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1.
S. D. Berry S. R. Davis E. M. Beattie N. L. Thomas A. K. Burrett H. E. Ward A. M. Stanfield M. Biswas A. E. Ankersmit-Udy P. E. Oxley J. L. Barnett J. F. Pearson Y. van der Does A. H. K. MacGibbon R. J. Spelman K. Lehnert R. G. Snell 《Genetics》2009,182(3):923-926
β-Carotene biochemistry is a fundamental process in mammalian biology. Aberrations either through malnutrition or potentially through genetic variation may lead to vitamin A deficiency, which is a substantial public health burden. In addition, understanding the genetic regulation of this process may enable bovine improvement. While many bovine QTL have been reported, few of the causative genes and mutations have been identified. We discovered a QTL for milk β-carotene and subsequently identified a premature stop codon in bovine β-carotene oxygenase 2 (BCO2), which also affects serum β-carotene content. The BCO2 enzyme is thereby identified as a key regulator of β-carotene metabolism.THE metabolism of β-carotene to form vitamin A is nutritionally important, and vitamin A deficiency remains a significant public health burden. Genetic variation may underlie individual differences in β-carotene metabolism and contribute to the etiology of vitamin A deficiency. Within an agricultural species, genetic variation provides opportunity for production improvements, disease resistance, and product specialization options. We have previously shown that natural genetic variation can be successfully used to inform bovine breeding decisions (Grisart et al. 2002; Blott et al. 2003). Despite numerous reports of quantitative trait loci (QTL), few causative mutations have been identified. We discovered a QTL for milk β-carotene content and report here the identification of a mutation in the bovine β-carotene oxygenase 2 (BCO2) gene responsible for this QTL. The mutation, which results in a premature stop codon, supports a key role for BCO2 in β-carotene metabolism.The QTL trial consisted of a Holstein-Friesian × Jersey cross in an F2 design and a half-sibling family structure (Spelman et al. 2001). Six F1 sires and 850 F2 female progeny formed the trial herd. To construct the genetic map, the pedigree (including the F1 sires, F1 dams, F2 daughters, and selected F0 grandsires: n = 1679) was genotyped, initially with 237 microsatellite markers, and subsequently, with 6634 SNP markers (Affymetrix Bovine 10K SNP GeneChip). A wide range of phenotypic measures relating to growth and development, health and disease, milk composition, fertility, and metabolism were scored on the F2 animals from birth to 6 years of age.To facilitate the discovery of QTL and genes regulating β-carotene metabolism, milk concentration of β-carotene was measured during week 6 of the animals'' second lactation (n = 651). Using regression methodology in a half-sib model (Haley et al. 1994; Baret et al. 1998), a QTL on bovine chromosome 15 (P < 0.0001; Figure 1A) was discovered. The β-carotene QTL effect on chromosome 15 was also significant (P < 0.0001) at two additional time points, in months 4 and 7 of lactation. Three of the six F1 sire families segregated for the QTL, suggesting that these three F1 sires would be heterozygous for the QTL allele (“Q”). To further define the most likely region within the QTL that would harbor the causative mutation, we undertook association mapping, using the 225 SNP markers that formed the chromosome 15 genetic map (Figure 1A). One SNP (“PAR351319”) was more closely associated with the β-carotene phenotype than any other marker (P = 2.522E−18). This SNP was located beneath the QTL peak. Further, the SNP was heterozygous in the three F1 sires that segregated for the QTL, and homozygous in the remaining three sires. On this basis, we hypothesized that the milk β-carotene phenotype would differ between animals on the basis of the genotype of SNP PAR351319.Open in a separate windowFigure 1.—Discovery of BCO2 mutation affecting milk β-carotene concentration. (A) The β-carotene QTL on bovine chromosome 15 (P < 0.0001) is shown by the red line. The maximum F-value at 21 cM was 7.15. The 95% confidence interval is shown by the shaded box. The association of each marker with milk β-carotene is shown by the blue dots, and the association of the BCO2 genotype is shown by the green diamond. A total of 233 informative markers (8 microsatellite markers and 225 single nucleotide polymorphisms) were included on the genetic map for BTA15. QTL detection was conducted using regression methodology in a line of descent model (Haley et al. 1994) and a half-sib model (Baret et al. 1998). Threshold levels were determined at the chromosomewide level using permutation testing (Churchill and Doerge 1998) and confidence intervals estimated using bootstrapping (Visscher et al. 1996). (B) The haplotypes of 10 representative animals for “QQ” and “qq” are shown for the SNP markers encompassing the SNP (“PAR351319”) most closely associated with the milk β-carotene phenotype. Light and dark gray boxes represent homozygous SNPs, while white boxes represent heterozygous SNPs. The genes present within the defined region are also shown. (C) The mutation in the bovine BCO2 gene is shown. The structure of the BCO2 gene is indicated by the horizontal bar, with vertical bars representing exons 1–12. The A > G mutation in exon 3 (red) causes a premature termination codon at amino acid position 80. (D) The mean concentration of β-carotene in the milk fat of “QQ,” “Qq,” and “qq” cows is shown. β-Carotene was measured by absorbance at 450 nm as previously described (Winkelman et al. 1999). Data are means ± SEM. The statistical significance was determined using ANOVA (***P < 0.0001; n = 651).We then made the following assumptions: that the effect of the QTL was additive, that the Q allele was present in the dam population, allowing the occurrence of homozygous (“QQ”) offspring, and that the QTL was caused by a single mutation, acting with a dominant effect on the milk β-carotene phenotype. Haplotypes encompassing the PAR351319 SNP were determined in the F2 offspring. A comparison of the phenotypic effect of homozygous Q, heterozygous and homozygous q individuals revealed that indeed, animals with the “QQ” genotype had a higher concentration of milk β-carotene than animals with the “qq” genotype (Figure 1D). We predicted that the region of homozygosity was likely to contain the causative gene and mutation. The extent of this region and the candidate genes contained within it are shown in Figure 1B. A total of 10 genes with known function, including BCO2, were located within the region. This information, combined with knowledge of the role BCO2 plays in β-carotene metabolism in other species (Kiefer et al. 2001), made BCO2 a good positional candidate for the QTL. We therefore sequenced the entire coding region (12 exons, ) of the BCO2 gene in each of the six F1 sires. An A > G mutation, which was heterozygous in the three F1 sires that segregated for the QTL, was discovered in exon three, 240 bp from the translation initiation site ( NC_007313.3Figure 1C). The three remaining sires were homozygous for the G allele, which encodes the 530-amino-acid BCO2 protein (). The A allele creates a premature stop codon resulting in a truncated protein of 79 amino acids. To determine whether this mutation was associated with the QTL, the remainder of the pedigree was genotyped. The BCO2 genotype was significantly associated with the milk β-carotene phenotype (P = 8.195E−29) The AA genotype (referred to as BCO2−/−) was present in 3.4% (n = 28) of the F2 population. The AG and GG genotypes (subsequently referred to as BCO2−/+ and BCO2+/+, respectively) were present in 32.8% (n = 269) and 63.8% (n = 523), respectively, of the F2 population.The effect of the premature stop codon on milk β-carotene content was striking. BCO2−/− cows produced milk with 78 and 55% more β-carotene than homozygous (GG) and heterozygous (AG) wild-type animals, respectively (P < 0.0001; NP_001101987Figure 2A). Consequently, the yellow color of the milk fat varied greatly (Figure 2B). The genotype effect on milk β-carotene content was similar at the other two time points measured during lactation (78 and 68% more β-carotene in milk from BCO2−/− cows compared to BCO2+/+ cows; data not shown).Open in a separate windowFigure 2.—Effect of BCO2 genotype on milk β-carotene content. (A) The mean concentration of β-carotene in the milk fat of BCO2−/−, BCO2−/+, and BCO2+/+ cows is shown. β-Carotene was measured by absorbance at 450 nm as previously described (Winkelman et al. 1999). Data are means ± SEM. The statistical significance was determined using ANOVA (***P < 0.0001; n = 651). (B) The effect of the BCO2 genotype on milk fat color is illustrated.No adverse developmental or health affects as a result of the A allele were observed at any stage throughout the lifespan of the animals. The BCO2−/− cows were fertile and milk yield was normal throughout lactation. Interestingly, quantitative real-time PCR showed fourfold lower levels of the BCO2 mRNA in liver tissue from BCO2−/− cows (data not shown).β-Carotene and vitamin A (retinol) concentrations were also measured in serum, liver, and adipose tissue samples, and vitamin A concentration was measured in milk samples from 14 F2 cows of each genotype. Serum β-carotene concentration was higher in BCO2−/− cows compared to the heterozygous and homozygous wild-type cows (P = 0.003; Figure 3A). Thus, the effect of the mutation on β-carotene concentration was similar for both milk and serum, showing that this effect was not confined to the mammary gland. Vitamin A concentration was higher in serum from BCO2−/− cows (P = 0.001; Figure 3B); however, the concentration did not differ in milk (13.1 μg/g fat vs. 14.1 μg/g fat for BCO2−/− and BCO2+/+ cows, respectively; P > 0.1). Liver β-carotene concentration did not differ between genotype groups (Figure 3C), but liver vitamin A was lower in BCO2−/− cows compared to BCO2+/+ cows (P < 0.03; Figure 3D). β-Carotene and vitamin A concentration did not differ between the genotype groups in adipose tissue (data not shown), suggesting tissue-specific effects of the BCO2 enzyme.Open in a separate windowFigure 3.—Effect of the BCO2 genotypes on concentration of β-carotene (A and C), and retinol (B and D), in serum (A and B), and liver (C and D). Subcutaneous adipose tissue biopsies (∼500 mg tissue), liver biopsies (∼100 mg tissue), and serum samples (10 ml) were taken from a subset of 42 cows (14 animals each BCO2−/−, BCO2−/+, and BCO2+/+ genotypes). β-Carotene and retinol measurements were determined using HPLC with commercial standards, on the basis of a published method (Hulshof et al. 2006). Data shown are means ± SEM. Significant differences are indicated by asterisks (*P < 0.05; **P < 0.01; ANOVA, n = 14 per genotype).While previous studies have shown a key role for β-carotene 15, 15′ monooxygenase (BCMO1) in catalyzing the symmetrical cleavage of β-carotene to vitamin A (von Lintig and Vogt 2000; von Lintig et al. 2001; Hessel et al. 2007) similar evidence for the role of the BCO2 enzyme in β-carotene metabolism is lacking. The physiological relevance of BCO2 has therefore been a topic of debate (Wolf 1995; Lakshman 2004; Wyss 2004). BCO2 mRNA and protein have been detected in several human tissues (Lindqvist et al. 2005), and the in vitro cleavage of β-carotene to vitamin A has been demonstrated (Kiefer et al. 2001; Hu et al. 2006). Our results provide in vivo evidence for BCO2-mediated conversion of β-carotene to vitamin A. BCO2−/− cows had more β-carotene in serum and milk and less vitamin A in liver, the main storage site for this vitamin.Our results show that a simple genetic test will allow the selection of cows for milk β-carotene content. Thus, milk fat color may be increased or decreased for specific industrial applications. Market preference for milk fat color varies across the world. Further, β-carotene enriched dairy foods may assuage vitamin A deficiency. Milk may be an ideal food for delivery of β-carotene, which is fat soluble and most efficiently absorbed in the presence of a fat component (Ribaya-Mercado 2002).In conclusion, we have discovered a naturally occurring premature stop codon in the bovine BCO2 gene strongly suggesting a key role of BCO2 in β-carotene metabolism. This discovery has industrial applications in the selection of cows producing milks with β-carotene content optimized for specific dairy products or to address a widespread dietary deficiency. More speculatively, it would be interesting to investigate possible effects of BCO2 variation in humans on the etiology of vitamin A deficiency. 相似文献
2.
