An intermediate polymer in the assembly of clathrin baskets

Clathrin (8 S) is known to polymerize into two varieties of basket structures (150 S or 300 S) under the normal buffer conditions [100 mM 2-(N-morpholino)ethanesulfonic acid (Mes), pH 5.9-6.7] used for the isolation of coated vesicles. However, it is now observed that under very low salt conditions (2 mM Mes, pH 5.9), it forms a homogeneous species with a sedimentation coefficient of 27 S. Increasing the salt concentration to 50 mM Mes completely converts all the 27S species into 150S baskets. Sedimentation equilibrium data show that this 27S species has a molecular weight that is 6 times that of the clathrin protomer and is the result of highly cooperative reversible self-association of the 8S protomer. Light-scattering studies show that the stabilities of 27S species and baskets (150 S or 300 S) are comparable. Fluorescent labeling of sulfhydryl groups with N-(1-anilinonaphthalenyl)maleimide indicates that the conformation of clathrin in 27S species and baskets (150 S or 300 S) is similar. Trypsin digestion reveals that in the 27S species clathrin has a conformation differing from that in both the 8S species and baskets.     

The evolution of sex-independent transmission ratio distortion involving multiple allelic interactions at a single locus in rice

Transmission ratio distortion (TRD) is frequently observed in inter- and intraspecific hybrids of plants, leading to a violation of Mendelian inheritance. Sex-independent TRD (siTRD) was detected in a hybrid between Asian cultivated rice and its wild ancestor. Here we examined how siTRD caused by an allelic interaction at a specific locus arose in Asian rice species. The siTRD is controlled by the S(6) locus via a mechanism in which the S(6) allele acts as a gamete eliminator, and both the male and female gametes possessing the opposite allele (S(6)(a)) are aborted only in heterozygotes (S(6)/S(6)(a)). Fine mapping revealed that the S(6) locus is located near the centromere of chromosome 6. Testcross experiments using near-isogenic lines (NILs) carrying either the S(6) or S(6)(a) alleles revealed that Asian rice strains frequently harbor an additional allele (S(6)(n)) the presence of which, in heterozygotic states (S(6)/S(6)(n) and S(6)(a)/S(6)(n)), does not result in siTRD. A prominent reduction in the nucleotide diversity of S(6) or S(6)(a) carriers relative to that of S(6)(n) carriers was detected in the chromosomal region. These results suggest that the two incompatible alleles (S(6) and S(6)(a)) arose independently from S(6)(n) and established genetically discontinuous relationships between limited constituents of the Asian rice population.     

Further characterization of agmatine binding to mitochondrial membranes: involvement of imidazoline I2 receptor

Agmatine, a divalent diamine with two positive charges at physiological pH, is transported into the matrix of liver mitochondria by an energy-dependent mechanism, the driving force of which is the electrical membrane potential. Its binding to mitochondrial membranes is studied by applying a thermodynamic treatment of ligand-receptor interactions on the analyses of Scatchard and Hill. The presence of two mono-coordinated binding sites S(1) and S(2), with a negative influence of S(2) on S(1), has been demonstrated. The calculated binding energy is characteristic for weak interactions. S(1) exhibits a lower binding capacity and higher binding affinity both of about two orders of magnitude than S(2). Experiments with idazoxan, a ligand of the mitochondrial imidazoline receptor I(2), demonstrate that S(1) site is localized on this receptor while S(2) is localized on the transport system. S(1) would act as a sensor of exogenous agmatine concentration, thus modulating the transport of the amine by its binding to S(2).     

A new self-compatibility haplotype in the sweet cherry 'Kronio', S5', attributable to a pollen-part mutation in the SFB gene

