Copy number of the 16S rRNA gene in Rickettsia prowazekii

Microfluidic digital PCR enables multigene analysis of individual environmental bacteria

Gene inventory and metagenomic techniques have allowed rapid exploration of bacterial diversity and the potential physiologies present within microbial communities. However, it remains nontrivial to discover the identities of environmental bacteria carrying two or more genes of interest. We have used microfluidic digital polymerase chain reaction (PCR) to amplify and analyze multiple, different genes obtained from single bacterial cells harvested from nature. A gene encoding a key enzyme involved in the mutualistic symbiosis occurring between termites and their gut microbiota was used as an experimental hook to discover the previously unknown ribosomal RNA-based species identity of several symbionts. The ability to systematically identify bacteria carrying a particular gene and to link any two or more genes of interest to single species residing in complex ecosystems opens up new opportunities for research on the environment.

Study of the five Rickettsia prowazekii proteins annotated as ATP/ADP translocases (Tlc): Only Tlc1 transports ATP/ADP, while Tlc4 and Tlc5 transport other ribonucleotides

The obligate intracytoplasmic pathogen Rickettsia prowazekii relies on the transport of many essential compounds from the cytoplasm of the eukaryotic host cell in lieu of de novo synthesis, an evolutionary outcome undoubtedly linked to obligatory growth in this metabolite-replete niche. The paradigm for the study of rickettsial transport systems is the ATP/ADP translocase Tlc1, which exchanges bacterial ADP for host cell ATP as a source of energy, rather than as a source of adenylate. Interestingly, the R. prowazekii genome encodes four open reading frames that are highly homologous to the well-characterized ATP/ADP translocase Tlc1. Therefore, by annotation, the R. prowazekii genome encodes a total of five ATP/ADP translocases: Tlc1, Tlc2, Tlc3, Tlc4, and Tlc5. We have confirmed by quantitative reverse transcriptase PCR that mRNAs corresponding to all five tlc homologues are expressed in R. prowazekii growing in L-929 cells and have shown their heterologous protein expression in Escherichia coli, suggesting that none of the tlc genes are pseudogenes in the process of evolutionary meltdown. However, we demonstrate by heterologous expression in E. coli that only Tlc1 functions as an ATP/ADP transporter. A survey of nucleotides and nucleosides has determined that Tlc4 transports CTP, UTP, and GDP. Intriguingly, although GTP was not transported by Tlc4, it was an inhibitor of CTP and UTP uptake and demonstrated a K(i) similar to that of GDP. In addition, we demonstrate that Tlc5 transports GTP and GDP. We postulate that Tlc4 and Tlc5 serve the primary function of maintaining intracellular pools of nucleotides for rickettsial nucleic acid biosynthesis and do not provide the cell with nucleoside triphosphates as an energy source, as is the case for Tlc1. Although heterologous expression of Tlc2 and Tlc3 was observed in E. coli, we were unable to identify substrates for these proteins.

Wolbachia endosymbionts in fleas (Siphonaptera)

Intracellular endosymbionts, Wolbachia spp., have been reported in many different orders of insects and in nematodes but not previously in fleas. This is the first conclusive report of Wolbachia spp. within members of the Siphonaptera. Using nested polymerase chain reaction (PCR) targeting of the 16S ribosomal RNA gene, we screened for Wolbachia spp. in fleas collected from 3 counties in Georgia and 1 in New York. The prevalence of Wolbachia spp. detected varied among the 6 different species screened: 21% in the cat flea Ctenocephalides felis (n = 604), 7% in the dog flea C. canis (n = 28), 25% in Polygenus gwyni (n = 8), 80% in Orchopeas howardi (n = 15), 94% in Pulex simulans (n = 255), and 24% in the sticktight flea Echidnophaga gallinacea (n = 101). Wolbachia spp. infection in fleas was confirmed by sequencing positive PCR products, comparing sequenced 16S ribosomal DNA (rDNA) with Wolbachia spp. sequences in GenBank using BLAST search, and subjecting sequence data to phylogenetic analysis. For further confirmation, 16S rDNA-positive samples were reamplified using the wsp gene.

