demethylation after the onset of transcription. Thus, there was an inverse correlation between methylation and expression of Pg1 genes, suggesting a role of DNA methylation in Pg1 gene regulation during normal differentiation, although not its primary role in gene activation. There was no detectable Pg1 mRNA in either primary or transplanted stomach cancers induced by N-methyl-N'-nitro-N-nitrosoguanidine. The methylation patterns of Pg1 genes were different from those of normal tissues that expressed the gene and of those that did not and no simple correlation was observed between methylation and expression of Pg1 genes. This result is consistent with a previous finding that DNA methylation is deranged in tumor cells.
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Affiliation(s)
- M Ichinose
- Department of Biophysics and Biochemistry, Faculty of Science, University of Tokyo, Japan
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21
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Abstract
How the size and shape of living structures are determined by genetic information is one of the fundamental problems in biology. Here I describe a study in which the size of a biological supramolecular structure was changed in a predictable way by in vitro genetics, with the size both before and after manipulation being exactly determined. I have studied the tail of bacteriophage lambda, whose length is determined by the length of the 'ruler protein', the product of gene H. The length of the tail can be decreased or increased by deleting the middle part of gene H or by forming a small duplication there, and the length of the tail is proportional to the size of the protein. These results can be regarded as a special case of protein engineering, namely supramolecular protein engineering.
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Tokiwa K, Niitsu H, Nakayashiki N, Kumagai R, Katsura I, Katsura S. [Preparation of anti-human-sweat serum]. Nihon Hoigaku Zasshi 1987; 41:102-8. [PMID: 3626135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Kumagai R, Niitsu H, Katsura I, Nakayashiki N, Katsura S. A case of a newborn infant with Hb M Iwate. TOHOKU J EXP MED 1986; 150:337-43. [PMID: 3824377 DOI: 10.1620/tjem.150.337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Hemoglobin of a newborn infant who was suspected to hereditarily have Hb M Iwate was examined. The infant hemolysate was separated into five fractions by column chromatography on Amberlite CG-50, and two of these fractions showed absorption spectra corresponding with that of Hb M Iwate. Five bands were found after the isoelectric focusing of the hemolysate, and two of these bands were brown. The two Hb M fractions obtained by column chromatography was focused to the positions of the brown bands. One of these Hbs M corresponded with Hb M Iwate (alpha M2 beta 2) from an adult carrier of this trait, but the other was not found in adult hemolysates. The latter species of Hb M was shown to be composed of the abnormal alpha chain and the normal gamma chain (alpha M2 gamma 2) by chain analysis, and was assumed to be specific for infants. A quantitative estimation of the hemoglobins in the infant hemolysate showed that there was no difference between the relative quantities of the fetal and adult forms of Hb M Iwate.
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24
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Abstract
A total of 940 amber mutants in gene E of bacteriophage lambda was isolated to study the structure-function relationship of the gene product, the major capsid protein. The mutants were mapped to 43 mutation sites, most of which have been located, albeit tentatively, at exact points in the known base sequence, by deletion mapping and by the specificity of mutagenesis and the patterns of suppression. The patterns of suppression were interpreted in terms of both the efficiency of insertion of amino acid residues by suppressors and the exchangeability of amino acid residues. The exchangeability seems to be related to the hydrophilicity of the residues themselves and their environment, as well as to the functional similarity between the replaced and the inserted amino acid residues. Suppression of two of the mutations resulted in the production of characteristic aberrant head-related structures, each showing a defect in a different functional site in the protein. This, together with the approximate positions of some specific missense mutations as determined in this study, revealed the distribution of the functional sites along the polypeptide chain of the gene E product.
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25
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Abstract
We have isolated viable mutants of bacteriophage lambda that have in-frame deletions in gene H, which codes for a minor tail protein. They produce correspondingly smaller but active gene H protein products and assemble shorter-tailed phage particles. The deficiency in tail length for each mutant corresponds to the calculated shortening of the gene H protein caused by the deletion. These results show that the H protein determines tail length and argue strongly for a scheme in which the H protein is a ruler or template that measures length during tail assembly.
