Molecular cloning of the cDNA for the major hemoglobin component from paramecium caudatum

Yamauchi, Kiyoshi; Mukai, Masanori; Ochiai, Takehiko; Usuki, Itaru

doi:10.1016/s0006-291x(05)80130-5

Cited by 13 publications

(5 citation statements)

References 11 publications

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“…The TATA box appears to be an indispensable orientation mechanism in archaeal transcription (Thomm 1996;Soppa 1999aSoppa , 1999bBell, Magill, and Jackson 2001;Slupska et al 2001) and is employed in a substantial fraction of metazoan genes (;42% in Drosophila and ;32% in human; Kutach and Kadonaga 2000;Suzuki et al 2001a;Ohler et al 2002) and most yeast genes (Struhl 1989;Choi et al 2002). Putative TATA boxes are also associated with the genes of Paramecium (Yamauchi et al 1992), Dictyostelium (Hori and Firtel 1994), and Entamoeba (Singh et al 1997). This wide phylogenetic distribution of TATA suggests that the stem eukaryote employed this sequence in transcription orientation.…”

Section: Introductionmentioning

confidence: 99%

The Evolution of Transcription-Initiation Sites

Lynch

Scofield

Hong

2005

Molecular Biology and Evolution

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Unlike the situation in prokaryotes, most eukaryotic messenger RNAs contain a moderately long 5' untranslated region (UTR). Such leader sequences impose a burden on eukaryotic genes by providing substrate for the mutational origin of premature translation-initiation codons, which generally result in defective proteins. To gain an insight into the expansion of 5' UTRs in eukaryotic genomes, we present a simple null model in which the evolution of transcription-initiation sites is entirely driven by the stochastic mutational flux of core-promoter sequences and premature translation-initiation codons. This model yields results consistent with a variety of heretofore disconnected observations, including the form of length distributions of 5' UTRs, the relatively low variance in UTR features among distantly related eukaryotes, the universal reliance on relatively simple core-promoter sequences, and the elevated density of introns in the 5' UTR. We suggest that the reduced effective population sizes of most eukaryotes impose a population-genetic environment conducive to the movement of core promoters to random positions, subject to the constraint imposed by the upstream accumulation of premature translation-initiation codons. If this hypothesis is correct, then selection for gene-specific regulatory features need not be invoked to explain either the origin of lengthy eukaryotic 5' UTRs or the 1,000-fold range of 5'-UTR lengths among genes within species. Nevertheless, once permanently established, expanded 5' UTRs may have provided a novel substrate for the evolution of mechanisms for posttranscriptional regulation of eukaryotic gene expression. These results provide a further example of how an increase in the power of random genetic drift can passively promote the evolution of forms of gene architecture that ultimately facilitate the evolution of organismal complexity.

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Section: Introductionmentioning

confidence: 99%

The Evolution of Transcription-Initiation Sites

Lynch

Scofield

Hong

2005

Molecular Biology and Evolution

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“…Partial genomic libraries in λEMBL3 and λgt11 were prepared and screened with a 0.4 kbp cDNA encoding the major hb gene (Yamauchi et al, 1992a). The longest 15 kbp fragment was obtained from the λEMBL3 library.…”

Section: Resultsmentioning

confidence: 99%

“…Partial genomic libraries of P. caudatum total genomic DNA were constructed using λEMBL3 and λgt11. These libraries were screened by plaque hybridization (Sambrook et al, 1989) using 32 Plabeled P. caudatum hb cDNA (Yamauchi et al, 1992a) under highly stringent conditions. The insert DNA of the longest clone from λEMBL3 library was digested with EcoRI or BamHI.…”

