The IStron CdISt1 of Clostridium difficile: molecular symbiosis of a group I intron and an insertion element

The IStron CdISt1 was first discovered as an insertion into the tcdA gene of the clinical isolate C34. It combines structural and functional properties of a group I intron at its 5'-end with those of an insertion element at its 3'-end. Up to date four different types could be found, mainly differing in their IS-element portions. Contrasting classical group I introns, CdISt1 is always integrated in ORFs encoding bacterial protein. In case CdISt1 had only the IS-element function such insertion would inactivate the protein encoded by the host gene. It is only due to the self-splicing activity of the group I intron parts that CdISt1 integration does not abolish protein function. Both elements seem to exist in molecular symbiosis and CdISt1 could thus be a prototype of a novel class of genetic elements. Moreover, integration of the CdISt1 into the genome could be advantageous for the bacterium, a motor function for evolution of bacterial proteins is discussed. In clinical practice CdISt1 might well serve as a tool for epidemiological studies of C. difficile infections.     

Production of exopolysaccharides by submerged culture of an enthomopathogenic fungus, Paecilomyces tenuipes C240 in stirred-tank and airlift reactors

The objective of this study was to investigate the effect of shearing effect on the production of exopolysaccharides (EPS) from an enthomopathogenic fungus, Paecilomyces tenuipes C240 in a stirred-tank reactor (STR) and in an airlift reactor (AR). The optimal agitation rate for the production of EPS in the STR was 150 rpm with the mycelial morphology of hairy pellets, where the final concentration and the specific production rate of EPS were 2.33 g l(-1) and 0.312 gg(-1) h(-1), respectively. However, the maximum concentration of biomass (21.06 g l(-1)) in the STR was obtained at a high agitation speed of 300 rpm. The specific production rate of EPS (0.456 gg(-1) h(-1)) in the AR was significantly higher than that achieved in the STR, in which the typical morphological form of mycelium was a loose clump. The three EPS groups in the STR (designated as STR-I, -II, and -III) and two groups of EPS in the AR (designated as AR-I and -II) were obtained from the culture filtrates by a gel filtration chromatography on Sepharose CL-6B. The molecular weights of STR-I, STR-II, STR-III, AR-I, and AR-II were determined to be 1,820, 25, 1.8, 1,160, and 6.7 kDa, respectively. An agitation rate of 150 rpm in the STR was selected as the optimal culture condition for maximum EPS production (2.33 g l(-1)), which was similar to the level achieved in the AR (2.30 g l(-1)). The carbohydrate composition in each EPS was quite different from each other: the major component was glucose (in STR-I, -III, and AR-I), mannose (in STR-II), and arabinose (in AR-II). In contrast, no significant difference in amino acid composition was observed.     

Translation elongation factor-1A1 (eEF1A1) localizes to the spine by domain III

In vertebrates, there are two variants of eukaryotic peptide elongation factor 1A (eEF1A; formerly eEF-1α), eEF1A1 and eEF1A2, which have three well-conserved domains (D(I), D(II), and D(III)). In neurons, eEF1A1 is the embryonic type, which is expressed during embryonic development as well as the first two postnatal weeks. In the present study, EGFP-tagged eEF1A1 truncates were expressed in cortical neurons isolated from rat embryo (E18-19). Live cell images of transfected neurons showed that D(III)-containing EGFP-fusion proteins (EGFP-D(III), -D(II)-III, -D(I)-III) formed clusters that were confined within somatodendritic domains, while D(III)-missing ones (EGFP-D(I), -D(II), -D(I)-II) and control EGFP were homogeneously D(I)spersed throughout the neuron incluD(I)ng axons. In dendrites, EGFP-D(III) was targeted to the heads of spine- and filopoD(I)a-like protrusions, where it was colocalized with SynGAPα, a postsynaptic marker. Our data inD(I)cate that D(III) of eEF1A1 meD(I)ates formation of clusters and localization to spines.     

Identification of novel splice variants of the human catalytic subunit Cbeta of cAMP-dependent protein kinase.

