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1,141 records · Page 64Linked to original sources
PubMed2006

Detection of a group II intron without an open reading frame in the alpha-toxin gene of Clostridium perfringens isolated from a broiler chicken.

A DNA insertion of 834 bp, designated CPF-G2Im, was identified within the alpha toxin gene (cpa) of Clostridium perfringens strain CPBC16ML, isolated from a broiler chicken. Sequence analysis of CPF-G2Im indicated that it was integrated 340 nucleotides downstream of the start codon of cpa. However, the insertion did not abolish the phospholipase C and hemolytic activities of CPBC16ML. To investigate the expression of its alpha toxin, the intact copy of cpa was cloned into an expression vector and transformed into Escherichia coli M15 cells. Immunoblotting analysis showed that the protein expressed from the transformant as well as in the culture supernatant of C. perfringens strain CPBC16ML had the expected molecular weight detected in reference strains of C. perfringens. Northern hybridization and reverse transcriptase PCR (RT-PCR) analysis revealed that the entire CPF-G2Im insertion was completely spliced from the cpa precursor mRNA transcripts. The sequence of the insertion fragment has 95% and 97% identity to two noncoding regions corresponding to sequences that flank a predicted group II RT gene present in the pCPF4969 plasmid of C. perfringens. However, an RT was not encoded by the CPF-G2Im fragment. Based on the secondary structure prediction analysis, CPF-G2Im revealed typical features of group II introns. The present study shows that CPF-G2Im is capable of splicing in both C. perfringens and E. coli. To our knowledge, this is the first report that a group II intron without an open reading frame (ORF) is located in the cpa ORF of C. perfringens.

Animals↗
PubMed2006

[Cloning of GmHSFA1 gene and its overexpression leading to enhancement of heat tolerance in transgenic soybean].

Heat shock transcription factors (HSFs) are important in regulating heat stress response by mediating expression of heat shock protein (HSP) genes in various plant species. In the present study, a novel GmHSFA1 with an ORF of 1,533 bp (full-length cDNA sequence of 1,781 bp) was cloned from soybean genome via comparative genomic approach and RACE (rapid amplification of cDNA ends). This gene encodes 510 amino acids consisting of a protein of 56.2 kDa (GenBank accession number: AY458843). Similar to other HSFs, GmHSFA1 has the basic modular structure including DBD, OD, NLS, and CTAD. BLAST analysis revealed the identity of 52.46% between amino acid sequences between GmHSFA1 and LpHSFA1 that has the highest similarity to GmHSFA1 in all HSFA1s in various plant species. The results from RT-PCR, Northern blotting, and transformation showed: 1) GmHsfA1 exhibited the constitutive expression patterns in different tissues of soybean; 2) The expression level of GmHsfA1 in transgenic plants was notably higher than that in non-transgenic plants; 3) Overexpression of GmHsfA1 activated transcription of GmHSP22 in transgenic plants under normal conditions and enhanced obviously expressions of GmHSP23 and GmHSP70 in transgenic plants under heat stress conditions; 4) Heat tolerant temperature (as high as 52 degrees C) of transgenic plants was remarkably higher than that of non-transgenic plants. These results preliminarily proved that the overexpression of GmHsfA1 possibly led to the notable enhancement of heat-tolerant level of transgenic plants by mediating the activation of transcription or improvement of expression of some GmHSPs in the GmHsfA1's downstream in transgenic plants, suggesting GmHSFA1 is a novel and functional heat shock transcription factor of soybean.

Amino Acid Sequence↗
PubMed1995

A TnphoA insertion within the Bradyrhizobium japonicum sipS gene, homologous to prokaryotic signal peptidases, results in extensive changes in the expression of PBM-specific nodulins of infected soybean (Glycine max) cells.

Bradyrhizobium japonicum mutant 132 was obtained by random TnphoA mutagenesis of strain 110spc4. A 6.5 kb BamHI kanamycin-resistance-coding DNA fragment of mutant 132 was used as a hybridization probe to clone the corresponding wild-type fragment. DNA sequence analysis of a 3213 bp BamHI-ClaI fragment revealed that three open reading frames (ORFs) were encoded in the same orientation. Based on sequence similarities to other proteins in the database, the second ORF was called sipS (signal peptidase). The TnphoA insertion in mutant 132 was found to be in frame near the 3' end of sipS. The resulting SipS-PhoA hybrid polypeptide was shown to be expressed in free-living B. japonicum and in Escherichia coli cultures. An immunoblot analysis with a polyclonal antibody directed against the alkaline phosphatase revealed the appearance of a weak signal of a 70 kDa polypeptide both in B. japonicum and in E. coli, in agreement with the calculated size of the hybrid polypeptide. A much stronger 52 kDa band was also detected. Mutant 132 was specifically disturbed in the interaction with soybean (Glycine max) when the bacteria were released from the infection threads. The bacteroids were not stably maintained within the symbiosome. Numerous vesicles were found in the plant cytosol, which finally resulted in the formation of large vacuoles within the infected nodule cells. Immunohistochemical analyses with antibodies directed against nodulins of the peribacteroid membrane indicated a lower expression of these proteins. The mutant phenotype was genetically complemented by a 4.4 kb BamHI fragment including sipS. Subfragments thereof also complemented a temperature-sensitive E. coli lepB mutant, demonstrating that the B. japonicum fragment was functionally replacing Lepts in E. coli. Genetic studies suggested that the three genes are organized in one common operon which is expressed from a promoter upstream of the sequenced region. Inactivation of the gene downstream of sipS did not result in a detectable phenotype.