'Kronio' is a Sicilian cultivar of sweet cherry (Prunus avium), nominally with the incompatibility genotype S(5)S(6), that is reported to be naturally self-compatible. In this work the cause of its self-compatibility was investigated. Test selfing confirmed self-compatibility and provided embryos for analysis; PCR with consensus primers designed to amplify S-RNase and SFB alleles showed that the embryos were of two types, S(5)S(5) and S(5)S(6), indicating that S(6) pollen failed, but S(5) succeeded, perhaps because of a mutation in the pollen or stylar component. Stylar RNase analysis indicated active S-RNases for both S(5) and S(6). The S-RNase alleles were cloned and sequenced; and sequences encode functional proteins. Cloning and sequencing of SFB alleles showed that S(6) was normal but S(5) had a premature stop codon upstream of the variable region HVa resulting in a truncated protein. Therefore, the self-compatibility can be attributed to a pollen-part mutation of S(5), designated S(5)', the first reported case of breakdown of self-incompatibility in diploid sweet cherry caused by a natural mutation at the S-locus. The second intron of the S-RNase associated with S(5)' contained a microsatellite smaller than that associated with S(5); primers designed to amplify across this microsatellite effectively distinguished S(5) from S(5)'. Analysis of some other Sicilian cherries with these primers indicated that S(5)' is also present in the Sicilian cultivar 'Maiolina a Rappu', and this proved to be self-compatible.     

Structure and density of ribosomal RNA and its complexes with proteins in a solution

X-ray and neutron scattering, as well as velocity sedimentation, were used to study the shape and dimensions (compactness) of isolated ribosomal (16S and 23S) RNA's and their complexes with ribosomal proteins. The neutron scattering of ribosomal particles in 42% 2H2O where the protein component is contrast-matched, were taken as a standard of comparison characterizing the dimensions and shape of the 16S and 23S RNA in situ. This comparison allowed the following conclusions: (1) The shape of the isolated 16S RNA at a sufficient Mg2+ concentration (e. g., in the reconstruction buffer) is similar to that of the 16S RNA in situ, but its compactness is somewhat less. (2) The 16S RNA in the complex with protein S4 has a shape and compactness similar to those of the isolated 16S RNA. (3) The 16S RNA in the complex with four core proteins, namely S4, S7, S8 and S15, has a shape and compactness similar to those of the isolated 16S RNA. (4). The six ribosomal proteins, S4, S7, S8, S15, S16, and S17, are necessary and sufficient for the 16S RNA to acquire a compactness similar to that in situ.     

A 12 S precursor to 5.8 S rRNA associated with rat liver nucleolar 28 S rRNA

The pre-rRNA and rRNA components of rat and mouse liver nucleolar RNA were analysed. It was shown that upon denaturation, part of the 32 S pre-rRNA is converted into 28 S rRNA and 12 S RNA. The 12 S RNA from mouse (Mr, 0.36 X 10(6)) is larger than the one from rat (Mr, 0.32 X 10(6). The 12 S RNA chain is intact and resists denaturation treatment. The non-covalent binding of this RNA with nucleolar 28 S rRNA is stronger than that of 5.8 S rRNA with 28 S rRNA. Hybridization with a rat internal-transcribed spacer rDNA fragment identifies 12 S RNA as corresponding to the 5'-end non-conserved segment of 32 S pre-rRNA, including 5.8 S rRNA. The significance of the formation of a 12 S precursor to 5.8 S rRNA in the biogenesis of ribosomes in mammalian cells is discussed.     

Sequence and structural diversity of the S locus genes from different lines with the same self-recognition specificities in Brassica oleracea

Self-incompatibility (SI) is a mechanism for preventing self-fertilization in flowering plants. In Brassica, it is controlled by a single multi-allelic locus, S, and it is believed that two highly polymorphic genes in the S locus, SLG and SRK, play central roles in self-recognition in stigmas. SRK is a putative receptor protein kinase, whose extracellular domain exhibits high similarity to SLG. We analyzed two pairs of lines showing cross-incompatibility (S(2) and S(2-b); S(13) and S(13-b)). In S(2) and S(2-b), SRKs were more highly conserved than SLGs. This was also the case with S(13) and S(13-b). This suggests that the SRKs of different lines must be conserved for the lines to have the same self-recognition specificity. In particular, SLG(2-b) showed only 88. 5% identity to SLG(2), which is comparable to that between the SLGs of different S haplotypes, while SRK(2-b) showed 97.3% identity to SRK(2) in the S domain. These findings suggest that the SLGs in these S haplotypes are not important for self-recognition in SI.     