Four different isoforms of the catalytic subunit of cAMP-dependent protein kinase, termed Calpha, Cbeta, Cgamma and PrKX have been identified. Here we demonstrate that the human Cbeta gene encodes six splice variants, designated Cbeta1, Cbeta2, Cbeta3, Cbeta4, Cbeta4ab and Cbeta4abc. The Cbeta splice variants differ in their N-terminal ends due to differential splicing of four different forms of exon 1 designated exon 1-1, 1-2, 1-3, 1-4 and three exons designated a, b and c. All these exons are located upstream of exon 2 in the Cbeta gene. The previously identified human Cbeta variant has been termed Cbeta1, and is similar to the Cbeta isoform identified in the mouse, ox, pig and several other mammals. Human Cbeta2, which is the homologue of bovine Cbeta2, has no homologue in the mouse. Human Cbeta3 and Cbeta4 are homologous to the murine Cbeta3 and Cbeta2 splice variants, whereas human Cbeta4ab and Cbeta4abc represent novel isofoms previously not identified in any other species. At the mRNA level, the Cbeta splice variants reveal tissue specific expression. Cbeta1 was most abundantly expressed in the brain, with low-level expression in several other tissues. The Cbeta3 and Cbeta4 splice variants were uniquely expressed in human brain in contrast to Cbeta2, which was most abundantly expressed in tissues of the immune system, with no detectable expression in brain. We suggest that the various Cbeta splice variants when complexed with regulatory subunits may give rise to novel holoenzymes of protein kinase A that may be important for mediating specific effects of cAMP.     

A new Ac-like transposon of Arabidopsis is associated with a deletion of the RPS5 disease resistance gene

The RPS5 and RFL1 disease resistance genes of Arabidopsis ecotype Col-0 are oriented in tandem and are separated by 1.4 kb. The Ler-0 ecotype contains RFL1, but lacks RPS5. Sequence analysis of the RPS5 deletion region in Ler-0 revealed the presence of an Ac-like transposable element, which we have designated Tag2. Southern hybridization analysis of six Arabidopsis ecotypes revealed 4-11 Tag2-homologous sequences in each, indicating that this element is ubiquitous in Arabidopsis and has been active in recent evolutionary time. The Tag2 insertion adjacent to RFL1 was unique to the Ler-0 ecotype, however, and was not present in two other ecotypes that lack RPS5. DNA sequence from the latter ecotypes lacked a transposon footprint, suggesting that insertion of Tag2 occurred after the initial deletion of RPS5. The deletion breakpoint contained a 192-bp insertion that displayed hallmarks of a nonhomologous DNA end-joining event. We conclude that loss of RPS5 was caused by a double-strand break and subsequent repair, and cannot be attributed to unequal crossing over between resistance gene homologs.     

Identification of a cis element for tissue-specific alternative splicing of chloroplast ascorbate peroxidase pre-mRNA in higher plants

Alternative splicing events in the 3'-terminal region of chloroplast ascorbate peroxidase (chlAPX) pre-mRNA in spinach and tobacco, which produced four types of mRNA variants, one form (tAPX-I) encoding thylakoid-bound APX (tAPX) and three forms (sAPX-I, -II, and -III) encoding stromal APX (sAPX), were regulated in a tissue-specific manner. The ratio of the level of sAPX mRNAs (sAPX-I, -II, and -III) to tAPX-I mRNA was close to 1 in leaf, whereas the ratio in root was greatly elevated due to an increase in sAPX-III and a decrease in tAPX-I resulting from the alternative excision of intron 11 and intron 12, respectively. A putative splicing regulatory cis element (SRE), which is highly conserved in the sequences of chlAPX genes of higher plants, was identified upstream of the acceptor site in intron 12. The deletion of the SRE sequence diminished the splicing efficiency of intron 12 in tobacco leaf in vivo. Gel-shift analysis showed that SRE interacts strongly with a nuclear protein from leaves but not those from the roots of spinach and tobacco. These results indicate that the tissue-specific alternative splicing of chlAPX pre-mRNA is regulated by the splicing enhancer SRE.     

A cytokinin mutant derived from cultured tobacco cells

Tissues cultured from the leaf lamina of wild-type Nicotiana tabacum L. cv. "Havana 425" plants require an exogenous source of cytokinin for rapid growth. In contrast, leaf tissues of plants heterozygous or homozygous for the partially dominant, monogenic habituated leaf (H1-1) trait, exhibit a cytokinin-autotrophic phenotype in culture. Here we show that the H1 trait can arise in culture. Cytokinin autotrophic variants were obtained by culturing wild-type tissues of leaf lamina successively on media containing reduced concentrations of the cytokinin, kinetin. Plants regenerated from clones of these variants exhibited the H1 phenotype, which segregated in breeding tests as expected for a dominant, monogenic trait. This trait, designated H1-2, is inherited at a different locus than the H1-1 trait described earlier. Our results show that cytokinin mutants can arise in cell culture and that at least two genes regulate the cytokinin requirement of cultured tobacco tissues.     

