Localization of the Drosophila MAGUK protein Polychaetoid is controlled by alternative splicing

The Drosophila membrane-associated guanylate kinase (MAGUK) protein Polychaetoid (Pyd) is required for dorsal closure of the embryo, sensory organ patterning, and cell fate specification in the developing eye. We demonstrate that pyd is alternatively spliced resulting in two isoforms that differ by the presence or absence of exon 6. To determine the role of alternative splicing in Pyd function, we generated antibodies specific for each isoform. We find that the exon 6⁺ form of Pyd is localized at adherens junctions of embryonic and imaginal epithelia, while the exon 6⁻ form is distributed broadly along the lateral membrane. These results suggest that localization of Pyd is controlled by alternative splicing and raise the possibility that exon 6 represents a distinct protein–protein interaction domain.     

The relative strengths of SR protein-mediated associations of alternative and constitutive exons can influence alternative splicing.

We have characterized the functional role of SR protein-mediated exon/exon associations in the alternative splicing of exon 5 of chicken cardiac troponin T (cTnT). We have previously shown that SR proteins can promote the association of the alternative exon 5 with the flanking constitutive exon 6 of this pre-mRNA. In this study, we have shown that when exons 2, 3, and 4 of the cTnT pre-mRNA are spliced together, the composite exon 2/3/4 contains an additional SR protein binding site. Furthermore, we have found that SR proteins can also promote interactions between the pairs of exons 2/3/4-5 and 2/3/4-6. We then asked whether the SR protein binding sites in these exons play a role in cTnT alternative splicing in vivo. We found that the SR protein binding sites in exons 2/3/4 and 6 promote exon 5 skipping, and it has previously been shown that the SR protein binding site in exon 5 promotes exon 5 inclusion. Consistent with these results, we find that the SR protein-mediated association of exon 2/3/4 with 6 is preferred over associations involving exon 5, in that exons 2/3/4 and 6 are more efficient than exon 5 in competing an SR protein-mediated exon/exon association. We suggest that the relative strengths of SR protein-mediated associations of alternative and constitutive exons play a role in determining alternative splicing patterns.     

The Rat Central Nervous System Expresses Alzheimer's Amyloid Precursor Protein APP695, but Not APP677 (L-APP Form)

Abstract: A novel splicing form of βA4 amyloid precursor protein (APP) lacking exon 15, corresponding to 18 residues, was first reported in leukocytes and then in ubiquitous organs. To determine which APP molecules (APP₆₉₅, APP₇₅₁, or APP₇₇₀) either with (N-APP) or without (L-APP; leukocytederived APP) exon 15 were expressed in various organs, we investigated the alternative splicing at exon 15 in the rat brain, kidney, heart, and testis by a PCR analysis of reverse-transcribed RNA and Southern blot analysis. Regarding APP₆₉₅ without exons 7 and 8, L-APP was either seldom or never expressed in the brain, whereas both N- and L-APP were expressed in other organs. On the other hand, regarding APP_751/770 containing exon 7, which codes for the Kunitz-type serine protease inhibitor domain, both N- and L-APP were expressed in all the organs examined, including the brain. These results suggest that a particular alternative regulation system related to exon 15 might be present in only APP₆₉₅ of the brain and influence the proteolytic processing of APP.     

The reaction between the superoxide anion radical and cytochrome c

1. 1. The superoxide anion radical (O₂⁻) reacts with ferricytochrome c to form ferrocytochrome c. No intermediate complexes are observable. No reaction could be detected between O₂⁻ and ferrocytochrome c.

2. 2. At 20 °C the rate constant for the reaction at pH 4.7 to 6.7 is 1.4 · 10⁶ M⁻¹ · s⁻¹ and as the pH increases above 6.7 the rate constant steadily decreases. The dependence on pH is the same for tuna heart and horse heart cytochrome c. No reaction could be demonstrated between O₂⁻ and the form of cytochrome c which exists above pH ≈ 9.2. The dependence of the rate constant on pH can be explained if cytochrome c has pKs of 7.45 and 9.2, and O₂⁻ reacts with the form present below pH 7.45 with k = 1.4 · 10⁶ M⁻¹ · s⁻¹, the form above pH 7.45 with k = 3.0 · 10⁵ M⁻¹ · s⁻¹, and the form present above pH 9.2 with k = 0.

3. 3. The reaction has an activation energy of 20 kJ mol⁻¹ and an enthalpy of activation at 25 °C of 18 kJ mol⁻¹ both above and below pH 7.45. It is suggested that O₂⁻ may reduce cytochrome c through a track composed of aromatic amino acids, and that little protein rearrangement is required for the formation of the activated complex.

