Protein interaction mapping on a functional shotgun sequence of Rickettsia sibirica

Protein interaction maps can reveal novel pathways and functional complexes, allowing 'guilt by association' annotation of uncharacterized proteins. To address the need for large-scale protein interaction analyses, a bacterial two-hybrid system was coupled with a whole genome shotgun sequencing approach for microbial genome analysis. We report the first large-scale proteomics study using this system, integrating de novo genome sequencing with functional interaction mapping and annotation in a high-throughput format. We apply the approach by shotgun sequencing and annotating the genome of Rickettsia sibirica strain 246, an obligate intracellular human pathogen among the Spotted Fever Group rickettsiae. The bacteria invade endothelial cells and cause lysis after large amounts of progeny have accumulated. Little is known about specific Rickettsial virulence factors and their mode of pathogenicity. Analysis of the combined genomic sequence and protein-protein interaction data for a set of virulence related Type IV secretion system (T4SS) proteins revealed over 250 interactions and will provide insight into the mechanism of Rickettsial pathogenicity.

Nuclear genes that encode mitochondrial proteins for DNA and RNA metabolism are clustered in the Arabidopsis genome

The plant mitochondrial genome is complex in structure, owing to a high degree of recombination activity that subdivides the genome and increases genetic variation. The replication activity of various portions of the mitochondrial genome appears to be nonuniform, providing the plant with an ability to modulate its mitochondrial genotype during development. These and other interesting features of the plant mitochondrial genome suggest that adaptive changes have occurred in DNA maintenance and transmission that will provide insight into unique aspects of plant mitochondrial biology and mitochondrial-chloroplast coevolution. A search in the Arabidopsis genome for genes involved in the regulation of mitochondrial DNA metabolism revealed a region of chromosome III that is unusually rich in genes for mitochondrial DNA and RNA maintenance. An apparently similar genetic linkage was observed in the rice genome. Several of the genes identified within the chromosome III interval appear to target the plastid or to be targeted dually to the mitochondria and the plastid, suggesting that the process of endosymbiosis likely is accompanied by an intimate coevolution of these two organelles for their genome maintenance functions.

Rickettsia-like mitochondrial motility in Drosophila spermiogenesis

Although it is generally accepted that mitochondria and chloroplasts are descended in evolution from bacteria, the potential contributions of their endosymbiont ancestors to specialized cellular pathways in development remain largely unexplored. Here we show that a motile behavior of mitochondria in Drosophila spermiogenesis is strikingly similar to the actin-based "comet tail" motility of several bacteria. A combination of electron and fluorescence microscopy demonstrates major reorganization and movement of mitochondria ahead of, and in close association with, dense conical arrays of actin filaments in the sperm individualization complex, which mediates the resolution of male germline syncytia into separate gametes. Because of several other parallels between the movement of the individualization complex and the motility behavior of some rickettsiae, the bacterial family from which mitochondria are most likely descended, this motility phenomenon is a strong candidate for a true vestige of endosymbiont behavior in contemporary mitochondria. The potential conservation of an ancient endosymbiont motility mechanism within a highly conserved feature of gametogenesis, the resolution of germline syncytia, may indicate a formative role for the endosymbiotic ancestor of mitochondria in the evolution of this developmental pathway.

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ

BACKGROUND

Shuffling and disruption of operons and horizontal gene transfer are major contributions to the new, dynamic view of prokaryotic evolution. Under the 'selfish operon' hypothesis, operons are viewed as mobile genetic entities that are constantly disseminated via horizontal gene transfer, although their retention could be favored by the advantage of coregulation of functionally linked genes. Here we apply comparative genomics and phylogenetic analysis to examine horizontal transfer of entire operons versus displacement of individual genes within operons by horizontally acquired orthologs and independent assembly of the same or similar operons from genes with different phylogenetic affinities.

