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J Hodgkin

Publications and source records attributed to J Hodgkin.

At least 37 records · Page 2Linked to original sources
PubMed1996

The tra-3 sex determination gene of Caenorhabditis elegans encodes a member of the calpain regulatory protease family.

The Caenorhabditis elegans sex determination gene tra-3 is required for the correct sexual development of the soma and germ line in hermaphrodites, while being fully dispensable in males. Genetic analysis of tra-3 has suggested that its product may act as a potentiator of another sex determination gene, tra-2. Molecular analysis reported here reveals that the predicted tra-3 gene product is a member of the calpain family of calcium-regulated cytosolic proteases, though it lacks the calcium binding regulatory domain. Calpains are regulatory processing proteases, exhibiting marked substrate specificity, and mutations in the p94 isoform underlie the human hereditary condition limb-girdle muscular dystrophy type 2A. The molecular identity of TRA-3 is consistent with previous genetic analysis which suggested that tra-3 plays a very selective modulatory role and is required in very small amounts. Based on these observations and new genetic data, we suggest a refinement of the position of tra-3 within the sex determination cascade and discuss possible mechanisms of action for the TRA-3 protein.

Amino Acid Sequence↗
PubMed1996

Evolution of sex determination in caenorhabditis: unusually high divergence of tra-1 and its functional consequences.

The tra-1 gene is a terminal regulator of somatic sex in Caenorhabditis elegans: high tra-1 activity elicits female development, low tra-1 activity elicits male development. To investigate the function and evolution of tra-1, we examined the tra-1 gene from the closely related nematode C. briggsae. Ce-tra-1 and Cb-tra-1 are unusually divergent. Each gene generates two transcripts, but only one of these is present in both species. This common transcript encodes TRA-1A, which shows only 44% amino acid identity between the species, a figure much lower than that for previously compared genes. A Cb-tra-1 transgene rescues many tissues of tra-1(null) mutants of C. elegans but not the somatic gonad or germ line. This transgene also causes nongonadal feminization of XO animals, indicating incorrect sexual regulation. Alignment of Ce-TRA-1A and Cb-TRA-1A defines several conserved regions likely to be important for tra-1 function. The phenotypic differences between Ce-tra-1(null) mutants rescued by Cb-tra-1 transgenes and wild-type C. elegans indicate significant divergence of regulatory regions. These molecular and functional studies suggest that evolution of sex determination in nematodes is rapid and genetically complex.

Amino Acid Sequence↗
PubMed1995

The nematode Caenorhabditis elegans and its genome.

Over the past two decades, the small soil nematode Caenorhabditis elegans has become established as a major model system for the study of a great variety of problems in biology and medicine. One of its most significant advantages is its simplicity, both in anatomy and in genomic organization. The entire haploid genetic content amounts to 100 million base pairs of DNA, about 1/30 the size of the human value. As a result, C. elegans has also provided a pilot system for the construction of physical maps of larger animal and plant genomes, and subsequently for the complete sequencing of those genomes. By mid-1995, approximately one-fifth of the complete DNA sequence of this animal had been determined. Caenorhabditis elegans provides a test bed not only for the development and application of mapping and sequencing technologies, but also for the interpretation and use of complete sequence information. This article reviews the progress so far toward a realizable goal--the total description of the genome of a simple animal.

Animals↗
PubMed1995

Dominant feminizing mutations implicate protein-protein interactions as the main mode of regulation of the nematode sex-determining gene tra-1.

The tra-1 gene is the terminal global selector of somatic sex in Caenorhabditis elegans: High tra-1 activity elicits female somatic development while low tra-1 activity elicits male development. Previous genetic studies defined a cascade of negatively interacting genes that regulates tra-1 activity in response to the primary sex-determining signal. Here, we investigate the last step in this regulatory cascade, by studying rare gain-of-function (gf) mutations of tra-1 that direct female somatic development irrespective of the upstream sex-determining signal. These mutations appear to abolish negative regulation of tra-1 in male tissues. We identify the lesions associated with 29 of these mutations and find that all affect a short stretch of amino acid residues present in both protein products of the tra-1 gene. Twenty-six alleles are associated with single nonconservative amino acid substitutions. Two alleles affect tra-1 RNA splicing and generate messages that omit part or all of the exon encoding this short stretch. These results suggest that sexual regulation of tra-1 is achieved post-translationally, by an inhibitory protein-protein interaction. The amino acid stretch altered by the tra-1(gf) mutations may define a site of interaction for negative regulators of tra-1. The stretch includes a potential phosphorylation site for glycogen synthase kinase 3 and may be conserved in the human gene GLI3, a homolog of tra-1 identified previously.

Alleles↗
PubMed1995

Isolation of dominant XO-feminizing mutations in Caenorhabditis elegans: new regulatory tra alleles and an X chromosome duplication with implications for primary sex determination.

