Strategy for protein isoform identification from expressed sequence tags and its application to peptide mass fingerprinting.

Expressed Sequence Tags (ESTs) are an invaluable resource for protein identification and characterisation in proteomics. They allow proteins to be identified in the absence of genome sequence data. When EST sequences are used for protein identification, they are usually first processed into contigs to reduce redundancy and generate longer sequences from the overlapping ESTs. However, the process of generating contigs may accidentally group biologically meaningful isoforms together. Here we report means of discovering isoforms in EST sequences and how to use this information in the framework of protein identification and characterisation with peptide mass fingerprinting. We illustrate our strategies with examples from the dbEST database as well as protein isoforms from two-dimensional polyacrylamide gels.

What place for polyacrylamide in proteomics?

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) continues to deliver high quality protein resolution and dynamic range for the proteomics researcher. To remain as the preferred method for protein separation and characterization, several key steps need to be implemented to ensure quality sample preparation and speed of analysis. Here, we describe the progress made towards establishing 2D-PAGE as the optimal separation tool for proteomics research.

Absence of SOX3 in the developing marsupial gonad is not consistent with a conserved role in mammalian sex determination.

Expression of Sox3 has been detected in the testes of humans and of developing and adult mice at the same time as Sox9 and Sry. The co-expression of these three related Sox genes in the mouse indifferent gonadal ridge led to the hypothesis that these three genes, encoding transcription factors with similar DNA target binding sites, may interact with each other in initiating testis differentiation. The location of SOX3 on the marsupial Dunnart X chromosome also makes it a candidate for the marsupial X-linked gene responsible for the SRY- and hormone-independent initiation of scrotum or mammary gland development. Here we show that although marsupial SOX3 is highly conserved at the genetic level and appears to have a conserved role in CNS development, its expression during sexual differentiation differs from that of mice and humans. SOX3 expression is absent from the developing marsupial genital ridge and from the scrotal and mammary primordia during the critical time of differentiation and throughout the time that SRY is expressed. The absence of expression in the developing gonad strongly suggests that SOX3 does not have a conserved role in mammalian sexual determination or differentiation.

Proteomics: capacity versus utility.

Until recently scientists studied genes or proteins one at a time. With improvements in technology, new tools have become available to study the complex interactions that occur in biological systems. Global studies are required to do this, and these will involve genomic and proteomic approaches. High-throughput methods are necessary in each case because the number of genes and proteins in even the simplest of organisms are immense. In the developmental phase of genomics, the emphasis was on the generation and assembly of large amounts of nucleic acid sequence data. Proteomics is currently in a phase of technological development and establishment, and demonstrating the capacity for high throughput is a major challenge. However, funding bodies (both in the public and private sector) are increasingly focused on the usefulness of this capacity. Here we review the current state of proteome research in terms of capacity and utility.

Temperature-dependent sex determination in the American alligator: expression of SF1, WT1 and DAX1 during gonadogenesis.

Sex determination in mammals and birds is chromosomal, while in many reptiles sex determination is temperature dependent. Morphological development of the gonads in these systems is conserved, suggesting that many of the genes involved in gonad development are also conserved. The genes SF1, WT1 and DAX1 play various roles in the mammalian testis-determining pathway. SF1 and WT1 are thought to interact to cause male-specific gene expression during testis development, while DAX1 is believed to inhibit this male-specific gene expression. We have cloned SF1 and DAX1 from the American alligator, a species with temperature-dependent sex determination (TSD). SF1, DAX1 and WT1 are expressed in the urogenital system/gonad throughout the period of alligator gonadogenesis which is temperature sensitive. SF1 appears to be expressed at a higher level in females than in males. This SF1 expression pattern is concordant with the observed pattern during chicken gonadogenesis, but opposite to that observed during mouse gonadogenesis. Although the observed sexual dimorphism of gonadal SF1 expression in alligators and chickens is opposite that observed in the mouse, it is probable that SF1 is involved in control of gonadal steroidogenesis in all these vertebrates. DAX1 and WT1 are both expressed during stages 22-25 of both males and females. However, there appear to be no sex differences in the expression patterns of these genes. We conclude that DAX1, WT1 and SF1 may be involved in gonadal development of the alligator. These genes may form part of a gonadal-development pathway which has been conserved through vertebrate evolution.

Temperature-dependent sex determination: upregulation of SOX9 expression after commitment to male development.

In mammals, birds and reptiles the morphological development of the gonads appear to be conserved. This conservation is evident despite the different sex determining switches employed by these vertebrate groups. Mammals exhibit chromosomal sex determination (CSD) where the key sex determining switch is the Y-linked gene, SRY. Although SRY is the trigger for testis determination in mammals, it is not conserved in other vertebrate groups. However, a gene closely related to SRY, the highly conserved transcription factor, SOX9, plays an important role in the testis pathway of mammals and birds. In contrast to the CSD mechanism evident in mammals and birds, many reptiles exhibit temperature dependent sex determination (TSD) where the egg incubation temperature triggers sex determination. Here we examine the expression of SOX9 during gonadogenesis in the American alligator, (Alligator mississippiensis), a reptile that exhibits TSD. Alligator SOX9 is expressed in the embryonic testis but not in the ovary. However, the timing of SOX9 upregulation in the developing testis is not consistent with a role for this gene in the early stages of alligator sex determination. Since SOX9 upregulation in male embryos coincides with the structural organisation of the testis, SOX9 may operate farther downstream in the vertebrate sex differentiation pathway than previously postulated.

