The cleavage specificity of RNase III

Krinke, Lothar; Wulff, Daniel L.

doi:10.1093/nar/18.16.4809

Cited by 66 publications

(54 citation statements)

References 33 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The extra stem-loop structures of R. capsulatus and R. sphaeroides have strong similarity to secondary structures that are recognized by RNase III in E. coli, i.e., stems of less than 20 consecutive bp that contain unpaired bases forming internal loops (7). A sequence that fits the consensus sequence proposed for RNase III cleavage in E. coli by Krinke and Wulff (27) is not present within these Rhodobacter stem-loops. However, even in E. coli, functional RNase III sites can differ significantly from this consensus sequence (7).…”

Section: Resultsmentioning

confidence: 84%

Cloning of a gene involved in rRNA precursor processing and 23S rRNA cleavage in Rhodobacter capsulatus

Kordes¹,

Jock²,

Fritsch³

et al. 1994

J Bacteriol

View full text Add to dashboard Cite

In Rhodobacter capsulatus wild-type strains, the 23S rRNA is cleaved into [16S] and [14S] rRNA molecules.Our data show that a region predicted to form a hairpin-loop structure is removed from the 23S rRNA during this processing step. We have analyzed the processing of rRNA in the wild type and in the mutant strain Fm65, which does not cleave the 23S rRNA. In addition to the lack of 23S rRNA processing, strain Fm65 shows impeded processing of a larger 5.6-kb rRNA precursor and slow maturation of 23S and 16S rRNAs from pre-23S and pre-16S rRNA species. Similar effects have also been described previously for Escherichia coli RNase III mutants. Processing of the 5.6-kb precursor was independent of protein synthesis, while the cleavage of 23S rRNA to generate 16S and 14S rRNA required protein synthesis. We identified a DNA fragment of the wild-type R. capsulatus chromosome that conferred normal processing of 5.6-kb rRNA and 23S rRNA when it was expressed in strain Fm65.The bacterial 50S ribosomal subunit is generally composed of a 23S and a 5S rRNA molecule and ribosomal proteins. However, some bacterial species have ribosomes that do not contain an intact 23S rRNA species. In vivo fragmentation of 23S rRNA has been reported for some cyanobacteria (10), for Agrobacterium tumefaciens (38), for Bdellovibrio bacteriovorus (34), for Salmonella species (5, 43), and for the closely related bacteria Rhodobacter sphaeroides (33), Rhodobacter capsulatus (28), and Paracoccus denitrificans (29). The biological significance of 23S rRNA fragmentation is not understood.Bacterial rRNA operons are transcribed into large precursor molecules often including tRNA sequences (23). These rRNA precursors are subsequently processed into the 23S, 16S, and 5S rRNA species. In Escherichia coli, two endoribonucleases that are involved in the processing of rRNA have been identified: RNase III and RNase E. RNase III cleaves doublestranded RNA regions with little sequence specificity (36,37) and is responsible for the generation of 23S and 16S rRNA precursor molecules from the larger 30S precursor (4, 44). RNase III is also responsible for the excision of intervening sequences from the rRNA of Salmonella species, resulting in fragmentation of the 23S rRNA (5). The enzymes involved in the final maturation of 16S and 23S rRNA from pre-16S and pre-23S rRNA have not been characterized; however, these reactions are most likely catalyzed by exoribonucleases (23,39). 5S rRNA is generated by cleavage of a 9S rRNA precursor that is catalyzed by the endoribonuclease RNase E (35). From comparison of different RNase E cleavage sites, the consensus sequence RAUUW (R = A or G; W = A or U) (14) has been postulated. RNase E cleaves single-stranded RNA regions with the maximal rate, when the cleavage site is preceded or followed by an mRNA hairpin-loop structure (14) (20), which is present in four copies on a single chromosome (15). The organization of the R. sphaeroides rrn operons is identical to the organization found in E. coli, with two tRNA genes in the 16...

show abstract

Section: Resultsmentioning

confidence: 84%

Cloning of a gene involved in rRNA precursor processing and 23S rRNA cleavage in Rhodobacter capsulatus

Kordes¹,

Jock²,

Fritsch³

et al. 1994

J Bacteriol

View full text Add to dashboard Cite

show abstract

“…Some of these transcripts show different patterns of expression, and the authors of that study suggested the presence of promoters internal to the operon. In the A. variabilis coxBAC operon, however, a sequence, 5Ј-AGAGATGACCA A-3Ј, strongly similar to RNase III cleavage sites (17) and located in a strand of the stem of a putative mRNA stem-loop structure, is detected in the region between the coxB and coxA open reading frames. The length from the coxB tsp to the possible cutting site is approximately 1,250 to 1,285 nucleotides.…”

