What causes the aphid 28S rRNA to lack the hidden break?

Ogino, K.; Eda-Fujiwara, Hiroko; Fujiwara, Haruhiko; Ishikawa, Hajime

doi:10.1007/bf02101106

Cited by 23 publications

(21 citation statements)

References 15 publications

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“…The two posttranscriptional processings, splitting of 5.8S rRNA and generation of the hidden break, apparently share a common mechanism that recognizes an A + U-rich stem-loop structure of rRNA (Fujiwara and Ishikawa 1986). In this context, it is conceivable that evolutionary bias in nucleotide composition toward G + C in variable regions, V6 in particular, of aphid 28S rRNA has invalidated the excision mechanism, just as in deuterostomes (Ogino et al 1990). In contrast, bias toward A + T in higher dipterans may have been such as to provide the pre-rRNA with an additional excision site at 5.8 rRNA.…”

Section: Discussionmentioning

confidence: 99%

“…While in most protostomes the hidden break of 28S rRNA is generated by excising a fixed length of polynucleotide from pre-rRNA posttranscriptionally (Ware et al 1985;Fujiwara and Ishikawa 1986), in aphids, like in deuterostomes, such an excision does not take place, leaving the 28S rRNA molecule covalently continuous (Ogino et al 1990). As for the aphid 18S rRNA, we determined its entire nucleotide sequence and demonstrated that it comprised 2,469 nucleotides, the longest 18S rRNA known at that time (Kwon et al 1991).…”

Section: Introductionmentioning

confidence: 99%

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Nucleotide sequence and presumed secondary structure of the 28S rRNA of pea aphid implication for diversification of insect rRNA

1996

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Determination of the entire nucleotide sequence of the aphid 28S ribosomal RNA gene (28S rDNA) revealed that it is 4,147 bp in length with a G + C content of 60.3%. Based on the nucleotide sequence, we constructed a presumed secondary-structure model of the aphid 28S rRNA which indicated that the aphid 28S rRNA is characterized by the length and high G + C content of its variable regions. The G + C content of the aphid's variable regions was much higher than that of the entire sequence of the 28S rRNA, which formed a striking contrast to those of Drosophila with the G + C content much lower than the entire 28S molecule. In this respect, the aphid 28S rRNA somewhat resembled those of vertebrates. This is the third report of a complete large-subunit rRNA sequence from an arthropod, and the first 28S rRNA sequence for a nondipterous insect.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Nucleotide sequence and presumed secondary structure of the 28S rRNA of pea aphid implication for diversification of insect rRNA

1996

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“…The genomic library was constructed by insertion of partial EcoRI digest of peaaphid DNA into the EMBL4 phage, as described in [7]. tDNA was screened by the plaque-hybridization method, using fragments of Boinbyx mori rDNA as probes [8].…”

Section: Dna Isolation Cloning Subcloning and Sequencingmentioning

confidence: 99%

Unique structure in the intergenic and 5′ external transcribed spacer of the ribosomal RNA gene from the pea aphid Acyrthosiphon pisum

Kwon

Ishikawa

1992

European Journal of Biochemistry

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We analyzed the DNA sequence of the 5' external transcribed spacer (ETS) and part of the intergenic transcribed spacer (IGS) of the aphid ribosomal RNA gene (rDNA). The 5' ETS of aphid rDNA consists of 843 nucleotides with a G/C content of 69 mo1/100 mol, far higher than that of any other known 5' ETS for insect rDNA. The IGS of aphid rDNA contained a characteristic array of repeated sequences of 247 nucleotides. The repeated sequences were identical. It was shown that the number of the repeating sequence is heterogeneous.In most eukaryotic organisms, ribosomal RNA genes (rDNA) are encoded in multiple copies and the 18S, 5.8s and 28s rRNA-coding regions are transcribed as a larger precursor (pre-rRNA) by RNA polymerase I, which undergoes a series of post-transcriptional processing steps yielding the 18S, 5.8s and 28s rRNA found in ribosomes [l]. The cis-regulatory sequence of transcription initiation of rDNA by RNA polymerase I is apparently species specific, and those for the rDNA of many animals, including human In the present study, we have analyzed the DNA sequence of the 5' external transcribed spacer (ETS) and part of the intergenic transcribed spacer (IGS) of aphid rDNA and suggested the presence of an array of characteristic repetitive sequences in IGS that may be involved in the transcriptioninitiation mechanism of this gene. MATERIALS AND METHODS MaterialsA long-established parthenogenetic clone of pea aphid, Acyrthosiphon pisum (Harris) was maintained on young broad-bean plants, Vicia faba L, at 15°C in a regime with a 12-h photo period. The collected aphids were stored at -80°C until use. DNA isolation, cloning, subcloning and sequencingHigh-molecular-mass genomic DNA was isolated from aphids by the method described in [6]. The genomic library was constructed by insertion of partial EcoRI digest of peaaphid DNA into the EMBL4 phage, as described in [7]. tDNA was screened by the plaque-hybridization method, using fragments of Boinbyx mori rDNA as probes [8]. An aphid rDNA clone, lApR8, was digested with XhoIIXbaI; the resulting fragments, encoding most of the IGS region, were subcloned into the same sites of the plasmid Bluescript SK'. Plasmid subclones of deletion series were constructed using a deletion kit (Takara Shuzo Co., Japan) and sequenced by the dideoxychain-termination method [9] using the Sequenase version 2.0 kit (U. S. Biochem. Co.). Sequence arrangement and dotmatrix analysis were performed using the DNASIS V6.00 program (Hi tachi Software Engineering Co., Japan). RNA isolation and S1-nuclease-protection assayTotal cellular RNA for S1-nuclease mapping was prepared by the method described in [lo]. For the Sl-nuclease-protection assay, 5' 32P end-labeling of DNA fragments, using hybridization conditions of end-labeled DNA fragments with total cellular RNA, was performed according to the method described in [ll]. Southern hybridization analysisPea-aphid genomic DNA and subcloned rDNA, pApR868, were partially or completely digested with restriction enzymes, and the resulting fragments were ...