Epigenetically inherited aggregates of the yeast prion [PSI+] cause genomewide readthrough translation that sometimes increases evolvability in certain harsh environments. The effects of natural selection on modifiers of [PSI+] appearance have been the subject of much debate. It seems likely that [PSI+] would be at least mildly deleterious in most environments, but this may be counteracted by its evolvability properties on rare occasions. Indirect selection on modifiers of [PSI+] is predicted to depend primarily on the spontaneous [PSI+] appearance rate, but this critical parameter has not previously been adequately measured. Here we measure this epimutation rate accurately and precisely as 5.8 × 10−7 per generation, using a fluctuation test. We also determine that genetic “mimics” of [PSI+] account for up to 80% of all phenotypes involving general nonsense suppression. Using previously developed mathematical models, we can now infer that even in the absence of opportunities for adaptation, modifiers of [PSI+] are only weakly deleterious relative to genetic drift. If we assume that the spontaneous [PSI+] appearance rate is at its evolutionary optimum, then opportunities for adaptation are inferred to be rare, such that the [PSI+] system is favored only very weakly overall. But when we account for the observed increase in the [PSI+] appearance rate in response to stress, we infer much higher overall selection in favor of [PSI+] modifiers, suggesting that [PSI+]-forming ability may be a consequence of selection for evolvability.THE yeast phenotype [PSI+] is characterized by prion aggregates of the protein Sup35. Cells are in either a [psi−] (normal) or [PSI+] state, depending on the absence or presence of the prion aggregates (Figure 1, a and b). Sup35 prion aggregates replicate in a similar fashion to mammalian prions but are cytoplasmic and, as such, the prion state is cytoplasmically inherited (Wickner et al. 1995).Open in a separate windowFigure 1.—Comparison between the three possible modes ([PSI+], genetic mimic, point mutation revertant) of the expression of 3′-UTR sequences in yeast. (a) The normal [psi−] phenotypic state; (b) the [PSI+] prion causes readthrough and low-level expression of 3′-UTRs across multiple genes, appearing at rate mPSI; (c) a genetic mimic of [PSI+] such as the sal3-4 mutant of Sup35 (Eaglestone et al. 1999) appearing at rate mmimic not reversible by the application of guanidine hydrochloride; (d) a point mutation in a single stop codon at rate μpoint, leading to incorporation of formerly 3′-UTR into a single coding sequence. (e) [PSI+] can act as a “stop-gap” mechanism, buying a lineage more time to acquire one or more adaptive stop codon readthrough point mutations. When this genetic assimilation is complete, [PSI+] can revert to [psi−] (Masel and Bergman 2003; Griswold and Masel 2009).When not part of an aggregate, Sup35 helps mediate translation termination in yeast (Stansfield et al. 1995b; Zhouravleva et al. 1995). Sup35 molecules that are incorporated into nonfunctional prion aggregates are presumably not available for translation termination, which can lead to the translation of stop codons by near-cognate tRNAs (Figure 1b) (Tuite and Mclaughlin 1982; Pure et al. 1985; Lin et al. 1986). This partial loss of Sup35 function leads to an increased frequency of readthrough translation of 3′-untranslated regions (3′-UTR) across all genes (Figure 1b). This increase is modest in wild-type yeast, from an average readthrough rate of 0.3% in [psi−] cells up to 1% in [PSI+] cells (Firoozan et al. 1991). Some [PSI+] yeast strains grow faster than [psi−] controls in certain harsh environments, suggesting that readthrough translation of some 3′-UTRs may be adaptive in certain conditions (True and Lindquist 2000; Joseph and Kirkpatrick 2008). This directly shows that [PSI+]-mediated capacitance may increase evolvability in the laboratory. [PSI+]-mediated phenotypes have a complex genetic basis, involving multiple loci (True et al. 2004).As an epigenetically inherited protein aggregate, [PSI+] can easily be lost after some generations (Cox et al. 1980). This returns the lineage to its normal [psi−] state and restores translation fidelity. If a subset of revealed phenotypic variation is adaptive, it may have lost its dependence on [PSI+] by this time (True et al. 2004). This process of genetic assimilation may, for example, involve one or more point mutations in stop codons, increasing readthrough up to 100% (Figure 1e) (Griswold and Masel 2009). This leaves the yeast with a new adaptive trait and with no permanent load of other, deleterious variation.In general, stop codons can be lost either directly through point mutations or indirectly through upstream indels. This leads to novel coding sequence coming from in-frame and out-of-frame 3′-UTRs, respectively. [PSI+] is expected to facilitate only the former, while mutation bias favors the latter. Yeasts show a much higher ratio of in-frame to out-of-frame 3′-UTR incorporation events than mammals do (Giacomelli et al. 2007), confirming a role for [PSI+] in capacitance-mediated evolvability in natural populations.The adaptive evolution both of evolvability in general (Sniegowski and Murphy 2006; Lynch 2007; Pigliucci 2008) and of capacitance in particular (Dickinson and Seger 1999; Wagner et al. 1999; Partridge and Barton 2000; Brookfield 2001; Pal 2001; Meiklejohn and Hartl 2002; Ruden et al. 2003) is highly controversial. In general, any costs of evolvability are borne in the present, while the benefits lie in the future, making it difficult for natural selection to favor an evolvability allele. For example, mutation rates seem to be set according to a trade-off between metabolic cost (favoring higher mutation rates) and the avoidance of deleterious effects (favoring lower mutation rates) (Sniegowski et al. 2000). The fact that mutation creates variation, the ultimate source of evolvability, is merely a fortuitous consequence of the metabolic cost of fidelity.Previous theoretical population genetic studies have, however, suggested that modifier alleles promoting the formation of [PSI+] might, unlike mutator alleles, be favored for their evolvability properties (King and Masel 2007; Masel et al. 2007; Griswold and Masel 2009; Masel and Griswold 2009). These models depend, however, on a number of parameter estimates. In particular, a number of predictions depend on the spontaneous rate of [PSI+] formation (Masel and Griswold 2009).
[PSI+] appearance rates and the fluctuation test:
The most widely cited spontaneous appearance rate for [PSI+] is mPSI ∼ 10−7–10−5, on the basis of experiments by Lund and Cox (1981). This estimate was calculated as the proportion of colonies scored as [PSI+] after growth over multiple generations from a single founding [psi−] clone. If [PSI+] happens to appear in the first generation of growth, this leads to a “jackpot” event with only one switching event, but many [PSI+] colonies. The proportion of colonies scored as [PSI+] therefore yields a systematic overestimation of the [PSI+] appearance rate.Various implementations of the fluctuation test (Luria and Delbrück 1943) can address such effects. The mutation rate experiment is replicated many times using independent populations, and a Luria–Delbrück distribution is fitted to the results across all replicates. In a simulation study, Stewart (1994) examined a number of estimators of the underlying Luria–Delbrück distribution and found that the maximum-likelihood estimator performed the best.Originally developed to study mutation rates, the fluctuation test can also be used for estimating epimutation rates. Fluctuation tests have been used to estimate the rate of gene silencing in Chinese hamster ovary cells (Holliday and Ho 1998) and in the yeast Schizosaccharomyces pombe (Singh and Klar 2002). However, fluctuation tests do not appear to be used routinely for epimutation rate estimates. For example, although the rates of spontaneous appearance and disappearance of [ISP+], a prion-like element in yeast, have been measured using the fluctuation test (Volkov et al. 2002), to the best of our knowledge there are no published estimates of the spontaneous rate of [PSI+] appearance as measured using a fluctuation test. Although results from the fluctuation test can be confounded by reverse epimutation, or back-switching, this is an issue only if the rate of back-switching is very high, e.g., 10−1–10−2 per generation (Saunders et al. 2003). This is not the case for [PSI+], for which the reverse epimutation rate (loss of [PSI+]) is <2 × 10−4 (Tank et al. 2007).Other [PSI+]-like phenotypes, including genetic mimics:
[PSI+] causes partial loss of Sup35 function, leading to elevated rates of translational readthrough at all stop codons (Figure 1b). There are many other spontaneous changes, presumably mutations, that also lead to elevated translational readthrough (Lund and Cox 1981). Mutations that affect readthrough at all stop codons (Figure 1c) (sometimes called “[PSI+]-like”) can be considered as genetic “mimics” because they produce the same phenotype as the Sup35 aggregate, but are generally not epigenetically inherited. A specific example of such a genetic mimic was characterized by Eaglestone et al. (1999), who identified the sal3-4 point mutation in the SUP35 gene. This leads to a defect in the Sup35 protein structure rendering the termination process less efficient (Eaglestone et al. 1999). The sal3-4 mutant can therefore be considered a partial loss-of-function genetic mimic of [PSI+], since it generates the same readthrough phenotype. Translation termination could also potentially be impaired through other point mutations or deletions, for example, in either the SUP35 or the SUP45 gene (Stansfield et al. 1995a) or in a tRNA that mutates to recognize stop codons at a higher rate. The presence of genetic mimics, whose effects are less reversible than those of [PSI+], can affect the evolution of the evolvability properties of the [PSI+] system such as its epimutation rate (Lancaster and Masel 2009). Note that genetic mimics are quite different from much rarer point mutations that convert stop codons into coding sequence (Figure 1d), resulting in readthrough at a single gene rather than multiple genes.Here we performed experiments to obtain accurate and precise estimates of the baseline appearance rates of both [PSI+] and [PSI+]-like phenotypes in permissive laboratory conditions, excluding stop codon point mutations that affect only a single gene. Our estimates are superior to previous estimates, since we use the fluctuation test. We consider the consequences of these estimates for the evolution of the [PSI+] system. 相似文献3.
Maize Mucronate1 is a dominant floury mutant based on a misfolded 16-kDa γ-zein protein. To prove its function, we applied RNA interference (RNAi) as a dominant suppressor of the mutant seed phenotype. A γ-zein RNAi transgene was able to rescue the mutation and restore normal seed phenotype. RNA interference prevents gene expression. In most cases, this is used to study gene function by creating a new phenotype. Here, we use it for the opposite purpose. We use it to reverse the creation of a mutant phenotype by restoring the normal phenotype. In the case of the maize Mucronate1 (Mc1) phenotype, interaction of a misfolded protein with other proteins is believed to be the basis for the Mc1 phenotype. If no misfolded protein is present, we can reverse the mutant to the normal phenotype. One can envision using this approach to study complex traits and in gene therapy.TRANSLUCENT or vitreous maize kernels are harder and able to sustain stronger mechanical strength during harvesting, transportation, and storage. There is a direct link between a vitreous seed phenotype and the type of storage proteins in the seed, collectively called zeins in maize. Zeins, encoded by a multigene family, constitute >60% of all maize seed proteins. They are classified into four groups (α-, β-, γ-, and δ-zein) on the basis of their structures (Esen 1987). Zeins are specifically synthesized in the endosperm ∼10 days after pollination (DAP) and deposited into protein bodies (Wolf et al. 1967; Burr and Burr 1976; Lending and Larkins 1992). Irregularly shaped protein bodies are found in floury or opaque kernel phenotypes (Coleman et al. 1997; Kim et al. 2004, 2006; Wu et al. 2010; Wu and Messing 2010). The terms “floury” and “opaque” were originally created on the basis of the genetic behaviors of the mutant allele causing the soft kernel texture. The floury mutants behave as semidominant or dominant mutants, as floury1 and floury2 do, while the opaque mutants are recessive, as opaque1 and opaque2 are (Hayes and East 1915; Lindstrom 1923; Emerson et al. 1935; Maize Genetics Cooperation 1939). Similar to floury2 with a single mutation in the signal peptide of a 22-kDa α-zein resulting in an unprocessed protein (Coleman et al. 1995), De*-B30 produces an unprocessed 19-kDa α-zein (Kim et al. 2004). It was hypothesized that the two mutant proteins with an unprocessed signal peptide are misfolded and docked in the membranes of the rough endoplasmic reticulum (RER), blocking the deposition of other zein proteins (Coleman et al. 1995; Kim et al. 2004). In Mucronate1 (Mc1), a 38-bp deletion in the C terminus of the 16-kDa γ-zein (γ16-zein) gene resulted in a frameshift and a protein with a different amino-acid tail. This modified 16-kDa γ-zein (Δγ16-zein) has altered solubility properties, which would explain the formation of irregular protein bodies. Because De*-B30 and Mc1 are semidominant and dominant, respectively, they belong to the floury mutant class.The γ-zein genes (γ27-zein and γ16-zein) are homologous copies because maize underwent allotetraploidization and both gene copies have been retained during diploidization (Xu and Messing 2008). The two γ-zeins and the 15-kDa β-zein have a redundant function in stabilizing protein-body formation (Wu and Messing 2010). Knockdown of both γ-zeins with a single RNA interference (RNAi) construct conditioned only partial opacity in the crown, the top of the kernel, as opposed to the remainder or gown area of the kernel. Consistent with its light kernel phenotype, protein bodies in such a γ-zein RNAi (γRNAi) mutant exhibited a slight alteration in morphology. This phenotype is clearly distinguishable from the Mc1 phenotype, which is far more severe. Therefore, if Mc1 is caused by a misfolded chimeric 16-kDa γ-zein, preventing its expression should restore normal kernel phenotype. Indeed, a simple cross of Mc1 with a maize line carrying the γRNAi transgene produced a non-floury phenotype, providing an example of RNAi as a dominant suppressor of a dominant phenotype and as a general tool in marker rescue.
