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D R Forsdyke

Publications and source records attributed to D R Forsdyke.

At least 19 recordsLinked to original sources

Haldane's rule: hybrid sterility affects the heterogametic sex first because sexual differentiation is on the path to species differentiation.

Prevention of recombination is needed to preserve both phenotypic differentiation between species and sexual phenotypic differentiation within species. For species differentiation (speciation), isolating barriers preventing recombination may be pre-zygotic (gamete transfer barriers), or post-zygotic (either a developmental barrier resulting in hybrid inviability, or a chromosomal-pairing barrier resulting in hybrid sterility). The sterility barrier is usually the first to appear and, although often initially only manifest in the heterogametic sex (Haldane's rule), is finally manifest in both sexes. For sexual differentiation, the first and only barrier is chromosomal-pairing, and always applies to the heterogametic sex. For regions of sex chromosomes affecting sexual differentiation there must be something analogous to the process generating the hybrid sterility seen when allied species cross. Explanations for Haldane's rule have generally assumed that the chromosomal-pairing barrier initiating evolutionary divergence into species is due to incompatibilities between gene products ("genic), or sets of gene products ("polygenic), rather than between chromosomes per se ("chromosomal"). However, if chromosomal incompatibilities promoting incipient sexual differentiation could also contribute to the process of incipient speciation, then a step towards speciation would have been taken in the heterogametic sex. Thus, incipient speciation, manifest as hybrid sterility when "varieties" are crossed, would appear at the earliest stage in the heterogametic sex, even in genera with homomorphic sex chromosomes (Haldane's rule for hybrid sterility). In contrast, it has been proposed that Haldane's rule for hybrid inviability needs differences in dosage compensation, so could not apply to genera with homomorphic sex chromosomes.

Animals↗

Crossover hot-spot instigator (Chi) sequences in Escherichia coli occupy distinct recombination/transcription islands.

Crossover hot-spot instigator (Chi) sequences (5'-GCTGGTGG-3') are orientation-dependent, strand-specific sequences implicated in RecA-mediated DNA recombination. In Escherichia coli and Haemophilus influenzae Chi and Chi-like sequences preferentially locate to approx. 1kb recombination 'islands' in the mRNA-synonymous strands of open reading frames (ORFs). Since mRNA-synonymous strands follow Szybalski's transcription direction rule in being G-rich, and the average ORF is about 1kb, then, on this basis alone, Chi sequences are seen to reside in 1kb G-rich 'islands'. However, RecA preferentially binds GT-rich sequences, suggesting that genomic context might potentiate Chi action. Consistent with this, we report for E. coli that 1kb sequence windows with Chi near their centres are a distinct subset of total 1kb windows, the mRNA-synonymous strands being preferentially enriched in both G and T. Chi function might be particularly important for bacteria that survive high temperature and radiation. These often exist in habitats where recombination with E. coli DNA would be unlikely, so canonical Chi sequences might not confer a selective disadvantage in this respect. In general, Chi sequences are not more frequent in thermophilic bacteria and Deinococcus radiodurans, than in E. coli and other mesophilic bacteria. Only two of five thermophilic bacteria examined showed preferential location of Chi sequences to mRNA-synonymous strands. In the thermophile Methanococcus jannaschii, windows containing the canonical Chi sequence do not form a distinct subset. We suggest that in thermophilic bacteria and D. radiodurans the Chi function may be achieved by sequences that differ from the canonical Chi sequence, or that the number of these sequences is sufficient, or that the Chi function is unnecessary.

Base Composition↗

Thermophilic bacteria strictly obey Szybalski's transcription direction rule and politely purine-load RNAs with both adenine and guanine.

When transcription is to the right of the promoter, the "top," mRNA-synonymous strand of DNA tends to be purine-rich. When transcription is to the left of the promoter, the top, mRNA-template strand tends to be pyrimidine-rich. This transcription-direction rule suggests that there has been an evolutionary selection pressure for the purine-loading of RNAs. The politeness hypothesis states that purine-loading prevents distracting RNA-RNA interactions and excessive formation of double-stranded RNA, which might trigger various intracellular alarms. Because RNA-RNA interactions have a distinct entropy-driven component, the pressure for the evolution of purine-loading might be greater in organisms living at high temperatures. In support of this, we find that Chargaff differences (a measure of purine-loading) are greater in thermophiles than in nonthermophiles and extend to both purine bases. In thermophiles the pressure to purine-load affects codon choice, indicating that some features of their amino acid composition (e.g., high levels of glutamic acid) might reflect purine-loading pressure (i.e., constraints on mRNA) rather than direct constraints on protein structure and function.