The highest priority: what microbial genomes are telling us about immunity

Study of microbial genomes has provided new insight into the functions that pathogens require for survival in the animal host. Small genome bacterial pathogens, defined as those < or = 1/3 the size of Escherichia coli, include chlamydiae, rickettsiae and ehrlichiae, mycoplasmas, and spirochetes. The small genome size is believed to result from reductive evolution, a process of initial mutation with loss of function followed by progressive accumulation of mutations and eventual gene deletion. This is most notable in the 1.1 Mb genome of Rickettsia prowazekki in which 24% of the genome is non-coding, as compared to approximately 10% in the 4.4 Mb E. coli. Consequently, these pathogens are thus presumed to retain only the most important functions for survival and propagation. There is consistent evidence from small genomes that the genetic deletion is primarily related to the loss of metabolic function and especially reduction of multiple overlapping pathways and duplicated genes. Thus, these pathogens undergo progressive reduction in their genomes yet maintain the ability to infect, survive within, and cause disease in animals. In the face of this reductive process, what genes and associated functions are maintained? Strikingly, these pathogens devote a high percentage of their genomes to paralogous families of polymorphic surface molecules. This retention suggests that evasion of the immune response is the highest priority of obligate microbial pathogens and provides a strategy for identifying protective antigens for vaccine development to control disease.

Evidence for conserved tRNA genes in the 16S-23S rDNA spacer sequence and two rrn operons of Xylella fastidiosa

The 16S-23S rDNA spacer of the type strain (ATCC 35879) of Xylella fastidiosa was amplified by PCR, cloned, and sequenced. The spacer sequence (455 bp) contains two tRNA (tRNA(ala) and tRNA(ile)) genes. Identical tRNA genes were also found in the 16S-23S spacer sequences of all the 51 strains of X. fastidiosa retrieved from the GenBank database. At this particular locus, the gene order of tRNA(ala)-tRNA(ile) is conserved among all the studied strains of Xylella and Xanthomonas, and different from those of other bacteria. Sequence analysis showed that Xanthomonas is the most closely related genus. Results from restriction endonuclease analysis suggested the presence of two rrn operons in the genome of a Xylella fastidiosa Pierce's disease strain.

Origin and evolution of the mitochondrial proteome

The endosymbiotic theory for the origin of mitochondria requires substantial modification. The three identifiable ancestral sources to the proteome of mitochondria are proteins descended from the ancestral alpha-proteobacteria symbiont, proteins with no homology to bacterial orthologs, and diverse proteins with bacterial affinities not derived from alpha-proteobacteria. Random mutations in the form of deletions large and small seem to have eliminated nonessential genes from the endosymbiont-mitochondrial genome lineages. This process, together with the transfer of genes from the endosymbiont-mitochondrial genome to nuclei, has led to a marked reduction in the size of mitochondrial genomes. All proteins of bacterial descent that are encoded by nuclear genes were probably transferred by the same mechanism, involving the disintegration of mitochondria or bacteria by the intracellular membranous vacuoles of cells to release nucleic acid fragments that transform the nuclear genome. This ongoing process has intermittently introduced bacterial genes to nuclear genomes. The genomes of the last common ancestor of all organisms, in particular of mitochondria, encoded cytochrome oxidase homologues. There are no phylogenetic indications either in the mitochondrial proteome or in the nuclear genomes that the initial or subsequent function of the ancestor to the mitochondria was anaerobic. In contrast, there are indications that relatively advanced eukaryotes adapted to anaerobiosis by dismantling their mitochondria and refitting them as hydrogenosomes. Accordingly, a continuous history of aerobic respiration seems to have been the fate of most mitochondrial lineages. The initial phases of this history may have involved aerobic respiration by the symbiont functioning as a scavenger of toxic oxygen. The transition to mitochondria capable of active ATP export to the host cell seems to have required recruitment of eukaryotic ATP transport proteins from the nucleus. The identity of the ancestral host of the alpha-proteobacterial endosymbiont is unclear, but there is no indication that it was an autotroph. There are no indications of a specific alpha-proteobacterial origin to genes for glycolysis. In the absence of data to the contrary, it is assumed that the ancestral host cell was a heterotroph.