Analysis of the progeny from the cross of Mc1 and γRNAi mutants:
Mc1 seeds (Stock ID U840I) were requested from the Maize Genetics Cooperation Stock Center. The γRNAi transgenic lines have been reported in previous work (Wu et al. 2010; Wu and Messing 2010). Twelve progeny kernels from the cross of the Mc1 mutant [homozygous for the dominant-negative mutant 16-kDa γ-zein alleles (Δγ16/Δγ16) and heterozygous for the γRNAi line (γRNAi/+)] were dissected at 18 DAP for segregation and mRNA accumulation analyses. For each kernel, the embryo and endosperm were separated for DNA and RNA extraction, respectively. As shown in Figure 1A, five and seven kernels were positive and negative for the amplification of the γRNAi gene with a specific primer set, exemplifying a 1:1 segregation of the γRNAi gene.Open in a separate windowFigure 1.—Segregation analysis of the accumulations of mRNAs and proteins from the cross of the Mc1 mutant and the γRNAi line by RT–PCR and SDS–PAGE. (A) γRNAi gene segregation from progeny (Δγ16/Δγ16 x γRNAi/+) by PCR amplification with a specific primer set (GFPF, ACAACCACTACCTGAGCAC and T35SHindIII, ATTAAGCTTTGCAGGTCACTGGATTTTGG). Kernels 3, 8, 9, 10, and 12 are positive for the γRNAi gene and the rest of them are negative. M, DNA markers from top to bottom band are 3, 2, 1.5, 1.4, and 1 kb. (B) RT–PCR analysis of mRNA accumulation from the normal γ16 and mutant Δγ16 alleles in the endosperms with the genotypes corresponding to the embryos analyzed above. Total RNA was extracted by using TRIzol reagent (Invitrogen). Two micrograms of RNA was digested with DNase I (Invitrogen) and then reverse-transcribed. Twenty-five nanograms of cDNA from each of the twelve endosperms was applied for PCR (25 cycles of 30 sec, 94 °C; 30 sec, 58 °C; and 1 min, 72 °C). A specific primer set (γ16F, ATGAAGGTGCTGATCGTTGC and γ16R, TCAGTAGTAGACACCGCCG) was designed for amplification of the full-length γ16-zein coding sequence (552 bp). The lower band (514 bp) from the mutant Δγ16 allele is 38 bp shorter than that from the normal allele (552 bp). Kernels 3, 8, 9, 10, and 12 with the γRNAi gene accumulated significantly less mRNA compared to those without the γRNAi gene (kernels 1, 2, 4, 5, 6, 7, and 11). BA, hybrid of B × A lines. M, DNA markers from top to bottom are 1 kb, 750 bp, and 500 bp. (C) Profile of zein accumulations of 20 kernels from the progeny as described in the text. The zein extraction method has been described elsewhere (Wu et al. 2009). The Δγ16-zein from Mc1 was not extracted by traditional total-zein extraction protocol (70% ethanol and 2% 2-mercaptoethanol). The γ27- and γ16-zeins were knocked down to a nondetectable level in kernels 1, 2, 3, 5, 7, 10, 12, 13, 16, and 20. In γRNAi-gene segregating progeny (kernels 4, 6, 8, 9, 11, 14, 15, 17, 18, and 19), the γ16-zein from the normal γ16 allele is marked by arrowheads. Protein loaded in each lane was equal to 500 μg fresh endosperm at 18 DAP. The size for each band is indicated by the numbers in the “kDa” columns. BA, hybrid of B × A lines; 1–20, kernels from the progeny described above; M, protein markers from top to bottom are 50, 25, 20, and 15 kDa.Due to the 38-bp deletion in the C terminus of the coding region, the Δγ16 allele is shorter than the normal one (Figure 1B). Therefore, most of Δγ16-zein was in the non-zein fraction. In progeny endosperms of another 20 kernels from the same cross described above segregating for the γRNAi gene, two types of γ16-zeins were synthesized: the normal γ16-zein in the ethanol-soluble zein fraction and the Δγ16-zein in the non-zein fraction. In progeny inheriting the γRNAi gene, the γ27- and γ16-zeins were reduced to nondetectable levels (Figure 1C). Although the Δγ16-zein is not in the ethanol-soluble zein fraction, the level of normal γ16-zein is a good indicator of the accumulation of the Δγ16-zein.Rescue of protein-body morphologies in the Mc1 mutant:
Regular protein bodies are round with distinct membrane boundaries (Figure 2A) and 1–2 μm in diameter at maturity. In homozygous and heterozygous Mc1 mutants (Δγ16/Δγ16 and Δγ16/+), protein bodies were irregularly shaped, some without discrete boundaries (Figure 2, C and D), which is quite different from the absence of normal γ27- or γ16-zeins in maize endosperm (Figure 2B). Indeed, protein bodies of the Mc1 mutant, blocked in the accumulation of Δγ16-zein, showed morphologies with no discernible difference from those in the γRNAi/+ line (Figure 2, B and E).Open in a separate windowFigure 2.—Transmission electron micrographs of protein bodies. The method has been described elsewhere (Wu and Messing 2010). (A) Nontransgenic BA. (B) γRNAi transgenic line (γRNAi/+). (C) Mc1 (Δγ16/Δγ16). (D) Cross of Mc1 mutant and nontransgenic hybrid of B × A lines (Δγ16/+). (E) Cross of Mc1 mutant (Δγ16/Δγ16) and heterologous γRNAi transgenic line (γRNAi/+). PB, protein body; RER, rough endoplasmic reticulum; CW, cell wall; Mt, mitochondria; SG, starch granule. Bars, 500 nm.Recovery of floury phenotype in progeny:
On the basis of these observations, it is reasoned that irregularly shaped protein bodies (Figure 2, C and D) in the Mc1 mutant cause the floury phenotype (Figure 3, A and B). Because knockdown of γ-zeins caused opacity only in the crown area (Figure 3C), one could envision that once the irregular protein bodies are restored, the kernel would become vitreous in the gown area of the kernel. Indeed, the progeny ear from the cross of Δγ16/Δγ16 and γRNAi/+ showed a 1:1 ratio of floury and vitreous kernels (Figure 3, D and F), and all kernels were vitreous when the Mc1 mutant was pollinated by a homozygous γRNAi line (Figure 3E).Open in a separate windowFigure 3.—Segregation of vitreous and floury kernels from a progeny ear. (A) Mc1 mutant with Δγ16/Δγ16 genotype. (B) The cross of the Mc1 mutant and the nontransgenic hybrid of B × A lines, showing floury phenotype as in A. (C) γRNAi transgenic line with partial opacity only in the crown area. (D) The cross of the Mc1 mutant (Δγ16/Δγ16) and the heterologous γRNAi transgenic line (γRNAi/+), showing a 1:1 ratio of vitreous and floury kernels. A row in the ear is marked with arrowheads and crosses to indicate vitreous and floury gowns of kernels. (E) Cross of the Mc1 mutant (Δγ16/Δγ16) and the γRNAi homozygous transgenic line (γRNAi/γRNAi), showing all vitreous kernels. (F) Truncated kernel phenotype. (Top) Mc1, cross of Mc1 × BA, and γRNAi transgenic line. (Bottom) Three vitreous and floury kernels from D.Conclusions:
RNAi can be used to rescue mutations that are dominant negative with a single cross, providing a useful tool in genetic analysis, plant breeding, and potentially in gene therapy in general. 相似文献4.