Adenine↗

Two levels of information in DNA: relationship of Romanes' "intrinsic" variability of the reproductive system, and Bateson's "residue" to the species-dependent component of the base composition, (C+G)%.

In 1886 Charles Darwin's research associate George Romanes published a paper entitled "Physiological Selection: An Additional Suggestion on the Origin of Species". This was criticized by his Victorian contemporaries and largely ignored by those who followed. However, the recent recognition of two levels of information in DNA suggests that Romanes had solved the major problems with Darwin's theory. It was apparent from the outset that the form of reproductive isolation likely to apply most generally to initial species divergence (hybrid sterility), would depend on differences, not in "primary" information ("genic"), but in "secondary" information ("chromosomal"). This viewpoint, further elaborated by Bateson & Saunders (1902), White (1978), and King (1993), is criticized by the genic school (Coyne & Orr, 1998) because it requires visible differences between chromosomes, and appears not to explain Haldane's rule. However, chromosomal differentiation with respect to the species-dependent component of base composition [(C+G)%; Forsdyke, 1996] appears to resolve these problems. Because it explained so much, it was easy to believe that the genic viewpoint explained everything. Romanes and Bateson thought otherwise. We are only just beginning to recognize what they were trying to tell us.

Animals↗

Accounting units in DNA.

Chargaff's first parity rule (%A=%T and %G=%C) is explained by the Watson-Crick model for duplex DNA in which complementary base pairs form individual accounting units. Chargaff's second parity rule is that the first rule also applies to single strands of DNA. The limits of accounting units in single strands were examined by moving windows of various sizes along sequences and counting the relative proportions of A and T (the W bases), and of C and G (the S bases). Shuffled sequences account, on average, over shorter regions than the corresponding natural sequence. For an E. coli segment, S base accounting is, on average, contained within a region of 10 kb, whereas W base accounting requires regions in excess of 100 kb. Accounting requires the entire genome (190 kb) in the case of Vaccinia virus, which has an overall "Chargaff difference" of only 0.086% (i.e. only one in 1162 bases does not have a potential pairing partner in the same strand). Among the chromosomes of Saccharomyces cerevisiae, the total Chargaff differences for the W bases and for the S bases are usually correlated. In general, Chargaff differences for a natural sequence and its shuffled counterpart diverge maximally when 1 kb sequence windows are employed. This should be the optimum window size for examining correlations between Chargaff differences and sequence features which have arisen through natural selection. We propose that Chargaff's second parity rule reflects the evolution of genome-wide stem-loop potential as part of short- and long-range accounting processes which work together to sustain the integrity of various levels of information in DNA.

Base Composition↗

Deviations from Chargaff's second parity rule correlate with direction of transcription.

The distribution of deviations from Chargaff's second parity rule was examined for overlapping sequence windows of a length (1 kb) predicted to be suitable for detecting correlations with functional features of DNA. For long genomic segments from E. coli, Saccharomyces cerevisiae, and Vaccinia virus, Chargaff differences for the W bases and/or for the S bases correlate with transcription direction and gene location. For W-rich genomes, the mRNA-synonymous strand contains regions which, if extruded from negatively supercoiled DNA, would fold to generate stem-loop structures with A-rich loops. Similarly, for S-rich genomes the loops would be G-rich. We suggest that the disposition of genes in nucleic acid sequences arises from their having to adapt to a preexisting mosaic of genomic regions, each distinguished by its potential to extrude single-strand loops enriched for a particular base (or two non-Watson-Crick pairing bases). The mosaic would have facilitated the intrastrand and interstrand accounting required for correction of mutations, and would have evolved in the early RNA world before the emergence of protein-encoding capacity. The preexisting mosaic would have determined transcription direction since there is pressure for all mRNAs of a cell to have purine-rich loops, thus decreasing loop-loop interactions which might lead to formation of "self" sense-antisense RNA duplexes.

