Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli.

The complete nucleotide sequence of the 16S RNA gene from the rrnB cistron of Escherichia coli has been determined by using three rapid DNA sequencing methods. Nearly all of the structure has been confirmed by two to six independent sequence determinations on both DNA strands. The length of the 16S rRNA chain inferred from the DNA sequence is 1541 nucleotides, in close agreement with previous estimates. We note discrepancies between this sequence and the most recent version of it reported from direct RNA sequencing [Ehresmann, C., Stiegler, P., Carbon, P. & Ebel, J.P. (1977) FEBS Lett. 84, 337-341]. A few of these may be explained by heterogeneity among 16S rRNA sequences from different cistrons. No nucleotide sequences were found in the 16S rRNA gene that cannot be reconciled with RNase digestion products of mature 16S rRNA.     

Classification of methanogenic bacteria by 16S ribosomal RNA characterization

The 16S ribosomal RNAs from 10 species of methanogenic bacteria have been characterized in terms of the oligonucleotides produced by T₁ RNase digestion. Comparative analysis of these data reveals the methanogens to constitute a distinct phylogenetic group containing two major divisions. These organisms appear to be only distantly related to typical bacteria.     

An intron within the 16S ribosomal RNA gene of the archaeon Pyrobaculum aerophilum.

The 16S rRNA genes of Pyrobaculum aerophilum and Pyrobaculum islandicum were amplified by the polymerase chain reaction, and the resulting products were sequenced directly. The two organisms are closely related by this measure (over 98% similar). However, they differ in that the (lone) 16S rRNA gene of Pyrobaculum aerophilum contains a 713-bp intron not seen in the corresponding gene of Pyrobaculum islandicum. To our knowledge, this is the only intron so far reported in the small subunit rRNA gene of a prokaryote. Upon excision the intron is circularized. A secondary structure model of the intron-containing rRNA suggests a splicing mechanism of the same type as that invoked for the tRNA introns of the Archaea and Eucarya and 23S rRNAs of the Archaea. The intron contains an open reading frame whose protein translation shows no certain homology with any known protein sequence.     

Mutational robustness of 16S ribosomal RNA, shown by experimental horizontal gene transfer in Escherichia coli

The bacterial ribosome consists of three rRNA molecules and 57 proteins and plays a crucial role in translating mRNA-encoded information into proteins. Because of the ribosome’s structural and mechanistic complexity, it is believed that each ribosomal component coevolves to maintain its function. Unlike 5S rRNA, 16S and 23S rRNAs appear to lack mutational robustness, because they form the structural core of the ribosome. However, using Escherichia coli Δ7 (null mutant of operons) as a host, we have recently shown that an active hybrid ribosome whose 16S rRNA has been specifically substituted with that from non–E. coli bacteria can be reconstituted in vivo. To investigate the mutational robustness of 16S rRNA and the structural basis for its functionality, we used a metagenomic approach to screen for 16S rRNA genes that complement the growth of E. coli Δ7. Various functional genes were obtained from the Gammaproteobacteria and Betaproteobacteria lineages. Despite the large sequence diversity (80.9–99.0% identity with E. coli 16S rRNA) of the functional 16S rRNA molecules, the doubling times (DTs) of each mutant increased only modestly with decreasing sequence identity (average increase in DT, 4.6 s per mutation). The three-dimensional structure of the 30S ribosome showed that at least 40.7% (628/1,542) of the nucleotides were variable, even at ribosomal protein-binding sites, provided that the secondary structures were properly conserved. Our results clearly demonstrate that 16S rRNA functionality largely depends on the secondary structure but not on the sequence itself.     

Molecular analysis of cloned human 18S ribosomal DNA segments.

A fraction of DNA from the human fetal lung fibroblast line IMR-90, 30-fold enriched for ribosomal DNA, was cloned in the lambda phage vector Charon 16A. Of 978 clones assayed by hybridization to a mixture of 125I-labeled 18S and 28S ribosomal RNA, 11 recombinants containing a 3.8-megadalton segment of human 18S ribosomal DNA were identified. Restriction endonuclease analysis of these clones demonstrated variation only in orientation of the human gene segment within the phage vector. Restriction sites that we had previously detected from analysis of restriction products of unfractionated human DNA by using the Southern transfer method were also present in the cloned DNA segment. Recombinant DNA technology thus provides a valid and efficient means to define structural conservation or variation within families of human genes.     

Mutant 16S ribosomal RNA: a codon-specific translational suppressor.