Prevalence of Ehrlichia chaffeensis (Rickettsiales: Rickettsiaceae) in Amblyomma americanum (Acari: Ixodidae) from the Georgia coast and Barrier Islands

Human monocytic ehrlichiosis is an emerging zoonosis caused by infection with Ehrlichia chaffeensis Anderson, Dawson, Jones & Wilson, which is transmitted to mammals by ixodid ticks. Prevalence of infected ticks and distribution of infection foci indicate relative risk of human exposure to ehrlichiosis and may be influenced by factors such as geographic isolation, human disturbance, and the availability of suitable mammalian reservoir hosts. To test, this, individual and pooled lone star ticks, Amblyomma americanum (L.), were collected from three populations from the Georgia coast (1 mainland site and two barrier islands) and screened for E. chaffeensis. A species-specific, nested polymerase chain reaction (PCR) assay was used to amplify a 572 bp fragment of the E. chaffeensis 16S rRNA gene from infected ticks. PCR product specificity was confirmed by nucleotide sequencing. Our results showed the prevalence of infected ticks to be 0.0% (n = 151), 0.9% (n = 111), and 9.3% (n = 129) for Sapelo Island, St. Catherine's Island, and Fort McAllister, respectively.

Acquisition and transmission of the agent of human granulocytic ehrlichiosis by Ixodes scapularis ticks

The purpose of the present study was to investigate the transmission of a human isolate of the agent of human granulocytic ehrlichiosis (HGE agent) from infected mice to larval ticks and to examine the population kinetics of the HGE agent in different stages of the tick life cycle. The HGE agent was quantitated by competitive PCR with blood from infected mice and with Ixodes scapularis ticks. The median infectious dose for C3H mice was 10(4) to 10(5) organisms when blood from an infected severe combined immunodeficient mouse was used as an inoculum. Uninfected larval ticks began to acquire infection from infected mice within 24 h of attachment, and the number of HGE agent organisms increased in larval ticks during feeding and after detachment of replete ticks. Molted nymphal ticks, infected as larvae, transmitted infection to mice between 40 and 48 h of attachment. Onset of feeding stimulated replication of the HGE agent within nymphal ticks. These studies suggest that replication of the HGE agent during and after feeding in larvae and during feeding in nymphs is a means by which the HGE agent overcomes inefficiencies in acquisition of infection by ticks and in tick-borne transmission to mammalian hosts.

Genomic rearrangements during evolution of the obligate intracellular parasite Rickettsia prowazekii as inferred from an analysis of 52015 bp nucleotide sequence

In this study a description is given of the sequence and analysis of 52 kb from the 1.1 Mb genome of Rickettsia prowazekii, a member of the alpha-Proteobacteria. An investigation was made of nucleotide frequencies and amino acid composition patterns of 41 coding sequences, distributed in 10 genomic contigs, of which 32 were found to have putative homologues in the public databases. Overall, the coding content of the individual contigs ranged from 59 to 97%, with a mean of 81%. The genes putatively identified included genes involved in the biosynthesis of nucleotides, macromolecules and cell wall structures as well as citric acid cycle component genes. In addition, a putative identification was made of a member of the regulatory response family of two-component signal transduction systems as well as a gene encoding haemolysin. For one gene, the homologue of metK, an internal stop codon was discovered within a region that is otherwise highly conserved. Comparisons with the genomic structures of Escherichia coli, Haemophilus influenzae and Bacillus subtilis have revealed several atypical gene organization patterns in the R. prowazekii genome. For example, R. prowazekii was found to have a unique arrangement of genes upstream of dnaA in a region that is highly conserved among other microbial genomes and thought to represent the origin of replication of a primordial replicon. The results presented in this paper support the hypothesis that the R. prowazekii genome is a highly derived genome and provide examples of gene order structures that are unique for the Rickettsia.