Animals↗

Heat shock proteins as mediators of aggregation-induced 'danger' signals: implications of the slow evolutionary fine-tuning of sequences for the antigenicity of cancer cells.

Organisms 'tune' to their environment through adaptations which confer a selective advantage. However, in complex systems, a primary change of positive adaptive value might have multiple minor secondary effects, usually of negative adaptive value, which could invoke further counter-adaptations. This 'fine-tuning', a 'debugging', mainly at the intracellular level, would appear an evolutionary burden detracting from the positive nature of the primary change. However, if the primary mutation is in a potential oncogene, secondary, short-term effects may include the recruitment, in an apparently random manner, of unmutated non-oncogene products into the antigenic repertoire of the cancer cell. This 'danger' signal, provided by the co-aggregation of oncogene and non-oncogene products, would be mediated by inducible heat-shock proteins (Hsps), and lead to display of corresponding MHC-peptide complexes. It was argued previously that T cells specific for peptides from most 'self' intracellular antigens are not eliminated during T cell 'education', and so would be available for subsequent immune activation by the corresponding peptides. These considerations might explain why cancer specific antigens have been so elusive, why cancer antigenicity is often individual specific, and why therapeutic approaches involving complexes of peptides with Hsps may be successful.

Antigens, Neoplasm↗

Correlation of chi orientation with transcription indicates a fundamental relationship between recombination and transcription.

Cross-over hot-spot instigator (Chi) sequences (5'-GCTGGTGG-3') are abundant, strand-specific, sequences, which locally increase recombination in Escherichia coli. Located within G-rich 'recombination islands', Chi orientations correlate with the orientations both of DNA replication and of transcription. Consistent with evidence from eukaryotic systems for a fundamental relationship between recombination and transcription, we find for E. coli Chi sequences, and for Haemophilus influenzae Chi-like sequences, that orientations correlate better with transcription than with replication. Complying with Szybalski's transcription direction rule, open reading frames in these prokaryotes have purine-rich mRNA-synonymous DNA strands. Hence, the G-richness of 'recombination islands' may reflect their correspondence with 'transcriptional islands' (genes). Comparison of a natural with the corresponding shuffled sequence, indicates a base order-dependent island unit of approx. 1kb. 1998 Elsevier Science B.V.

Base Composition↗

An alternative way of thinking about stem-loops in DNA. A case study of the human G0S2 gene.

Single strands extruded from duplex DNA have the potential to form stem-loop structures, which may be involved in the homology search preceding recombination. The total stem-loop potential in a sequence window can be analysed in terms of the relative contributions of base composition and base order. There are at least 10 base composition-determined parameters of relevance to the energetics of stem-loop formation. These are the quantities of the four bases themselves, and six derived parameters: ATmin, CGmin, Chargaff differences for the W and S bases, and two base products. The quantities of the least represented base of a Watson-Crick base pair (ATmin, CGmin) might provide an index of the total stem potential of a widow. The degrees to which one base of a Watson-Crick pair exceeds the other (the Chargaff differences for the W bases and for the S bases) might provide an index of the total loop potential of a window. Base products (A x T, C x G) might provide an index both of stem and of loop potentials. Multiple regression analysis of the relationship of the 10 parameters to the energetics of stem-loop formation in the G0S2 gene reveals major roles of S bases, and of base products. While base composition may primarily serve genome or genome sector "strategies", it becomes of local relevance in the case of CpG islands. Base order serves many local "strategies", whose demands may conflict. Base order serves the encoding of protein or of recognition motifs for regulatory factors. On the other hand there appear to be circumstances under which base order synergizes with, or antagonises, base composition in determining total stem-loop potential. Antagonism is evident when the base composition-dependent component of the stem-loop potential of a region is greater than the total stem-loop potential of that region.

DNA↗

Expression and processing of G0/G1 switch gene 24 (G0S24/TIS11/TTP/NUP475) RNA in cultured human blood mononuclear cells.