Molecular characterization of a new arcelin-5 gene

Arcelins are insecticidal proteins found in some wild accessions of the common bean, Phaseolus vulgaris. They are grouped in six allelic variants and arcelin-5 is the variant with the highest inhibitory effect on the development of Zabrotes subfasciatus larvae. Characterization of the protein and its genes resulted in the identification of three polypeptides and the isolation of two genes that encode the Arc5a and Arc5b polypeptides. Here we describe a new gene, Arc5-III. The protein it encodes has 81% amino acid identity with the derived amino acid sequences of Arc5-I and Arc5-II. The Arc5-III gene is highly expressed in developing seeds and at a much lower level in roots. Data obtained by a combination of two-dimensional gel electrophoresis, protein sequencing and MALDI-TOF mass spectrometry analysis support the conclusion that Arc5-III encodes a polypeptide present in Arc5c band. Using ion-exchange chromatography, three fractions containing arcelin-5 polypeptides were eluted by increasing the salt concentration. The three fractions contain various amounts of the three arc-5 polypeptides and inhibit the growth of Zabrotes subfasciatus larvae differentially, suggesting differences in insecticidal activity among the arcelin-5 isoforms.     

ESCRT-0 Is Not Required for Ectopic Notch Activation and Tumor Suppression in Drosophila

Multivesicular endosome (MVE) sorting depends on proteins of the Endosomal Sorting Complex Required for Transport (ESCRT) family. These are organized in four complexes (ESCRT-0, -I, -II, -III) that act in a sequential fashion to deliver ubiquitylated cargoes into the internal luminal vesicles (ILVs) of the MVE. Drosophila genes encoding ESCRT-I, -II, -III components function in sorting signaling receptors, including Notch and the JAK/STAT signaling receptor Domeless. Loss of ESCRT-I, -II, -III in Drosophila epithelia causes altered signaling and cell polarity, suggesting that ESCRTs genes are tumor suppressors. However, the nature of the tumor suppressive function of ESCRTs, and whether tumor suppression is linked to receptor sorting is unclear. Unexpectedly, a null mutant in Hrs, encoding one of the components of the ESCRT-0 complex, which acts upstream of ESCRT-I, -II, -III in MVE sorting is dispensable for tumor suppression. Here, we report that two Drosophila epithelia lacking activity of Stam, the other known components of the ESCRT-0 complex, or of both Hrs and Stam, accumulate the signaling receptors Notch and Dome in endosomes. However, mutant tissue surprisingly maintains normal apico-basal polarity and proliferation control and does not display ectopic Notch signaling activation, unlike cells that lack ESCRT-I, -II, -III activity. Overall, our in vivo data confirm previous evidence indicating that the ESCRT-0 complex plays no crucial role in regulation of tumor suppression, and suggest re-evaluation of the relationship of signaling modulation in endosomes and tumorigenesis.     

Characterization of extradiol dioxygenases from a polychlorinated biphenyl-degrading strain that possess higher specificities for chlorinated metabolites

Recent studies demonstrated that 2,3-dihydroxybiphenyl 1,2-dioxygenase from Burkholderia sp. strain LB400 (DHBDLB400; EC 1.13.11.39) cleaves chlorinated 2,3-dihydroxybiphenyls (DHBs) less specifically than unchlorinated DHB and is competitively inhibited by 2',6'-dichloro-2,3-dihydroxybiphenyl (2',6'-diCl DHB). To determine whether these are general characteristics of DHBDs, we characterized DHBDP6-I and DHBDP6-III, two evolutionarily divergent isozymes from Rhodococcus globerulus strain P6, another good polychlorinated biphenyl (PCB) degrader. In contrast to DHBDLB400, both rhodococcal enzymes had higher specificities for some chlorinated DHBs in air-saturated buffer. Thus, DHBDP6-I cleaved the DHBs in the following order of specificity: 6-Cl DHB > 3'-Cl DHB approximately DHB approximately 4'-Cl DHB > 2'-Cl DHB > 4-Cl DHB > 5-Cl DHB. It also cleaved its preferred substrate, 6-Cl DHB, three times more specifically than DHB. Interestingly, some of the worst substrates for DHBDP6-I were among the best for DHBDP6-III (4-Cl DHB > 5-Cl DHB approximately 6-Cl DHB approximately 3'-Cl DHB > DHB > 2'-Cl DHB approximately 4'-Cl DHB; DHBDP6-III cleaved 4-Cl DHB two times more specifically than DHB). Generally, each of the monochlorinated DHBs inactivated the enzymes more rapidly than DHB. The exceptions were 4-Cl DHB for DHBDP6-I and 2'-Cl DHB for DHBDP6-III. As observed in DHBDLB400, chloro substituents influenced the reactivity of the dioxygenases with O2. For example, the apparent specificities of DHBDP6-I and DHBDP6-III for O2 in the presence of 2'-Cl DHB were lower than those in the presence of DHB by factors of >60 and 4, respectively. DHBDP6-I and DHBDP6-III shared the relative inability of DHBDLB400 to cleave 2',6'-diCl DHB (apparent catalytic constants of 0.088 +/- 0.004 and 0.069 +/- 0.002 s(-1), respectively). However, these isozymes had remarkably different apparent K(m) values for this compound (0.007 +/- 0.001, 0.14 +/- 0.01, and 3.9 +/- 0.4 micro M for DHBDLB400, DHBDP6-I, and DHBDP6-III, respectively). The markedly different reactivities of DHBDP6-I and DHBDP6-III with chlorinated DHBs undoubtedly contribute to the PCB-degrading activity of R. globerulus P6.     