Section: Discussionmentioning

confidence: 99%

The coxBAC Operon Encodes a Cytochrome c Oxidase Required for Heterotrophic Growth in the Cyanobacterium Anabaena variabilis Strain ATCC 29413

et al. 2001

View full text Add to dashboard Cite

Three genes, coxB, coxA, and coxC, found in a clone from a gene library of the cyanobacterium Anabaena variabilis strain ATCC 29413, were identified by hybridization with an oligonucleotide specific for aa 3 -type cytochrome c oxidases. Deletion of these genes from the genome of A. variabilis strain ATCC 29413 FD yielded strain CSW1, which displayed no chemoheterotrophic growth and an impaired cytochrome c oxidase activity. Photoautotrophic growth of CSW1, however, was unchanged, even with dinitrogen as the nitrogen source. A higher cytochrome c oxidase activity was detected in membrane preparations from dinitrogen-grown CSW1 than from nitrate-grown CSW1, but comparable activities of respiratory oxygen uptake were found in the wild type and in CSW1. Our data indicate that the identified cox gene cluster is essential for fructose-dependent growth in the dark, but not for growth on dinitrogen, and that other terminal respiratory oxidases are expressed in this cyanobacterium. Transcription analysis showed that coxBAC constitutes an operon which is expressed from two transcriptional start points. The use of one of them was stimulated by fructose.

show abstract

“…In two cases involving RNase III cleavage sites (41,49), GU pairs gave a strong mutant phenotype and so were thought to be disruptive of a structure which was stabilized by a GC pair at the same position. Since the sequence specificity of RNase III is relaxed (8,32), it is argued that these effects are due only to weakened pairing.…”

Section: Discussionmentioning

confidence: 99%

Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium

1997

View full text Add to dashboard Cite

The RpoS transcription factor (also called S or 38 ) is required for the expression of a number of stationary-phase and osmotically inducible genes in enteric bacteria. RpoS is also a virulence factor for several pathogenic species, including Salmonella typhimurium. The activity of RpoS is regulated in response to many different signals, at the levels of both synthesis and proteolysis. Previous work with rpoS-lac protein fusions has suggested that translation of rpoS requires hfq function. The product of the hfq gene, host factor I (HF-I), is a ribosome-associated, site-specific RNA-binding protein originally characterized for its role in replication of the RNA bacteriophage Q␤ of Escherichia coli. In this study, the role of HF-I was explored by isolating suppressor mutations that map to the region directly upstream of rpoS. These mutations increase rpoS-lac expression in the absence of HF-I and also confer substantial independence from HF-I. DNA sequence analysis of the mutants suggests a model in which the RNA secondary structure near the ribosome binding site of the rpoS mRNA plays an important role in limiting expression in the wild type. Genetic tests of the model confirm its predictions, at least in part. It seems likely that the mutations analyzed here activate a suppression pathway that bypasses the normal HF-I-dependent route of rpoS expression; however, it is also possible that some of them identify a sequence element with an inhibitory function that is directly counteracted by HF-I.The rpoS gene encodes a specificity factor for RNA polymerase (44, 46, 59) which is required for the transcription of many genes expressed during the onset of stationary phase. RpoS-dependent adaptations to nutrient limitation and starvation identified so far in Escherichia coli include not only shifts in metabolic pathways but also resistance mechanisms protective against life-threatening stresses such as high osmolarity, heat shock, elevated H 2 O 2 , and UV light (reviewed in references 26 and 37). RpoS is also a virulence factor for Salmonella typhimurium (16) and other enteric bacteria. The regulation of this regulatory protein is itself complex: RpoS abundance can be increased by a variety of inducing treatments (37). Control of RpoS can occur both at the level of synthesis and by proteolysis (27,34,65); in this respect it is reminiscent of heat shock sigma factor (RpoH) regulation (66). It has also been demonstrated that RpoS abundance is positively regulated by ppGpp (23), and this may provide a unifying mechanism for the multitude of RpoS inducers. An hns mutant, lacking the abundant DNA-binding protein H-NS, has an increased level of RpoS in exponential phase, and this effect is remarkable because it occurs through increases in both translation and protein stability (2, 65). Genetic evidence suggests that RpoS is degraded by the energy-dependent ClpXP protease (52) with the help of other factors (42,48,58).The E. coli hfq gene product, host factor I (HF-I), was discovered through its role in the in vitro replicati...

show abstract

The cleavage specificity of RNase III

Cited by 66 publications

References 33 publications

Cloning of a gene involved in rRNA precursor processing and 23S rRNA cleavage in Rhodobacter capsulatus

Cloning of a gene involved in rRNA precursor processing and 23S rRNA cleavage in Rhodobacter capsulatus

The coxBAC Operon Encodes a Cytochrome c Oxidase Required for Heterotrophic Growth in the Cyanobacterium Anabaena variabilis Strain ATCC 29413

Mutations that increase expression of the rpoS gene and decrease its dependence on hfq function in Salmonella typhimurium

Contact Info

Product

Resources

About