Thiago R. Benatti Fernando H. Valicente Rajat Aggarwal Chaoyang Zhao Jason G. Walling Ming-Shun Chen Sue E. Cambron Brandon J. Schemerhorn Jeffrey J. Stuart 《Genetics》2010,184(3):769-777
Two nonoverlapping autosomal inversions defined unusual neo-sex chromosomes in the Hessian fly (Mayetiola destructor). Like other neo-sex chromosomes, these were normally heterozygous, present only in one sex, and suppressed recombination around a sex-determining master switch. Their unusual properties originated from the anomalous Hessian fly sex determination system in which postzygotic chromosome elimination is used to establish the sex-determining karyotypes. This system permitted the evolution of a master switch (Chromosome maintenance, Cm) that acts maternally. All of the offspring of females that carry Cm-associated neo-sex chromosomes attain a female-determining somatic karyotype and develop as females. Thus, the chromosomes act as maternal effect neo-W''s, or W-prime (W′) chromosomes, where ZW′ females mate with ZZ males to engender female-producing (ZW′) and male-producing (ZZ) females in equal numbers. Genetic mapping and physical mapping identified the inversions. Their distribution was determined in nine populations. Experimental matings established the association of the inversions with Cm and measured their recombination suppression. The inversions are the functional equivalent of the sciarid X-prime chromosomes. We speculate that W′ chromosomes exist in a variety of species that produce unisexual broods.SEX chromosomes are usually classified as X, Y, Z, or W on the basis of their pattern of segregation and the gender of the heterogametic sex (Ohno 1967). However, when chromosome-based sex determination occurs postzygotically, the same nomenclature confounds important distinctions and may hide interesting evolutionary phenomena. The Hessian fly (Mayetiola destructor), a gall midge (Diptera: Cecidomyiidae) and an important insect pest of wheat, presents an excellent example (Stuart and Hatchett 1988, 1991). In this insect, all of the female gametes and all of the male gametes have the same number of X chromosomes (Figure 1A); no heterogametic sex exists. Nevertheless, Hessian fly sex determination is chromosome based; postzygotic chromosome elimination produces different X chromosome to autosome ratios in somatic cells (male A1A2X1X2/A1A2OO and female A1A2X1X2/A1A2X1X2, where A1 and A2 are the autosomes, X1 and X2 are the X chromosomes, and the paternally derived chromosomes follow the slash) (Stuart and Hatchett 1991; Marin and Baker 1998). Thus, Hessian fly “X” chromosomes are defined by their haploid condition in males, rather than by their segregation in the gametes.Open in a separate windowFigure 1.—Chromosome behavior and sex determination in the Hessian fly. (A) Syngamy (1) establishes the germ-line chromosome constitution: ∼32 maternally derived E chromosomes (represented as a single white chromosome) and both maternally derived (black) and paternally derived (gray) autosomes and X chromosomes. During embryogenesis, while the E chromosomes are eliminated, the paternally derived X chromosomes are either retained (2) or excluded (3) from the presumptive somatic cells. When the paternally derived X chromosomes are retained (2), a female-determining karyotype is established. When they are eliminated (3), a male-determining karyotype is established. Thelygenic mothers carry Cm (white arrow), which conditions all of their offspring to retain the X chromosomes. Recombination occurs during oogenesis (4). All ova contain a full complement of E chromosomes and a haploid complement of autosomes and X chromosomes. Chromosome elimination occurs during spermatogenesis (5). Sperm contain only the maternally derived autosomes and X chromosomes. (B) The segregation of Cm (white dot) on a Hessian fly autosome among monogenic families. Thelygenic females produce broods composed of equal numbers of thelygenic (Cm/−) and arrhenogenic (−/−) females (box 1). Arrhenogenic females produce males (box 2). (C) Matings between monogenic and amphigenic families. Cm (white dot) is dominant to the amphigenic-derived chromosomes (gray dot) and generates all-female offspring (box 3). Amphigenic-derived chromosomes are dominant to the arrhenogenic-derived chromosomes (no dot) and generate offspring of both sexes (box 4).An autosomal, dominant, genetic factor called Chromosome maintenance (Cm) complicates Hessian fly sex determination further (Stuart and Hatchett 1991). Cm has a maternal effect that acts upstream of X chromosome elimination during embryogenesis (Figure 1A). It prevents X chromosome elimination so that all of the offspring of Cm-bearing mothers obtain a female-determining karyotype. Cm-bearing females produce only female offspring and are therefore thelygenic. The absence of Cm usually has the opposite effect; all of the offspring of most Cm-lacking females obtain a male-determining karyotype. These Cm-lacking females produce only male offspring and are therefore arrhenogenic. Like a sex-determining master switch, Cm is usually heterozygous and present in only one sex (Figure 1B). Thus, thelygenic females (Cm/−) are “heterogametic,” as their Cm-containing gametes and Cm-lacking gametes produce thelygenic (Cm/−) and arrhenogenic (−/−) females in a 1:1 ratio. Collectively, thelygenic and arrhenogenic females are called monogenic because they produce unisexual families. However, some Hessian fly females produce broods of both sexes and are called amphigenic. No mating barrier between monogenic and amphigenic families exists (Figure 1C), but amphigenic females have always been found in lower abundance (Painter 1930; Gallun et al. 1961; Stuart and Hatchett 1991). In experimental matings, the inheritance of maternal phenotype was consistent with the segregation of three Cm alleles (Figure 1C): a dominant thelygenic allele, a hypomorphic amphigenic allele, and a null arrhenogenic allele (Stuart and Hatchett 1991).Here we report the genetic and physical mapping of Cm on Hessian fly autosome 1 (A1). Two nonoverlapping inversions were identified that segregated perfectly with Cm. The most distal inversion was present in all thelygenic females examined. The more proximal inversion extended recombination suppression. These observations suggested that successive inversions evolved to suppress recombination around Cm after it arose. The inversions therefore appear to have evolved in response to the forces that shaped vertebrate Y and W chromosomes (Charlesworth 1996; Graves and Shetty 2001; Rice and Chippindale 2001; Carvalho and Clark 2005). We therefore believe the inversion-bearing chromosomes may be classified as maternal effect neo-W''s. 相似文献
5.
Fachuang Lu Jane M. Marita Catherine Lapierre Lise Jouanin Kris Morreel Wout Boerjan John Ralph 《Plant physiology》2010,153(2):569-579
Caffeic acid O-methyltransferase (COMT) is a bifunctional enzyme that methylates the 5- and 3-hydroxyl positions on the aromatic ring of monolignol precursors, with a preference for 5-hydroxyconiferaldehyde, on the way to producing sinapyl alcohol. Lignins in COMT-deficient plants contain benzodioxane substructures due to the incorporation of 5-hydroxyconiferyl alcohol (5-OH-CA), as a monomer, into the lignin polymer. The derivatization followed by reductive cleavage method can be used to detect and determine benzodioxane structures because of their total survival under this degradation method. Moreover, partial sequencing information for 5-OH-CA incorporation into lignin can be derived from detection or isolation and structural analysis of the resulting benzodioxane products. Results from a modified derivatization followed by reductive cleavage analysis of COMT-deficient lignins provide evidence that 5-OH-CA cross couples (at its β-position) with syringyl and guaiacyl units (at their O-4-positions) in the growing lignin polymer and then either coniferyl or sinapyl alcohol, or another 5-hydroxyconiferyl monomer, adds to the resulting 5-hydroxyguaiacyl terminus, producing the benzodioxane. This new terminus may also become etherified by coupling with further monolignols, incorporating the 5-OH-CA integrally into the lignin structure.Lignins are polymeric aromatic constituents of plant cell walls, constituting about 15% to 35% of the dry mass (Freudenberg and Neish, 1968; Adler, 1977). Unlike other natural polymers such as cellulose or proteins, which have labile linkages (glycosides and peptides) between their building units, lignins’ building units are combinatorially linked with strong ether and carbon-carbon bonds (Sarkanen and Ludwig, 1971; Harkin, 1973). It is difficult to completely degrade lignins. Lignins are traditionally considered to be dehydrogenative polymers derived from three monolignols, p-coumaryl alcohol 1h (which is typically minor), coniferyl alcohol 1g, and sinapyl alcohol 1s (Fig. 1; Sarkanen, 1971). They can vary greatly in their composition in terms of their plant and tissue origins (Campbell and Sederoff, 1996). This variability is probably determined and regulated by different activities and substrate specificities of the monolignol biosynthetic enzymes from different sources, and by the carefully controlled supply of monomers to the lignifying zone (Sederoff and Chang, 1991).Open in a separate windowFigure 1.The monolignols 1, and marker compounds 2 to 4 resulting from incorporation of novel monomer 15h into lignins: thioacidolysis monomeric marker 2, dimers 3, and DFRC dimeric markers 4.Recently there has been considerable interest in genetic modification of lignins with the goal of improving the utilization of lignocellulosics in various agricultural and industrial processes (Baucher et al., 2003; Boerjan et al., 2003a, 2003b). Studies on mutant and transgenic plants with altered monolignol biosynthesis have suggested that plants have a high level of metabolic plasticity in the formation of their lignins (Sederoff et al., 1999; Ralph et al., 2004). Lignins in angiosperm plants with depressed caffeic acid O-methyltransferase (COMT) were found to derive from significant amounts of 5-hydroxyconiferyl alcohol (5-OH-CA) monomers 15h (Fig. 1) substituting for the traditional monomer, sinapyl alcohol 1s (Marita et al., 2001; Ralph et al., 2001a, 2001b; Jouanin et al., 2004; Morreel et al., 2004b). NMR analysis of a ligqnin from COMT-deficient poplar (Populus spp.) has revealed that novel benzodioxane structures are formed through β-O-4 coupling of a monolignol with 5-hydroxyguaiacyl units (resulting from coupling of 5-OH-CA), followed by internal trapping of the resultant quinone methide by the phenolic 5-hydroxyl (Ralph et al., 2001a). When the lignin was subjected to thioacidolysis, a novel 5-hydroxyguaiacyl monomer 2 (Fig. 1) was found in addition to the normal guaiacyl and syringyl thioacidolysis monomers (Jouanin et al., 2000). Also, a new compound 3g (Fig. 1) was found in the dimeric products from thioacidolysis followed by Raney nickel desulfurization (Lapierre et al., 2001; Goujon et al., 2003).Further study with the lignin using the derivatization followed by reductive cleavage (DFRC) method also confirmed the existence of benzodioxane structures, with compounds 4 (Fig. 1) being identified following synthesis of the authentic parent compounds 9 (Fig. 2). However, no 5-hydroxyguaiacyl monomer could be detected in the DFRC products. These facts imply that the DFRC method leaves the benzodioxane structures fully intact, suggesting that the method might therefore be useful as an analytical tool for determining benzodioxane structures that are linked by β-O-4 ethers. Using a modified DFRC procedure, we report here on results that provide further evidence for the existence of benzodioxane structures in lignins from COMT-deficient plants, that 5-OH-CA is behaving as a rather ideal monolignol that can be integrated into plant lignins, and demonstrate the usefulness of the DFRC method for determining these benzodioxane structures.Open in a separate windowFigure 2.Synthesis of benzodioxane DFRC products 12 (see later in Fig. 6 for their structures). i, NaH, THF. ii, Pyrrolidine. iii, 1g or 1s, benzene/acetone (4/1, v/v). iv, DIBAL-H, toluene. v, Iodomethane-K2CO3, acetone. vi, Ac2O pyridine. 相似文献
6.