RESULTS

Since a substantial number of operons have been identified experimentally in only a few model bacteria, evolutionarily conserved gene strings were analyzed as surrogates of operons. The phylogenetic affinities within these predicted operons were assessed first by sequence similarity analysis and then by phylogenetic analysis, including statistical tests of tree topology. Numerous cases of apparent horizontal transfer of entire operons were detected. However, it was shown that apparent horizontal transfer of individual genes or arrays of genes within operons is not uncommon either and results in xenologous gene displacement in situ, that is, displacement of an ancestral gene by a horizontally transferred ortholog from a taxonomically distant organism without change of the local gene organization. On rarer occasions, operons might have evolved via independent assembly, in part from horizontally acquired genes.

CONCLUSIONS

The discovery of in situ gene displacement shows that combination of rampant horizontal gene transfer with selection for preservation of operon structure provides for events in prokaryotic evolution that, a priori, seem improbable. These findings also emphasize that not all aspects of operon evolution are selfish, with operon integrity maintained by purifying selection at the organism level.

Reduction of bacterial genome size and expansion resulting from obligate intracellular lifestyle and adaptation to soil habitat

Prokaryotic organisms are exposed in the course of evolution to various impacts, resulting often in drastic changes of their genome size. Depending on circumstances, the same lineage may diverge into species having substantially reduced genomes, or such whose genomes have undergone considerable enlargement. Genome reduction is a consequence of obligate intracellular lifestyle rendering numerous genes expendable. Another consequence of intracellular lifestyle is reduction of effective population size and limited possibility of gene acquirement via lateral transfer. This causes a state of relaxed selection resulting in accumulation of mildly deleterious mutations that can not be corrected by recombination with the wild type copy. Thus, gene loss is usually irreversible. Additionally, constant environment of the eukaryotic cell renders that some bacterial genes involved in DNA repair are expandable. The loss of these genes is a probable cause of mutational bias resulting in a high A+T content. While causes of genome reduction are rather indisputable, those resulting in genome expansion seem to be less obvious. Presumably, the genome enlargement is an indirect consequence of adaptation to changing environmental conditions and requires the acquisition and integration of numerous genes. It seems that the need for a great number of capabilities is common among soil bacteria irrespective of their phylogenetic relationship. However, this would not be possible if soil bacteria lacked indigenous abilities to exchange and accumulate genetic information. The latter are considerably facilitated when housekeeping genes are physically separated from adaptive loci which are useful only in certain circumstances.

Mechanisms of immunity against rickettsiae. New perspectives and opportunities offered by unusual intracellular parasites

Investigation of the biology, pathology and immunology of rickettsial diseases offers new insights useful not only for the field of rickettsiology, but more importantly for the understanding of general principles of host-intracellular parasite relationships and, in particular, the immune interaction between endothelial cells and immune cells in the context of infection.

Intracellular movements of Rickettsia conorii and R. typhi based on actin polymerization

Human vascular endothelial, Vero and human embryonic lung cells infected with rickettsiae for 24 h or 48 h were labelled for polymerized actin with NBD-phallacidin. Between 20 and 68% of the intracellular Rickettsia conorii had an actin tail of between 0.33 and 15 microns, with the longest tails being observed in Vero cells. In the case of R. typhi less than 1% of the organisms had actin tails and these were considerably shorter than those of R. conorii. These findings provide new information concerning the different cytopathic effects observed with the two rickettsial species.

Rickettsia japonica sp. nov., the etiological agent of spotted fever group rickettsiosis in Japan

We propose the name Rickettsia japonica sp. nov. (with type strain YH [= ATCC VR-1363]) for a serologically specific species of spotted fever group rickettsiae that are pathogenic for humans (J. Infect. Dis. 159:1122-1126, 1989; J. Clin. Microbiol. 28:1177-1180, 1990). The biologic and genomic characteristics of the organism (G+C content, 31.2 +/- 0.7 mol%) are essentially the same as those of other pathogenic spotted fever group rickettsiae, although the R. japonica isolates cause a persistent infection in Vero cells for many subcultures.

