Evolution and diversity of Rickettsia bacteria

Background

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant neuromuscular disorder associated with the partial deletion of integral numbers of 3.3 kb D4Z4 DNA repeats within the subtelomere of chromosome 4q. A number of candidate FSHD genes, adenine nucleotide translocator 1 gene (ANT1), FSHD-related gene 1 (FRG1), FRG2 and DUX4c, upstream of the D4Z4 array (FSHD locus), and double homeobox chromosome 4 (DUX4) within the repeat itself, are upregulated in some patients, thus suggesting an underlying perturbation of the chromatin structure. Furthermore, a mouse model overexpressing FRG1 has been generated, displaying skeletal muscle defects.

Results

In the context of myogenic differentiation, we compared the chromatin structure and tridimensional interaction of the D4Z4 array and FRG1 gene promoter, and FRG1 expression, in control and FSHD cells. The FRG1 gene was prematurely expressed during FSHD myoblast differentiation, thus suggesting that the number of D4Z4 repeats in the array may affect the correct timing of FRG1 expression. Using chromosome conformation capture (3C) technology, we revealed that the FRG1 promoter and D4Z4 array physically interacted. Furthermore, this chromatin structure underwent dynamic changes during myogenic differentiation that led to the loosening of the FRG1/4q-D4Z4 array loop in myotubes. The FRG1 promoter in both normal and FSHD myoblasts was characterized by H3K27 trimethylation and Polycomb repressor complex binding, but these repression signs were replaced by H3K4 trimethylation during differentiation. The D4Z4 sequences behaved similarly, with H3K27 trimethylation and Polycomb binding being lost upon myogenic differentiation.

Conclusion

We propose a model in which the D4Z4 array may play a critical chromatin function as an orchestrator of in cis chromatin loops, thus suggesting that this repeat may play a role in coordinating gene expression.     

Complete genome sequence of Rickettsia heilongjiangensis, an emerging tick-transmitted human pathogen

Rickettsia heilongjiangensis is an emerging tick-transmitted human pathogen causing far-Eastern spotted fever. Here we report the complete sequence and the main features of the genome of R. heilongjiangensis (strain 054).     

The emerging genetic diversity of hereditary spastic paraplegia in Korean patients

Hereditary Spastic Paraplegias (HSP) are a group of rare inherited neurological disorders characterized by progressive loss of corticospinal motor-tract function. Numerous patients with HSP remain undiagnosed despite screening for known genetic causes of HSP. Therefore, identification of novel genetic variations related to HSP is needed. In this study, we identified 88 genetic variants in 54 genes from whole-exome data of 82 clinically well-defined Korean HSP families. Fifty-six percent were known HSP genes, and 44% were composed of putative candidate HSP genes involved in the HSPome and originally reported neuron-related genes, not previously diagnosed in HSP patients. Their inheritance modes were 39, de novo; 33, autosomal dominant; and 10, autosomal recessive. Notably, ALDH18A1 showed the second highest frequency. Fourteen known HSP genes were firstly reported in Koreans, with some of their variants being predictive of HSP-causing protein malfunction. SPAST and REEP1 mutants with unknown function induced neurite abnormality. Further, 54 HSP-related genes were closely linked to the HSP progression-related network. Additionally, the genetic spectrum and variation of known HSP genes differed across ethnic groups. These results expand the genetic spectrum for HSP and may contribute to the accurate diagnosis and treatment for rare HSP.     

Deubiquitinating enzymes: their diversity and emerging roles

A growing number of important regulatory proteins within cells are modified by conjugation of ubiquitin, a well-conserved 76-amino-acid polypeptide. The ubiquitinated proteins are targeted to proteasome for degradation or alternative metabolic fates, such as triggering of plasma membrane endocytosis and trafficking to vacuoles or lysosomes. Deubiquitination, reversal of this modification, is being recognized as an important regulatory step. Deubiquitinating enzymes are cysteine proteases that specifically cleave off ubiquitin from ubiquitin-conjugated protein substrates as well as from its precursor proteins. Genome sequencing projects have identified more than 90 deubiquitinating enzymes, making them the largest family of enzymes in the ubiquitin system. This review will concentrate on recent important findings as well as new insights into the diversity and emerging roles of deubiquitinating enzymes in the ubiquitin-dependent pathway.     