A Genetic Screen for Suppressors of a Mutated 5′ Splice Site Identifies Factors Associated With Later Steps of Spliceosome Assembly 下载免费PDF全文
MaryAnn Dassah Sophie Patzek Valerie M. Hunt Pedro E. Medina Alan M. Zahler 《Genetics》2009,182(3):725-734
Many alleles of human disease genes have mutations within splicing consensus sequences that activate cryptic splice sites. In Caenorhabditis elegans, the unc-73(e936) allele has a G-to-U mutation at the first base of the intron downstream of exon 15, which results in an uncoordinated phenotype. This mutation triggers cryptic splicing at the −1 and +23 positions and retains some residual splicing at the mutated wild-type (wt) position. We previously demonstrated that a mutation in sup-39, a U1 snRNA gene, suppresses e936 by increasing splicing at the wt splice site. We report here the results of a suppressor screen in which we identify three proteins that function in cryptic splice site choice. Loss-of-function mutations in the nonessential splicing factor smu-2 suppress e936 uncoordination through changes in splicing. SMU-2 binds SMU-1, and smu-1(RNAi) also leads to suppression of e936. A dominant mutation in the conserved C-terminal domain of the C. elegans homolog of the human tri-snRNP 27K protein, which we have named SNRP-27, suppresses e936 uncoordination through changes in splicing. We propose that SMU-2, SMU-1, and SNRP-27 contribute to the fidelity of splice site choice after the initial identification of 5′ splice sites by U1 snRNP.PRE-mRNA splicing takes place in a large ribonucleoprotein complex called the spliceosome (Burge et al. 1999). Components of this splicing machinery assemble at conserved signal sequences within the pre-mRNA. The 5′ splice site consensus sequence M−3A−2G−1 | G+1U+2R+3A+4G+5U+6 and the 3′ splice site consensus sequence Y−3A−2G−1 | R+1 (M is either A or C; R is a purine, and Y is a pyrimidine) define the limits of the intron. Base-pairing interactions between the 5′ end of the U1 snRNA and the 5′ splice site consensus sequence occur early in spliceosome assembly. It is the nearly invariable GU dinucleotide at the first two positions of the 5′ end of the intron that defines the beginning of the intron. The 5′ consensus sequence is essential but insufficient for splice site selection, as 5′ splice sites with weaker consensus matches may require additional determinants for proper activation (Sanford et al. 2005).Mutations that disrupt the 5′ consensus splice signal can lead to genetic disease in humans (Nelson and Green 1990; Cohen et al. 1994). Approximately 15% of point mutations that cause genetic diseases affect pre-mRNA splicing consensus sequences (Krawczak et al. 1992). For some specific disease genes, as many as 50% of the known heritable alleles alter splicing (Teraoka et al. 1999; Ars et al. 2000; Roca et al. 2003; Pagenstecher et al. 2006). Among all the positions of the 5′ splice site consensus sequence, the highest proportion of human disease mutations occur at the +1G position (Buratti et al. 2007). The fidelity of pre-mRNA splice site choice is largely disrupted by this defect, since this mutation causes splicing at this site to be either abolished or outcompeted by the activation of nearby cryptic 5′ splice sites (Nelson and Green 1990; Cohen et al. 1994). Cryptic splice sites are used only when the wild-type splice donor is disrupted by mutation, as they tend to have very weak splice donor consensus sequences outside of a 5′-GU dinucleotide that defines the beginning of the intron (Roca et al. 2003). Suppression of mutations to the 5′ splice site consensus sequence in vivo has been achieved through the expression of U1 snRNAs containing compensatory base substitutions (Zhuang and Weiner 1986); however, suppression of mutations to the +1 position of the intron using reverse genetic approaches has not been successful (Newman et al. 1985; Nelson and Green 1990; Cohen et al. 1994).We have used a specific allele of the Caenorhabditis elegans unc-73 gene, e936, which contains a G-to-U mutation at the first nucleotide of intron 16 (Steven et al. 1998), as a model for studying cryptic splice site choice (Roller et al. 2000; Zahler et al. 2004). unc-73 encodes a RAC guanine nucleotide exchange factor that is expressed in neurons and is important for axon guidance (Steven et al. 1998). The e936 allele induces the use of three different cryptic 5′ splice sites (Figure 1A). Two of these 5′ splice sites, located at the −1 and +23 positions, define introns beginning with GU. The third 5′ splice site used is at the mutated wild-type (wt) position and is referred to as “wt” since splicing at this site still produces wild-type unc-73 mRNA and protein, even though the intron begins with UU (Roller et al. 2000). Use of either the −1 or the +23 cryptic site causes a shift in the reading frame and loss of gene function. In e936 animals, 90% of the stable messages of unc-73 are out-of-frame, yet the phenotype is not as severe as for other alleles in this gene. This indicates that the 10% of steady-state messages that are in frame have some functional role.Open in a separate windowFigure 1.—(A) Diagram of the unc-73 gene between exons 15 and 16. The positions of the −1 and +23 cryptic 5′ splice sites are indicated by arrows. The intronic e936 (+1G → U) point mutation is highlighted. (B) γ-32P-labeled RT–PCR results across the cryptic splicing region of unc-73(e936) for different strains. Lanes 1, 2, and 3 are loaded with RT–PCR reactions from wild type (N2), unc-73(e936);sup-39(je5), and unc-73(e936) RNA, respectively. The lines carrying the suppressor alleles and e936 follow in lanes 4–10 as indicated. (C) The unc-73 genomic sequence from exon 15 (uppercase letters) and intron 15 (lowercase letters). The locations of the az23 and e936 mutational substitutions are indicated below. The position of the −9 cryptic splice donor activated in e936az23 is indicated by an arrow above.In a previous genetic screen for extragenic suppressors of e936 movement defects, Way and colleagues identified sup-39 (Run et al. 1996). It was subsequently shown that mutations in sup-39 alter cryptic splice site choice of e936 (Roller et al. 2000). sup-39 encodes a U1 snRNA gene with a compensatory mutation at the position that normally base pairs with the +1G. This allows sup-39 to base pair with an intron with a +1U (Zahler et al. 2004). This dominant suppressor increases usage of the mutated splice site and improves the fraction of in-frame messages from e936 from 10 to 33%, with a dramatic improvement in coordination. A similar mutant U1 snRNA suppressor with a different compensatory substitution, sup-6(st19), was found to suppress the intronic +1G to A transition of unc-13(e309) to allow for splicing at the mutated wild-type site, even though the intron begins with AU instead of GU (Zahler et al. 2004).We are interested in identifying additional factors that play a role in cryptic 5′ splice site choice. To do this, we took advantage of unc-73(e936), in which modest increases in the use of the wt splice site lead to dramatic increases in coordination, as a sensitive screen for changes in cryptic splice site choice. In this article we report that the proteins SMU-1 and SMU-2, which are nonessential factors previously shown to have a role in alternative splicing (Spartz et al. 2004), have a role in selection of cryptic 5′ splice sites. We also report the identification of a new dominant suppressor of cryptic splicing, snrp-27, which encodes a C. elegans homolog of the human tri-snRNP 27K protein. 相似文献
7.
Sara Kaliman Christina Jayachandran Florian Rehfeldt Ana-Sun?ana Smith 《Biophysical journal》2014,106(7):L25-L28
It is well established that MDCK II cells grow in circular colonies that densify until contact inhibition takes place. Here, we show that this behavior is only typical for colonies developing on hard substrates and report a new growth phase of MDCK II cells on soft gels. At the onset, the new phase is characterized by small, three-dimensional droplets of cells attached to the substrate. When the contact area between the agglomerate and the substrate becomes sufficiently large, a very dense monolayer nucleates in the center of the colony. This monolayer, surrounded by a belt of three-dimensionally packed cells, has a well-defined structure, independent of time and cluster size, as well as a density that is twice the steady-state density found on hard substrates. To release stress in such dense packing, extrusions of viable cells take place several days after seeding. The extruded cells create second-generation clusters, as evidenced by an archipelago of aggregates found in a vicinity of mother colonies, which points to a mechanically regulated migratory behavior.Studying the growth of cell colonies is an important step in the understanding of processes involving coordinated cell behavior such as tissue development, wound healing, and cancer progression. Apart from extremely challenging in vivo studies, artificial tissue models are proven to be very useful in determining the main physical factors that affect the cooperativity of cells, simply because the conditions of growth can be very well controlled. One of the most established cell types in this field of research is the Madin-Darby canine kidney epithelial cell (MDCK), originating from the kidney distal tube (1). A great advantage of this polarized epithelial cell line is that it retained the ability for contact inhibition (2), which makes it a perfect model system for studies of epithelial morphogenesis.Organization of MDCK cells in colonies have been studied in a number of circumstances. For example, it was shown that in three-dimensional soft Matrigel, MDCK cells form a spherical enclosure of a lumen that is enfolded by one layer of polarized cells with an apical membrane exposed to the lumen side (3). These structures can be altered by introducing the hepatocyte growth factor, which induces the formation of linear tubes (4). However, the best-studied regime of growth is performed on two-dimensional surfaces where MDCK II cells form sheets and exhibit contact inhibition. Consequently, the obtained monolayers are well characterized in context of development (5), mechanical properties (6), and obstructed cell migration (7–9).Surprisingly, in the context of mechanics, several studies of monolayer formation showed that different rigidities of polydimethylsiloxane gels (5) and polyacrylamide (PA) gels (9) do not influence the nature of monolayer formation nor the attainable steady-state density. This is supposedly due to long-range forces between cells transmitted by the underlying elastic substrate (9). These results were found to agree well with earlier works on bovine aortic endothelial cells (10) and vascular smooth muscle cells (11), both reporting a lack of sensitivity of monolayers to substrate elasticity. Yet, these results are in stark contrast with single-cell experiments (12–15) that show a clear response of cell morphology, focal adhesions, and cytoskeleton organization to substrate elasticity. Furthermore, sensitivity to the presence of growth factors that are dependent on the elasticity of the substrate in two (16) and three dimensions (4) makes this result even more astonishing. Therefore, we readdress the issue of sensitivity of tissues to the elasticity of the underlying substrate and show that sufficiently soft gels induce a clearly different tissue organization.We plated MDCK II cells on soft PA gels (Young’s modulus E = 0.6 ± 0.2 kPa), harder PA gels (E = 5, 11, 20, 34 kPa), and glass, all coated with Collagen-I. Gels were prepared following the procedure described in Rehfeldt et al. (17); rigidity and homogeneity of the gels was confirmed by bulk and microrheology (see the Supporting Material for comparison). Seeding of MDCK II cells involved a highly concentrated solution dropped in the middle of a hydrated gel or glass sample. For single-cell experiments, cells were dispersed over the entire dish. Samples were periodically fixed up to Day 12, stained for nuclei and actin, and imaged with an epifluorescence microscope. Details are described in the Supporting Material.On hard substrates and glass it was found previously that the area of small clusters expands exponentially until the movement of the edge cannot keep up with the proliferation in the bulk (5). Consequently, the bulk density increases toward the steady state, whereas the density of the edge remains low. At the same time, the colony size grows subexponentially (5). This is what we denote “the classical regime of growth”. Our experiments support these observations for substrates with E ≥ 5 kPa. Specifically, on glass, colonies start as small clusters of very low density of 700 ± 200 cells/mm2 (Fig. 1, A and B), typically surrounded by a strong actin cable (Fig. 1, B and C). Interestingly, the spreading area of single cells (Fig. 1
A) on glass was found to be significantly larger, i.e., (2.0 ± 0.9) × 10−3 mm2. After Day 4 (corresponding cluster area of 600 ± 100 mm2), the density in the center of the colony reached the steady state with 6,800 ± 500 cells/mm2, whereas the mean density of the edge profile grew to 4,000 ± 500 cells/mm2. This density was retained until Day 12 (cluster area 1800 ± 100 mm2), which is in agreement with previous work (9).Open in a separate windowFigure 1Early phase of cluster growth on hard substrates. (A) Well-spread single cells, and small clusters with a visible actin cable 6 h after seeding. (B) Within one day, clusters densify and merge, making small colonies. (C) Edge of clusters from panel B.In colonies grown on 0.6 kPa gels, however, we encounter a very different growth scenario. The average spreading area of single cells is (0.34 ± 0.3) × 10−3 mm2, which is six times smaller than on glass substrates (Fig. 2
A). Clusters of only few cells show that cells have a preference for cell-cell contacts (a well-established flat contact zone can be seen at the cell-cell interface in Fig. 2
A) rather than for cell-substrate contacts (contact zone is diffusive and the shape of the cells appears curved). The same conclusion emerges from the fact that dropletlike agglomerates, resting on the substrate, form spontaneously (Fig. 2
A), and that attempts to seed one single cluster of 90,000 cells fail, resulting in a number of three-dimensional colonies (Fig. 2
A). When the contact area with the substrate exceeds 4.7 × 10−3 mm2, a monolayer appears in the center of such colonies (Fig. 2
B). The colonies can merge, and if individual colonies are small, the collapse into a single domain is associated with the formation of transient irregular structures (Fig. 2
B). Ultimately, large elliptical colonies (average major/minor axis of e = 1.8 ± 0.6) with a smooth edge are formed (Fig. 2
C), unlike on hard substrates where circular clusters (e = 1.06 ± 0.06) with a ragged edge comprise the characteristic phenotype.Open in a separate windowFigure 2Early phase of cluster growth on soft substrates. (A) Twelve hours after seeding, single cells remain mostly round and small. They are found as individual, or within small, three-dimensional structures (top). The latter nucleate a monolayer in their center (bottom), if the contact area with the substrate exceeds ∼5 × 10−3 mm2. (B) Irregularly-shaped clusters appear due to merging of smaller droplets. A stable monolayer surrounded by a three-dimensional belt of densely packed cells is clearly visible, even in larger structures. (C) All colonies are recorded on Day 4.Irrespective of cluster size, in the new regime of growth, the internal structure is built of two compartments (Fig. 2
B):
- 1.The first is the edge (0.019 ± 0.05-mm wide), a three-dimensional structure of densely packed cells. This belt is a signature of the new regime because on hard substrates the edge is strictly two-dimensional (Fig. 1 C).
- 2.The other is the centrally placed monolayer with a spatially constant density that is very weakly dependent on cluster size and age (Fig. 3). The mean monolayer density is 13,000 ± 2,000 cells/mm2, which is an average over 130 clusters that are up to 12 days old and have a size in the range of 10−3 to 10 mm2, each shown by a data point in Fig. 3. This density is twice the steady-state density of the bulk tissue in the classical regime of growth.Open in a separate windowFigure 3Monolayer densities in colonies grown on 0.6 kPa substrates, as a function of the cluster size and age. Each cluster is represented by a single data point signifying its mean monolayer density. (Black lines) Bulk and (red dashed lines) edge of steady-state densities from monolayers grown on glass substrates. Error bars are omitted for clarity, but are discussed in the Supporting Material.
8.
9.
