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H T Jacobs

Publications and source records attributed to H T Jacobs.

At least 55 records · Page 3Linked to original sources
PubMed1995

Multisite oligonucleotide-mediated mutagenesis: application to the conversion of a mitochondrial gene to universal genetic code.

Using multisite oligonucleotide-mediated mutagenesis in conjunction with a mutagenesis selection procedure and rapid screening by allele-specific oligonucleotide hybridization has allowed us to develop a reliable protocol that enables a large number of base changes to be introduced rapidly into a piece of DNA, with the minimum number of manipulations. We have applied this protocol to generate synthetic versions of four mouse mitochondrial genes capable of being expressed in the nucleus/cytosol.

Amino Acid Sequence↗
PubMed1994

Apparent functional independence of the mitochondrial and nuclear transcription systems in cultured human cells.

We have constructed a series of reporter constructs which test the effects of sequence elements from the control region of human mitochondrial DNA on expression in the nucleus, as assayed by transient expression in cultured human cells. The mitochondrial heavy-strand promoter (HSP) was unable to function as a promoter in nuclear DNA. Neither the HSP, nor the binding region for the mitochondrial transcription factor mtTF1 from the light-strand promoter, had any significant or systematic modulatory effects upon transcription from strong or weak RNA polymerase II (pol II) promoters, in three different human cell lines. The same finding held true regardless of orientation with respect to the start site of transcription. Similar results were obtained with a rho 0 derivative of one of these lines, indicating that mitochondrial promoter sequences in the nucleus cannot modulate transcription in response to altered mtDNA copy number. These results support the view that the nuclear and mitochondrial transcription systems in human cells are functionally independent, and do not communicate through factors recognizing shared sequence elements, as suggested by studies in yeast.

Base Sequence↗
PubMed1994

A novel mitochondrial point mutation in a maternal pedigree with sensorineural deafness.

We have detected a novel mitochondrial mutation in a maternal pedigree, at least 13 of whose members have sensorineural hearing loss of varying severity, but who exhibit no other pathological features. The mutation, at np 7445, converts the 3' terminal T residue of tRNA-ser(UCN) to a C, and also brings about a silent alteration to the COI stop codon. The mutation destroys an XbaI site, within which a second mutation, at np 7444, has previously been reported in association with Leber's hereditary optic neuropathy. Predominantly mutant mtDNA was found in all 13 family members surveyed, whether or not they are overtly affected by deafness, and some individuals appeared homoplasmic, within the limits of detection. The novel mutation was not found in over 600 normal controls, nor in any of 27 other maternally unrelated individuals with deafness Other mutations found in mitochondrial disorders were also absent from this pedigree.

Adolescent↗
PubMed1994

Bilateral sensorineural hearing loss in members of a maternal lineage with mitochondrial point mutation.

Pure-tone audiometry was carried out on members of a recently described maternal lineage with sensorineural deafness, harbouring a novel mitochondrial mutation in the gene for tRNA-ser(UCN). This revealed a characteristic pattern of symmetrical bilateral sensorineural hearing losses in each affected individual, predominantly affecting the high-frequencies, but with considerable variability between individuals. No clear correlation was observed between age and severity, but most subjects reported progressive worsening of their condition. Some members of the lineage were found to be heteroplasmic for the tRNA-ser(UCN) mutation. However, the severity of hearing loss was poorly correlated with the representation of the mutant mtDNA, indicating that other, as yet unidentified factors must be involved in the aetiology of this disorder.

Adolescent↗
PubMed1993

Two distinct, sequence-specific DNA-binding proteins interact independently with the major replication pause region of sea urchin mtDNA.

We have identified a second DNA-binding protein in sea urchin embryo mitochondria, which interacts with a binding site in the major replication pause region, at the junction of the genes for ATP synthase subunit 6 and cytochrome c oxidase subunit III (COIII). We provisionally designate this protein mtPBP2, to distinguish it from the previously characterized mitochondrial pause-region binding protein mtPBP1, whose properties and binding site are quite distinct. The high-affinity binding site for mtPBP2 lies at the 5' end of the COIII gene, and exhibits partial dyad symmetry, although modification interference analysis indicates that recognition is complex. Binding of mtPBP2 to this site induces a bend of approximately 45 degrees in the DNA. Southwestern blots show that mtPBP1 and 2 are both single polypeptides, of apparent molecular weights 25 kD and 18 kD respectively. In vitro, mtPBP1 and mtPBP2 bind independently to their high-affinity sites, which are separated by about 50 bp.