A review of Scymnodes Blackburn, with the description of a new Australian species and its larva (Coleoptera: Coccinellidae)

Abstract. The genus Scymnodes is reviewed both taxonomically and biologically, and its nineteen constituent species placed into two subgenera. S.(Dolinus) Weise is made a subjective synonym of S. (Scymnodes) Blackburn, S.(Apolinus) is proposed as a new name for Platyomus Mulsant (nee Schoenherr) and Rhynchortalia wallacei Crotch is transferred to S. (Scymnodes) as a new combination. S.(S.)bellus , sp.n. is described. Its larva is also described and comparisons made with those of S.(A.)lividigaster and the platynaspine Phymatosternus lewisi (Crotch). Comments are made on the habits of the S.(S.)bellus larva, which was observed to feed on ants.     

Ambiguous coding is required for the lethal interaction between methylated DNA bases and DNA mismatch repair

The thiopurine 6-thioguanine (S6G) is used to treat acute leukaemia. Its cytotoxic effect requires an active DNA mismatch repair (MMR) system. S6G is incorporated into DNA where a small fraction undergoes in situ conversion to S6-thiomethylguanine (S6meG). After replication, S6meG-containing base pairs interact with MMR. This interaction is ultimately lethal and MMR-defective cells are resistant to S6G. Here, we report that growing human cells extensively incorporate the thiopyrimidine nucleoside 4-thiothymidine (S4TdR) into their DNA. The incorporated thiopyrimidine (S4T) can also undergo facile S-methylation to 4-thiomethylthymine (S4meT). The rate of methylation of S4TdR in model substrates is similar to that for the conversion of S6G to S6meG indicating that the DNA of cells grown in S4TdR will contain significant levels of S4meT. Despite this, S4TdR is not associated with MMR-related cell death. We demonstrate that, in contrast to S6meG, neither DNA S4T nor S4meT codes ambiguously. S4T retains the coding properties of unmodified T, whereas S4meT behaves like a normal cytosine and exclusively directs the incorporation of guanine. The preferred S4meT:G base pair is also a poor substrate for binding by the hMutSalpha mismatch recognition factor. We suggest that the ability of S4meT to produce a structurally acceptable base pair during replication underlies the absence of MMR-related death in cells treated with S4TdR.     

Cladistic analysis of the fire ants of the Solenopsis saevissima species-group (Hymenoptera: Formicidae)

Results are presented from a phylogenetic study of the fire ants comprising the Solenopsis saevissima species-group (Hymenoptera: Formicidae). Six most-parsimonious trees were identified following a cladistic analysis utilizing 18 taxa and 36 morphological characters derived from three castes and two developmental stages. A strict consensus tree recovered the following relationships: ( S. daguerrei (( S. electra , S. pusilignis ) ( S. saevissima ( S. pythia ( S. interrupta , S. 'undescribed species' , S. weyrauchi ( S. richteri , S. invicta ( S. megergates ( S. quinquecuspis , S. macdonaghi )))))))). This phylogenetic hypothesis implies trends in fire ant evolution towards both polygyny (multiple egg-laying queens per colony) and large major worker size. The phylogeny also provides a test of Emery's Rule, which is not supported in its strictest sense because the social parasite S. daguerrei is not the sister species to its host species. A modified version of Emery's Rule is supported, because the social parasite is the sister species to a larger clade containing its hosts, as well as nonhosts.     

Inheritance of S(f)-RNase in Japanese apricot ( Prunus mume) and its relation to self-compatibility

Self-compatible cultivars of Japanese apricot ( Prunus mume Shieb. et Zucc.), a tree species that normally shows S-RNase-based self-incompatiblity, have a horticultural advantage over self-incompatible cultivars. Inheritance of self-compatibility and a common S(f)-RNase allele that is observed in self-compatible cultivars was investigated using progenies from controlled crosses. Total DNAs were isolated from the parents and progenies of seven crosses that included at least one self-compatible cultivar as a parent. These DNAs were PCR-amplified with the Pru-C2 and PCE-R primer pair to determine S-haplotypes of the parents and progenies. A novel S-haplotype, S(8), was found. In all crosses examined, the S(f)-RNase gene was inherited from either the seed or pollen parent as a pistil S-allele in a non-functional S-haplotype. Self-compatibility of about 20 trees each from reciprocal crosses of 'Benisashi ( S(7) S(f))' and 'Shinpeidayu ( S(3) S(f))', and 26 selections from 16 different crosses was tested by pollination and pollen-tube growth studies. Cosegregation of the S(f)-RNase allele and self-compatibility was confirmed with all but selection 1K0-26 ( S(3) S(7)). Selection 1K0-26 ( S(3) S(7)) that originated from 'Benisashi ( S(7) S(f))' x 'Koshinoume ( S(3) S(f))' appeared to be self-compatible even without the S(f)-RNase allele. The possible role of pollen- S, a presumably existing pollen component of gametophytic self-incompatibility, is discussed.     