A strain of Caenorhabditis elegans was constructed that permits selection of dominant or sex-linked mutations that transform XO animals (normally male) into fertile females, using a feminizing mutation, tra-2(e2046gf), which by itself does not sexually transform XO males. Twenty-three mutations were isolated after chemical mutagenesis and found to fall into both expected classes (four dominant tra-1 mutations and eight recessive xol-1 mutations) and novel classes. The novel mutations include 10 second-site mutations of tra-2, which are called eg mutations, for enhanced gain-of-function. The tra-2(gf, eg) alleles lead to complete dominant transformation of XO animals from fertile male into fertile female. Also isolated was a duplication of the left end of the X chromosome, eDp26, which has dominant XO lethal and feminizing properties, unlike all previously isolated duplications of the X chromosome. The properties of eDp26 indicate that it carries copies of one or more numerator elements, which act as part of the primary sex-determination signal, the X:A ratio. The eDp26 duplication is attached to the left tip of the X chromosome in inverted orientation and consequently can be used to generate unstable attached-X chromosomes.

Animals↗
PubMed1994

Regulatory rearrangements and smg-sensitive alleles of the C. elegans sex-determining gene tra-1.

The tra-1 gene is the terminal regulator in the sex determination pathway in C. elegans, directing all aspects of somatic sexual differentiation. Recessive loss-of-function (lf) mutations in tra-1 masculinize XX animals (normally somatically female), while dominant gain-of-function mutations feminize XO animals (normally male). Most tra-1 (lf) mutations can be fitted into a simple allelic series of somatic masculinization, but a small number of lf alleles do not fit into this series. Here we show that three of these mutations are associated with DNA rearrangements 5' to the coding region. One allele is an inversion that may be subject to a position effect. We also report the isolation of a new class of tra-1 alleles that are responsive to mutations in the smg system of RNA surveillance. We show that two of these express RNAs of aberrant size. We suggest that the smg-sensitive mutations may identify a carboxy-terminal domain required for negative regulation of tra-1 activity.

Alleles↗
PubMed1994

Epigenetics and the maintenance of gene activity states in Caenorhabditis elegans.

The nematode Caenorhabditis elegans has been the subject of many detailed investigations in developmental biology. Molecular analyses have failed to detect covalent alterations to DNA, such as methylation or rearrangement, during development of C. elegans. Genetic experiments indicate that imprinting of gamete genomes does not occur to any significant extent. The maintenance of gene activity states in this organism may depend predominantly on regulatory gene circuitry. Some possible examples of maintenance circuits are discussed.

Animals↗
PubMed1994

Identification of a candidate primary sex determination locus, fox-1, on the X chromosome of Caenorhabditis elegans.

Sex in Caenorhabditis elegans (XX hermaphrodite, XO male) is determined by the X:A ratio, which is the ratio of X chromosome number to autosomal set number. Recent genetic results with X chromosome duplications have suggested that there may be only a small number of major numerator sites on the X chromosome that contribute to this ratio. Mapping of duplication endpoints delimited a region of less than 300 kb, likely to contain one such element. Cosmid clones from this region were tested for numerator activity by constructing transgenic lines carrying extra copies of each tested cosmid. Most cosmid arrays have no effect on the viability of either XX or XO animals. One cosmid array was found to be viable in XX animals, but lethal and feminizing in XO animals, consistent with it containing a major numerator element. Further experiments defined a region of 12-30 kb with apparent numerator activity, which is designated fox-1, 'Feminizing locus On X'. A cDNA clone hybridizing across part of this region encodes a predicted RNA-binding protein.

Amino Acid Sequence↗
PubMed1993

Zinc fingers in sex determination: only one of the two C. elegans Tra-1 proteins binds DNA in vitro.

The tra-1 gene of Caenorhabditis elegans is a major developmental regulator that promotes female development. Two mRNAs are expressed from the tra-1 locus as a result of alternative mRNA processing. One mRNA encodes a protein with five zinc fingers and the other a protein with only the first two zinc fingers. We have derived a preferred in vitro DNA binding site for the five finger protein by selection from random oligonucleotides. The two finger protein does not bind to DNA in vitro. Moreover, removal of the first two fingers from the five finger protein does not eliminate binding and has little effect on its preferred binding site. We find that a protein sequence amino-terminal to the finger domain also appears to play a role in DNA binding.

Alternative Splicing↗
PubMed1993

Molecular cloning and duplication of the nematode sex-determining gene tra-1.