We have isolated an unusual codon-specific translational suppressor in Escherichia coli. The suppressor resulted from a spontaneous mutation in a chromosomal gene during a selection for suppressors of the auxotrophic nonsense mutation trpA(UGA211). The suppressor allows readthrough of UGA mutations at two positions in trpA and at two sites in bacteriophage T4. It does not, however, suppress amber (UAG) or ochre (UAA) mutations that were tested in both genomes, some of which were at the same positions as the suppressible UGA mutations. The suppressor also does not allow mistranslation of the UGA-related trpA missense mutations UGG at positions 211 and 234, AGA at 211 and 234, CGA at 211, or UGU and UGC at 234. The suppressor mutation was mapped by genetic procedures to position 89 on the E. coli genetic map. Localization of the suppressor mutation to rrnB was achieved by cloning it in the low-copy-number plasmid pEJM007 by in vivo recombination from the chromosome. Recloning in bacteriophage M13 and subsequent DNA sequence analysis allowed the identification of the suppressor mutation as a deletion of the cytidylic acid residue at nucleotide position 1054 of the 16S ribosomal RNA. The mutant EcoRI-Xba I fragment from the suppressor gene was recloned, from M13, in an otherwise wild-type rrnB in the plasmid pEJM007, and UGA suppression was examined. The UGA-suppressing activity of the reconstructed suppressor-containing pEJM007 was indistinguishable from that of the original recombinant suppressor-containing plasmid. This result demonstrates that the C1054 deletion in 16S rRNA is both necessary and sufficient for UGA suppression. The existence of this mutant suggests an important role for rRNA in codon recognition, at least for accurate polypeptide chain termination.     

Variation among human 28S ribosomal RNA genes.

We report the complete 5025-base sequence of the human 28S rRNA gene. Variability within the species has been demonstrated by sequencing a variable region from six separately cloned genes. This region is one of three large subunit rRNA regions that show extreme sequence and size variation among species. The interspecies differences suggest species-specific functions for these sections, while the intraspecies heterogeneity indicates differences among ribosomes. Comparison of the human gene with a partial sequence from the chimpanzee 28S gene yields divergence rates for the two species: 0.8% for conserved regions of the gene and 3.7% for a variable region. The rapid divergence rates of variable regions in the ribosomal gene may permit answers to the question of time of separation of closely related species.     

Involvement of bases 787-795 of Escherichia coli 16S ribosomal RNA in ribosomal subunit association.

A nine-base DNA oligomer [d(GTATCTAAT)] was used to probe the accessibility and function of bases in the region 787-795 of Escherichia coli 16S rRNA. Hybridization of the cDNA [d(GTATCTAAT)] to 16S rRNA in situ was carried out by binding the probe to intact 30S ribosomal subunits. Nitrocellulose filter binding showed that cDNA hybridization saturated with increasing probe concentration, suggesting that the probe was binding to a discrete site or sites. RNase H digestion of the rRNA under the DNA . rRNA hybrid and sequencing of the resultant RNA fragments verified that the cDNA probe bound specifically to the 787-795 region. Hybridization experiments using the cDNA probe showed that bases in the 787-795 region of 16S rRNA are exposed on the surface of 30S subunits. The functional role of bases 787-795 was then tested by assaying various ribosomal activities with the cDNA in place. Results of these functional assays demonstrate that this 16S rRNA region is directly involved in the association of 30S and 50S subunits.     

In vitro methylation of Escherichia coli 16S ribosomal RNA and 30S ribosomes.

Treatment of synthetic 30S particles lacking all of the normally methylated nucleotides with S-adenosyl-[3H]methionine and either an S100 or ribosomal high salt wash extract resulted in ribosome-dependent incorporation of [3H]methyl groups into trichloroacetic acid-insoluble material. No incorporation was observed when naturally methylated isolated 30S particles were used, showing that methylation at unnatural sites did not occur. Enzymatic hydrolysis of the labeled RNA to nucleosides followed by HPLC analysis identified the [3H]methylated residues. Activities for the formation of N6-methyladenosine, N6-dimethyladenosine, 5-methylcytidine (m5C), 3-methyluridine, and N2-methylguanosine were found. Fractionation by ammonium sulfate partially resolved the different activities. All of the fractions with m5C activity were 6-8 times more active on synthetic unmethylated 16S RNA than on synthetic 30S ribosomes, whereas the N2-methylguanosine activity preferred 30S ribosomes to 16S RNA by a factor of more than 10. The N6-methyladenosine and N6-dimethyladenosine activities were 30S ribosome-specific. The m5C activity present in the 55-85% ammonium sulfate fraction of the high salt wash yielded a maximum of 1.0 mol of m5C per mol of 16S RNA, although two m5C residues, positions 967 and 1407, are found in vivo. RNase protection by hybridization with the appropriate oligodeoxynucleotide identified the methylated residue as C-967. Methylation of m5C-967 did not require prior methylation of G-966, and methylation of A-1518 and A-1519 was not dependent on prior methylation of G-1516.     