Isolation of immunoglobulin class switch variants from hybridoma lines secreting anti-idiotope antibodies by sequential sublining

The combination of a sensitive radioimmunoassay with a simple limiting dilution approach designated as sequential sublining (ssl) allowed us to isolate spontaneous class switch variants from two hybridoma lines secreting monoclonal anti-idiotope antibodies against a germ-line encoded antibody with defined hapten-binding specificity. We obtained two families of antibodies, one of which consists of IgG1, IgG2b, and IgG2a, the other consisting of IgG1, IgG2b, IgG2a, and IgE antibodies. The members of a family possess identical anti-idiotypic specificity. We describe serologic and biochemical properties of the class switch variants as well as the frequency and order of "forward" and "reverse" switching, and we compare the ssl approach to other related methods. The ssl allows the rapid isolation of somatic mutants, which have acquired a new predefined antigenic determinant, without complicated equipment and even when the frequency of the mutants is as low as 10(-6) or 10(-7).     

In vivo analyses of the roles of essential Omp85-related proteins in the chloroplast outer envelope membrane

Two different, essential Omp85 (Outer membrane protein, 85 kD)-related proteins exist in the outer envelope membrane of Arabidopsis (Arabidopsis thaliana) chloroplasts: Toc75 (Translocon at the outer envelope membrane of chloroplasts, 75 kD), encoded by atTOC75-III; and OEP80 (Outer Envelope Protein, 80 kD), encoded by AtOEP80/atTOC75-V. The atToc75-III protein is closely related to the originally identified pea (Pisum sativum) Toc75 protein, and it forms a preprotein translocation channel during chloroplast import; the AtOEP80 protein is considerably more divergent from pea Toc75, and its role is unknown. As knockout mutations for atTOC75-III and AtOEP80 are embryo lethal, we employed a dexamethasone-inducible RNA interference strategy (using the pOpOff2 vector) to conduct in vivo studies on the roles of these two proteins in older, postembryonic plants. We conducted comparative studies on plants silenced for atToc75-III (atToc75-III↓) or AtOEP80 (AtOEP80↓), as well as additional studies on a stable, atToc75-III missense allele (toc75-III-3/modifier of altered response to gravity1), and our results indicated that both proteins are important for chloroplast biogenesis at postembryonic stages of development. Moreover, both are important for photosynthetic and nonphotosynthetic development, albeit to different degrees: atToc75-III↓ phenotypes were considerably more severe than those of AtOEP80↓. Qualitative similarity between the atToc75-III↓ and AtOEP80↓ phenotypes may be linked to deficiencies in atToc75-III and other TOC proteins in AtOEP80↓ plants. Detailed analysis of atToc75-III↓ plants, by electron microscopy, immunoblotting, quantitative proteomics, and protein import assays, indicated that these plants are defective in relation to the biogenesis of both photosynthetic and nonphotosynthetic plastids and preproteins, confirming the earlier hypothesis that atToc75-III functions promiscuously in different substrate-specific import pathways.     

New alternatively spliced variants of calmodulin-dependent protein kinase II from rabbit liver

Polymerase chain reaction analysis revealed four alternatively spliced variants of each of the γ and δ isoforms of calmodulin-dependent protein kinase II (CaM-kinase II) in rabbit liver. Among the four variants of the γ isoform, two were novel ones, designated as CaM-kinase II γ-H and γ-I. The γ-I variant possessed both of the two deletable exons, D2a and D2b, which had never been found together in any variant. Sequence analysis of the γ-I indicated that the D2a was upstream of the D2b and that they were contiguous with each other in the γ-I. Among the four variants of the δ isoform, two were also novel ones, designated as CaM-kinase II δ-11 and δ-12, and the other two were the already-reported ones, δ-2 and δ-6. The δ-11 and δ-12 were identical to the δ-2 and δ-6, respectively, except that three bases (CAG) located at a splicing junction was deleted in the δ-11 and δ-12, suggesting two splicing sites of a single intron. Thus, the diverse splicing patterns may produce many more variants than those so far considered.