Alkaline Phosphatase↗
PubMed2004

Biosynthesis of the dichloroacetyl component of chloramphenicol in Streptomyces venezuelae ISP5230: genes required for halogenation.

Five ORFs were detected in a fragment from the Streptomyces venezuelae ISP5230 genomic DNA library by hybridization with a PCR product amplified from primers representing a consensus of known halogenase sequences. Sequencing and functional analyses demonstrated that ORFs 11 and 12 (but not ORFs 13-15) extended the partially characterized gene cluster for chloramphenicol (Cm) biosynthesis in the chromosome. Disruption of ORF11 (cmlK) or ORF12 (cmlS) and conjugal transfer of the insertionally inactivated genes to S. venezuelae gave mutant strains VS1111 and VS1112, each producing a similar series of Cm analogues in which unhalogenated acyl groups replaced the dichloroacetyl substituent of Cm. 1H-NMR established that the principal metabolite in the disrupted strains was the alpha-N-propionyl analogue. The sequence of CmlK implicated the protein in adenylation, and involvement in halogenation was inferred from biosynthesis of analogues by the cmlK-disrupted mutant. A role in generating the dichloroacetyl substituent was supported by partial restoration of Cm biosynthesis when a cloned copy of cmlK was introduced in trans into VS1111. Complementation of the mutant also indicated that inactivation of cmlK rather than a polar effect of the disruption on cmlS expression had interfered with dichloroacetyl biosynthesis. The deduced CmlS sequence resembled sequences of FADH2-dependent halogenases. Conjugal transfer of cmlK or cmlS into S. venezuelae cml-2, a chlorination-deficient strain with a mutation mapped genetically to the Cm biosynthesis gene cluster, did not complement the cml-2 lesion, suggesting that one or more genes in addition to cmlK and cmlS is needed to assemble the dichloroacetyl substituent. Insertional inactivation of ORF13 did not affect Cm production, and the products of ORF14 and ORF15 matched Streptomyces coelicolor A3(2) proteins lacking plausible functions in Cm biosynthesis. Thus cmlS appears to mark the downstream end of the gene cluster.

Amino Acid Sequence↗
PubMed2001

Structural analysis of the -1 ribosomal frameshift elements in giardiavirus mRNA.

The RNA polymerase of giardiavirus (GLV) is synthesized as a fusion protein through a -1 ribosomal frameshift in a region where gag and pol open reading frames (ORFs) overlap. A heptamer, CCCUUUA, and a potential pseudoknot found in the overlap were predicted to be required for the frameshift. A 68-nucleotide (nt) cDNA fragment containing these elements was inserted between the GLV 5' 631-nt cDNA and the out-of-frame luciferase gene that required a -1 frameshift within the 68-nt fragment for expression. Giardia lamblia trophozoites transfected with the transcript of this construct showed a frameshift frequency at 1.7%, coinciding with the polymerase-to-capsid protein ratio in GLV. The heptamer is required for the frameshift but can be replaced with other sequences of the same motif. Mutations placing stop codons in the 0 or -1 frame, located directly before or after the heptamer, implicated the latter as the site for the -1 frameshift. Shortening or destroying the putative stem decreased the frameshift efficiency threefold; the efficiency was fully recovered by mutations to restore the stem. Deleting 18 nt from the 3' end of the 68-nt fragment, which formed the second stem in the putative pseudoknot, had no effect on the frequency of the frameshift. Chemical probing of the RNA secondary structure in the frameshift region showed that bases resistant to chemical modification were clustered in the putative stem structures, thus confirming the presence of the postulated stem-loop, while all the bases in the loop were chemically modified, thus ruling out their capability of forming a pseudoknot. These results confirmed the conclusion based on data from the mutation study that there is but a simple stem-loop downstream from the heptamer. Together, they constitute the structural elements for a -1 ribosomal frameshift in the GLV transcript.

Giardiavirus↗
PubMed1997

Identification of two novel isoforms of the ZNF162 gene: a growing family of signal transduction and activator of RNA proteins.

