Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.30.1 (S1 nuclease)
 3,660 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The genetic information, carried on mRNA 6 of feline infectious peritonitis virus (FIPV) strain 79-1146, was determined by sequence analysis of cDNA clones derived from the 3' end of the FIPV genome. Two ORFs were found, encoding polypeptides of 11K (ORF-1) and 22K (ORF-2). The FIPV sequence was compared to the 3' end sequence of transmissible gastroenteritis virus (TGEV). ORF-1 has a homologous counterpart (ORF-X3) in the TGEV genome; both ORFs are located at the same position relative to the nucleocapsid gene. However, as a result of an in-frame insertion or deletion, ORF-1 is 69 nucleotides larger than ORF-X3. A similar event has occurred immediately downstream of ORF1: a 624-nucleotide segment, containing the complete ORF-2, is absent in the TGEV sequence. Most sequence similarity (98.5%) was found in the 3' noncoding sequences. ORF-X3 and ORF-1 are preceded by the sequence AACTAAAC, which is assumed to be the transcription-initiation signal in FIPV and TGEV (P.A. Kapke and D.A. Brian (1986) Virology 151, 41-49). By S1 nuclease analysis, the 5' end of FIPV RNA 6 was mapped immediately upstream of this sequence. A 700-nucleotide TGEV-specific RNA was found by cross-hybridization with an FIPV 3' end probe, suggesting that TGEV ORF-X3 is also carried on a separate mRNA. The differences at the 3' ends of the FIPV and TGEV genomes may be the result of RNA recombination events.
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PMID:Sequence analysis of the 3'-end of the feline coronavirus FIPV 79-1146 genome: comparison with the genome of porcine coronavirus TGEV reveals large insertions. 320 47

Production of actinorhodin, a polyketide antibiotic made by Streptomyces coelicolor A3(2), normally occurs only in stationary-phase cultures. S1 nuclease protection experiments showed that transcription of actII-ORF4, the activator gene required for expression of the biosynthetic structural genes, increased dramatically during the transition from exponential to stationary phase. The increase in actII-ORF4 expression was followed by transcription of the biosynthetic structural genes actIII and actVI-ORF1, and by the production of actinorhodin. The presence of actII-ORF4 on a multicopy plasmid resulted in enhanced levels of actII-ORF4 mRNA, and transcription of actIII and actinorhodin production during exponential growth, suggesting that actinorhodin synthesis in rapidly growing cultures is normally limited only by the availability of enough of the activator protein. bldA, which encodes a tRNA(Leu)UUA that is required for the efficient translation of a single UUA codon in the actII-ORF4 mRNA, was transcribed throughout growth. Moreover, translational fusions of the 5' end of actII-ORF4 that included the UUA codon to the ermE reporter gene demonstrated the presence of functional bldA tRNA in young, exponentially growing cultures and no increase in the efficiency of translation of UUA codons, relative to UUG codons, was observed during growth. The normal growth-phase-dependent production of actinorhodin in the liquid culture conditions used in these experiments appears to be mediated at the transcriptional level through activation of the actII-ORF4 promoter.
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PMID:Stationary-phase production of the antibiotic actinorhodin in Streptomyces coelicolor A3(2) is transcriptionally regulated. 768 65

Genetic instability in Streptomyces ambofaciens DSM 40697 is correlated with genomic instability characterized by multiple rearrangements (deletions and/or amplifications) occurring in a large unstable region. We have focused on one of the two amplifiable DNA loci which were mapped in this region: the amplifiable unit of DNA locus 6 (AUD6). The nucleotide sequence of one AUD6 fragment of 1.9 kb reveals the presence of two open reading frames (ORF1 and ORF2) on the basis of the typical Streptomyces base composition at each of the three positions within codons. ORF1 shows some similarity with a gene encoding a regulatory protein. The presence of potential genes in this unstable locus was unexpected because deletions occurred with high frequency within this region in the genetic instability-derived mutant strains. However, transcription analyses by S1 nuclease protection experiments on the wild-type strain showed transcription of both ORF1 and ORF2. Moreover, the amplified strain reveals increased transcription of ORF1 but no transcription of ORF2. The amplification therefore results in a switch in transcription. The unstable region of S. ambofaciens DSM 40697 therefore is not a 'silent' region because at least some loci are transcribed.
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PMID:Analysis of genome instability in Streptomyces ambofaciens. 827 41