The human G0/G1 switch (G0S) gene, G0S24, and its rodent immediate-early homolog (TIS11, TTP, NUP475) are part of a mammalian gene family whose members encode CCCH zinc finger domains and domains similar to part of the large subunit of RNA polymerase II and to the Mei2 regulator of G1 arrest in fission yeast. We compared the RNA expression of G0S24 with that of other G0S genes in cultured blood mononuclear cells and examined the levels of various RNA processing intermediates. Freshly isolated cells contained high levels of several G0S RNAs, which declined by 24 h, suggesting transient spontaneous stimulation during cell purification (Heximer et al., 1996). However, in cells preincubated for 24 h, G0S24 RNA levels remained much higher than those of other G0S genes (107+/-42 x 10(6) molecules/microg of RNA); stimulation with lectin (Con-A) further increased G0S24 RNA, much of which remained nuclear. Like those of FOS/G0S7, EGR1/G0S30 and of the gene encoding the regulator of G protein signalling 1 (RGS1), G0S24 RNA levels increased more in response to a protein kinase C activator than to a calcium ionophore, whereas the opposite held for FOSB/G0S3 and RGS2/G0S8. With appropriate PCR primer pairs, we showed a G0S24 RNA processing intermediate, which crossed the exon-1/intron boundary, and nonpolyadenylated nuclear RNA extending into the 3' flank, where there is a second CpG island. The concentration of the latter intermediate (1.2+/-0.2 x 10(6) molecules/microg of RNA), which increased transiently on cell stimulation, did not account for all G0S24 nuclear RNA. The levels of G0S24 RNA and both intermediates were increased by the protein synthesis inhibitor cycloheximide, consistent with regulation by a labile repressor.

Base Sequence↗

The normal copy of the G0S19-3-associated, CpG island-containing, upstream sequence is downstream of G0S19-2/MIP1alpha in association with a TRE17 oncogene.

The G0S19-1/MIP1alpha and G0S19-2/MIP1alpha genes locate to human chromosomes 17q and encode similar copies of the beta-chemokine G0S19/MIP1alpha. The G0S19-3 gene, present in 1 in 4 humans, is a 5' truncated version of G0S19-2; a CpG island-containing upstream sequence (CpG-US), rich in potential transcriptional activation motifs, replaces much of the first intron and the first exon. Sequences hybridizing with the CpG-US sequence, normally exist in all human genomes. Thus, it appears that there has been recombination between a duplicated G0S19 gene and a duplicated CpG-US-like sequence. We have isolated sequences hybridizing with the CpG-US sequence from a human genomic library in bacteriophage lambda. Restriction mapping and sequencing shows a CpG-US-like sequence approximately 8 kb downstream of G0S19-2 (hence, named CpG-DS sequence). The sequence is contiguous with a TRE17 oncogene-associated sequence (GenBank locus HSTRE175). Members of the TRE17 family are known to locate to chromosome 17q (Onno et al., 1993b), and have sequence characteristics suggestive of positive Darwinian selection. Linkage with a TRE17 oncogene may have arisen by recombination and imply no functional relationship. However, it is possible that the CpG-DS may normally regulate TRE17 expression. PCR and sequencing studies indicate the close proximity of other chemokine-related sequences in the 17q11.2 region.

Amino Acid Sequence↗

Chargaff difference analysis of the bithorax complex of Drosophila melanogaster.

Much of the fruit fly genome is compact ("Escherichia coli mode"), indicating a genome-wide selection pressure against DNA with little adaptive function. However, in the bithorax complex (BX-C) homeodomain genes are widely dispersed with large introns ("mammalian mode"). Chargaff difference analysis of compact bacterial and viral genomes has shown that most mRNAs have the potential to form stem-loop structures with purine-rich loops. Thus, for many taxa if transcription is to the right, the top (mRNA synonymous) DNA strand has purine-rich loop potential, and if transcription is to the left, the top (template) strand has pyrimidine-rich loop potential. The best indicator bases for transcription direction are A and T for AT-rich genomes, and C and G for CG-rich genomes. Consistent with this, Chargaff difference analysis of BX-C genes and several non-BX-C genes shows that, whatever the mode, mRNAs have the potential to form stem-loop structures with A-rich loops. We confirm that many potential open reading frames in the BX-C are unlikely to be functional. Conversely, we suggest that a few unassigned open reading frames may actually be functional. Since apparent organization in the mammalian mode cannot be explained in terms of unacknowledged open reading frames, yet the fruit fly genome is under pressure to be compact, it is likely that many BX-C functions do not involve the encoding of proteins.

Animals↗

Cyclosporin A inhibits early mRNA expression of G0/G1 switch gene 2 (G0S2) in cultured human blood mononuclear cells.