A Mutant S3 RNase of Petunia inflata Lacking RNase Activity Has an Allele-Specific Dominant Negative Effect on Self-Incompatibility Interactions

Gametophytic self-incompatibility in the Solanaceae is controlled by a multiallelic locus called the S locus. Growth of pollen tubes in the pistil is inhibited when the pollen has one of the two S alleles carried by the pistil. The products of a number of pistil S alleles[mdash]S proteins or S RNases[mdash]have been identified, and their role in controlling the pistil's ability to reject self-pollen has been positively established. In contrast, the existence of pollen S allele products has so far been inferred entirely from genetic evidence. Here, we introduced a modified S3 gene of Petunia inflata encoding an S3 RNase lacking RNase activity into P. inflata plants of the S2S3 genotype to determine whether the production of the mutant protein, designated S3(H93R), would have any effect on the ability of the transgenic plants to reject S2 and S3 pollen. Analysis of the self-incompatibility behavior of 49 primary transgenic plants and the progeny of three plants (H30, H37, and H40) that produced S3(H93R) in addition to producing wild-type levels of endogenous S2 and S3 RNases revealed that S3(H93R) had a dominant negative effect on the function of the S3 RNase in rejecting self-pollen; however, it had no effect on the function of the S2 RNase. One likely explanation of the results is that S3(H93R) competes with the S3 RNase for binding to a common molecule, which is presumably the product of the pollen S3 allele.     

Sporophytic self-incompatibility in Senecio squalidus L (Asteraceae)--the search for S

Senecio squalidus (Oxford Ragwort) is being used as a model species to study the genetics and molecular genetics of self-incompatibility (SI) in the Asteraceae. S. squalidus has a strong system of sporophytic SI (SSI) and populations within the UK contain very few S alleles probably due to a population bottleneck experienced on its introduction to the UK. The genetic control of SSI in S. squalidus is complex and may involve a second locus epistatic to S. Progress towards identifying the female determinant of SSI in S. squalidus is reviewed here. Research is focused on plants carrying two defined S alleles, S(1) and S(2). S(2) is dominant to S(1) in pollen and stigma. RT-PCR was used to amplify three SRK-like cDNAs from stigmas of S(1)S(2) heterozygotes, but the expression patterns of these cDNAs suggest that they are unlikely to be directly involved in SI or pollen-stigma interactions in contrast to SSI in the Brassicaceae. Stigma-specific proteins associated with the S(1) allele and the S(2) allele have been identified using isoelectric focusing and these proteins have been designated SSP1 (Stigma S-associated Protein 1) and SSP2. SSP1 and SSP2 cDNAs have been cloned by 3' and 5' RACE and shown to be allelic forms of the same gene, SSP. The expression of SSP and its linkage to the S locus are currently being investigated. Initial results show SSP to be expressed exclusively in stigmas and developmentally regulated, with maximal expression occurring at and just before anthesis when SI is fully functional, SSP expression being undetectable in immature buds. Together these data suggest that SSP is a strong candidate for a Senecio S-gene.     

Sequential recognition of two distinct sites in sigma(S) by the proteolytic targeting factor RssB and ClpX

sigma(S) (RpoS), the master regulator of the general stress response in Escherichia coli, is a model system for regulated proteolysis in bacteria. sigma(S) turnover requires ClpXP and the response regulator RssB, whose phosphorylated form exhibits high affinity for sigma(S). Here, we demonstrate that recognition by the RssB/ClpXP system involves two distinct regions in sigma(S). Region 2.5 of sigma(S) (a long alpha-helix) is sufficient for binding of phosphorylated RssB. However, this interaction alone is not sufficient to trigger proteolysis. A second region located in the N-terminal part of sigma(S), which is exposed only upon RssB-sigma(S) interaction, serves as a binding site for the ClpX chaperone. Binding of the ClpX hexameric ring to sigma(S)-derived reporter proteins carrying the ClpX-binding site (but not the RssB-binding site) is also not sufficient to commit the protein to degradation. Our data indicate that RssB plays a second role in the initiation of sigma(S) proteolysis that goes beyond targeting of sigma(S) to ClpX, and suggest a model for the sequence of events in the initiation of sigma(S) proteolysis.     