Min Xu Hargeet K. Brar Sehiza Grosic Reid G. Palmer Madan K. Bhattacharyya 《Genetics》2010,184(1):53-63
Active endogenous transposable elements, useful tools for gene isolation, have not been reported from any legume species. An active transposable element was suggested to reside in the W4 locus that governs flower color in soybean. Through biochemical and molecular analyses of several revertants of the w4-m allele, we have shown that the W4 locus encodes dihydroflavonol-4-reductase 2 (DFR2). w4-m has arisen through insertion of Tgm9, a 20,548-bp CACTA-like transposable element, into the second intron of DFR2. Tgm9 showed high nucleic acid sequence identity to Tgmt*. Its 5′ and 3′ terminal inverted repeats start with conserved CACTA sequence. The 3′ subterminal region is highly repetitive. Tgm9 carries TNP1- and TNP2-like transposase genes that are expressed in the mutable line, T322 (w4-m). The element excises at a high frequency from both somatic and germinal tissues. Following excision, reinsertions of Tgm9 into the DFR2 promoter generated novel stable alleles, w4-dp (dilute purple flowers) and w4-p (pale flowers). We hypothesize that the element is fractured during transposition, and truncated versions of the element in new insertion sites cause stable mutations. The highly active endogenous transposon, Tgm9, should facilitate genomics studies specifically that relate to legume biology.IN soybean [Glycine max (L.) Merr.], five loci W1, W3, W4, Wm, and Wp control the pigmentations in flowers and hypocotyls (Palmer et al. 2004). Soybean plants with genotype W1_ w3w3 W4_ Wm_ Wp_ produce wild-type purple flowers (Figure 1) and purple hypocotyls. Mutations at the W4 locus in the W1_ background result in altered pigment accumulation patterns in petals and reduced levels of purple pigments in flowers and hypocotyls. Four mutant alleles, w4, w4-m, w4-dp, and w4-p have been mapped to this locus. The w4 allele represents a spontaneous mutation, which produces near-white flowers (Figure 1) and green hypocotyls (Hartwig and Hinson 1962; Groose and Palmer 1991). The w4-m allele was identified from a cross between two experimental breeding lines with white and purple flowers, respectively (Palmer et al. 1989; Weigelt et al. 1990). w4-m is characterized by variegated flowers (Figure 1) and green hypocotyls with purple sectors (Groose et al. 1988).Open in a separate windowFigure 1.—Variation in flower color among soybean lines carrying different W4 alleles.w4-m has been proposed to harbor a class II transposable element (Palmer et al. 1989). Presumably, somatic excision of the putative transposable element results in the variegated (Groose et al. 1988) and germinal excision wild-type phenotypes, purple flowers and purple pigments on hypocotyls (Palmer et al. 1989; Groose et al. 1990). The mutable line carrying w4-m undergoes germinal reversion at a very high frequency, about 6% per generation (Groose et al. 1990). Approximately 1% of the progeny derived from germinal revertants contain new mutations in unlinked loci, presumably resulting from reinsertion of the element (Palmer et al. 1989). For example, female partial-sterile 1 (Fsp1), female partial-sterile 2 (Fsp2), female partial-sterile 3 (Fsp3), and female partial-sterile 4 (Fsp4) were isolated from progenies of germinal revertants with purple flowers and were mapped to molecular linkage groups (MLG) C2, A2, F, and G, respectively (Kato and Palmer 2004). Similarly, 36 male-sterile, female-sterile mutants mapped to the st8 region on MLG J (Kato and Palmer 2003; Palmer et al. 2008a), 24 necrotic root (rn) mutants mapped to the rn locus on MLG G (Palmer et al. 2008b), and three Mdh1-n y20 mutants, mapped to a chromosomal region on MLG H (Palmer et al. 1989; Xu and Palmer 2005b), were isolated among progenies of germinal revertants.In addition to germinal revertants with purple flowers, the w4 mutable line also generated intermediate stable revertants that produce flowers with variable pigment intensities ranging from purple to near-white (Figure 1). Two stable intermediate revertants, w4-dp and w4-p, are allelic to W4. Plants carrying w4-dp or w4-p alleles produce dilute purple flowers or pale flowers, respectively (Figure 1) (Palmer and Groose 1993; Xu and Palmer 2005a).Pigment formation requires two types of genes: structural genes that encode anthocyanin biosynthetic enzymes [e.g., CHS (chalcone synthase), F3H (flavanone 3-hydroxylase), DFR (dihydroflavonol-4-reductase), ANS (anthocyanidin synthase); Figure S1] and regulatory genes that control expression of structural genes (Holton and Cornish 1995). Among the five genes, W1, W3, W4, Wp, and Wm, controlling pigment biosynthesis in soybean, four have been characterized at the molecular level (Figure S1). W1 encodes a flavonoid 5′, 3′-hydroxylase (Zabala and Vodkin 2007). W3 cosegregates with a DFR gene, Wp encodes a flavonone 3-hydroxylase (F3H), and Wm encodes a flavonol synthase (FLS) (Fasoula et al. 1995; Zabala and Vodkin 2005; Takahashi et al. 2007).Nine CACTA-type class II transposable elements, Tgm1, Tgm2, Tgm3, Tgm4, Tgm5, Tgm6, Tgm7, Tgm-Express1, and Tgmt*, have been reported in soybean (Rhodes and Vodkin 1988; Zabala and Vodkin 2005, 2008). Tgm-Express1 causes mutation in Wp (Zabala and Vodkin 2005) and Tgmt* () in T that encodes a flavonoid 3′ hydroxylase (F3′H) ( EU190440Zabala and Vodkin 2003, 2008). The objectives of the present study were to characterize the W4 locus and then investigate whether the w4-m allele harbors an active transposable element. Our results showed that a CACTA-like transposable element located in a dihydroflavonol-4-reductase gene causes variegated flower phenotype in soybean. 相似文献
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11.
Rigoberto Rios-Estepa Iris Lange James M. Lee B. Markus Lange 《Plant physiology》2010,152(4):2105-2119
We have previously reported the use of a combination of computational simulations and targeted experiments to build a first generation mathematical model of peppermint (Mentha × piperita) essential oil biosynthesis. Here, we report on the expansion of this approach to identify the key factors controlling monoterpenoid essential oil biosynthesis under adverse environmental conditions. We also investigated determinants of essential oil biosynthesis in transgenic peppermint lines with modulated essential oil profiles. A computational perturbation analysis, which was implemented to identify the variables that exert prominent control over the outputs of the model, indicated that the essential oil composition should be highly dependent on certain biosynthetic enzyme concentrations [(+)-pulegone reductase and (+)-menthofuran synthase], whereas oil yield should be particularly sensitive to the density and/or distribution of leaf glandular trichomes, the specialized anatomical structures responsible for the synthesis and storage of essential oils. A microscopic evaluation of leaf surfaces demonstrated that the final mature size of glandular trichomes was the same across all experiments. However, as predicted by the perturbation analysis, differences in the size distribution and the total number of glandular trichomes strongly correlated with differences in monoterpenoid essential oil yield. Building on various experimental data sets, appropriate mathematical functions were selected to approximate the dynamics of glandular trichome distribution/density and enzyme concentrations in our kinetic model. Based on a χ2 statistical analysis, simulated and measured essential oil profiles were in very good agreement, indicating that modeling is a valuable tool for guiding metabolic engineering efforts aimed at improving essential oil quality and quantity.The essential oil distilled from peppermint (Mentha × piperita) leaves is used in numerous consumer products (e.g. chewing gum, toothpaste, and mouthwash), as a flavor in the confectionary and pharmaceutical industries, and as a source of active ingredients for aromatherapy. Peppermint oil consists primarily of p-menthane-type monoterpenes, with smaller amounts of other monoterpenes and very minor quantities of sesquiterpenes (Rohloff, 1999). The essential oil is synthesized and accumulated in specialized anatomical structures called peltate glandular trichomes (Gershenzon et al., 1989; McCaskill et al., 1992). These trichomes contain secretory cells, arranged in an eight-celled disc, which are responsible for the synthesis of the oil. Nascent essential oil is secreted into an emerging cavity formed by the separation of a preformed layer of cuticular material (Amelunxen, 1965). Over the last two decades, the entire complement of genes and enzymes involved in the peppermint monoterpenoid essential oil biosynthetic pathway has been characterized (for review, see Croteau et al., 2005).Transgenic peppermint plants have been generated in efforts aimed at modulating essential oil yield and composition. Mahmoud and Croteau (2001) reported that, by overexpressing the gene encoding 1-deoxy-d-xylulose 5-phosphate reductoisomerase (DXR), oil yield increases (compared with wild-type plants) of up to 50% were observed. Antisense suppression of the (+)-menthofuran synthase (MFS) gene led to a dramatic decrease in the amounts of the undesirable side product (+)-menthofuran (elite transgenic line designated MFS7a; Mahmoud and Croteau, 2001). A slight increase in overall monoterpene yields was reported for transgenic plants with increased expression levels of the gene encoding (−)-limonene synthase (LS; Diemer et al., 2001), whereas only negligible effects on yield were detected in an independent study (Krasnyansky et al., 1999). Transgenic plants overexpressing the gene coding for (−)-limonene 3-hydroxylase (L3H) did not accumulate increased levels of the recombinant protein, and the composition and yield of the essential oils were the same as in wild-type controls; however, cosuppression of the L3H gene resulted in a vastly increased accumulation of the intermediate (−)-limonene, without notable effects on oil yield (elite transgenic line designed L3H20; Mahmoud et al., 2004).Mathematical modeling can be a powerful tool to support metabolic engineering efforts, including those performed with peppermint. Stoichiometric modeling only requires knowledge of the topology of reactions in the pathway and inputs/outputs. This is a particularly useful approach to determine flux distributions and the systemic characteristics of metabolic networks (for review, see Llaneras and Picó, 2008). When experimental designs supporting metabolic and isotopic steady state are employed, isotope labeling data can be utilized for the development of quantitative flux maps of metabolic pathways (for review, see Libourel and Shachar-Hill, 2008). For dynamic systems, kinetic modeling is regarded as the generally most suitable method (McNeil et al., 2000; Poolman et al., 2004; Bruggeman and Westerhoff, 2006; Rios-Estepa and Lange, 2007; Mendes et al., 2009). Building on the rich body of published data on the enzymology and physiology of the peppermint monoterpene pathway (for review, see Croteau et al., 2005), we recently developed a first generation kinetic model to simulate the dynamics of peppermint monoterpene composition (Rios-Estepa et al., 2008). Modeling indicated that the monoterpene profiles observed in leaves of plants grown under low-light conditions could be explained if one assumed that (+)-menthofuran, a dead-end side product, acted as a heretofore unknown competitive inhibitor against (+)-pulegone, the primary substrate of the branch point enzyme (+)-pulegone reductase (PR; Fig. 1). Follow-up biochemical studies established that this prediction was correct (Rios-Estepa et al., 2008), thus illustrating the utility of an approach that integrates mathematical modeling with experimental testing.Open in a separate windowFigure 1.Outline of p-menthane monoterpene biosynthesis in peppermint glandular trichomes. The following enzymes are involved in this pathway: 1, 1-deoxy-d-xylulose 5-phosphate synthase; 2, 1-deoxy-d-xylulose 5-phosphate reductoisomerase; 3, 2C-methyl-d-erythritol 4-phosphate cytidyltransferase; 4, 4-(cytidine 5′-diphospho)-2C-methyl-d-erythritol kinase; 5, 2C-methyl-d-erythritol 2,4-cyclodiphosphate synthase; 6, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate synthase; 7, (E)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase; 8, isopentenyl diphosphate isomerase; 9, geranyl diphosphate synthase; 10, (−)-limonene synthase; 11, (−)-limonene 3-hydroxylase; 12, (−)-trans-isopiperitenol dehydrogenase; 13, (−)-trans-isopiperitenone reductase; 14, (+)-cis-isopulegone isomerase; 15, (+)-menthofuran synthase; 16a, (+)-pulegone reductase [(−)-menthone-forming activity]; 16b, (+)-pulegone reductase [(+)-isomenthone-forming activity]; 17a, (−)-menthone:(−)-menthol reductase [(−)-menthol-forming activity]; 17b, (−)-menthone:(−)-menthol reductase [(+)-neoisomenthol-forming activity]; 18a, (−)-menthone:(+)-neomenthol reductase [(+)-neomenthol-forming activity]; 18b, (−)-menthone:(+)-neomenthol reductase [(+)-isomenthol-forming activity]. The subcellular compartmentation of p-menthane metabolic enzymes is color coded as follows: Cyt (blue), cytosol; ER (orange), endoplasmic reticulum; Lpl (green), leucoplasts; Mit (red), mitochondria. The inhibitory effects of (+)-menthofuran on (+)-pulegone reductase and geranyl diphosphate on isopentenyl diphosphate isomerase are indicated by red arcs with orthogonal red lines. Names of selected metabolites are shown in the colors that are used to indicate the corresponding profiles in Figures 2 to 55.As part of this study, a computational perturbation analysis was used to predict factors with the potentially greatest impacts on peppermint essential oil yield and composition (specific biosynthetic enzymes and the density of oil-synthesizing trichomes). To test these modeling predictions experimentally, we first acquired biometric data with peppermint plants grown under several environmental conditions known to adversely affect oil accumulation (Burbott and Loomis, 1967; Clark and Menary, 1980) and the transgenic line MFS7a, for which an altered essential oil profile had been reported earlier (Mahmoud and Croteau, 2001). Building on these experimental data sets, we then developed a second generation model that accounts for biochemical, developmental, environmental, and genotypic factors of essential oil formation. This updated model was then used to simulate monoterpenoid essential oil profiles for the transgenic line MFS7a grown under low-light environmental stress conditions and the transgenic line L3H20, which had previously been shown to have vastly reduced expression levels of the gene encoding L3H. In both cases, simulated and measured monoterpene patterns were very similar, indicating that mathematical modeling has great potential for guiding efforts aimed at developing peppermint lines with high oil yields and favorable composition, even under adverse environmental conditions. 相似文献
12.