Presence of Bacterial 16S Ribosomal RNA Gene Segments in Human Intestinal Lymph Follicles

Background: There is currently no information regarding microbial agents inside the intestinal lymph follicles. Methods: Biopsy or resected specimens, mostly from macroscopically normal areas, were sectioned with a cryostat. DNA was extracted from microdissected samples, exclusively from the lymph follicle. Amplification of DNA was performed using universal primers designed from conserved regions of bacterial 16S ribosomal RNA (rRNA). Several clones with inserts of around 400 base pairs were subjected to DNA sequence analysis followed by a database homology search. Results: Bacterial 16S rRNA gene segments were detected in the lymph follicle in 2 of 14 (14%) non-inflammatory bowel disease (IBD) cases, 4 of 14 (28%) Crohn disease cases, and in 2 of 5 (40%) ulcerative colitis cases. Nineteen 16S rRNA gene segments were recognized in the eight positive cases. Five segments showed 100% identity to known bacterial 16S rRNAs, namely staphylococcus species, Streptococcus sanguis, and Paracoccus marcusii. However, the other 14 segments showed below 100% identity, indicating either the presence of unknown bacteria or of bacteria without known DNA data. No single identified or unidentified bacterium, characteristic of IBD, including Mycobacterium paratuberculosis and Listeria monocytogenes, was detected. Conclusions: The present study confirms the presence of bacterial 16S rRNA gene segments in human intestinal lymph follicles and paves the way for new investigations into the microbiology of the lymph follicle. Whether or not bacteria inside the lymph follicle is a primary stimulus in IBD has yet to be clarified.     

Changes in intestinal mucosa above lymph follicles during carcinogenesis in rats

Summary p Changes in the intestinal mucosa during carcinogenesis were investigated in 36 rats after weekly s.c. injection of 20 mg dimethylhydrazine/kg body-weight. More changes were seen in the large than in the small intestine. In the first week, 60% of colonic lymphoid plaques displayed various crypt abscesses and glandular regenerations. These mucosal changes correspond to the glands covering the lymph follicles, in direct contact with lymphoid cells. Beginning in week 8, dysplastic glands developed in these mucosal areas above the lymph follicles. The number of lymphoid plaques with dysplastic glands in the large intestine increased week by week, attaining 75% in week 20. At the end of week 12 the first adenocarcinoma was detected in the cecum by light microscopy, and classified as a poorly differentiated adenocarcinoma with signet ring cells infiltrating the lymph follicles which contained endocrine cells. The majority of adenocarcinomas (10 cases) occurred in week 20. of these, 7 were localized above the lymphatic plaques in the intestine.Endocrine cells were found in varying numbers in 6 of 10 adenocarcinomas. Three endocrine cell carcinomas, corresponding to human adenocarcinoids or goblet cell carcinoids, developed within the intestinal mucosa; all were identified as poorly differentiated intestinal adenocarcinomas, two of them situated above lymph follicles. These suprafollicular tumors developing from the glandular base, were composed of mucoid cells, endocrine cells, and undifferentiated cells. Microcarcinomas are considered as initial stages of endocrine cell carcinoma.The trend of tumor development above colonic lymph follicles, and the histogenesis of endocrine cell carcinomas and de novo carcinomas is discussed.Dedicated to Professor E. Grundmann on the occasion of his 65th birthday, September 28, 1986Supported by A. v. Humboldt-Stiftung and Ministerium für Wissenschaft und Forschung NRW, grant IV B5-FA 9843Fellow of the Alexander-von-Humboldt-Stiftung     

Processing of the 5'' end of Escherichia coli 16S ribosomal RNA.

We have isolated and partially characterized an endonuclease involved in processing the 5' end of 16S rRNA of Escherichia coli. A mutant strain that is deficient in this enzyme accumulates a new precursor of 16S rRNA, named 16.3S rRNA. This rRNA has the 3' end of mature 16S rRNA but is about 60 nucleotides longer at the 5' end. In vitro, the enzyme preparation cleaves an RNA fragment of about 60 nucleotides from the 5' end of 16.3S rRNA in 30S ribosomal subunits, yielding the mature 5' end of 16S rRNA. In the mutant strain the 16.3S rRNA is associated with a full complement of 21 ribosomal proteins in 30S subunits. These particles, which comprise 50% of the total 30S subunits, are present on polyribosomes.     

Influence of 16S ribosomal RNA gene polymerase chain reaction and sequencing on antibiotic management of bone and joint infections

INTRODUCTION:

Amplification of the 16S ribosomal RNA gene by polymerase chain reaction (PCR) followed by analysis of generated sequences can be an important adjunct to conventional cultures.