Assembly of the central domain of the 30S ribosomal subunit: roles for the primary binding ribosomal proteins S15 and S8

Assembly of the 30S ribosomal subunit occurs in a highly ordered and sequential manner. The ordered addition of ribosomal proteins to the growing ribonucleoprotein particle is initiated by the association of primary binding proteins. These proteins bind specifically and independently to 16S ribosomal RNA (rRNA). Two primary binding proteins, S8 and S15, interact exclusively with the central domain of 16S rRNA. Binding of S15 to the central domain results in a conformational change in the RNA and is followed by the ordered assembly of the S6/S18 dimer, S11 and finally S21 to form the platform of the 30S subunit. In contrast, S8 is not part of this major platform assembly branch. Of the remaining central domain binding proteins, only S21 association is slightly dependent on S8. Thus, although S8 is a primary binding protein that extensively contacts the central domain, its role in assembly of this domain remains unclear. Here, we used directed hydroxyl radical probing from four unique positions on S15 to assess organization of the central domain of 16S rRNA as a consequence of S8 association. Hydroxyl radical probing of Fe(II)-S15/16S rRNA and Fe(II)-S15/S8/16S rRNA ribonucleoprotein particles reveal changes in the 16S rRNA environment of S15 upon addition of S8. These changes occur predominantly in helices 24 and 26 near previously identified S8 binding sites. These S8-dependent conformational changes are consistent with 16S rRNA folding in complete 30S subunits. Thus, while S8 binding is not absolutely required for assembly of the platform, it appears to affect significantly the 16S rRNA environment of S15 by influencing central domain organization.     

Changes in S1P1 and S1P2 expression during embryonal development and primitive endoderm differentiation of F9 cells

Sphingosine 1-phosphate (S1P) is a ligand for S1P family receptors (S1P(1)-S1P(5)). Of these receptors, S1P(1), S1P(2), and S1P(3) are ubiquitously expressed in adult mice, while S1P(4) and S1P(5) are tissue specific. However, little is known of their expression during embryonal development. We performed Northern blot analyses in mouse embryonal tissue and found that such expression is developmentally regulated. We also examined the expression of these receptors during primitive endoderm (PrE) differentiation of mouse F9 embryonal carcinoma (EC) cells, a well-known in vitro endoderm differentiation system. S1P(2) mRNA was abundantly expressed in F9 EC cells, but little S1P(1) and no S1P(3), S1P(4), or S1P(5) mRNA was detectable. However, S1P(1) mRNA expression was induced during EC-to-PrE differentiation. Studies using small interference RNA of S1P(1) indicated that increased S1P(1) expression is required for PrE differentiation. Thus, S1P(1) may play an important function in PrE differentiation that is not substituted for by S1P(2).     

S1 constrains S4 in the voltage sensor domain of Kv7.1 K+ channels

Voltage-gated K(+) channels comprise a central pore enclosed by four voltage-sensing domains (VSDs). While movement of the S4 helix is known to couple to channel gate opening and closing, the nature of S4 motion is unclear. Here, we substituted S4 residues of Kv7.1 channels by cysteine and recorded whole-cell mutant channel currents in Xenopus oocytes using the two-electrode voltage-clamp technique. In the closed state, disulfide and metal bridges constrain residue S225 (S4) nearby C136 (S1) within the same VSD. In the open state, two neighboring I227 (S4) are constrained at proximity while residue R228 (S4) is confined close to C136 (S1) of an adjacent VSD. Structural modeling predicts that in the closed to open transition, an axial rotation (approximately 190 degrees) and outward translation of S4 (approximately 12 A) is accompanied by VSD rocking. This large sensor motion changes the intra-VSD S1-S4 interaction to an inter-VSD S1-S4 interaction. These constraints provide a ground for cooperative subunit interactions and suggest a key role of the S1 segment in steering S4 motion during Kv7.1 gating.     