A new plasmid was isolated from the haloalkaliphilic archaeon, Natronobacterium sp. strain AS7091 and named pNB101. Sequence analysis revealed that pNB101 consists of 2,538 bp, in which three major open reading frames (ORF1, ORF2, and ORF3) were identified in the same strand. The ORF1 encodes a putative replication (Rep) protein with three typical motifs (I, II, and III) found in rolling-circle (RC) replicating plasmids. The putative double-stranded origin (DSO) and single-stranded origin (SSO) were detected within ORF3 and downstream of ORF1, respectively. S1 nuclease digestion and Southern blot analysis demonstrated the existence of the single-stranded DNA (ssDNA) intermediate from pNB101, which corresponds to the leading strand in RC replication and was further confirmed by strand-specific RNA probes. A single transcript for ORF1 ( rep) was detected by Northern blotting, and the 5' end of this transcript was determined by primer extension. Both results indicate that the three motifs (I-III) are located at the very end of the N-terminal of this Rep protein. Northern blot analysis also revealed that the ORF3 was transcribed at a very high level, which may play an important role in plasmid replication because the putative DSO is located in this gene. Together, our results indicate that pNB101, the first plasmid isolated from haloalkaliphilic Archaea, represents a novel RC-replicating plasmid.
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PMID:Complete sequence and molecular characterization of pNB101, a rolling-circle replicating plasmid from the haloalkaliphilic archaeon Natronobacterium sp. strain AS7091. 1506 75

Two small cryptic plasmids, pTJ86-1 and pTJ86-2, identified in Cupriavidus taiwanensis strain TJ86, were detected and characterized. Complete sequencing of pTJ86-1 and pTJ86-2 revealed these plasmids to be 2221 and 2229bp in length with a GC content of 61.7% and 61.6%, respectively. Both plasmids harbored four open reading frames (ORF1, 2, 3 and 4). Only the predicted ORF1 gene product of both plasmids (436 amino acids) was homologous to Rep proteins previously identified on plasmids replicated using a rolling-circle replication (RCR). A double-stranded origin (DSO) of replication, highly conserved in the group III (cluster III) RCR plasmids, was identified and located immediately upstream of this putative Rep gene. In addition, both plasmids contained a putative single-stranded origin of replication (SSO) exhibiting similarity to the ssoA-type. Detection of single-stranded plasmid DNA by Southern analysis and S1 nuclease digestion confirmed that the cryptic plasmid replicated via an RCR mechanism. A potential shuttle vector, pS4-tet(R), was constructed by ligation of pTJ86-1 to the cloning vector pBluescript II SK(+) along with the insertion of a tetracycline-resistance (tet(R)) gene. It was successfully used for the transformation of genera Burkholderia and Cupriavidus.
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PMID:Characterization and application of a rolling-circle-type plasmid from Cupriavidus taiwanensis. 1719 53

Plasmid isolation of kimchi-derived Weissella cibaria KLC140 revealed six different plasmids. The smallest plasmid, pKW2124, was DNA sequenced and characterized, showing 2,124 bp with a GC content of 36.39% and five putative open reading frames (ORFs). In silico analysis of these ORFs showed ORF1 encodes a putative replication protein similar to rolling circular replication proteins from other lactic acid bacteria. However, a single-stranded intermediate was not detected when S1 nuclease was treated, suggesting it may follow theta replication. Interestingly, the replication initiation site of this plasmid is 100% identical to other plasmids from lactic acid bacteria, suggesting it may function for replication initiation. To construct a surface layer expression vector, pTSLGFP, slpA encoding the surface layer protein from Lactobacillus acidophilus was PCR amplified and fused with the gfp gene, forming a SLGFP fused gene. The plasmid pKW2124 was cloned into the XbaI site of pUC19, forming an Weissella-E. coli shuttle vector pKUW22. NheI-linearized pTSLGFP was ligated into pKUWCAT containing pKUW22 and the chloramphenicol acetyltransferase gene from pEK104, resulting in an 8.6 kb pKWCSLGFP surface layer expression vector. After transformation of this vector into W. cibaria KLC140, a GFP fluorescence signal was detected on the surface of the transformant, substantiating production of SLGFP fused protein and its secretion. This is the first report for construction of a Weissella surface layer expression vector, which may be useful for surface layer production of beneficial proteins in Weissella.
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PMID:Sequence analysis of a cryptic plasmid pKW2124 from Weissella cibaria KLC140 and construction of a surface display vector. 2356 10


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