4. 4. No reduction of ferricytochrome c by HO₂ radicals could be demonstrated at pH 1.2–6.2 but at pH 5.3, HO₂ radicals oxidize ferrocytochrome c with a rate constant of about 5 · 10⁵–5 · 10⁶ M⁻¹ · s⁻¹

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干旱胁迫下表观遗传机制对转C4型PEPC基因水稻种子萌发的影响

为探究干旱胁迫下表观遗传机制对高表达玉米(Zea mays) C₄型PEPC转基因水稻(Oryza sativa)种子萌发的影响, 以转C₄型PEPC水稻(PC)和野生型水稻Kitaake (WT)为试材, 采用10% (m/v)聚乙二醇6000 (PEG6000)模拟干旱条件, 通过单独和联合施用PEG6000、DNA甲基化抑制剂5-氮杂胞苷(5azaC)和可变剪接抑制剂大环内酯类(PB)进行种子发芽实验, 测定种子活力、萌发过程中可溶性糖和可溶性蛋白含量、α-淀粉酶活性以及PEPC、糖信号相关基因和部分剪接因子基因的表达。结果表明, 0.25 µmol·L^-1PB处理对2种供试水稻在干旱条件下种子萌发均表现出显著抑制作用, 使干旱条件下种子萌发过程中可溶性总糖、蔗糖、葡萄糖和果糖含量以及可溶性蛋白含量均有所下降, PB也抑制糖信号-蔗糖非发酵1 (SNF1)相关蛋白激酶(SnRKs)家族和剪接因子丝氨酸/精氨酸富集蛋白家族(SR proteins)相关基因的表达以及α-淀粉酶的活性, 但对PC的抑制作用小于WT。5 µmol·L^-15azaC处理对干旱条件下种子萌发的效果与可变剪接抑制剂相反。5 µmol·L ^-1 5azaC联合PEG6000干旱处理部分减缓了干旱对水稻种子发芽率的抑制作用, 使供试材料发芽率升高, 表明DNA甲基化和可变剪接机制参与了水稻芽期干旱耐性, 其中对PC的作用更大。     

Effects of Epigenetic Mechanisms on C4 Phosphoenolpyruvate Carboxylase Transgenic Rice (Oryza sativa) Seed Germination Under Drought Stress

为探究干旱胁迫下表观遗传机制对高表达玉米(Zea mays) C₄型PEPC转基因水稻(Oryza sativa)种子萌发的影响, 以转C₄型PEPC水稻(PC)和野生型水稻Kitaake (WT)为试材, 采用10% (m/v)聚乙二醇6000 (PEG6000)模拟干旱条件, 通过单独和联合施用PEG6000、DNA甲基化抑制剂5-氮杂胞苷(5azaC)和可变剪接抑制剂大环内酯类(PB)进行种子发芽实验, 测定种子活力、萌发过程中可溶性糖和可溶性蛋白含量、α-淀粉酶活性以及PEPC、糖信号相关基因和部分剪接因子基因的表达。结果表明, 0.25 μmol·L^-1PB处理对2种供试水稻在干旱条件下种子萌发均表现出显著抑制作用, 使干旱条件下种子萌发过程中可溶性总糖、蔗糖、葡萄糖和果糖含量以及可溶性蛋白含量均有所下降, PB也抑制糖信号-蔗糖非发酵1 (SNF1)相关蛋白激酶(SnRKs)家族和剪接因子丝氨酸/精氨酸富集蛋白家族(SR proteins)相关基因的表达以及α-淀粉酶的活性, 但对PC的抑制作用小于WT。5 μmol·L^-15azaC处理对干旱条件下种子萌发的效果与可变剪接抑制剂相反。5 μmol·L ^-1 5azaC联合PEG6000干旱处理部分减缓了干旱对水稻种子发芽率的抑制作用, 使供试材料发芽率升高, 表明DNA甲基化和可变剪接机制参与了水稻芽期干旱耐性, 其中对PC的作用更大。     

A model for the involvement of Okazaki fragments maturation in the expansion of short tandem repeats

Mutations were accumulated with a wide variety in the p53 pseudogene of various wild mouse species and subspecies captured at different localities, as extensively observed in the exon 4 – exon 5 region. The rate of mutation accumulation in the mouse p53 pseudogene was estimated to be 1.4–2.1×10⁻⁸ mutations/bp/year, which is 20–30 times faster than that of the functional p53 and makes the dating possible for the time range of 10⁶ years or more. From comparison of the mutation spectrum, the origin of laboratory mice was identified to one of two M. m. domesticus groups.     