Animals↗
PubMed1993

Characterization of a high-affinity binding site for a DNA-binding protein from sea urchin embryo mitochondria.

Based on electrophoretic mobility shift assays, DNase I footprinting and modification interference analyses we have identified a sequence-specific DNA-binding protein in blastula stage mitochondria of the sea urchin Strongylocentrotus purpuratus, which interacts with a binding site around the major pause site for DNA replication. This region straddles the boundary of the genes for ATP synthase subunit 6 and cytochrome c oxidase subunit III, and contains also a prominent origin of lagging-strand synthesis. The protein is thermostable, and its natural high-affinity binding site comprises the sequence 5'-AGCCT(N7)AGCAT-3'. Binding studies have demonstrated that two copies of the imperfect repeat, as well as the 7 bp spacing between them, are essential for tight binding. Based on the location of its binding site, we tentatively designate the protein mitochondrial pause-region binding protein (mtPBP) 1.

Animals↗
PubMed1992

Replication origins and pause sites in sea urchin mitochondrial DNA.

We have used a combination of one- and two-dimensional agarose gel electrophoresis, and solution hybridization to strand-specific probes, to map the replication origin of sea urchin mitochondrial DNA and to investigate the structure of replication intermediates. These assays are consistent with replication initiating unidirectionally from the D-loop region by D-loop expansion, as in vertebrates. A prominent site of initiation of lagging-strand synthesis lies at, or near to, the boundary between the genes for ATPase 6 and COIII, which is also close to a pause site for leading-strand synthesis. These findings suggest a role for pause sites in the regulation of mitochondrial transcription and replication, possibly involving template-binding proteins.

Animals↗
PubMed1991

Structural similarities between a mitochondrially encoded polypeptide and a family of prokaryotic respiratory toxins involved in plasmid maintenance suggest a novel mechanism for the evolutionary maintenance of mitochondrial DNA.

Subunit 8 of mitochondrial ATP synthase (A8), a mitochondrially encoded polypeptide, has no known homologue in any prokaryotic or plastid ATP synthase, suggesting that it has been recruited to its present role in the enzyme from an extraneous source. The polypeptide is poorly conserved at the primary sequence level, but shows a well-conserved hydropathy profile. The hydropathy profiles of A8 from diverse taxa were compared with those of the hok family of prokaryotic respiratory toxins, some of whose members are involved in plasmid maintenance, through postsegregational killing of cells that lose the plasmid at cell division. Such comparisons revealed a highly significant degree of similarity, suggesting a functional relationship. Based on these findings, it is proposed that A8 evolved from a hok-like protein, whose original role was the maintenance of an extrachromosomal replicon in the endosymbiont ancestor of mitochondria. An aggressive mechanism for the evolutionary maintenance of mitochondrial DNA overcomes many of the failings of traditional explanations for its retention as a separate genome.

Biological Evolution↗
PubMed1989

Sea urchin egg mitochondrial DNA contains a short displacement loop (D-loop) in the replication origin region.

Based on solution hybridization using single-stranded probes, native mitochondrial DNA extracted from sea urchin eggs contains a displacement-loop (D-loop) of approximately 70-80 nt. This maps to the single extended unassigned sequence of the genome, between the genes for tRNA(thr) and tRNA(pro), which also appears to contain the origin of first-strand replication. The D-loop commences at or close to a site of supercoil-dependent S1 nuclease hypersensitivity, adjacent to a run of 20 consecutive C residues, terminates near to the boundary of tRNA(thr), and appears to be composed at least partly of RNA, based on the sensitivity of the assays to RNase H. These experiments imply that the mechanisms of replication initiation in sea urchin and vertebrate mtDNAs are very similar, and suggest that the developmental restriction on mtDNA synthesis in eggs and embryos is maintained at the level of D-loop extension.

Animals↗
PubMed1989

Do ribosomes regulate mitochondrial RNA synthesis?