The mosquito Anopheles gambiae has heteromorphic sex chromosomes, while the mosquito Aedes aegypti has homomorphic sex chromosomes. We use retrotransposed gene duplicates to show an excess of movement off the An. gambiae X chromosome only after the split with Ae. aegypti, suggesting that their ancestor had homomorphic sex chromosomes.HETEROMORPHIC sex chromosomes, both XX/XY and ZZ/ZW systems, have evolved independently multiple times in both animals and plants (Bull 1983; Charlesworth 1996; Rice 1996). Sex chromosomes are thought to evolve from a pair of autosomes that acquire a new sex-determining locus. Theory suggests that natural selection will favor tight linkage between the newly arisen sex-determining locus and sexually antagonistic alleles (i.e., genes that are beneficial in one sex, but detrimental in the other), which favors the suppression of recombination near the sex-determining locus (Charlesworth et al. 2005). In some species, this nonrecombining region includes only a small portion of the sex chromosome (hereafter referred to as homomorphic sex chromosomes), whereas in other species, this region encompasses most of the sex chromosomes (heteromorphic sex chromosomes). In many species the nonrecombining region progressively expands from only the portion near the sex-determining locus to nearly the full extent of the sex chromosomes (Lahn and Page 1999; Lawson Handley et al. 2004; Nicolas et al. 2005). However, the broad phylogenetic distribution of homomorphic sex chromosomes suggests that this progression does not happen in every species (e.g., Matsubara et al. 2006; Tsuda et al. 2007), although why it should occur in some lineages and not in others is unknown. As noted by Gilchrist and Haldane (1947, p. 187): “It is a striking fact that this [the suppression of recombination across the sex chromosome] has not happened in many large and successful groups.”Within the order Diptera, there are a wide variety of sex chromosomes and sex-determination mechanisms, including XY, ZW, multiple-X, and homomorphic systems, often varying within the same family (Marin and Baker 1998; Schutt and Nothiger 2000; Sanchez 2008). The mosquito Anopheles gambiae (a species in the subfamily Anophelinae) has fully differentiated heteromorphic X and Y chromosomes that show no evidence of recombination (Krzywinski et al. 2004). The mosquito Aedes aegypti (subfamily Culicinae) has a nonrecombining sex-determining region that spans only a few megabases on chromosome 1; this chromosome is homologous to chromosomes X and 2R of An. gambiae (Nene et al. 2007). An. gambiae and Ae. aegypti diverged ∼150 million years ago (Krzywinski et al. 2006).Because of the rapid turnover of sex-chromosome systems among the Diptera, it is not clear if the common ancestor of Ae. aegypti and An. gambiae had only a sex-determining region (i.e., homomorphic sex chromosomes) or fully differentiated heteromorphic sex chromosomes (Rai and Black 1999). The generally accepted model of sex-chromosome evolution, in which homomorphic sex chromosomes progressively suppress recombination and become heteromorphic, predicts that the common ancestor of Ae. aegypti and An. gambiae had homomorphic sex chromosomes (Figure 1A). This implies that evolution of heteromorphic sex chromosomes in An. gambiae occurred in a short period of time after the split between these two lineages and before the radiation of the Anophelines and that the homomorphic sex chromosomes of Ae. aegypti have been nearly static over evolutionary time. Alternatively, the common ancestor may have had nearly or fully differentiated sex chromosomes, and Ae. aegypti evolved from heteromorphic sex chromosomes to having only a small sex-determining region (Figure 1B; Rao and Rai 1987). We imagine this transition may have occurred by one of two mechanisms: either the sex-determining locus was transposed from the ancestral sex chromosome to an autosome or, in an XO sex-determination system, one of the “numerator” genes located on the X chromosome sustained an inactivating mutation, effectively making a karyotypic XX individual into a genetically male XO individual. (The precise mechanism of sex determination in Ae. aegypti is not known.)Open in a separate windowFigure 1.—Hypotheses for sex-chromosome evolution in Anopheles gambiae and Aedes aegypti. (A) The ancestor of An. gambiae and Ae. aegypti had homomorphic sex chromosomes and heteromorphism evolved along the Anopheline lineage. (B) The ancestor of An. gambiae and Ae. aegypti had heteromorphic chromosomes and homomorphism evolved along the Culicine lineage.To determine the state of the mosquito common ancestor, we examined genes duplicated by retrotransposition in the An. gambiae genome. Several organisms with heteromorphic sex chromosomes, including mammals and Drosophila, have an excess of retrotransposed genes moving from the X chromosome to autosomes compared to genes moving between autosomes or from the autosomes to the X (Betran et al. 2002; Emerson et al. 2004; Vinckenbosch et al. 2006; Meisel et al. 2009). This pattern is further found to be strongly associated with the origin of new X chromosomes in both mammals and Drosophila (Potrzebowski et al. 2008; Meisel et al. 2009), although it continues long after X chromosomes arise. While there are many hypotheses for the evolutionary forces that drive gene movement off X chromosomes—including sexual antagonism and meiotic sex-chromosome inactivation (e.g., Hense et al. 2007)—it is likely that all of these forces also act in mosquitoes, implying excess movement off the heteromorphic X in this clade as well. We reasoned that if the common ancestor of Ae. aegypti and An. gambiae had homomorphic sex chromosomes (Figure 1A), there should be an excess of retrogene movement off the X chromosome in An. gambiae only after the divergence of the two lineages (i.e., since An. gambiae evolved a differentiated X chromosome). In contrast, if the common ancestor had fully heteromorphic chromosomes (Figure 1B), then our prediction is that there will be an excess of gene movement off the An. gambiae X on both the shared ancestral branch and the Anopheles-specific branch after the split with Aedes. (Note that the Ae. aegypti genome is largely not assembled onto chromosomes, precluding a similar analysis in this species.)We collected data on all functional, intact duplicates in the An. gambiae genome and all orthologs between An. gambiae and Ae. aegypti from Ensembl version 54. When genes are retrotransposed there will be introns in the parental copy, but no introns in the daughter copy, allowing us to polarize gene movement. Although introns may be lost—and more rarely gained—over time, the rate of such changes is quite low (Coulombe-Huntington and Majewski 2007). Nevertheless, unless a parental gene loses all of its introns and the daughter gene gains introns, such changes will merely cause us to miss events rather than to assign them to an incorrect chromosome. Using gene-tree/species-tree reconciliation (Goodman et al. 1979), we identified retrotransposition events in the An. gambiae genome that have occurred since the split with Drosophila melanogaster and assigned them to a branch on the basis of the timing of the inferred duplication event in the gene tree. Calculating the expected number of movements on the basis of the equations presented in Betran et al. (2002), we find that an excess of movement off the X chromosome has in fact occurred since the split with D. melanogaster (χ2 = 23.83, d.f. = 2, P = 6.7 × 10−6). We then divided the retrotransposition events into those that occurred before the divergence of An. gambiae and Ae. aegypti and those that occurred only in An. gambiae since the split. We determined that there is a 400% excess of retrotransposition events off the X chromosome since the An. gambiae and Ae. aegypti split (Figure 2: χ2 = 51.97, d.f. = 2, P = 5.2 × 10−12). However, there is no excess of retrotransposition off the X chromosome prior to the split between An. gambiae and Ae. aegypti (Figure 2: χ2 = 1.51, d.f. = 2, P = 0.47). This strongly suggests a recent origin of fully differentiated heteromorphic sex chromosomes in An. gambiae.Open in a separate windowFigure 2.—Retroposition events off the X chromosome. There is an excess of genes moving off the X chromosome on the An. gambiae-specific lineage, but not on the branch leading to the common ancestor of An. gambiae and Ae. aegypti.The deepest split between species within the subfamily Anophelinae—all of which have fully differentiated sex chromosomes—occurs soon after the split with the Culicinae (Krzywinski et al. 2006). This implies that the evolution of heteromorphic sex chromosomes must have occurred very soon after the split with Ae. aegypti. To determine whether there was a burst of retrotransposition off the X following this split, we examined the amino acid sequence identity between X-to-autosome retrotransposed proteins and their parental paralogs. A comparison of these distributions indicates that there is no difference in the percentage of identity of genes retrotransposed off the An. gambiae X chromosome and one-to-one orthologs between An. gambiae and Ae. aegypti (71.1% vs. 70.7%, t-test, P = 0.92; JTT amino acid distances, 0.508 vs. 0.436, t-test, P = 0.57). Given the fact that functional retrotransposed genes have been found to evolve more rapidly than single-copy genes (Betran et al. 2002), these results support the idea that these duplication events occurred soon after the split between An. gambiae and Ae. aegypti.Our results have important implications for two further areas of research. First, a recent article (Moyle et al. 2010) proposed that X-to-autosome duplication events could be partly responsible for the large X-effect—the disproportionate effect of the X chromosome on reproductive isolation (Coyne and Orr 2004). This is because gene movement between chromosomes can itself cause reproductive isolation (e.g., Masly et al. 2006), and any excess movement involving the X will lead to an excess of reproductive isolation loci mapping to this chromosome. One prediction of this model is that species showing the large X-effect should also show an excess of X-to-autosome gene movement. As An. gambiae does in fact exhibit patterns consistent with the large X-effect (Slotman et al. 2005), our demonstration of an excess of movement off the X supports this model.Second, it has been proposed that the excess movement off the X in Drosophila is the cause of the deficit of male-biased genes on the X in the same species (e.g., Vibranovski et al. 2009), although the number of retrotransposed genes is much smaller than the number of missing male-biased genes (Betran et al. 2002; Parisi et al. 2003). We have previously shown that there is no deficit of male-biased genes on the An. gambiae X chromosome, at any significance level (Hahn and Lanzaro 2005). Given the observed excess of gene movement off the X presented here, we therefore find little support for a causal link between movement and genome-wide patterns of male-biased gene expression.Our results suggest that retrogene movement is a general feature of sex-chromosome evolution and support the hypothesis that the common ancestor of An. gambiae and Ae. aegypti had homomorphic sex chromosomes. It appears that the nonrecombining region around the sex-determining locus in An. gambiae expanded rapidly after the divergence with Ae. aegypti. Further investigation into the causes of the rapid expansion in the An. gambiae lineage and the long-term stasis in the Ae. aegypti lineage is clearly warranted. 相似文献
13.
