Biomedical subjects

R Okimoto

Publications and source records attributed to R Okimoto.

25 records · Page 2Linked to original sources

PubMed1991

Repeated sequence sets in mitochondrial DNA molecules of root knot nematodes (Meloidogyne): nucleotide sequences, genome location and potential for host-race identification.

Within a 7 kb segment of the mtDNA molecule of the root knot nematode, Meloidogyne javanica, that lacks standard mitochondrial genes, are three sets of strictly tandemly arranged, direct repeat sequences: approximately 36 copies of a 102 ntp sequence that contains a TaqI site; 11 copies of a 63 ntp sequence, and 5 copies of an 8 ntp sequence. The 7 kb repeat-containing segment is bounded by putative tRNAasp and tRNAf-met genes and the arrangement of sequences within this segment is: the tRNAasp gene; a unique 1,528 ntp segment that contains two highly stable hairpin-forming sequences; the 102 ntp repeat set; the 8 ntp repeat set; a unique 1,068 ntp segment; the 63 ntp repeat set; and the tRNAf-met gene. The nucleotide sequences of the 102 ntp copies and the 63 ntp copies have been conserved among the species examined. Data from Southern hybridization experiments indicate that 102 ntp and 63 ntp repeats occur in the mtDNAs of three, two and two races of M.incognita, M.hapla and M.arenaria, respectively. Nucleotide sequences of the M.incognita Race-3 102 ntp repeat were found to be either identical or highly similar to those of the M.javanica 102 ntp repeat. Differences in migration distance and number of 102 ntp repeat-containing bands seen in Southern hybridization autoradiographs of restriction-digested mtDNAs of M.javanica and the different host races of M.incognita, M.hapla and M.arenaria are sufficient to distinguish the different host races of each species.

Animals↗

PubMed1990

Evidence for the frequent use of TTG as the translation initiation codon of mitochondrial protein genes in the nematodes, Ascaris suum and Caenorhabditis elegans.

Data obtained from alignments of nucleotide sequences of mitochondrial (mt) DNA molecules of the nematode worms Ascaris suum and Caenorhabditis elegans indicate that in six of the mt-protein genes of A. suum and three of the mt-protein genes of C. elegans TTG is used as the translation initiation codon. Also, GTT seems to be the translation initiation codon of the A. suum COIII gene. All of the five remaining A. suum mt-protein genes appear to begin with ATT and the remaining nine C. elegans mt-protein genes appear to begin with either ATT or ATA. Therefore, in contrast to all other metazoan mtDNAs sequenced so far, it is likely that none of the nematode mt-protein genes use the standard ATG translation initiation codon. Some A. suum and C. elegans mt-protein genes end in T or TA, suggesting that, as found in other metazoan mitochondria, 3'-terminal polyadenylation is occasionally necessary to generate complete translation termination codons in transcripts of nematode mt-protein genes.

Amino Acid Sequence↗

PubMed1990

A set of tRNAs that lack either the T psi C arm or the dihydrouridine arm: towards a minimal tRNA adaptor.

The mitochondrial DNA (mtDNA) molecules of the nematode worms, Caenorhabditis elegans and Ascaris suum contain 22 putative genes for non-standard forms of tRNAs. The inferred transcripts can be folded into 20 separate structures each resembling a tRNA whose T psi C arm and variable loop are replaced with a simple loop of 6-12 nucleotides. In two further structures [that resemble tRNAs for ser(UCN) and ser(AGN)], the dihydrouridine arm is replaced by a loop of 5-8 nucleotides. By hybridizing mt-tRNA gene-specific oligonucleotide probes to nematode RNAs, we have obtained evidence for transcription of at least nine C.elegans and three A.suum mt-tRNA genes. Each transcript (tRNA) is the exact size predicted from the respective DNA sequence, to which three nucleotides, presumably CCA, have been added following transcription. An exception was C.elegans mt-tRNAasn, most molecules of which had one nucleotide (plus CCA) more than predicted from the gene. The data presented strongly support the conclusion that the functional mt-tRNAs of nematode worms are direct transcripts (with only CCA addition) of the structurally unusual mt-tRNA genes. There is no evidence of trans-splicing or RNA editing to add the sequences missing from these nonstandard tRNAs. We presume, therefore, that the non-standard forms are active in mitochondrial protein synthesis.