Ecosystem dynamics, biological diversity and emerging infectious diseases

In this article, we summarize the major scientific developments of the last decade on the transmission of infectious agents in multi-host systems. Almost sixty percent of the pathogens that have emerged in humans during the last 30-40 years are of animal origin and about sixty percent of them show an important variety of host species besides humans (3 or more possible host species). In this review, we focus on zoonotic infections with vector-borne transmission and dissect the contrasting effects that a multiplicity of host reservoirs and vectors can have on their disease dynamics. We discuss the effects exerted by host and vector species richness and composition on pathogen prevalence (i.e., reduction, including the dilution effect, or amplification). We emphasize that, in multiple host systems and for vector-borne zoonotic pathogens, host reservoir species and vector species can exert contrasting effect locally. The outcome on disease dynamics (reduced pathogen prevalence in vectors when the host reservoir species is rich and increased pathogen prevalence when the vector species richness increases) may be highly heterogeneous in both space and time. We then ask briefly how a shift towards a more systemic perspective in the study of emerging infectious diseases, which are driven by a multiplicity of hosts, may stimulate further research developments. Finally, we propose some research avenues that take better into account the multi-host species reality in the transmission of the most important emerging infectious diseases, and, particularly, suggest, as a possible orientation, the careful assessment of the life-history characteristics of hosts and vectors in a community ecology-based perspective.     

The library of Rickettsia prowazekii genes

The DNA of Rickettsia provazekii strain E was cleaved by PstI restriction endonuclease under the conditions of partial restriction. The fragments were inserted into the PstI site of pBR325 and cloned in this plasmid. E. coli strain HB101 was used as a recipient for cloning. 880 clones sensitive to ampicillin and resistant to tetracycline were selected from 5120 transformants. The cloning of rickettsial DNA has been confirmed by the blot hybridization technique. Analysis of individual and net probes of the hybrid DNA by gel electrophoresis makes it possible to conclude that 90% of the selected clones harbour hybrid plasmids, the size of the cloned fragments rangers from 0.9 to 10.4 Kb, the obtained library of clones contains 70% of the whole genome of Rickettsia provazekii.     

Within-host genetic diversity of endemic and emerging parvoviruses of dogs and cats

Viral emergence can result from the adaptation of endemic pathogens to new or altered host environments, a process that is strongly influenced by the underlying sequence diversity. To determine the extent and structure of intrahost genetic diversity in a recently emerged single-stranded DNA virus, we analyzed viral population structures during natural infections of animals with canine parvovirus (CPV) or its ancestor, feline panleukopenia virus (FPV). We compared infections that occurred shortly after CPV emerged with more recent infections and examined the population structure of CPV after experimental cross-species transmission to cats. Infections with CPV and FPV showed limited genetic diversity regardless of the analyzed host tissue or year of isolation. Coinfections with genetically distinct viral strains were detected in some cases, and rearranged genomes were seen in both FPV and CPV. The sporadic presence of some sequences with multiple mutations suggested the occurrence of either particularly error-prone viral replication or coinfection by more distantly related strains. Finally, some potentially organ-specific host effects were seen during experimental cross-species transmission, with many of the mutations located in the nonstructural protein NS2. These included residues with evidence of positive selection at the population level, which is compatible with a role of this protein in host adaptation.     

Genomic comparison of Rickettsia helvetica and other Rickettsia species

We report the complete and annotated genome sequence of Rickettsia helvetica strain C9P9, which was first isolated in 1979 from Ixodes ricinus ticks in Switzerland and is considered a human pathogen.     