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26
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Katsura S, Tokiwa K, Kumaga R, Niitsu H, Nakayashiki N, Sato M, Wada M, Katsura I. [Specificity of anti-human HbA0 goat-serum for human HbA0]. Nihon Hoigaku Zasshi 1984; 38:155-62. [PMID: 6207325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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27
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Abstract
Missense mutants of bacteriophage lambda that produce small proheads were found among prophage mutants defective in the major head protein gpE. Measurements of the sedimentation coefficient and molecular weight of the small proheads showed that they have the T = 4 structure composed of 240 molecules of gpE instead of the wild-type T = 7 structure composed of 420 molecules of gpE. When the phage mutants were grown in groE mutants of Escherichia coli, they produced small unprocessed proheads, which contained a smaller number (about 60) of the core protein (gpNu3) molecules than normal unprocessed proheads, which contain about 180 molecules of gpNu3. This shows that the major head protein determines the size of not only the shell but also the core of unprocessed proheads. These mutants by themselves produce very few mature small-headed phage particles, partly because the lambda DNA molecule, whose cos sites are separated at a distance of 48,500 bases, is too long to be packaged into the small proheads. However, the small proheads can package shorter DNA in vivo and in vitro at somewhat reduced efficiency, if the length or a multiple of the length between the cos sites of the DNA is 13,000 to 19,000 bases.
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Abstract
Coated vesicles, which are found in many eucaryotic cells, seem to play a role in the transfer of membrane and in the uptake and secretion of proteins. They have polyhedral structures whose faces consist of twelve pentagons and a variable number of hexagons and at whose vertices always three edges meet. To study the stability of such structures theoretically I first enumerate all the topologically distinct polyhedra under the conditions that they have at most ten hexagonal faces. Then I estimate their strain energy assuming Hookean elasticity and considering only interactions of short range. The results show that the three structures of coated vesicles which Crowther et al. (1976) reported have the lowest energy among all the polyhedra under certain conditions. Thus, the seemingly complex structures of coated vesicles can be constructed from only one species of structural units according to the principle of lowest strain energy.
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Kawaguchi K, Noda H, Katsura I. Structure and inherent properties of the bacteriophage lambda head shell. III. Spectroscopic studies on the expansion of the prohead. J Mol Biol 1983; 164:573-87. [PMID: 6221116 DOI: 10.1016/0022-2836(83)90051-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The head shell of bacteriophage lambda expands by about 20% in diameter when it packages the DNA molecule in vivo. The expansion reaction is essentially a conformational change of the major head protein molecules to a state of lower free energy and can also be triggered in vitro by treatment with 4 M-urea. In order to investigate the conformational change, we have measured the circular dichroism, fluorescence and difference absorption spectra of the lambda head shell before and after the expansion by the treatment with urea. The far-ultraviolet circular dichroism spectra and the fluorescence spectra show that the expansion is not accompanied by a great change in the secondary structure (29% alpha-helix, 23% beta-structure) and the environment (non-polar) of the tryptophan residues of the major head protein molecule. On the other hand, by measurements of the circular dichroism and difference absorption spectra in the near-ultraviolet region as well as by chemical modification experiments with tetranitromethane, we have found that one or two tyrosine residues of the major head protein are transferred from a polar, solvent-exposed to a non-polar, solvent-unexposed environment during the expansion. Judging from these results, the conformational change seems to be mainly intermolecular or interdomainal rather than intradomainal.
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30
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Yanagida M, Hiraoka Y, Katsura I. Dynamic behaviors of DNA molecules in solution studied by fluorescence microscopy. Cold Spring Harb Symp Quant Biol 1983; 47 Pt 1:177-87. [PMID: 6345057 DOI: 10.1101/sqb.1983.047.01.023] [Citation(s) in RCA: 79] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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31
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Tsukagoshi N, Yamada H, Tsuboi A, Udaka S, Katsura I. Hexagonal surface array in a protein-secreting bacterium, Bacillus brevis 47. Biochim Biophys Acta 1982; 693:134-42. [PMID: 7150585 DOI: 10.1016/0005-2736(82)90479-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Bacillus brevis 47, a protein-secreting bacterium, contained two major proteins with approximate molecular weights of 150 000 and 130 000 in the cell wall. The cell surface was covered with a hexagonally arranged array of six structural units about 4 nm in diameter with a lattice constant of 14.5 nm. The regular array structure as well as the chemical composition of cell envelopes remained the same regardless of the growth conditions. A mutant, strain 47-57, which was isolated as a phage resistant colony, contained only the 150 000 protein as a major cell wall protein. Although the mutant had hexagonally arranged arrays with the same lattice constant as that of wild-type cells, the distribution of mass in the unit cell differed considerably from that of the wild-type cells. The number of structural units in the unit cell of the mutant was reduced from six to three. Taking these results together with filtered images of the wild-type and mutant envelopes, two possible models for the surface array of B. brevis 47 are discussed.