By differential screening of a cDNA library obtained from a GM-CSF-dependent human myeloid leukemia cell line (GF-D8), we identified two novel isoforms of the recently described ZNF162 gene, which is apparently linked to multiple endocrine neoplasia type 1. The shorter of these new isoforms, called B3, presents an open reading frame (ORF) of 1713 bp coding for 571 amino acids. Its nucleotide sequence is homologous to the cDNA coding for the ABCDF isoform of ZNF162, except for a 4-nucleotide insertion that results in a frame shift of the ORF starting from nucleotide 1725 of the ZNF162 sequence. As a consequence, the predicted translation product of B3 contains the consensus sequence of the A motif (G-X-X-X-X-G-K-S) of the "ATP/ GTP binding site," which is characteristic of several protein families including protein kinases. Moreover, B3 shows the use of a different stop codon and contains a different tyrosine-rich COOH terminus. The longer isoform, called B4, differs from the ABCDEF isoform of ZNF162 by the insertion, at position 2137, of 383 nucleotides leading to a different, proline-rich COOH terminus. The complex transcription pattern of the ZNF162 gene is characterized by four transcripts, of approximately 3.9, 3.7, 3.2, and 2.9 kb, in GF-D8 cells. The 3.7- and 2.9-kb transcripts are expressed in resting GF-D8 cells. Upon stimulation with GM-CSF the expression of these mRNAs is up-regulated in parallel with the induction of two additional transcripts of 3.9 and 3.2 kb. The same pattern of expression has also been observed in freshly isolated myeloid leukemia cells and normal CD34+ stem cells. In light of these data, and since GM-CSF is known to stimulate signal transduction pathways, it becomes relevant that all the different isoforms of ZNF162 contain the KH module, which is a sequence motif present in proteins playing a major role in regulating cellular RNA metabolism. A search for functional domains demonstrates that ZNF162 belongs to a new and growing family of genes dubbed STAR (signal transduction and activator of RNA) proteins that are thought to play a downstream role in cell signaling and also in RNA binding. The mammalian members include Sam68, which is a target of Src, Fyn, and Grb2, and the newly cloned mouse quaking proteins (qkI) necessary in early embryogenesis and myelination. Moreover, since ZNF162 is highly conserved from yeast to humans, it implies that this new pathway has a significant function.

Amino Acid Sequence↗
PubMed2001

Coumarin formation in novobiocin biosynthesis: beta-hydroxylation of the aminoacyl enzyme tyrosyl-S-NovH by a cytochrome P450 NovI.

BACKGROUND: Coumarin group antibiotics, such as novobiocin, coumermycin A1 and clorobiocin, are potent inhibitors of DNA gyrase. These antibiotics have been isolated from various Streptomyces species and all possess a 3-amino-4-hydroxy-coumarin moiety as their structural core. Prior labeling experiments on novobiocin established that the coumarin moiety was derived from L-tyrosine, probably via a beta-hydroxy-tyrosine (beta-OH-Tyr) intermediate. Recently the novobiocin gene cluster from Streptomyces spheroides was cloned and sequenced and allows analysis of the biosynthesis of the coumarin at the biochemical level using overexpressed and purified proteins. RESULTS: Two open reading frames (ORFs), NovH and NovI, from the novobiocin producer S. spheroides have been overexpressed in Escherichia coli, purified and characterized for tyrosine activation and oxygenation which are the initial steps in coumarin formation. The 65 kDa NovH has two predicted domains, an adenylation (A) and a peptidyl carrier protein (PCP), reminiscent of non-ribosomal peptide synthetases. Purified NovH catalyzes L-tyrosyl-AMP formation by its A domain, can be posttranslationally phosphopantetheinylated on the PCP domain, and accumulates the covalent L-tyrosyl-S-enzyme intermediate on the holo PCP domain. The second enzyme in the pathway, NovI, is a 45 kDa heme protein that functions as a cytochrome P450-type monooxygenase with specificity for the tyrosyl-S-NovH acyl enzyme. The product beta-OH-tyrosyl-S-NovH was detected by alkaline release and high performance liquid chromatography analysis of radioactive [3H]beta-OH-Tyr and by mass spectrometry. Also detected was 4-OH-benzaldehyde, a retro aldol breakdown product of beta-OH-Tyr. The amino acid released was (3R,2S)-3-OH-Tyr by comparison with authentic standards. CONCLUSIONS: This work establishes that NovH and NovI are responsible for the formation of a beta-OH-Tyr intermediate that is covalently tethered to NovH in novobiocin biosynthesis. Comparable A-PCP/P450 pairs for amino acid beta-hydroxylation are found in various biosynthetic gene clusters, such as ORF19/ORF20 in the chloroeremomycin cluster for tyrosine, CumC/CumD in the coumermycin A1 cluster for tyrosine, and NikP1/NikQ in the nikkomycin cluster for histidine. This phenomenon of covalent docking of the amino acid in a kinetically stable thioester linkage prior to chemical modification by downstream tailoring enzymes, could represent a common strategy for controlling the partitioning of the amino acid for incorporation into secondary metabolites.

Acylation↗