Temperature-dependent sex determination in the American alligator: AMH precedes SOX9 expression.

Gonadal morphogenesis is very similar among mammals, birds, and reptiles. Despite this similarity, each group utilises quite different genetic triggers for sex determination. In mammals, testis development is initiated by action of the Y-chromosome gene SRY. Current evidence suggests that SRY may act together with a related gene, SOX9, to activate another gene(s) in the pathway of testicular differentiation. A downstream candidate for regulation by SRY and SOX9 is AMH. In mouse, Sox9 is expressed in the Sertoli cells of the embryonic testis and it precedes the onset of Amh expression. During mouse gonadogenesis, Amh is confined to the embryonic testis, although it later shows postnatal expression in the ovary. Reptiles such as the American alligator, which exhibit temperature-dependent sex determination (TSD) do not have dimorphic sex chromosomes and apparently no SRY orthologue. SOX9 is expressed during testis differentiation in the alligator; however, it appears to be expressed too late to cause testis determination. Here we describe the cloning and expression of the alligator AMH gene and show that AMH expression precedes SOX9 expression during testis differentiation. This is the opposite to that observed in the mouse where SOX9 precedes AMH expression. The data presented here, as well as findings from recent expression studies in the chick, suggest that AMH expression is not regulated by SOX9 in the non-mammalian vertebrates.

Developmental expression of the androgen receptor during virilization of the urogenital system of a marsupial.

In the marsupial tammar wallaby, virilization begins approximately 3 wk after the onset of testosterone synthesis. In the eutherian mammal, in contrast, the onset of virilization of the male urogenital tract occurs shortly after the onset of androgen synthesis. Androgen action requires the presence of the androgen receptor to mediate a response in target tissues. We therefore investigated the developmental expression of the androgen receptor (AR) in both sexes of the tammar wallaby. AR gene transcript was detected in fetal gonad and brain as early as Day 19 of the 26.5-day gestation, 7 days earlier than the first rise in testicular testosterone (Days 0-5 postpartum [p.p.]). Immunoreactive AR was identified in the male urogenital sinus (UGS) 2 days before birth and in the female UGS and mammary glands by the day of birth. AR was present in the UGS, vagina, and prostate until Day 152 p.p., the oldest age examined. AR was identified in the gubernaculum testis at Day 2 p.p. and became more abundant by Day 32. In the phallus of both sexes, AR was identified by Day 4 p.p. and until Day 157, the oldest age examined. AR was not detected in the scrotum at any age from the day of birth to Day 157. Maturation of the phallus, wolffian duct, and epididymis was marked by appearance of epithelial immunostaining. AR was localized in the epithelium of the UGS in females by Day 50 p.p. but was not found in the epithelium of the male UGS up to Day 152 p.p., the oldest examined. AR were found in the mesenchyme of the UGS of male and female tammars 3-4 wk before virilization is first evident in the male at Day 25 p.p. We conclude that the presence of AR is not the initiating signal for virilization of the UGS in this marsupial male.

A human candidate spermatogenesis gene, RBM1, is conserved and amplified on the marsupial Y chromosome.

Three genes, RBM1, DAZ and TSPY, map to a small region of the long arm of the human Y chromosome which is deleted in azoospermic men. RBM1, but not DAZ or TSPY, has a Y-linked homologue in marsupials which is transcribed in the testis. This suggests that RBM1 has been retained on the Y chromosome because of a critical male-specific function. Marsupial RBM1 is closely related to human RBM1, but, like the related autosomal gene hnRNPG, lacks the amplification of an exon. This suggests that RBM1 evolved from hnRNPG at least 130 million years ago and has undergone internal amplification in primates, as well as independent amplification in several therian [corrected] lineages.

Widespread expression of the testis-determining gene SRY in a marsupial.

There is compelling evidence from mutation analysis and transgenesis that the SRY gene isolated from human and mouse encodes the testis-determining factor on the mammalian Y chromosome. However, how SRY achieves this function is unclear. Although marsupials have been separated from eutherian mammals for approximately 100 million years, homologues of SRY have been localised to the Y chromosome of two unrelated marsupial species, the tammar wallaby and the Darling Downs dunnart. Gonadal development is fundamentally similar in eutherian and marsupial mammals, but the timing of morphological events is different. Fetal Sry transcripts are confined to somatic cells of the male mouse genital ridge between 10.5-12.5 days post coitum, corresponding with the onset of testis differentiation. Analysis of Sry gene expression in the genital ridge of normal and germ cell-deficient fetal mice has established that this gene acts in the somatic cell lineage, and is presumed to induce the formation of Sertoli cells. This assumption can be tested more critically in the tammar, where the equivalent stages of testis differentiation are observed over a 7-day period. We have examined the relationship of SRY expression to testis differentiation in the tammar wallaby. We show the marsupial SRY gene cannot be exclusively coupled to Sertoli cell differentiation, as this gene is expressed in the male fetus from several days before genital ridge formation until 40 days after birth. SRY transcripts are also present in a variety of extra-gonadal tissues in the developing young and adult male, a pattern of SRY expression similar to that observed in humans. These data indicate that, in addition to a role in testis determination, SRY may have other functions [corrected].