Cyclosporin A (CsA) may achieve its immunosuppressive effects by inhibiting the calcium- and calmodulin-dependent phosphatase calcineurin which is required for activation of target genes by members of the NFAT (nuclear factor of activated T cells) transcription factor family. Among these target genes is the gene encoding interleukin-2 (IL2), a cytokine facilitating progression through the G1 phase of the cell cycle. However, IL2 does not reverse CsA inhibition, suggesting that at least one other NFAT-sensitive gene may be involved. The human G0/G1 switch gene, G0S2, has potential NFAT-binding sites in the 5' flank and encodes a small basic potential phosphoprotein of unknown function. Using a sensitive, reverse transcription-polymerase chain reaction (RT-PCR) assay, G0S2 mRNA levels were assayed in cultured blood mononuclear cells. Freshly isolated cells contain high levels of G0S2 mRNA which rapidly decline. This "spontaneous stimulation" is also noted with some other G0S genes and has been attributed to some aspect of the isolation procedure. In cells that have been preincubated to lower mRNA levels, there is a transient increase in G0S2 mRNA, peaking between 1-2 h, in response to Concanavalin-A (ConA), or to the combination of phorbol ester (TPA), and the calcium ionophore, ionomycin. Both these responses are inhibited by CsA. Our results suggest that G0S2 expression is required to commit cells to enter the G1 phase of the cell cycle, and that, while not excluding other possible targets, early inhibition of G0S2 expression by CsA may be important in achieving immunosuppression. G0S2 may be of value as a reporter gene for analyzing the mechanism of action of CsA and its influence on the positive and negative selection of lymphocytes in response to self and not-self antigens.

Amino Acid Sequence↗

Comparison of mRNA expression of two regulators of G-protein signaling, RGS1/BL34/1R20 and RGS2/G0S8, in cultured human blood mononuclear cells.

RGS1 and RGS2 are members of a new class of regulators of G-protein signaling identified by their selective mRNA expression either in phorbol ester (TPA)-stimulated human B lymphocytes (RGS1/1R20/BL34) or in blood mononuclear cells treated with the T-cell lectin concanavalin A (ConA) and cycloheximide (RGS2/G0S8). The RGS1 gene shows low basal mRNA expression in freshly purified blood mononuclear cells, which increases upon incubation for a day. In contrast, RGS2 initially shows high basal levels of mRNA expression, which subsequently decrease. Expression of both genes increases in response to ConA, with RGS2 mRNA levels increasing briskly to a maximum between 0.5 and 1 hr and decreasing to baseline by 6 hr, whereas the RGS1 mRNA increase is delayed reaching a maximum between 1 and 2 hr. RGS1 mRNA levels increase much more in response to a protein kinase C activator (TPA), than to a calcium ionophore (ionomycin), whereas the opposite is true for RGS2. We suggest that ConA elevates RGS2 on the basis of its ability to increase intracellular calcium, and that RGS2 may be involved in the regulation of intracellular calcium. The distinction between RGS1 and RGS2 is further emphasized by studies indicating that recombinant RGS2 does not bind in vitro to two members of the G(i) subfamily of G-protein alpha-subunits for which recombinant RGS1 has high affinity.

GTP-Binding Proteins↗

Different biological species "broadcast" their DNAs at different (G+C)% "wavelengths".

Radio can be used as a metaphor for the transmission of information by DNA through time and space. Just as different radio transmitters broadcast at different wavelengths to prevent interference, so different biological species "broadcast" their DNAs at different (G+C)% "wavelengths" to prevent recombination. It is postulated that species differences in (G+C)% prevent recombination. First, evidence is presented supporting the early Crick-Sobell stem-loop model for genetic recombination, which proposes that the rate-limiting step in recombination is the recognition ("kissing") of complementary sequences in the loops of stem-loop structures extruded from supercoiled DNA. Then, various ways in which differences in (G+C)% might impede complementary loop interactions are outlined. The strength of the postulate is that it brings together a variety of disparate observations in fields that have not previously been seen as related. Thus, explanations are apparent for why most mutations are not selectively neutral (the "neutralist/selectionist" debate), why introns were present in the earliest genes (the "introns-early/introns-late" debate), and the origin of species.