Energy metabolism of monocytic Ehrlichia

We investigated if the monocytic Ehrlichia are totally dependent on their host cells for energy, or, as Rickettsia, are capable of some ATP synthesis in vitro. The Miyayama strain of Ehrlichia sennetsu and the Maryland and Illinois strains of Ehrlichia risticii were cultivated in a mouse macrophage cell line, separated from host cell constituents by procedures that included Renografin or Percoll gradient centrifugation, and tested after cryopreservation. Cells incubated without a metabolizing substrate contained little, if any, ATP. When the Ehrlichia cells were incubated for 1 hr at 34 degrees C with glutamine, significant amounts of ATP were detected. The amounts of ATP attained with glutamine were decreased in some instances by the addition of atractyloside, an inhibitor of adenine nucleotide translocase in mitochondria, and were decreased consistently and to a greater extent by 2,4-dinitrophenol. When ATP, instead of glutamine, was added to the ehrlichiae, upon incubation the amount of ATP was markedly decreased. Comparable responses under all these conditions were obtained with Rickettsia typhi, although the final ATP levels were higher. Control preparations derived from uninfected mouse macrophages or from the discards of the Ehrlichia purification procedures contained negligible amounts of ATP, which were not increased by incubation with glutamine. We conclude that with respect to ATP metabolism, the monocytic Ehrlichia resemble Rickettsia more closely than Chlamydia, even though Ehrlichia resemble Chlamydia in their intracellular location in the phagosomes and in possibly having a developmental cycle.

Metabolism and genetics of chlamydias and rickettsias

Chlamydial and rickettsial diseases pose a hazard to man and to domesticated and wild animals. The virulence mechanisms which aid the establishment of these obligate intracellular parasites in the eukaryotic host are still not within our grasp. Recent knowledge of the biochemical stratagem, the metabolic capabilities and the genetic diversity of these microbes illustrate fundamental differences in ecology and evolutionary divergence. The preferred site of intracellular residence determines the strategy for uptake, for nutrient assimilation and also for evasion of the host's immunological defenses. The Chlamydia, Rickettsia, and Coxiella are the most extensively studied of the genera. Whereas the Ehrlichia and Cowdria are poorly understood, they are also the most intriguing of the Rickettsiae. A number of antigenically and genetically distinct species are identified for the genera Chlamydia, Rickettsia, and Ehrlichia, whereas the Coxiella and Cowdria may not represent such a wide diversity. Recent information on the genetic heterogeneity of the chromosomal and plasmid DNAs of the strains of Coxiella suggest the diversity is greater than was originally envisioned. New information regarding the antigenic structure of Cowdria and their cellular tropisms suggests that they are closely related to the Ehrlichia. In this review we compare the metabolic capabilities and the genetic diversity of these different intracellular bacteria.

Biochemistry of rickettsiae: recent advances

The application of new biotechnology to the study of the biochemistry of rickettsiae was a prominent feature of the presentations at the 3rd International Symposium on Rickettsiae and Rickettsial Diseases, held in Smolenice near Bratislava in September 1984. This review is an attempt to summarize recent advances leading up to these presentations as well as the studies that have been reported in the two years since the meeting. Since rickettsiae are intracellular parasites, most reviews deal with the interaction of rickettsiae with host cells. It is useful, however, to focus also--as we have done--on the properties of rickettsiae that can be demonstrated in the absence of their hosts, although, undoubtedly, many of these properties reflect adaptation to an intracellular microenvironment.

