Sequence diversity of intervening sequences (IVSs) in the 23S ribosomal RNA in Salmonella spp

Nucleic acid-based biotechnologies for food-borne pathogen detection using routine time-intensive culture-based methods and fast molecular diagnostics

Diseases caused by food-borne pathogens constitute a major burden to consumers, food business operators, and national governments. Bacterial and viral pathogens are the major biotic factors influencing food safety. A vast array of culture dependent analytical methods and protocols have been developed. Recently, nucleic acid-based methods have begun to replace or complement culture-based methods for routine use in food control laboratories. Basic advantages provided by nucleic acid-based technologies are faster speed and more information, such as sub-species identification, antibiotic resistance, and food microbiology. In particular, PCR and alternative methods have been developed to a stage that provides good speed, sensitivity, specificity, and reproducibility with minimized risk of carryover contamination. This review briefly summarizes currently available and developing molecular technologies that may be candidates for involvement in microbiological molecular diagnostic methods in the next decade.

Delineation of two Helicobacter bilis genomospecies: implications for systematics and evolution

The evolution and taxonomy of Helicobacter bilis strains isolated in Italy and Finland were studied by phylogenetic analysis of different genes, comparative analysis of small rRNA gene intervening sequence (IVS), amplified fragment length polymorphism analysis and DNA-DNA hybridization. The results of this study divided the H. bilis strains into two distinct and divergent genomic groups. In the absence of a specific phenotype or pathotype to distinguish these groups, however, they may be referred to as two genomospecies: H. bilis sensu stricto and Helicobacter sp. FL56. The phylogenetic network of gyrB and ureB gene sequences, as well as the comparative analysis of small rRNA gene IVS, suggests independent evolution of the two genomospecies. In particular, Helicobacter sp. FL56 seems to be the result of adaptation of an ancestral H. bilis strain in a new host. The phenomenon of adaptation to different hosts, or different intestinal niches in the same host, associated with high mutation and recombination rates could explain the evolution and the complex taxonomy of the genus Helicobacter. A comprehensive phylogenomics study of this genus would be useful to properly investigate this hypothesis.

Extremely acidophilic protists from acid mine drainage host Rickettsiales-lineage endosymbionts that have intervening sequences in their 16S rRNA genes

During a molecular phylogenetic survey of extremely acidic (pH < 1), metal-rich acid mine drainage habitats in the Richmond Mine at Iron Mountain, Calif., we detected 16S rRNA gene sequences of a novel bacterial group belonging to the order Rickettsiales in the Alphaproteobacteria. The closest known relatives of this group (92% 16S rRNA gene sequence identity) are endosymbionts of the protist Acanthamoeba. Oligonucleotide 16S rRNA probes were designed and used to observe members of this group within acidophilic protists. To improve visualization of eukaryotic populations in the acid mine drainage samples, broad-specificity probes for eukaryotes were redesigned and combined to highlight this component of the acid mine drainage community. Approximately 4% of protists in the acid mine drainage samples contained endosymbionts. Measurements of internal pH of the protists showed that their cytosol is close to neutral, indicating that the endosymbionts may be neutrophilic. The endosymbionts had a conserved 273-nucleotide intervening sequence (IVS) in variable region V1 of their 16S rRNA genes. The IVS does not match any sequence in current databases, but the predicted secondary structure forms well-defined stem loops. IVSs are uncommon in rRNA genes and appear to be confined to bacteria living in close association with eukaryotes. Based on the phylogenetic novelty of the endosymbiont sequences and initial culture-independent characterization, we propose the name "Candidatus Captivus acidiprotistae." To our knowledge, this is the first report of an endosymbiotic relationship in an extremely acidic habitat.

Atypical processing in domain III of 23S rRNA of Rhizobium leguminosarum ATCC 10004(T) at a position homologous to an rRNA fragmentation site in protozoa

For still unknown reasons, the 23S rRNA of many alpha-Proteobacteria shows a unique fragmentation pattern compared to other bacteria. The 23S rRNA processing involves RNase III and additional, yet unidentified enzymes. The alpha-proteobacterium Rhizobium leguminosarum ATCC 10004(T) possesses two fragmentation sites in its 23S rRNA. The first one harbors an intervening sequence in helix 9 which is cleaved by RNase III. We demonstrate that the mature 5' end of the resulting 2.6-kb rRNA fragment is generated by additional removal of helix 10. A fraction of the 2.6-kb rRNA is further processed in domain III, giving rise to two 1.3-kb rRNA fragments. We mapped the domain III fragmentation site and found it to be at a position which has only been reported for trypanosomatid protozoa. This fragmentation site is also unique in that it lacks an intervening sequence. We found that the simultaneous occurrence of 2.6-kb and 1.3-kb rRNA fragments is not due to interoperonal sequence differences but rather reflects slow processing. The different characteristics of the two fragmentation sites in the 23S rRNA suggest that they are processed by different mechanisms. Interestingly, the amount of 2.6-kb rRNA varies during culture growth. We observed a transient increase in the relative amount of 2.6-kb rRNA fragments during the first hours after inoculation, which points to changes in the ratio of rRNA synthesis rate to domain III processing rate during the growth of a culture.

Commonly conserved genetic fragments revealed by genome profiling can serve as tracers of evolution

We developed a method to produce, identify and analyze DNA fragments for the purpose of taxonomic classification. Genome profiling (GP) is a strategy that identifies genomic DNA fragments common to closely related species without prior knowledge of the DNA sequence. Random PCR, one of the key technologies of GP, is used to produce fragments and may be used even when there are mutations at the priming site. These fragments can then be distinguished based on the information of mobility and melting pattern when subjected to temperature gradient gel electrophoresis (TGGE). Corresponding fragments among several species, designated as commonly conserved genetic fragments (CCGFs), likely have the same genetic origin or correspond to the same gene. The criteria for identification of CCGFs has been defined and presented here. To assess this prediction, some of the fragments were sequenced and were confirmed to be CCGFs. We show that genome profiles bearing evolutionarily conserved CCGFs can be used to classify organisms and trace evolutionary pathways, among other profound applications.

Intervening sequences in rrl genes and fragmentation of 23S rRNA in genera of the family Enterobacteriaceae

Intervening sequences (IVSs) in the rrl genes for 23S rRNA are transcribed but later removed by RNase III without religation during RNA processing, leading to fragmented rRNA. We examined about 240 strains of the family Enterobacteriaceae for presence of IVSs using PCR. No IVSs were detected in strains belonging to Escherichia, Shigella, Enterobacter, Erwinia, Ewingella, Hafnia, Kluyvera, Morganella, Pantoea, or Serratia. Previously unreported IVSs were detected in Klebsiella oxytoca, Citrobacter amalonaticus, and Providencia stuartii; previously reported IVSs are in species of Salmonella, Proteus, Providencia, and Yersinia. The sporadic distribution of IVSs indicates lateral genetic transfer of IVSs.