Animals↗

Stem-loop potential in MHC genes: a new way of evaluating positive Darwinian selection?

The domains of polymorphic major histocompatibility complex (MHC) proteins which interact with peptides and T-cell receptors are considered to have been under positive evolutionary selection pressure. Evidence for this is a high ratio of non-synonymous to synonymous mutations in the corresponding genomic domains. By this criterion snake venom phospholipase A2 genes have also been under positive selection pressure. Recent studies of the latter genes indicate that positive selection has overridden an evolutionary pressure on base order which normally promotes the potential to extrude single-strand stem-loops from supercoiled duplex DNA ( fold pressure ). This has resulted in base order-dependent stem-loop potential being shifted to introns, which are highly conserved between species. It is now shown that, like snake venom phospholipase A2 genes, the domains of polymorphic MHC genes which appear to have responded to positive selection pressure have decreased base order-dependent stem-loop potential. The evolutionary pressure to generate stem-loop potential (believed to be important for recombination) has been overridden less in exons under negative purifying selection than in exons under positive Darwinian selection. Thus, base order-dependent stem-loop potential shows promise as an independent indicator of positive selection.

Animals↗

Sequence analysis and expression in cultured lymphocytes of the human FOSB gene (G0S3).

G0S3 is a member of a set of putative G0/G1 switch regulatory genes (G0S genes) selected by screening cDNA libraries prepared from human blood mononuclear cells cultured for 2 hr with lectin and cycloheximide. The sequence shows high homology with the murine FOSB gene, which encodes a component of the AP1 transcriptional regulator. Comparison of cDNA and genomic sequences reveals a 4-exon structure characteristic of the FOS family of genes. Freshly isolated cells show high levels of FOSB/G0S3 and FOS/G0S7 mRNAs, which decline rapidly during incubation in culture medium. The kinetics of expression suggest that the high initial levels are caused by the isolation procedure, and do not reflect constitutive expression. In cells preincubated for a day, levels of FOS mRNA reach a maximum 20 min after the addition of lectin and decline to control levels over the next 3 hr. Levels of FOSB mRNA reach a maximum 40 min after the addition of lectin and decline to control levels over the next 6 hr. In freshly isolated cells, both FOS and FOSB mRNAs increase dramatically in response to the protein synthesis inhibitor cycloheximide. In preincubated cells, the cycloheximide response is decreased, especially in the case of FOSB. These differences in expression of FOS and FOSB suggest different roles and regulation. Regions of low base order-dependent stem-loop potential in the region of the gene are defined. These indicate where base order has been adapted for purposes other than stem-loop stability (e.g., encoding proteins or gene regulation). Regions of low potential in a 68.5-kb genomic segment containing the FOSB gene suggest that the potential may help locate genes in uncharted DNA sequences.

Adult↗

A "stealth" approach to inhibition of lymphocyte activation by oligonucleotide complementary to the putative G0/G1 switch regulatory gene G0S30/EGR1/NGFI-A.

The putative G0/G1 switch regulatory gene G0S30/EGR1/NFGI-A show increased expression shortly after adding concanavalin-A (ConA) to cultured T lymphocytes. However, it is reported that lymphocytes from mice in which the gene has been deleted proliferate normally in response to ConA. This suggests that G0S30 expression is not critical for the response. Paradoxically, others report that proliferation of ConA-stimulated rat lymphocytes is inhibited by an antisense oligonucleotide complementary to G0S30. Because the G0S30 sequence is highly conserved between species, we used a similar oligonucleotide (differing by 1 base) to show for humans that the response to ConA is also inhibited. However, no oligonucleotide-induced changes in the concentrations of G0S30 protein or mRNA are detectable. This suggests that the oligonucleotide is not acting by influencing the expression of G0S30, and may be targeting another gene. The phosphorothioated oligonucleotide was maximally inhibitory at a 50 nM concentration, which is near to the "physiological" concentration found with CpG-containing oligonucleotides to activate mouse B lymphocytes. In the present work, increasing the concentration above 50 nM, or adding further quantities of control oligonucleotides, decreased the inhibition. It is suggested that by using low oligonucleotide concentrations (the "stealth" approach), one may avoid "tripping" an endogenous defense system directed against exogenous oligonucleotides, yet still get sufficient uptake to inhibit lymphocyte activation.

Base Sequence↗