The mechanism of sex-specific splicing at the doublesex gene is different between Drosophila melanogaster and Bombyx mori

We have previously reported that Bmdsx, a homologue of the sex-determining gene, doublesex (dsx), was found to be sex-specifically expressed in various tissues at larval, pupal, and adult stages in the silkworm, Bombyx mori, and was alternatively spliced to yield male- and female-specific mRNAs. To reveal sex-specific differences in splicing patterns of Bmdsx pre-mRNA, the genomic sequence was determined and compared with male- and female-specific Bmdsx cDNA sequences. The open reading frame (ORF) consisted of five exons. Exons 3 and 4 were specifically incorporated into the female type of Bmdsx mRNA. On the other hand, exon 2 was spliced to exon 5 to produce the male type mRNA of Bmdsx. As in the case of Drosophila dsx, the OD2 domain was separated by a female-specific intron into sex-independent and sex-dependent regions. Sex-specific splicing occurred in equivalent positions in the Drosophila dsx gene. However, unlike Drosophila dsx, the female-specific introns showed no weak 3′ splice sites, and the TRA/TRA-2 binding site related sequences were not found in the female-specific exon, nor even in any other regions of the Bmdsx gene. Moreover, an in vitro splicing reaction consisting of HeLa cell nuclear extracts showed that the female-type of Bmdsx mRNA represented the default splicing. These findings suggest that the structural features of the sex-specific splicing patterns of Bmdsx pre-mRNA are similar to those of Drosophila dsx but the regulation of sex-specific alternative splicing of Bmdsx pre-mRNA is different.     

Promotion of exon 6 inclusion in HuD pre-mRNA by Hu protein family members

The Hu RNA-binding protein family consists of four members: HuR/A, HuB, HuC and HuD. HuR expression is widespread. The other three neuron-specific Hu proteins play an important role in neuronal differentiation through modulating multiple processes of RNA metabolism. In the splicing events examined previously, Hu proteins promote skipping of the alternative exons. Here, we report the first example where Hu proteins promote inclusion of an alternative exon, exon 6 of the HuD pre-mRNA. Sequence alignment analysis indicates the presence of several conserved AU-rich sequences both upstream and downstream to this alternatively spliced exon. We generated a human HuD exon 6 mini-gene reporter construct that includes these conserved sequences. Hu protein over-expression led to significantly increased exon 6 inclusion from this reporter and endogenous HuD. Studies using truncated and mutant HuD exon 6 reporters demonstrate that two AU-rich sequences located downstream of exon 6 are important. RNAi knockdown of Hu proteins decreased exon 6 inclusion. An in vitro splicing assay indicates that Hu proteins promote HuD exon 6 inclusion directly at the level of splicing. Our studies demonstrate that Hu proteins can function as splicing enhancers and expand the functional role of Hu proteins as splicing regulators.     

Identification of a cDNA encoding a novel C18-Δ polyunsaturated fatty acid-specific elongating activity from the docosahexaenoic acid (DHA)-producing microalga, Isochrysis galbana

Isochrysis galbana, a marine prymnesiophyte microalga, is rich in long chain polyunsaturated fatty acids such as docosahexaenoic acid (C22:6n-3, Δ^{4,7,10,13,16,19}). We used a polymerase chain reaction-based strategy to isolate a cDNA, designated IgASE1, encoding a polyunsaturated fatty acid-elongating activity from I. galbana. The coding region of 263 amino acids predicts a protein of 30 kDa that shares only limited homology to animal and fungal proteins with elongating activity. Functional analysis of IgASE1, by expression in Saccharomyces cerevisiae, was used to determine its activity and substrate specificity. Transformed yeast cells specifically elongated the C18-Δ⁹ polyunsaturated fatty acids, linoleic acid (C18:2n-6, Δ^9,12) and -linolenic acid (C18:3n-3, Δ^9,12,15), to eicosadienoic acid (C20:2n-6, Δ^11,14) and eicosatrienoic acid (C20:3n-3, Δ^11,14,17), respectively. To our knowledge this is the first time such an elongating activity has been functionally characterised. The results also suggest that a major route for eicosapentaenoic acid (C20:5n-3, Δ^5,8,11,14,17) and docosahexaenoic acid syntheses in I. galbana may involve a Δ⁸ desaturation pathway.     