Sequence and copy number of the Xanthomonas campestris pv. campestris gene encoding 16S rRNA

A 6.7-kb Sau3A1 fragment containing ribosomal RNA genes was cloned from the chromosome of Xanthomonas campestris pv. campestris strain 17 by a PCR-based strategy. Nucleotide sequence was determined for the 16S rRNA gene (1,544 nt). This gene has a G+C content of 54.9% which is similar to the 16S rRNA genes of Escherichia coli and Pseudomonas aeruginosa but different from the value reported for the whole X. campestris chromosome (64%). Sequence alignment revealed that AGGAGG is consensus for ribosome binding, with the internal GGAG to be paired most frequently with the anti-Shine-Dalgarno sequence. This consensus sequence was found in the regions upstream from the initiation codon of 98 Xanthomonas genes among 116 aligned, but not in the remaining genes. This suggests that about 16% of the Xanthomonas genes do not possess typical ribosome binding sites and another mechanism may be required for recognition of correct translation initiation sites. Two rrn operons were detected in Xc17 chromosome by pulsed-field gel electrophoresis and Southern hybridization.

Synthesis of functional eukaryotic ribosomal RNAs in trans: development of a novel in vivo rDNA system for dissecting ribosome biogenesis

Active 18S and 25S ribosomal RNAs were produced in trans in yeast, from plasmids containing RNA polymerase II transcription signals and rDNA fragments with unique hybridization tags. Analyses were carried out in cells with temperature-sensitive RNA polymerase I. Functional rRNAs were derived from separate 18S and 5.8/25S rRNA coding units, however, active 25S rRNA could be produced only by cotranscription with 5.8S rRNA. The results demonstrate that the polycistronic organization of the large rDNA operon is not required for successful processing of rRNA or assembly of functional ribosomes. The split operon system should facilitate future efforts to dissect eukaryotic ribosome biogenesis.

A chimeric disposition of the elongation factor genes in Rickettsia prowazekii

An exceptional disposition of the elongation factor genes is observed in Rickettsia prowazekii, in which there is only one tuf gene, which is distant from the lone fus gene. In contrast, the closely related bacterium Agrobacterium tumefaciens has the normal bacterial arrangement of two tuf genes, of which one is tightly linked to the fus gene. Analysis of the flanking sequences of the single tuf gene in R. prowazekii shows that it is preceded by two of the four tRNA genes located in the 5' region of the Escherichia coli tufB gene and that it is followed by rpsJ as well as associated ribosomal protein genes, which in E. coli are located downstream of the tufA gene. The fus gene is located within the str operon and is followed by one tRNA gene as well as by the genes secE and nusG, which are located in the 3' region of tufB in E. coli. This atypical disposition of genes suggests that intrachromosomal recombination between duplicated tuf genes has contributed to the evolution of the unique genomic architecture of R. prowazekii.

Codon usage and base composition in Rickettsia prowazekii

Codon usage and base composition in sequences from the A + T-rich genome of Rickettsia prowazekii, a member of the alpha Proteobacteria, have been investigated. Synonymous codon usage patterns are roughly similar among genes, even though the data set includes genes expected to be expressed at very different levels, indicating that translational selection has been ineffective in this species. However, multivariate statistical analysis differentiates genes according to their G + C contents at the first two codon positions. To study this variation, we have compared the amino acid composition patterns of 21 R. prowazekii proteins with that of a homologous set of proteins from Escherichia coli. The analysis shows that individual genes have been affected by biased mutation rates to very different extents: genes encoding proteins highly conserved among other species being the least affected. Overall, protein coding and intergenic spacer regions have G + C content values of 32.5% and 21.4%, respectively. Extrapolation from these values suggests that R. prowazekii has around 800 genes and that 60-70% of the genome may be coding.