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“…The genomic library was screened [5] by the plaque-hybridization method using fragments from Bombyx mori ribosomal DNA as probes [6].…”

Section: Dna Isolation and Cloningmentioning

confidence: 99%

“…Aphids also share another characteristic feature with vertebrates in that their 28s rRNA lacks the hidden break that all the other insect rRNA have [34]. This is, at least, partly due to the exceptional G + C richness of the central gap region of the aphid 28s rRNA gene [5]. These, taken together, are suggestive of the very unique molecular evolution of this group of insect.…”

Section: Lrnplicationsmentioning

confidence: 99%

The longest 18S ribosomal RNA ever known

Kwon

Ogino

Ishikawa

1991

European Journal of Biochemistry

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An EMBL4 recombinant phage which encodes one of the full length of the aphid ribosomal DNA has been isolated from the aphid genomic library. Determination of the complete nucleotide sequence of the aphid 18s rRNA gene revealed that it is 2469 bp with a G + C content of 59%. The aphid 18s rRNA gene studied here is the longest and has the highest G + C content among the 18s rRNA genes examined so far. Evidence provided by the S1 nuclease assay suggests that the aphid 18s rRNA gene examined in this study is not a pseudogene containing an insertion sequence. Based on the nucleotide sequence of the 18s rRNA gene, we constructed a presumed secondary-structure model of the aphid 18s rRNA. In the aphid 18s rRNA, the eucaryote-specific E21 and 41 region are supposed to be longer and more complex than the counterparts of other 18s rRNA.It is generally known that rRNA share high similarity among various species. The small ribosomal subunit RNA (18s rRNA), which are encoded by nuclear genomes, have lengths close to 1800 bp and share significant nucleotide sequence identity with similar secondary structures. So far, 62 complete 18s rRNA sequences of eucaryotes, among which six vertebrates, four arthropods and one nematode are included, have been published [l] and extensively used as molecular clocks for evolutionary studies. Previously, we suggested that the aphid 18s rRNA has a molecular mass significantly larger than those of other eucaryotic 18s rRNA, suggesting that this exceptional structure may provide a clue to understand the general functions of the rRNA in the eucaryotic ribosomes To study the exceptional structure of this molecule further, we have cloned the aphid 18s rRNA gene and determined its entire nucleotide sequence. Also, based on the result we have presumed its secondary structure taking special note of the eucaryote-specific E21 region. 121. MATERIALS AND METHODS MaterialsA long-established parthenogenetic clone of the pea aphid, Acyrthosiphon pisum (Harris) was reared on young broadbean plants, Viciujaba L, at 15 "C in a short-day regime with a 12-h photo period. The collected aphids were stored at -80 "C until use. DNA isolation and cloningHigh-molecular-mass genomic DNA was isolated from the aphids by the method described [ 3 ] . EcoRI partial digests ofCorrespondence fo H. Ishikawa, Zoological Institute, Faculty of Science, University of Tokyo, Hongo 7-3-1, Tokyo, Japan 113 aphid DNA were ligated into EMBL4 at EcoRI sites using T4 ligase, packaged as described [4] and introduced into Escherichia coli LE392. The genomic library was screened [5] by the plaque-hybridization method using fragments from Bombyx mori ribosomal DNA as probes [6]. Subcloning and sequencingIsolation of bacteriophage DNA, subcloning of the fragment into plasmid Bluescript SK' and KS' , transformation into E. coli XL1 Blue, plasmid growth, isolation of plasmid DNA and restriction enzyme digestions were performed according to the standard methods described [4]. Plasmid subclones of deletion series were constructed and sequenced b...

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What causes the aphid 28S rRNA to lack the hidden break?

Cited by 23 publications

References 15 publications

Nucleotide sequence and presumed secondary structure of the 28S rRNA of pea aphid implication for diversification of insect rRNA

Nucleotide sequence and presumed secondary structure of the 28S rRNA of pea aphid implication for diversification of insect rRNA

Unique structure in the intergenic and 5′ external transcribed spacer of the ribosomal RNA gene from the pea aphid Acyrthosiphon pisum

The longest 18S ribosomal RNA ever known

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