[Biochemical and genetical study of Rickettsia]

The review deals with the phenomenology in the studies on characteristics of surface antigenic and immunogenic structures of Rickettsia, their cellular membranes, the processes of metabolic cooperation and interaction with the host cells, and the structure of Rickettsia genome. The data on active antigenic and immunogenic proteins distribution in inner and outer membranes and on osmotically active functioning cellular membrane, including the specific substrate carriers, are discussed. The materials, are presented on the specific ADP-ATP transport system, slightly different from the mitochondrial one, in evidence that Rickettsia utilize ATP in two pathways: endogenous and exogenous. The metabolic regulatory processes, controlled by adenine nucleotides are discussed that could be used as a means of fitting to constantly changing conditions of Rickettsia ecological niche. The Rickettsia deficiency in AMP catabolism enzyme could be used for allosteric-regulation of citrate synthase, the key enzyme in the Krebs cycle. The data on the mol mass of Rickettsia DNA (1 x 10(9)) and the characteristics of plasmids are presented. In conclusion new data on molecular cloning of Rickettsia genes in vector plasmids and the restriction analysis of specific DNA sequences are discussed.

Ornithine metabolism in the genus Rochalimaea

Ornithine metabolism was studied in two strains of the trench fever rickettsia Rochalimaea quintana, Fuller and Guadalupe, and in the vole agent, a strain of Rochalimaea but not necessarily of Rochalimaea quintana. The metabolic activity of intact cells and cell-free extracts was measured by monitoring the evolution of 14CO2 from [1-14C]ornithine. Low levels of activity were obtained with all three strains, but requirements for the demonstration of this activity differed. With the cells of the Fuller and Guadalupe strains, the decarboxylation of ornithine was almost completely dependent on added pyruvate or succinate, presumably as sources of energy for transport. This enhancement was not prevented by the presence of chloramphenicol. The activity of the vole agent, on the other hand, required the complete medium. This activity was prevented by chloramphenicol added at the same time as the medium but not by chloramphenicol added after 1 h of incubation. In cell-free extracts, the demonstration of ornithine decarboxylase activity in the vole agent required prior induction with medium containing ornithine, whereas in the other two strains, the activity was constitutive. The activities of the extracts of the Fuller strain and the vole agent differed also in pH optimum, which was somewhat lower for the vole agent, and in the added pyridoxal phosphate requirement, which was greater for the Fuller strain. Comparable experiments with Rickettsia typhi and Rickettsia prowazekii failed to reveal evidence of ornithine metabolism.

Rickettsial permeability. An ADP-ATP transport system

The obligate intracellular parasitic bacterium, Rickettsia prowazeki, has a carrier-mediated transport system for ADP and ATP. The transport of nucleotides was measured by membrane filtration assays; the assay was shown not to harm the relatively labile rickettsiae. The nucleotide transport system was shown to reside in the rickettsiae, not in the contaminating yolk sac mitochondria of the preparation. The influx of nucleotide had an activation energy of 12 to 13 kcal above 22 deg-rees (an apparent transition temperature), and 30 kcal below this value. The uptake of nucleotide was independent of the Mg2+ concentration, but was markedly stimulated by the phosphate concentration. The pH optimum of the influx of nucleotide was pH 7. The specificity of the transport system was remarkable in that it required a specific moiety in each portion of the nucleotide, i.e. an adenine base, a ribose sugar, and two or three, but not one, phosphates. Of the wide variety of compounds tested, the system could transport only ADP, ATP, and (beta, gamma-methylene) adenosine 5'-triphosphate. The influx of nucleotide was a saturable process; half-maximum velocity was achieved at a nucleotide concentration of about 75 muM. ADP and ATP were competitive inhibitors of each other's transport. Although at least 95% of the labeled intracellular nucleotide was exchangeable, efflux of labeled nucleotide was observed only in the presence of unlabeled nucleotide in the medium. Half-maximum efflux was achieved at a concentration of about 75 muM. A large intracellular to extracellular concentration gradient of labeled nucleotide was maintained in the presence of metabolic inhibitors and uncouplers, which completely abolished rickettsial hemolysis. While having no effect on the steady state, KCN and DNP accelerated both influx and efflux. Measurements of the endogenous pool of adenine nucleotides in isolated rickettsiae show that is was large (5 mM), and that these unlabeled nucleotides exchanged, on approximately a 1/1 basis, with exogenously added nucleotide. These studies support the proposal that rickettsiae are not "leaky" to adenine nucleotides or to small molecules in general, and that they have a carrier-mediated transport system which allows an exchange of host and parasite ADP and ATP.