Transcriptional analysis of the 16s rRNA gene in Rickettsia prowazekii

The control of rRNA synthesis in the etiological agent of epidemic typhus, Rickettsia prowazekii, a slowly growing obligate intracytoplasmic bacterium, was investigated. Transcription of the rickettsial 16S rRNA gene (rrs), of which there is only a single copy, was controlled by a single promoter region, and the site for the initiation of transcription (base A) was found 117 bp upstream of the rrs coding region for the mature product. The promoter region contained an Escherichia coli promoter-like sequence, TTGACA-N17-TATAAC, centered 139 bp upstream of the coding region for the mature product. To investigate whether transcription of the rickettsial rrs responds to amino acid starvation conditions, total RNA was isolated from R. prowazekii-infected mouse L929 cells with or without methionine starvation. The level of newly synthesized 16S rRNA precursors in R. prowazekii, as analyzed by ribonuclease protection assays, decreased significantly after methionine starvation for 6 h and then recovered within 12 h after the addition of methionine. The chemical half-lives of the 16S rRNA precursors in the methionine-starved rickettsiae did not differ significantly from those in the normal rickettsiae. These results suggest that R. prowazekii regulates transcription of the rrs in response to amino acid starvation conditions.

Genomic evolution drives the evolution of the translation system

Our thesis is that the characteristics of the translational machinery and its organization are selected in part by evolutionary pressure on genomic traits have nothing to do with translation per se. These genomic traits include size, composition, and architecture. To illustrate this point, we draw parallels between the structure of different genomes that have adapted to intracellular niches independently of each other. Our starting point is the general observation that the evolutionary history of organellar and parasitic bacteria have favored bantam genomes. Furthermore, we suggest that the constraints of the reductive mode of genomic evolution account for the divergence of the genetic code in mitochondria and the genetic organization of the translational system observed in parasitic bacteria. In particular, we associate codon reassignments in animal mitochondria with greatly simplified tRNA populations. Likewise, we relate the organization of translational genes in the obligate intracellular parasite Rickettsia prowazekii to the processes supporting the reductive mode of genomic evolution. Such findings provide strong support for the hypothesis that genomes of organelles and of parasitic bacteria have arisen from the much larger genomes of ancestral bacteria that have been reduced by intrachromosomal recombination and deletion events. A consequence of the reductive mode of genomic evolution is that the resulting translation systems may deviate markedly from conventional systems.

A single rRNA gene region in Bradyrhizobium japonicum

Bradyrhizobium japonicum contains only a single rRNA (rrn) gene region, despite its comparatively large genome size of 8,700 kb. The nucleotide sequence revealed an organization of rRNA and tRNA genes that is frequently found in bacteria: 5'-rrs (16S rRNA)-ileT (tRNA(Ile))-alaT (tRNA(Ala))-rrl (23S rRNA)-rrf (5S rRNA)-3'. The 5' end of the primary transcript, one of the 16S rRNA processing sites, and the 5' end of the mature 16S rRNA were determined by primer extension. DNA hybridization experiments showed that the slowly growing Bradyrhizobium strains generally have only a single copy of the 16S rRNA gene, whereas the faster-growing Rhizobium species contain three rrs copies.

Characterization of a putative 23S-5S rRNA operon of Buchnera aphidicola (endosymbiont of aphids) unlinked to the 16S rRNA-encoding gene

Buchnera aphidicola (Ba) is an endosymbiont of the aphid Schizaphis graminum. In order to obtain information on highly expressed genes, we have chosen to study Ba genes coding for rRNAs. Previously, the single-copy rrs gene was cloned and sequenced [Munson et al., Gene 137 (1993) 171-178], and found to constitute a single transcription unit unlinked to rrl and rrf. In the present study, a 6.1-kb Ba DNA fragment containing rrl was cloned into Escherichia coli (Ec) and sequenced. Based on sequence similarity to Ec, the following genes were identified: aroE-tRNA(Glu)-rrl-rrf-cysS. AroE and CysS had 48 and 54% amino acid (aa) identity, respectively, to the corresponding Ec proteins; tRNA(Glu), rrl and rrf had 80-90% nucleotide (nt) identity with the corresponding genes of Ec rrnB. Ba tRNA(Glu)-rrl-rrs appears to be part of a single transcriptional unit; a putative promoter and a Rho-independent terminator were identified. Comparisons of sequences of aroE-rrl from endosymbionts of seven additional species of aphids indicated conservation of the -35 (TTGACT) and -10 (TGTAA/TT) promoter regions, and boxA, tRNA(Glu) and boxC. Secondary structure analysis indicated that the Ba tRNA(Glu)-rrl-rrf operon resembled the homologous region of Ec rrnB. The results of this and previous studies indicate that Ba differs from most bacteria in having the single-copy rRNA genes organized into two transcription units.

