Complete nucleotide sequences of the nuclear pseudogenes for cytochrome oxidase subunit I and the large mitochondrial ribosomal RNA in the sea urchin Strongylocentrotus purpuratus

Howard T. Jacobs, Brenda Grimes

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Nucleotide sequencing of the sea urchin nuclear genomic homologues of two mitochondrial genes, cytochrome oxidase subunit I (COI) and 16 S ribosomal RNA, shows clearly that they are both pseudogenes. The COI homologue has accumulated numerous single-base changes causing non-conservative amino acid substitutions, as well as many small insertions and deletions, most of which result in frameshifts. There is no continuous open reading frame and eight unmutated TGA codons persist. A genomic repetitive element is found between the break points of two rearrangements that have occurred in the region. By solution hybridization in RNA excess, we were unable to detect transcripts colinear with the complete nuclear COI sequence, using Strongylocentrotus purpuratus gastrula RNA, at a detection limit of 10-6 of total RNA. Transcripts restricted to the 3′ end of the COI pseudogene may be present, however, but at an extremely low level. Comparison of the 16 S/COI junctions in nuclear and mitochondrial DNA suggests a possible complementary DNA-mediated conversion of the 16 S pseudogene subsequent to its original transposition into nuclear DNA. We have estimated the likely age of the nuclear sequence element from the divergence between nuclear and mitochondrial sequences and from cross-hybridization with the genomes of other sea urchin species. With both methods, an age of more than 30 million years is suggested.

Original languageEnglish (US)
Pages (from-to)509-527
Number of pages19
JournalJournal of molecular biology
Volume187
Issue number4
DOIs
StatePublished - Feb 20 1986

Fingerprint

Strongylocentrotus purpuratus
Pseudogenes
Ribosomal RNA
Sea Urchins
Electron Transport Complex IV
RNA
Gastrula
Mitochondrial Genes
Terminator Codon
Amino Acid Substitution
Mitochondrial DNA
Open Reading Frames
Limit of Detection
Nucleotides
Complementary DNA
mitochondrial RNA
Genome
DNA

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology

Cite this

@article{b3535cb33cc74ffb90285a6be3751935,
title = "Complete nucleotide sequences of the nuclear pseudogenes for cytochrome oxidase subunit I and the large mitochondrial ribosomal RNA in the sea urchin Strongylocentrotus purpuratus",
abstract = "Nucleotide sequencing of the sea urchin nuclear genomic homologues of two mitochondrial genes, cytochrome oxidase subunit I (COI) and 16 S ribosomal RNA, shows clearly that they are both pseudogenes. The COI homologue has accumulated numerous single-base changes causing non-conservative amino acid substitutions, as well as many small insertions and deletions, most of which result in frameshifts. There is no continuous open reading frame and eight unmutated TGA codons persist. A genomic repetitive element is found between the break points of two rearrangements that have occurred in the region. By solution hybridization in RNA excess, we were unable to detect transcripts colinear with the complete nuclear COI sequence, using Strongylocentrotus purpuratus gastrula RNA, at a detection limit of 10-6 of total RNA. Transcripts restricted to the 3′ end of the COI pseudogene may be present, however, but at an extremely low level. Comparison of the 16 S/COI junctions in nuclear and mitochondrial DNA suggests a possible complementary DNA-mediated conversion of the 16 S pseudogene subsequent to its original transposition into nuclear DNA. We have estimated the likely age of the nuclear sequence element from the divergence between nuclear and mitochondrial sequences and from cross-hybridization with the genomes of other sea urchin species. With both methods, an age of more than 30 million years is suggested.",
author = "Jacobs, {Howard T.} and Brenda Grimes",
year = "1986",
month = "2",
day = "20",
doi = "10.1016/0022-2836(86)90330-X",
language = "English (US)",
volume = "187",
pages = "509--527",
journal = "Journal of Molecular Biology",
issn = "0022-2836",
publisher = "Academic Press Inc.",
number = "4",

}

TY - JOUR

T1 - Complete nucleotide sequences of the nuclear pseudogenes for cytochrome oxidase subunit I and the large mitochondrial ribosomal RNA in the sea urchin Strongylocentrotus purpuratus

AU - Jacobs, Howard T.

AU - Grimes, Brenda

PY - 1986/2/20

Y1 - 1986/2/20

N2 - Nucleotide sequencing of the sea urchin nuclear genomic homologues of two mitochondrial genes, cytochrome oxidase subunit I (COI) and 16 S ribosomal RNA, shows clearly that they are both pseudogenes. The COI homologue has accumulated numerous single-base changes causing non-conservative amino acid substitutions, as well as many small insertions and deletions, most of which result in frameshifts. There is no continuous open reading frame and eight unmutated TGA codons persist. A genomic repetitive element is found between the break points of two rearrangements that have occurred in the region. By solution hybridization in RNA excess, we were unable to detect transcripts colinear with the complete nuclear COI sequence, using Strongylocentrotus purpuratus gastrula RNA, at a detection limit of 10-6 of total RNA. Transcripts restricted to the 3′ end of the COI pseudogene may be present, however, but at an extremely low level. Comparison of the 16 S/COI junctions in nuclear and mitochondrial DNA suggests a possible complementary DNA-mediated conversion of the 16 S pseudogene subsequent to its original transposition into nuclear DNA. We have estimated the likely age of the nuclear sequence element from the divergence between nuclear and mitochondrial sequences and from cross-hybridization with the genomes of other sea urchin species. With both methods, an age of more than 30 million years is suggested.

AB - Nucleotide sequencing of the sea urchin nuclear genomic homologues of two mitochondrial genes, cytochrome oxidase subunit I (COI) and 16 S ribosomal RNA, shows clearly that they are both pseudogenes. The COI homologue has accumulated numerous single-base changes causing non-conservative amino acid substitutions, as well as many small insertions and deletions, most of which result in frameshifts. There is no continuous open reading frame and eight unmutated TGA codons persist. A genomic repetitive element is found between the break points of two rearrangements that have occurred in the region. By solution hybridization in RNA excess, we were unable to detect transcripts colinear with the complete nuclear COI sequence, using Strongylocentrotus purpuratus gastrula RNA, at a detection limit of 10-6 of total RNA. Transcripts restricted to the 3′ end of the COI pseudogene may be present, however, but at an extremely low level. Comparison of the 16 S/COI junctions in nuclear and mitochondrial DNA suggests a possible complementary DNA-mediated conversion of the 16 S pseudogene subsequent to its original transposition into nuclear DNA. We have estimated the likely age of the nuclear sequence element from the divergence between nuclear and mitochondrial sequences and from cross-hybridization with the genomes of other sea urchin species. With both methods, an age of more than 30 million years is suggested.

UR - http://www.scopus.com/inward/record.url?scp=0023053133&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0023053133&partnerID=8YFLogxK

U2 - 10.1016/0022-2836(86)90330-X

DO - 10.1016/0022-2836(86)90330-X

M3 - Article

C2 - 3012091

AN - SCOPUS:0023053133

VL - 187

SP - 509

EP - 527

JO - Journal of Molecular Biology

JF - Journal of Molecular Biology

SN - 0022-2836

IS - 4

ER -