Growth and physiology of rickettsiae

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Rickettsiae and rickettsial diseases

This paper summarizes present knowledge on rickettsiae and rickettsial diseases, and on their epidemiological characteristics, control, and public health significance. There are many natural foci of rickettsial diseases, from where the disease may spread to other areas in the world under changing socioeconomic conditions. Because of rapid long-distance travel, sporadic cases of serious rickettsial diseases may today appear far from endemic areas where the infection occurred. Even in endemic areas the disease may be misdiagnosed and deaths may occur as a result of inadequate treatment. Rapid treatment of rickettsial infections (preferably with tetracyclines) is therefore most important. Epidemic louse-borne typhus, though no longer subject to the International Health Regulations, remains one of the diseases in the WHO epidemiological surveillance programme. This disease continues to be a major cause of morbidity and mortality in some parts of Africa and it is present also in parts of the Americas and of Asia. Scrub typhus remains a continuing and serious public health problem in areas of South-East Asia and in the Western Pacific. The annual number of reported cases of Rocky Mountain spotted fever in the USA showed an increase during the last two decades, which may be due to improved recognition as well as to increased outdoor activities and migration of people from the city centres to the suburbs. Related forms of tick-borne typhus occur in South America, the Mediterranean region, Africa, South-East Asia, the Far East, and the Western Pacific. Increasing in number, though still sporadic, are reports of serious illness from chronic Q fever infection in many parts of the world.

Metabolism of Rickettsia typhi and Rickettsia akari in irradiated L cells

L cells that had been exposed to 3,000 r of (60)Co the previous day were used to study the growth and metabolism of Rickettsia typhi and R. akari. Viable (unirradiated) L cells were used to study the effect of rickettsial infection on host-cell metabolism. Monolayers were infected with a rickettsial multiplicity of 1.2 and given Eagle's minimal essential medium containing 25 mmN-2-hydroxyethylpiperazine-N'-2'-ethanesulfonic acid buffer and 10% calf serum. At various intervals, cycloheximide (2 mug/ml) was added to one set of cultures, to inhibit eukaryotic protein and deoxyribonucleic acid (DNA) metabolism; phosphate-buffered saline (PBS) was added to another set. After 1 hr, the cultures received a mixture of 15 (14)C-labeled amino acids or adenine-8-(14)C. The cultures were harvested 16 hr later and were tested for incorporation of labeled carbon into the fraction precipitated by cold trichloroacetic acid. Viable cells were exposed to thymidine-2-(14)C for 2-hr periods. Infectivity of R. typhi increased to a peak of 150 to 400 hemolytic units/culture on day 4; the titer remained approximately the same on days 5 and 6, and declined rapidly on day 7. Total amino acid incorporation was about the same in infected and uninfected cultures up to day 6, but metabolic activity was reduced to a negligible level on day 7 in infected cells. Cycloheximide-resistant activity was higher in the infected cultures, with a peak equivalent to one-half the total activity at day 4 to 5. Total as well as cycloheximide-resistant adenine incorporation was higher in the infected cells between days 3 and 5 after infection, with a peak at day 3 to 4. Somewhat similar results were obtained with R. akari, except that the cycle of infection and of cycloheximide-resistant activity proceeded and was completed more rapidly. (14)C-DNA of both rickettsiae was isolated from infected cultures that had received labeled adenine. With labeled thymidine, which was not incorporated by the rickettsiae, it was shown that R. typhi and R. akari differ considerably in their effects on the host cell. R. typhi elicited moderate inhibition, whereas R. akari infection led to a complete inhibition of thymidine incorporation by the third day, at the time of highest rickettsial activity. It is concluded that rickettsiae have the necessary enzymes for protein and nucleic acid synthesis, but, thus far, these enzymes have been activated or induced only in an intracellular environment.