Validation of trans-acting elements that promote exon 7 skipping of SMN2 in SMN2-GFP stable cell line

Spinal muscular atrophy is a genetic disease in which the SMN1 gene is deleted. The SMN2 gene exists in all of the patients. Alternative splicing of these two genes are different. More than 90% of exon 7 included form is produced from SMN1 pre-mRNA, whereas only ～20% of exon 7 included form is produced from SMN2 pre-mRNA. Only exon 7 inclusion form produces functional protein. Exon 7 skipped SMN isoform is unstable. Here we constructed a GFP reporter system that recapitulates the alternative splicing of SMN1 and SMN2 pre-mRNA. We designed a system in which GFP protein is expressed only when exon 7 of is included in alternative splicing. The stable cell that expresses SMN1-GFP produces ～4 times more GFP protein than the stable cell line that expresses SMN2-GFP; as demonstrated by microscopy, FACS analysis and immunoblotting. In addition the ratio of exon 7 inclusion and skipping of SMN1-GFP and SMN2-GFP pre-mRNA was similar to endogenous SMN1 and SMN2 pre-mRNA as shown in RT-PCR. Furthermore the knockdown with hnRNP A1 shRNA, a known protein which promotes exon 7 skipping of SMN2, induces exon 7 inclusion of exon 7 in SMN2-GFP pre-mRNA in SMN2-GFP cell line. We conclude that we have established the stable cell lines that recapitulate alternative splicing of the SMN1 and SMN2 genes. The stable cell line can be used to identify the trans-acting elements with siRNA.     

Zooplankton feeding ecology: bacterivory by metazoan microzooplankton

Bacterivory by the rotifer Brachionus plicatilis Müller, nauplii and copepodites of the copepods Centropages Krøyer sp. and Acartia tonsa Dana, and the tintinnid Favella panamensis Kofoid & Campbell was examined using fluorescently labelled bacteria (FLB) and epifluorescence microscopy. FLB were < 1 μm in diameter, and were offered at environmental concentrations (1.47−9.08 × 10⁶ cells·ml⁻¹). FLB were visible within rotifers, nauplii, copepodites, and tintinnids, confirming ingestion. Rotifer clearance rates (32–418 μl·animal⁻¹·h⁻¹) exhibited no relation with FLB concentration. In some cases rates of clearance of FLB by rotifers were different with alternative phytoplankton food (Nanochloris Naumann sp.) than in replicates with FLB alone, whereas in other cases presence of alternative food exhibited no clear effects on rates of ingestion of FLB. Clearance rates for all six naupliar stages of A. tonsa nauplii (0–320 μl·animal⁻¹·h⁻¹) were stage-related, with higher rates by NIII-VI nauplii than NI-II nauplii. Nauplii had higher rates of clearance of FLB in the absence of alternative phytoplankton food (Isochrysis Parke sp.). Clearance rates of FLB by a single stage of Centropages sp. nauplii, A. tonsa CI copepodites and F. panamensis (each obtained at only a single food concentration of either 1.5 or 5.0 × 10⁶ cells·ml⁻¹) were within the range of 85–142 μl·animal⁻¹·h⁻¹. These ranges were similar to those of rotifers and A. tonsa nauplii. This is the first report of FLB ingestion by metazoan marine microzooplankton. Although rotifers and ciliates might be expected to ingest small particles such as FLB using ciliary induced feeding currents, the means by which nauplii and copepodites eat FLB is less clear. We propose that they may “eat” bacteria as they “drink” to osmoregulate.     

Catalysis of plastocyanin electron self-exchange by redox-inert multivalent cations

Electron self-exchange in solutions of the ‘blue’ copper protein plastocyanin is catalysed by the redox-inert multivalent cations Mg²⁺ or Co(NH₃)³⁺₆. Measurements of specific ¹H-NMR line broadening with 50% reduced solutions in the presence of these cations show that electron exchange proceeds through encounters of cation-protein complexes which dissociate at high ionic strength. In the presence of 8mM (5 equivalents/total protein) Co(NH₃)³⁺₆, with 10 mM cacodylate (pH^*6.0) as background electrolyte, the bimolecular rate constant at 25°C is 7 × 10⁴ M⁻¹·s⁻¹. For comparison, the ‘electrostatically screened’ rate constant measured in 0.1 M KCl in the absence of added multivalent cations is ˜ 4 × 10³ M¹·s⁻¹.

Plastocyanin Electron self-exchange NMR Protein-protein interaction Multivalent cation Blue copper protein