We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we study the distribution of the total branch lengths of its sample genealogies. Within the coalescent approximation we have obtained a general expression—Equation 20—for the moments of this distribution with a given arbitrary dependence of the population size on time. We investigate how the frequency of population-size variations alters the total branch length.MODELS for gene genealogies of biological populations often assume a constant, time-independent population size N. This is the case for the Wright–Fisher model (Fisher 1930; Wright 1931), for the Moran model (Moran 1958), and for their representation in terms of the coalescent (Kingman 1982). In real biological populations, by contrast, the population size changes over time. Such fluctuations may be due to catastrophic events (bottlenecks) and subsequent population expansions or just reflect the randomness in the factors determining the population dynamics. Many authors have argued that genetic variation in a population subject to size fluctuations may nevertheless be described by the Wright–Fisher model, if one replaces the constant population size in this model by an effective population size of the form(1)where Nl stands for the population size in generation l. The harmonic average in Equation 1 is argued to capture the significant effect of catastrophic events on patterns of genetic variation in a population: if, for example, a population went through a recent bottleneck, a large fraction of individuals in a given sample would originate from few parents. This in turn would lead to significantly reduced genetic variation, parameterized by a small value of Neff. (See, e.g., Ewens 1982 for a review of different measures of the effective population size and Sjödin et al. 2005 and Wakeley and Sargsyan 2009 for recent developments of this concept.)The concept of an effective population size has been frequently used in the literature, implicitly assuming that the distribution of neutral mutations in a large population of fluctuating size is identical to the distribution in a Wright–Fisher model with the corresponding constant effective population size given by Equation 1. However, recently it was shown that this is true only under certain circumstances (Kaj and Krone 2003; Nordborg and Krone 2003; Jagers and Sagitov 2004). It is argued by Sjödin et al. (2005) that the concept of an effective population size is appropriate when the timescale of fluctuations of Nl is either much smaller or much larger than the typical time between coalescent events in the sample genealogy. In these limits it can be proved that the distribution of the sample genealogies is exactly given by that of the coalescent with a constant, effective population size.More importantly, it follows from these results that, in populations with variable size, the coalescent with a constant effective population size is not always a valid approximation for the sample genealogies. Deviations between the predictions of the standard coalescent model and empirical data are frequently observed, and there are a number of different statistical tests quantifying the corresponding discrepancies (see, for example, Tajima 1989, Fu and Li 1993, and Zeng et al. 2006). The analysis of such deviations is of crucial importance in understanding, for example, human genetic history (Garrigan and Hammer 2006). But while there is a substantial amount of work numerically quantifying deviations, often in terms of a single number, little is known about their qualitative origins and their effect upon summary statistics in the population in question.The question is thus to understand the effect of population-size fluctuations on the patterns of genetic variation, in particular for the case where the scale of the population-size fluctuations is comparable to the time between coalescent events in the ancestral tree. As is well known, many empirical measures of genetic variation can be computed from the total branch length of the sample genealogy (the expected number of single-nucleotide polymorphisms, for example, is proportional to the average total branch length).The aim of this article is to analyze the distribution of the scaled total branch length Tn for a sample genealogy in a population of fluctuating size, as illustrated in Figure 1. For the genealogy of n ≥ 2 lineages sampled at the present time, the expression ⌊NTn⌋ gives the total branch length in terms of generations. Here ⌊Nt⌋ is the largest integer ≤Nt, and the scaling factor N is a suitable measure of the number of genes in the population and serves as a counterpart of the constant generation size of the standard Wright–Fisher model.Open in a separate windowFigure 1.—The effect of population-size oscillations on the genealogy of a sample of size n = 17 (schematic). Left, genealogy described by Kingman''s coalescent for a large population of constant size, illustrated by the light blue rectangle; right, sinusoidally varying population size. Coalescence is accelerated in regions of small population sizes and vice versa. This significantly alters the tree and gives rise to changes in the distribution of the number of mutations and of the population homozygosity.A motivating example is given in Figure 2, which shows numerically computed distributions ρ(Tn) of the total branch lengths Tn for a particular population model with a time-dependent carrying capacity. The model is described briefly in the Figure 2 legend and in detail in a model for a population with time-dependent carrying capacity. As Figure 2 shows, the distributions depend in a complex manner on the form of the size changes. We observe that when the frequency of the population-size fluctuations is very small (Figure 2a), the distribution is well described by the standard coalescent result(2)(Hein et al. 2005). When the frequency is very large (Figure 2e), Equation 2 also applies, but with a different time scaling reflecting an effective population size: t on the right-hand side (rhs) in Equation 2 is replaced by t/c with c = N/Neff. Apart from these special limits, however, the form of the distributions appears to depend in a complicated manner upon the frequency of the population-size variation. The observed behavior is caused by the fact that coalescence proceeds faster for smaller population sizes and more slowly for larger population sizes, as illustrated in Figure 1. But the question is how to quantitatively account for the changes shown in Figure 2.Open in a separate windowFigure 2.—Numerically computed distributions of the scaled total branch lengths Tn in genealogies of samples of size n = 10. The model employed in the simulations is outlined in a model for a population with time-dependent carrying capacity. It describes a population subject to a time-varying carrying capacity, Kl = K0(1 + ɛ sin(2πνl)). The frequency of the time changes is determined by ν, and l = 1, 2, 3, … labels discrete generations forward in time. The parameter N = K0 describes the typical population size, which is taken here to be equal to the time-averaged carrying capacity. a–e show for populations with increasingly rapidly oscillating carrying capacity. The dashed red line in a shows that in the limit of low frequencies the standard coalescent result, Equation 2, is obtained. The dashed red line in e shows that also in the limit of large frequencies the standard coalescent result is obtained, but now with an effective population size. The dashed red line in d is a two-parameter distribution, Equation 41, derived in comparison between numerical simulations and coalescent predictions. Further numerical and analytical results on the frequency dependence of the moments of these distributions are shown in Figure 4. Parameter values used: K0 = 10,000, ɛ = 0.9, and r = 1 (see a model for a population with time-dependent carrying capacity for the exact meaning of the intrinsic growth rate r) and (a) νN = 0.001, (b) νN = 0.1, (c) νN = 0.316, (d) νN = 1, and (e) νN = 100.We show in this article that the results of the simulations displayed in Figure 2 are explained by a general expression—Equation 20—for the moments of the distributions shown in Figure 2. Our general result is obtained within the coalescent approximation valid in the limit of large population size. But we find that in most cases, the coalescent approximation works very well down to small population sizes (a few hundred individuals). Our result enables us to understand and quantitatively describe how the distributions shown in Figure 2 depend upon the frequency of the population-size oscillations. It makes possible to determine, for example, how the variance, skewness, and the kurtosis of these distributions depend upon the frequency of demographic fluctuations. This in turn allows us to compute the population homozygosity and to characterize genetic variation in populations with size fluctuations.The remainder of this article is organized as follows. The next section summarizes our analytical results for the moments of the total branch length. Following that, we describe the model employed in the computer simulations. Then, corresponding numerical results are compared to the analytical predictions. And finally, we summarize how population-size fluctuations influence the distribution of total branch lengths and conclude with an outlook. 相似文献
14.
Sylvain Glémin 《Genetics》2010,185(3):939-959
GC-biased gene conversion (gBGC) is a recombination-associated process mimicking selection in favor of G and C alleles. It is increasingly recognized as a widespread force in shaping the genomic nucleotide landscape. In recombination hotspots, gBGC can lead to bursts of fixation of GC nucleotides and to accelerated nucleotide substitution rates. It was recently shown that these episodes of strong gBGC could give spurious signatures of adaptation and/or relaxed selection. There is also evidence that gBGC could drive the fixation of deleterious amino acid mutations in some primate genes. This raises the question of the potential fitness effects of gBGC. While gBGC has been metaphorically termed the “Achilles'' heel” of our genome, we do not know whether interference between gBGC and selection merely has practical consequences for the analysis of sequence data or whether it has broader fundamental implications for individuals and populations. I developed a population genetics model to predict the consequences of gBGC on the mutation load and inbreeding depression. I also used estimates available for humans to quantitatively evaluate the fitness impact of gBGC. Surprising features emerged from this model: (i) Contrary to classical mutation load models, gBGC generates a fixation load independent of population size and could contribute to a significant part of the load; (ii) gBGC can maintain recessive deleterious mutations for a long time at intermediate frequency, in a similar way to overdominance, and these mutations generate high inbreeding depression, even if they are slightly deleterious; (iii) since mating systems affect both the selection efficacy and gBGC intensity, gBGC challenges classical predictions concerning the interaction between mating systems and deleterious mutations, and gBGC could constitute an additional cost of outcrossing; and (iv) if mutations are biased toward A and T alleles, very low gBGC levels can reduce the load. A robust prediction is that the gBGC level minimizing the load depends only on the mutational bias and population size. These surprising results suggest that gBGC may have nonnegligible fitness consequences and could play a significant role in the evolution of genetic systems. They also shed light on the evolution of gBGC itself.GC-BIASED gene conversion (gBGC) is increasingly recognized as a widespread force in shaping genome evolution. In different species, gene conversion occurring during double-strand break recombination repair is thought to be biased toward G and C alleles. In heterozygotes, GC alleles undergo a kind of molecular meiotic drive that mimics selection (reviewed in Marais 2003). This process can rapidly increase the GC content, especially around recombination hotspots (Spencer et al. 2006), and, more broadly, can affect genome-wide nucleotide landscapes (Duret and Galtier 2009a). For instance, it is thought to play a role in shaping isochore structure evolution in mammals (Galtier et al. 2001; Meunier and Duret 2004; Duret et al. 2006) and birds (Webster et al. 2006). Direct experimental evidence of gBGC mainly comes from studies in yeast (Birdsell 2002; Mancera et al. 2008; but see Marsolier-Kergoat and Yeramian 2009) and humans (Brown and Jiricny 1987). However, associations between recombination and the nucleotide landscape and frequency spectra biased toward GC alleles provide indirect evidence in very diverse organisms (Organisms Direct evidence Indirect evidence Achille''s heel evidence References Yeast Meiotic segregation bias Mancera et al. (2008) Mitotic and mitotic heteromismatch correction bias Correlation between GC and recombination Birdsell (2002) Mammals Mitotic heteromismatch correction bias Brown and Jiricny (1987) Correlation between GC*/GC and recombination Duret and Arndt (2008); Meunier and Duret (2004) Biased frequency spectrum toward GC alleles Galtier et al. (2001); Spencer et al. (2006) GC bias associated with high dN/dS near recombination hotspot Berglund et al. (2009; Galtier et al. (2009) Birds Correlation between GC and recombination International Chicken Genome Sequencing Consortium (2004) Turtles Correlation between GC and chromosome size Kuraku et al. (2006) Drosophila Correlation between GC and recombination Marais et al. (2003) Biased frequency spectrum toward GC alleles Galtier et al. (2006) Nematodes Correlation between GC and recombination Marais et al. (2001) Grasses Correlation between GC and outcrossing/selfing Glémin et al. (2006) Correlation between GC* and recombination and outcrossing/selfing Outcrossing increases dN/dS for genes with high GC* Haudry et al. (2008) Green algae Correlation between GC and recombination Jancek et al. (2008) Paramecium Correlation between GC and chromosome size Duret et al. (2008)