OBJECTIVE:

To determine how the results of this approach influence physicians’ decisions regarding the management of bone and joint infections.

METHOD:

Clinical and laboratory findings of patients seen at the Queen Elizabeth II Health Sciences Centre (Halifax, Nova Scotia) between December 2005 and September 2009 were reviewed. Patients who had negative cultures but likely or possible bone and joint infections were further evaluated using 16S rRNA PCR. The impact of the 16S rRNA PCR result on antibiotic management was evaluated and it was assessed whether untreated patients with negative 16S rRNA PCR subsequently presented with infections, suggesting a false-negative result.

RESULT:

A total of 36 patients (mean age 62 years) were reviewed. Thirty-two patients were evaluated by infectious disease consultants; of these, 20 were considered likely to have infections. Seventeen patients were admitted with suspected prosthetic joint infections. Twenty-nine patients received antimicrobial treatment before the sample for the 16S rRNA PCR assay was obtained. Of the 36 patients, 26 (72.2%) were treated appropriately with modifications to their antibiotic regimen in response to the 16S rRNA PCR assay results. Antimicrobials were discontinued for 19 patients based on negative PCR assay and, in seven patients, antibiotics were changed based on a positive result. There were no relapses among patients with negative PCR assay in whom antibiotics were discontinued.

CONCLUSION:

16S ribosomal RNA gene PCR and sequencing is a valuable tool in the guidance of antimicrobial therapy for bone and joint infections.     

Evidence for functional interaction between elongation factor Tu and 16S ribosomal RNA.

Translation of the genetic code requires the accurate selection of elongation factor (EF)-Tu.GTP.tRNA ternary complexes at the ribosomal acceptor site, or A site. Several independent lines of evidence have implicated the universally conserved 530 loop of 16S rRNA in this process; yet its precise role has not been identified. Using an allele-specific chemical probing strategy, we have examined the functional defect caused by a dominant lethal G-->A substitution at position 530. We find that mutant ribosomes are impaired in EF-Tu-dependent binding of aminoacyl-tRNA in vitro; in contrast, nonenzymatic binding of tRNA to the A and P sites is unaffected, indicating that the defect involves an EF-Tu-related function rather than tRNA-ribosome interactions per se. In vivo, the mutant ribosomes are found in polysomes at low levels and contain reduced amounts of A-site-bound tRNA, but normal levels of P-site tRNA, in agreement with the in vitro results; thus the dominant lethal phenotype of mutations at G530 can be explained by impaired interaction of mutant ribosomes with ternary complex. These results provide evidence for a newly defined function of 16S rRNA--namely, modulation of EF-Tu activity during translation.     

Electron microscopic determination of the binding sites of ribosomal proteins S4 and S8 on 16S RNA.

Specific complexes.early in the assembly of Escherichia coli ribosomes were examined in the electron microscope. Complexes between ribosomal protein S4 or S8 and 16S RNA were fixed gently with formaldehyde and then denatured for protein-free spreading. Binding of each protein was found to preserve an easily recognized configuration in the RNA that allows the sites of protein binding to be determined. S8--16S RNA complexes have a single hairpin loop near the middle of the 16S RNA, 798 +/- 21 bases from one end and 657 +/- 26 bases from the other. S4-16S RNA complexes have two adjacent loops at one end with 250--450 bases. This structure probably arises from the simultaneous binding of S4 to three noncontiguous sites on the RNA. Measurements of these complexes place the binding sites near the 5' end, at more than one site 250--585 nucleotides from the 5' end and 645 +/- 45 bases from the 3' end. The latter site has not been recognized previously as a distinct S4 binding site. This approach allows the binding sites to be determined without knowledge of the nucleotide sequence and gives insight into the configuration of the rRNA in the assembling ribisome.     

Complete DNA sequence analysis for 16S ribosomal RNA gene of the leproma-derived, cultivable and nerve-invading mycobacterium HI-75.

The complete 1493 nucleotide sequence of the 16SrRNA gene of the leproma-derived and cultivable mycobacterium HI-75 strain was analyzed to elucidate the taxonomic characteristics by direct sequencing of the polymerase chain reaction (PCR) products. The results revealed that the sequence of mycobacterium HI-75 was mostly similar to that of Mycobacterium scrofulaceum with 5 bases differences in the sequenced 1493 bases (0.35%) of the 16SrRNA gene. M. leprae differed from the strain with 47 bases (3.3%). Sasaki and Hamit reported the nerve-invasive activity of the inoculated mycobacterium HI-75 in nude mice or the 131I-treated immunocompromised Swiss mice. The results indicate that mycobacterium HI-75 could be a mutant of M. scrofulaceum possessing the ability to invade the peripheral nerve in addition to developing leproma-like lesions.