Molecular analysis of the endosymbionts of tsetse flies: 16S rDNA locus and over-expression of a chaperonin

Based on 16S rDNA sequence comparison, intracellular mycetome-associated endosymbionts (P-endosymbionts) of tsetse flies (Diptera: Glossinidae) form a distinct lineage within the gamma-3 subdivision of proteobacteria, related to the free-living bacterium Escherichia coli, midgut S-endosymbionts of various insects including tsetse flies, and to the P-endosymbiont lineage of aphids, Buchnera aphidicola. Gene organization and expression of several loci in intracellular microorganisms have revealed differences from free-living bacteria. This study analyses two of these characteristics in tsetse endosymbionts; the copy number and gene organization of rDNA operations and the nature of the abundant protein(s) synthesized by these microorganisms. Results indicate that Glossina morsitans morsitans S-endosymbionts have multiple (seven) rDNA operons coding for 16S (rrs) followed by 23S (rrl) gene sequences, whereas tsetse P-endosymbionts have a single, similarly organized rDNA operon. In tsetse mycetocytes in vitro, P-endosymbionts synthesize a predominant protein of 60 kDa in size (p60) which by Western blot analysis shows immunological cross-reactivity with the abundant 63 kDa (p63) protein of B. aphidicola. p63 (also referred to as symbionin) has been characterized as a molecular chaperone, structurally and functionally similar to the groEL protein of E. coli. Under in vitro conditions, tsetse S-endosymbionts synthesize high levels of a similarly-sized protein that cross-reacts with p63 chaperonin. Antisera against the tsetse p60 protein also recognizes p63 protein of B. aphidicola, suggesting that the abundant tsetse endosymbiont protein is a chaperonin.

Detection of Buchnera, the primary prokaryotic endosymbiont of aphids, using the polymerase chain reaction

Members of the genus Buchnera constitute a distinct prokaryotic lineage containing the primary endosymbionts of aphids (Homoptera: Aphidoidea). Using synthetic oligonucleotides in conjunction with the polymerase chain reaction, we propose three approaches for the identification of members of this genus. The first is based on unique sequences within rrs (gene coding for 16S ribosomal RNA). The second is based on a different and unique organization of the ribosomal RNA operons of Buchnera and the close proximity of aroE upstream of rrl (gene coding for 23S rRNA). The third is based on the linkage relationship of argS which is upstream of rrs. Validation of these three approaches requires their more extensive application.

Identification of tlc and gltA mRNAs and determination of in situ RNA half-life in Rickettsia prowazekii

RNAs of Rickettsia prowazekii, an obligate intracytoplasmic bacterium, have been identified and analyzed by an RNase protection assay. Total RNA, a mixture of host cell RNA and rickettsial RNA, was isolated from rickettsia-infected mouse L929 cells by the hot-phenol method. After hybridization with specific antisense RNA probes and digestion with RNase, the protected products were analyzed by electrophoresis and autoradiography. The results show that there is only one mRNA species for the ATP/ADP translocase gene (tlc) but two mRNA species for the citrate synthase gene (gltA). RNA half-lives were determined by measuring the RNA remaining after addition of rifampin. The half-lives of tlc mRNA, gltA mRNA I, and gltA mRNA II in R. prowazekii are 8.4 +/- 0.6, 12.3 +/- 1.3, and 20.5 +/- 1.8 min, respectively. However, the half-lives of tlc mRNA and gltA mRNA I in recombinant Escherichia coli strains are 2.9 +/- 0.1 and 1.4 +/- 0.1 min, respectively. The 16S rRNA in R. prowazekii was also examined and shown to be stable.