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32
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Katsura I. Structure and function of the major tail protein of bacteriophage lambda. Mutants having small major tail protein molecules in their virion. J Mol Biol 1981; 146:493-512. [PMID: 6456359 DOI: 10.1016/0022-2836(81)90044-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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33
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Katsura I. Assembly systems in molecular biology: a graph theory of genetic complementation between two related species. J Theor Biol 1981; 88:503-12. [PMID: 7278301 DOI: 10.1016/0022-5193(81)90279-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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34
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Katsura I, Aoki H. [Clinical results of dental TDZ in prosthodontic field (author's transl)]. Shikai Tenbo 1980; 56:1069-74. [PMID: 7017970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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35
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Katsura I. Structure and inherent properties of the bacteriophage lambda head shell. II Isolation and initial characterization of prophage mutants defective in gene E. J Mol Biol 1980; 142:387-98. [PMID: 6450837 DOI: 10.1016/0022-2836(80)90278-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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36
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Katsura I. Structure and inherent properties of the bacteriophage lambda head shell. I. Polyheads produced by two defective mutants in the major head protein. J Mol Biol 1978; 121:71-93. [PMID: 660651 DOI: 10.1016/0022-2836(78)90263-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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37
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38
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39
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Katsura I. Isolation of lambda prophage mutants defective in structural genes: their use for the study of bacteriophage morphogenesis. Mol Gen Genet 1976; 148:31-42. [PMID: 792680 DOI: 10.1007/bf00268543] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mutants of coliphage lambda defective in structural genes were isolated and characterized. The isolation method consisted in lysogenizing bacteria with mutagenized phage and testing for inability to form plaques after heat induction. The mutants were propagated as prophages in the lysogens. Mutants in the region of the tail-genes U, V, G and H were enriched for by a selection method based on recombination and complementation with known mutants, and they were mapped by deletion mapping with newly isolated lambdadg's. The lysates of all the mutants were examined by electron microscopy. Some of the mutants showed phenotypes different from those of known amber mutants in the same genes. They are interpreted as producing partially active, altered gene products and might be useful for the studies of morphogenesis and of the mechanism of infection.
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41
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Katsura I. [Morphogenesis of the tail of bacteriophage lambda (author's transl)]. Tanpakushitsu Kakusan Koso 1976; 21:687-95. [PMID: 796887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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42
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43
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Kül PW, Katsura I. Morphogenesis of the tail of bacteriophage lambda. Virology 1975; 63:221-37. [PMID: 1111212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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44
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Kühl PW, Katsura I. Morphogenesis of the tail of bacteriophage lambda I. In vitro intratail complementation. Virology 1975; 63:221-237. [PMID: 18621349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/1974] [Indexed: 05/26/2023]
Abstract
By studying nonsense mutants in ten of the 11 known tail genes of bacteriophage lambda we obtained the following results. Concentrated tail(-)-lysates complement each other in nearly all possible (45) combinations. The efficiency of complementation is very dependent on physical parameters (lysis procedure, concentration, temperature) and on the mutants used for complementation (i.e., type of precursors present, absence or presence of abortive structures, polarity effects of some nonsense mutants). Gene product dosage experiments, in which the ratio of concentrations of the different precursors present in different lysates is varied up to four orders of magnitude, allow us to distinguish five classes of intratail complementations. By these studies we detected that the morphogenetic action of at least two gene products, pV and pM, is extremely concentration-dependent. Furthermore the gene product dosage experiments allow us to deduce for five gene products the following sequence of morphogenetic action during lambda tail assembly: (pJ,pM), (pV,pU), pZ. Finally, we find that our in vitro complementation data are consistent with already known polarity properties of nonsense tail(-)-mutants of phage lambda.
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Affiliation(s)
- P W Kühl
- Department of Microbiology, Biozentrum der Universität Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland
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45
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Katsura I, Kühl PW. Morphogenesis of the tail of bacteriophage lambda. II. In vitro formation and properties of phage particles with extra long tails. Virology 1975; 63:238-51. [PMID: 1089336 DOI: 10.1016/0042-6822(75)90388-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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46
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47
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Katsura I, Noda H. Structure and polymorphism of light meromyosin aggregates. J Biochem 1973; 73:257-68. [PMID: 4575557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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48
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Katsura I, Noda H. Further studies on the formation of reconstituted myosin filaments. J Biochem 1973; 73:245-56. [PMID: 4709619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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49
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50
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