Animals↗

PubMed1987

Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms.

The complete nucleotide sequence of the mitochondrial DNA (mtDNA) molecule of the parasitic nematode worm Ascaris suum has been determined. This molecule lacks genes for tRNAs of the standard form. Instead, 21 sequences are found that can be folded into structures that resemble tRNAs in which the T psi C arm and variable loop are missing and replaced with a single loop of between 4 and 12 nucleotides. Considerations of various properties of these sequences, including the number, predicted anticodons, conserved nucleotides, direction of transcription, base composition, and relative gene arrangements are consistent with the interpretation that they are genes for a different sort of tRNA. Transfer RNA genes with a similar potential secondary structure are found in mtDNA of the free-living nematode Caenorhabditis elegans, suggesting that this unusual form of tRNA is used by all nematode mitochondria.

Animals↗

PubMed1983

Coordinate gene expression during somatic embryogenesis in carrots.

There are several biochemical differences between the callus and the embryos of carrot culture. Callus tissue produces callus-specific proteins and a conditioning factor that is necessary for the synthesis of callus-specific proteins. By contrast, embryos produce embryo-specific proteins [Sung, Z. R. & Okimoto, R. (1981) Proc. Natl. Acad. Sci. USA 78, 3683-3687] and develop the capability to inactivate cycloheximide [Sung, Z. R., Lazar, G. J. & Dudits, D. (1981) Plant Physiol. 68, 261-264]. A mutant, WCH105, that can inactivate cycloheximide in the callus as well as in the embryos produces the embryo-specific proteins instead of the callus-specific proteins and fails to produce the conditioning factor by the callus tissue. Callus tissues also produce a conditioning factor for callus growth. This factor is not the same as the conditioning factor for the synthesis of the callus-specific proteins, as WCH105 can grow as callus. The existence of WCH105 demonstrates that the callus-specific and embryo-specific traits are coordinately regulated, but in an opposite manner. A common mechanism apparently activates one set and inactivates the other set of functions. WCH105 seems to be impaired in this mechanism.

Journal Article↗

PubMed1981

Embryonic proteins in somatic embryos of carrot.

The translational profile of cultured carrot cells (callus) was compared with that of the somatic embryos derived from them. The two tissues synthesize almost the same number and kinds of polypeptides except for two "embryonic" proteins. These were found in the somatic embryos but were nearly undetectable in the callus. Both embryo development and the production of embryonic proteins were induced by the same trigger (transfer of the callus to fresh medium) and were suppressed by the same factor (2,4-dichlorophenoxyacetic acid). But the appearance and disappearance of the proteins occurred several days prior to embryo formation and to the conversion of embryo to callus, respectively. Carrot cell lines incapable of embryogenesis could not synthesize the embryonic proteins. These findings indicate that the embryonic proteins play a key role in the process of embryo development. The function of these proteins is presently unknown; however, they can serve as early developmental markers for studying the mechanisms underlying somatic embryogeny in plants.

Journal Article↗

PubMed1980

The anaerobic proteins of maize.

Anaerobic treatment drastically alters the pattern of protein synthesized by maize primary roots. During the first hour of anaerobiosis, aerobic protein synthesis is halted and there is an increase in the synthesis of a class of polypeptides with approximate molecular weights of 33,000 daltons. During the second hour of anaerobic treatment, the synthesis of another small group of polypeptides is initated. This group, the anerboic polypeptides (ANPs), accounts for > 70% of total protein synthesis after 5 hr of anaerobiosis, and is synthesized in basically the same ratio until root death (approximately 70 hr). The alcohol dehydrogenase polypeptides are major ANPs. RNA isolated from roots treated anaerobically for at least 24 hr directs the translation of only the anaerobic polypeptides. However, RNA from roots treated anaerobically for only 5 hr directs translation of both anaerobic and aerobic polypeptides. Thus an early response to anaerobic treatment is the suppression of aerobic message translation. Although the anaerobic polypeptides share a formal similarity to heat-shock proteins in animals, it is probable that the anaerobic genes are an adaptation to flooding.

Anaerobiosis↗