The autosomal sex-determining gene tra-1 plays a major role in controlling sexual phenotype in the nematode Caenorhabditis elegans. This gene is the terminal global regulator in a well-characterized cascade of sex-determining genes. It governs all aspects of somatic sexual differentiation, and it also has important functions in governing germ-line differentiation. Previous genetic analyses have led to the characterization of many loss-of-function (masculinizing) and gain-of-function (dominant feminizing) alleles, and to models for the functions and regulation of tra-1. The gene was cloned by identifying linked transposon insertions, about 200 kb away from tra-1. From this starting point a series of YAC, cosmid and phage clones were assembled into a genomic walk covering over 400 kb. Much of this region was found to be unrepresented in the cosmid database that covers most of the C. elegans genome. This deficit is largely or wholly due to the presence of sequences that cannot be cloned in rec+bacterial hosts. The ratio of physical map distances to recombinational map distances in the tra-1 region of the genome appears to be unusually low, indicating considerable local map expansion. The location of tra-1 within the cloned region was determined using a variety of tra-1 mutations that are associated with physical rearrangements of the gene. One of these is a 14-kb deletion, which behaves as a null allele. Another rearrangement, eDp24, is a tandem duplication of 22kb. Genetic analysis demonstrates that eDp24 carries two incomplete copies of tra-1, and that these copies appear to interact, suggesting some form of negative autoregulation at this locus. Three variant forms of the tra-1 locus have been identified in different natural isolates of C. elegans.

Alleles↗
PubMed1992

Molecular analysis of the C. elegans sex-determining gene tra-1: a gene encoding two zinc finger proteins.

The tra-1 gene is the terminal control gene for somatic sex determination in the nematode Caenorhabditis elegans. Here we identify two tra-1 mRNAs: one is a 1.5 kb transcript that peaks in abundance in the second larval stage, and the other is a 5 kb transcript that is present at relatively constant abundance throughout development. Both RNAs occur at similar levels in both sexes, suggesting that regulation of tra-1 is posttranscriptional. Neither RNA is germline restricted. The two RNAs are colinear at their 5' ends: the shorter RNA encodes a protein with two zinc finger motifs, and the longer RNA encodes a protein with five zinc fingers. The identification of eight nonsense mutations confirms that these are authentic tra-1 RNAs and demonstrates that the longer one is essential for tra-1 activity. The transcription pattern reveals that alternative mRNA processing governs the number of zinc fingers in the resulting tra-1 protein. The tra-1 fingers are strikingly similar to those of three other proteins, the products of the human GLI and GLI3 and Drosophila cubitus interruptus Dominant (ciD) genes.

Amino Acid Sequence↗
PubMed1992

Genetic sex determination mechanisms and evolution.

Different animal groups exhibit a surprisingly diversity of sex determination systems. Moreover, even systems that are superficially similar may utilize different underlying mechanisms. This diversity is illustrated by a comparison of sex determination in three well-studied model organisms: the fruitfly Drosophila melanogaster, the nematode Caenorhabditis elegans, and the mouse. All three animals exhibit male heterogamety, extensive sexual dimorphism and sex chromosome dosage compensation, yet the molecular and cellular processes involved are now known to be quite unrelated. The similarities must have arisen by convergent evolution. Studies of sex determination demonstrate that evolution can produce a variety of solutions to the same basic problems in development.

Animals↗
PubMed1991

More is not better: brood size and population growth in a self-fertilizing nematode.

The normal form of the nematode Caenorhabditis elegans is a self-fertilizing hermaphrodite, which produces from the same germ-line tissue first a limited number of sperm and then a larger number of oocytes. Self-progeny brood sizes are determined by the number of sperm, and most of the oocytes remain unfertilized. Therefore it might seem selectively advantageous to increase the number of sperm, and hence the size of the brood. A mutation that leads to a 50% increase in sperm production allows a comparison of population growth rates between the wild type (mean brood 327 progeny) and the mutant (mean brood 499 progeny). Wild-type populations grow faster, as measured by food consumption, indicating that increased brood size is not advantageous. The mutant appears to be at a disadvantage because the additional spermatogenesis leads to a delay in the onset of oogenesis, and hence to an increase in the minimum generation time. In support of the notion of an optimal brood size, it was found that different natural isolates of this species have self-fertilities similar to that of the standard laboratory strain, in the range 250-350 progeny per worm.

Animals↗
PubMed1991

Tests for parental imprinting in the nematode Caenorhabditis elegans.

The mutation him-6 (e1423) leads to generalized chromosomal nondisjunction during meiosis in oogenesis and spermatogenesis of C. elegans. As a result, gametes nullisomic or disomic for each of the six chromosomes occur at appreciable frequency. Crosses utilizing marked him-6 strains were used to generate and identify exceptional euploid progeny which had received both homologues of a marked autosome either from the male parent or from the female parent. Examples of all ten possible exceptions were identified and found to be viable and fertile. These results (together with previous data for the X chromosome) indicate that major chromosomal imprinting effects do not occur during gametogenesis in this organism.

Animals↗