The marsupial male: a role model for sexual development.

Sexual differentiation in male marsupials has many similarities with that of eutherians. Marsupials have an XX-XY sex determining mechanism, and have a homologue of the testis-determining SRY gene on their Y-chromosome. However, the development pattern of SRY gene expression is different from the mouse in that it is expressed for a much longer period. SRY is expressed in a range of non-gonadal tissues in male pouch young and adults which is similar to the human pattern, and raises questions as to its particular role(s) in sexual differentiation. Similarly Müllerian inhibiting substance (MIS) is produced in the developing testis over a longer period than in the mouse. Since ovaries cultured with MIS or transplanted into male recipient pouch young develop tubular structures, MIS may induce Sertoli cell formation. Testosterone is produced by the neonatal testis, and this stimulates Wolffian duct development to form the vas deferens and epididymis. Virilization of urogenital sinus is also androgen-dependent. However, virilization of the prostate and phallus occurs more than three weeks after the onset of testosterone production, suggesting that the timing of this may be regulated by delayed activation of the androgen receptor pathway. Unlike in eutherians, differentiation of the scrotum and mammary glands is not dependent on testicular hormones, but is independently regulated by an X-linked genetic mechanism. Clearly marsupials provide a unique perspective to help us clarify the mechanisms underlying sexual development in all mammals.

PCR amplification of SRY-related gene sequences reveals evolutionary conservation of the SRY-box motif.

SRY (sex-determining region of the Y chromosome) has recently been identified as a key regulatory gene in mammalian sex determination. The open reading frame of this gene contains an 80-amino-acid motif, the SRY-box, which shares a high degree of homology with a DNA-binding domain found in the high-mobility-group (HMG) proteins HMG1 and HMG2. The SRY box motif is highly conserved in several sequence-specific DNA-binding proteins that are known to act as transcription factors. Here we describe the use of degenerate PCR primers to identify SRY-related sequences containing the SRY-box motif from the genomic DNA of a variety of species. The results of this study suggest that in a diverse array of species SRY-related genes may serve as transcription factors that regulate a variety of developmental pathways, including sex determination.

Putting the heat on sex determination.

Sex determination and differentiation are inherently fascinating to both layperson and geneticist. Major advances have accelerated interest in the molecular genetic events mediating these processes in nematodes, flies, mice and humans. Far less attention has been paid to those organisms, particularly reptiles, where sex is determined by environmental cues. However, recent experimental evidence suggests that the two modes of sex determination may not only share common genetic elements, but may also be regulated by similar mechanisms. We argue that the ability to manipulate sex by temperature provides a particularly suitable model for exploring the molecular basis of this fundamental biological process.

Sex determination in loggerhead turtles: differential expression of two hnRNP proteins.

Sex determination in the loggerhead turtle, Caretta caretta, is controlled by incubation temperature during a critical period of embryogenesis. As heat-shock gene expression is temperature-dependent and has been shown to be associated with early developmental regulation in several organisms, we studied the constitutive expression of hsp70 and hsp90 in embryonic brain and urinogenital tissues to see if these proteins are differentially expressed during the sex-determining period in embryos incubated at male- (26 degrees C) and female- (32 degrees C) determining temperatures. The level of expression of hsp70 and hsp90, as determined from monoclonal antibody staining, is similar in both sexes during the sex-determining period. However, AC88, a monoclonal antibody that identifies hsp90 in several systems, recognised two additional protein bands (Mr 42 and 46 x 10(3)), which are differentially expressed in the urinogenital tissue of developing male and female embryos during the sex-determining period. While the 42K and 46K proteins appear in the urinogenital tissue of developing female (32 degrees C) embryos until stage 25, they are not expressed in the male (26 degrees C) urinogenital system after stage 24. Subsequent experiments have identified both turtle proteins as heterogeneous nuclear ribonucleoprotein particles (hnRNPs). As several hnRNP proteins have specific RNA-binding sites and are involved in mRNA processing reactions, the 46K protein may mediate post-transcriptional control of specific RNA transcripts required for sexual differentiation in C. caretta.

Multiple paternity in the loggerhead turtle (Caretta caretta).

Genotypic ratios within clutches of loggerhead turtle (Caretta caretta) embryos, from the Mon Repos rookery (Queensland), deviate significantly from the Mendelian ratios expected on the null hypothesis of single paternity. One-third of all clutches provide evidence for multiple insemination, indicating that multiple mating constitutes the major breeding pattern for C. caretta. Clutches from two females indicate that C. caretta females may mate between nestings.