Section: Isolation and Characterization Of Genomic Clonesmentioning

confidence: 99%

Extreme heterogeneous composition of the Paramecium caudatum macronuclear genomic DNA between hemoglobin and nucleosome assembly protein-1 genes

et al. 2010

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The intergenic region between the hemoglobin (hb) and nucleosome assembly protein-1 (nap-1) genes in the Paramecium caudatum macronuclear genome was previously found to be heterogeneously composed. Cloning of this intergenic region from the macronuclear genomic DNA identified four unique DNA fragments of different sizes. Sequencing of the cloned fragments revealed extreme heterogeneity and characteristics of both internal eliminated sequence (IES) and imprecise internal deletion sequences (IIDSs) in the intergenic region. Missing sequences were an AT-rich and direct repeats existed in their boundaries. Southern blotting of the total genomic DNA and polymerase chain reaction (PCR) of the total genomic DNAs indicated that there exist a dozen DNA fragments of different sizes in this intergenic region. It is likely that the heterogeneity found in the P. caudatum macronuclear genome results from the variable removal of an intergenic region.

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“…The amino acid sequence was determined directly by protein sequencing. Codon selections (ϩ) were made on the basis of the highest frequency in the codon usage reported for Paramecium proteins (Martindale, 1989;Dupuis, 1992;Yamauchi et al 1992). The amino acid residue that was mismatched between the determined protein sequence and the deduced protein sequence ( Figure 2B) is shown in parentheses.…”

Section: Resultsmentioning

confidence: 99%

“…Hybridization and washing were performed as described above (Sambrook et al, 1989). Probes used for hybridization were the p36-C EcoRI fragment of the cDNA as described above, the 0.4-kbp P. caudatum hemoglobin cDNA (Yamauchi et al 1992), and the 0.5-kbp P. caudatum genomic DNA encoding the glyceraldehyde-3-phosphate dehydrogenase. The last probe was produced by PCR with two specific primers (O'Hara and Mikami, unpublished observations).…”

Section: Northern Blottingmentioning

confidence: 99%

Cloning and Sequencing of a Protein Involved in Phagosomal Membrane Fusion inParamecium

Yamauchi

Aihara

Ishida

et al. 1999

MBoC

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An mAb was raised to the C5 phagosomal antigen in Paramecium multimicronucleatum. To determine its function, the cDNA and genomic DNA encoding C5 were cloned. This antigen consisted of 315 amino acid residues with a predicted molecular weight of 36,594, a value similar to that determined by SDS-PAGE. Sequence comparisons uncovered a low but significant homology with a Schizosaccharomyces pombe protein and the C-terminal half of the beta-fructofuranosidase protein of Zymomonas mobilis. Lacking an obvious transmembrane domain or a possible signal sequence at the N terminus, C5 was predicted to be a soluble protein, whereas immunofluorescence data showed that it was present on the membranes of vesicles and digestive vacuoles (DVs). In cells that were minimally permeabilized but with intact DVs, C5 was found to be located on the cytosolic surface of the DV membranes. Immunoblotting of proteins from the purified and KCl-washed DVs showed that C5 was tightly bound to the DV membranes. Cryoelectron microscopy also confirmed that C5 was on the cytosolic surface of the discoidal vesicles, acidosomes, and lysosomes, organelles known to fuse with the membranes of the cytopharynx, the DVs of stages I (DV-I) and II (DV-II), respectively. Although C5 was concentrated more on the mature than on the young DV membranes, the striking observation was that the cytopharyngeal membrane that is derived from the discoidal vesicles was almost devoid of C5. Approximately 80% of the C5 was lost from the discoidal vesicle-derived membrane after this membrane fused with the cytopharyngeal membrane. Microinjection of the mAb to C5 greatly inhibited the fusion of the discoidal vesicles with the cytopharyngeal membrane and thus the incorporation of the discoidal vesicle membranes into the DV membranes. Taken together, these results suggest that C5 is a membrane protein that is involved in binding and/or fusion of the discoidal vesicles with the cytopharyngeal membrane that leads to DV formation.

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Molecular cloning of the cDNA for the major hemoglobin component from paramecium caudatum

Cited by 13 publications

References 11 publications

The Evolution of Transcription-Initiation Sites

The Evolution of Transcription-Initiation Sites

Extreme heterogeneous composition of the Paramecium caudatum macronuclear genomic DNA between hemoglobin and nucleosome assembly protein-1 genes

Cloning and Sequencing of a Protein Involved in Phagosomal Membrane Fusion inParamecium

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