Interhaplotypic heterogeneity and heterochromatic features may contribute to recombination suppression at the S locus in apple (Malusxdomestica)

Gametophytic self-incompatibility (GSI) is controlled by a complex S locus containing the pistil determinant S-RNase and pollen determinant SFB/SLF. Tight linkage of the pistil and pollen determinants is necessary to guarantee the self-incompatibility (SI) function. However, multiple probable pollen determinants of apple and Japanese pear, SFBBs (S locus F-box brothers), exist in each S haplotype, and how these multiple genes maintain the SI function remains unclear. It is shown here by high-resolution fluorescence in situ hybridization (FISH) that SFBB genes of the apple S ( 9 ) haplotype are physically linked to the S ( 9 ) -RNase gene, and the S locus is located in the subtelomeric region. FISH analyses also determined the relative order of SFBB genes and S-RNase in the S ( 9 ) haplotype, and showed that gene order differs between the S ( 9 ) and S ( 3 ) haplotypes. Furthermore, it is shown that the apple S locus is located in a knob-like large heterochromatin block where DNA is highly methylated. It is proposed that interhaplotypic heterogeneity and the heterochromatic nature of the S locus help to suppress recombination at the S locus in apple.     

Systematic relationships within the dasyurid marsupial tribe Sminthopsini--a multigene approach.

We report analyses of complete DNA sequences of the mitochondrial cytochrome b (1146 bp), 12S rRNA (974 bp), partial control region (371 bp) loci, and the nuclear protamine P1 (616 bp) gene from all but one species (Sminthopsis butleri) of the dasyurid marsupial tribe Sminthopsini, as well as several outgroups. Parsimony analyses of combined nuclear and mitochondrial data suggest that Antechinomys is sister to a clade consisting of Sminthopsis and Ningaui. Parsimony, maximum-likelihood, and mixed-model distance analyses consistently resolve several species groups within Sminthopsis. The Macroura group includes S. macroura, S. virginiae, S. douglasi, and S. bindi; S. butleri is also included here on the basis of partial 12S rRNA sequences. S. crassicaudata is resolved as sister to the Macroura clade. The Murina group includes S. murina, S. leucopus, S. gilberti, S. dolichura, and S. archeri. S. griseoventer and S. aitkeni are resolved as a clade, and there is moderate support for a group consisting of the genetically divergent species S. psammophila, S. hirtipes, S. youngsoni, and S. ooldea (possibly along with S. longicaudata and S. granulipes). Compositions of species groups are partially congruent with clades previously proposed on the basis of morphological data. Radiations within Sminthopsini appear to be coincident with major environmental changes since the mid-Miocene.     

Steinernema cholashanense n. sp. (Rhabditida, Steinernematidae) a new species of entomopathogenic nematode from the province of Sichuan, Chola Shan Mountains, China

During a random survey of entomopathogenic nematodes in the provinces of Sichuan and Gansu (eastern Tibet) in 2004, soil samples from several sites were collected and tested for the incidence of entomopathogenic nematodes. A new species was collected in this survey and it is described herein as Steinernema cholashanense n. sp. Steinernema cholashanense n. sp. is characterized by morphology and morphometry of the IJ and male. For the IJ, the new species can be recognized by the average body length 843 microm, esophagus length 125 microm, H%=39% and E%=81%. The lateral field pattern is 2, 5, 7, 4, 2. The male of the first generation is characterized by spicule shape and length and especially with prominent velum and the presence of a mucron on both generations. The average body length of the IJ of S. cholashanense n. sp. (843 microm) is shorter than that of S. oregonense (980 microm), S. kraussei (951 microm) and S. litorale (909 microm), similar to that of S. feltiae (849 microm), but longer than that of S. weiseri (740 microm), S. jollietti (711 microm) and S. hebeiense (658 microm). Esophagus length of the new species (125 microm) is closer to that of S. jollieti (123 microm) but longer than that of S. weiseri (113 microm) and shorter than that of S. oregonense (132 microm), S. kraussei (134 microm) and S. feltiae (136 microm). E% of the new species (81) is similar to that of S. kraussei (80), but smaller than that of S. jollieti (88), S. weiseri (95), S. oregonense (100) and S. feltiae (119). Spicule head length of the new species is almost the same as its width, this character is similar to that of S. kraussei but it is different from this species by its prominent velum. The new species can be recognized further by characteristics of sequences of ITS and D2D3 regions and cross hybridization with closely related species, S. feltiae, S. kraussei and S. oregonense.