The levels of different classes of mitochondrially encoded transcripts are developmentally regulated in sea urchin embryos, as a result of selection between mutually exclusive synthetic pathways. I propose a simple model to explain these observations, based on a dual role for mitochondrial ribosomes and translation factors in RNA synthesis as well as in translation. This effect may be exerted either at the transcriptional or post-transcriptional level (or both), and is potentially generalizable to mammalian mtDNA and to other systems.

Animals↗
PubMed1989

Conserved tRNA gene cluster in starfish mitochondrial DNA.

Partial sequencing of mtDNA from four long-diverged species of starfish reveals the existence of a conserved cluster of 13 tRNA genes, organized in a manner similar to that of the tRNA cluster of sea urchin mtDNA, but located at a position distant from the presumed replication origin. These findings suggest that a clustered organization of tRNA genes may have been present in the ancestral mitochondrial genome, and raise the possibility that tRNAs may have catalyzed the dispersal rather than the accumulation of the genes which encode them.

Amino Acid Sequence↗
PubMed1989

Mutually exclusive synthetic pathways for sea urchin mitochondrial rRNA and mRNA.

The structure and abundance of mitochondrial transcripts in sea urchin embryos were investigated by a combination of RNA blot-hybridization, S1 mapping, and primer extension assays. Between the egg and blastula stages, the relative abundance of mitochondrial rRNAs declined slightly, while that of mitochondrial mRNAs increased up to 10-fold. Fine mapping of the termini of the rRNAs and of the adjacent transcripts indicated that, although they appeared to be butt-joined at their 5' ends to the upstream transcripts, tRNA-Phe 5' to the small subunit (12S) rRNA and NADH dehydrogenase subunit 2 mRNA 5' to the large subunit (16S) rRNA, respectively, their 3' ends were found to overlap the 5' ends of the downstream transcripts. 12S rRNA was found to extend 7 to 13 nucleotides into the sequence of tRNA-Glu; 16S rRNA was shown to terminate 3 to 5 nucleotides inside the coding region of cytochrome oxidase subunit 1 (COI) and 8 to 10 nucleotides from the mapped 5' end of COI mRNA. The rRNAs and the downstream transcripts must therefore be synthesized by distinct pathways, either by alternative processing of the same primary transcript(s) or by processing of different precursors. In either case, the events which select the ribosomal 3' ends preclude the production of functional transcripts of the downstream genes from the same precursor molecule. No developmental alterations in transcript structure were detected. We propose that mitochondrial RNA levels are regulated in early development by the selection of alternate and mutually exclusive RNA-processing pathways.

Animals↗
PubMed1988

Nucleotide sequence and gene organization of sea urchin mitochondrial DNA.

The 15,650 base-pair mitochondrial genome of the sea urchin Strongylocentrotus purpuratus has been cloned and sequenced. It exhibits a novel organization that suggests the primacy of post-transcriptional gene regulation. The same 13 polypeptides, two rRNAs and 22 tRNAs are encoded as in other animal mitochondrial DNAs, but are organized with extreme economy; non-coding information between genes is almost completely absent, some stop codons are generated post-transcriptionally and tRNA sequences are interspersed between only a minority of other structural genes. The genome uses a variant genetic code, in which AAA specifies asparagine, ATA isoleucine, TGA tryptophan and AGN serine, and has an unusual pattern of codon bias. The order of genes shows several differences from that of vertebrates. The genes for the large (16 S) ribosomal RNA and for NADH dehydrogenase subunit 4L (ND4L) are in different positions, located respectively between those encoding ND2 and cytochrome oxidase subunit I (COI) and between COI and COII. This organization is conserved amongst at least four regular echinoids diverging by some 225 million years. Most tRNA genes are also in different positions. The only long unassigned sequence in the genome (121 base-pairs) is located within a cluster of 15 tRNA genes. It contains elements resembling some of those found in the displacement (D) loop of vertebrate mtDNAs, notably polypurine/polypyrimidine tracts that may play a role in regulating transcription and the initiation of replication. The separation of the ribosomal RNA genes from each other and from the putative control region imposes special demands on the transcription of the genome.

Animals↗
PubMed1986

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

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.

Amino Acid Sequence↗