Partitioning the net effect of host diversity on an emerging amphibian pathogen

The ‘dilution effect’ (DE) hypothesis predicts that diverse host communities will show reduced disease. The underlying causes of pathogen dilution are complex, because they involve non-additive (driven by host interactions and differential habitat use) and additive (controlled by host species composition) mechanisms. Here, we used measures of complementarity and selection traditionally employed in the field of biodiversity–ecosystem function (BEF) to quantify the net effect of host diversity on disease dynamics of the amphibian-killing fungus Batrachochytrium dendrobatidis (Bd). Complementarity occurs when average infection load in diverse host assemblages departs from that of each component species in uniform populations. Selection measures the disproportionate impact of a particular species in diverse assemblages compared with its performance in uniform populations, and therefore has strong additive and non-additive properties. We experimentally infected tropical amphibian species of varying life histories, in single- and multi-host treatments, and measured individual Bd infection loads. Host diversity reduced Bd infection in amphibians through a mechanism analogous to complementarity (sensu BEF), potentially by reducing shared habitat use and transmission among hosts. Additionally, the selection component indicated that one particular terrestrial species showed reduced infection loads in diverse assemblages at the expense of neighbouring aquatic hosts becoming heavily infected. By partitioning components of diversity, our findings underscore the importance of additive and non-additive mechanisms underlying the DE.     

Ultrastructure of the Surface of Rickettsia prowazeki and Rickettsia akari

Negative-contrast electron microscopy revealed that the outer layer of the envelope of rickettsiae is composed of a matrix of tetragonally arranged subunits. The layer projects approximately 7 nm from the cell wall. It is suggested that this outer layer is analogous to the structure considered capsule-like in morphology.     

Metabolic Activity of the Trench Fever Rickettsia, Rickettsia quintana

A study of the metabolic activity of Rickettsia quintana was carried out by conventional Warburg and radioisotope techniques with intact cells harvested while growing in the fluid counterpart of the medium of Vinson and Fuller. Like other rickettsiae, R. quintana did not utilize glucose, but did metabolize glutamate and glutamine. Unlike typhus rickettsiae, R. quintana did not require a diluent high in K⁺ for metabolic activity, and it utilized glutamine more efficiently than glutamate. In typical experiments, this microorganism produced 1.6 to 2.0 μmoles of CO₂ from glutamine per mg of rickettsial protein per hr at 37 C, while consuming 1.5 to 1.7 μmoles of O₂. R. quintana also utilized, in descending order, succinate, α-ketoglutarate, glutamate, pyruvate, and citrate; the first-named substrate was utilized more rapidly than glutamine. R. quintana, like typhus rickettsiae, has a glutamate-oxaloacetate transaminase because aspartate was isolated, by means of thin-layer chromatography, as one of the end products of the utilization of glutamine. When the microorganisms were incubated with glutamine-¹⁴C and unlabeled intermediates of the citric acid cycle, labeled dicarboxylic acids of the cycle were recovered. Labeled tricarboxylic acids, however, were not recovered, possibly because of cellular impermeability to the corresponding unlabeled intermediates. In the case of cis-aconitate, it was shown that this substrate interfered with the uptake of glutamine. These observations are believed to provide convincing evidence that glutamine is utilized through the citric acid cycle and that R. quintana, with the differences noted, resembles other rickettsiae.     

Development of the mouse retina: emerging morphological diversity of the ganglion cells

The time course and regulatory mechanisms of dendritic development are subjects of intense interest. We approached these problems by investigating dendritic morphology of retinal ganglion cells (RGCs) at four early postnatal stages. The RGCs develop from a diffusely stratified and poorly differentiated group at birth (P0), to 16 distinct, morphologically well-defined subtypes before eye opening (P13). Even before bipolar cells make synaptic contacts with the RGCs (P8), most adultlike RGC subtypes are already present. Similar to previous studies in other mammalian species, our results indicate that the initiation of the RGC morphological maturation is independent of light stimulation and of formation of glutamatergic synapses. This study narrowed down the window of RGCs morphological maturation and highlighted a few early postnatal events as potential factors controlling the developmental process. Because mouse is the most popular mammalian model for genetic manipulation, this study provided a foundation for further exploring regulatory mechanisms of RGC dendritic development.     

Genomic comparison of Rickettsia honei strain RBT and other Rickettsia Species

Rickettsia honei strain RB(T) was isolated from a febrile patient on Flinders Island, Australia, in 1991 and has been demonstrated to be the agent of Flinders Island spotted fever, a disease transmitted to humans by ticks. The comparison of this 1.27-Mb genome with other Rickettsia genomes provides additional insight into the mechanisms of evolution in Rickettsia species.     

Action of tetracycline and rifampicin on Rickettsia prowazekii and Rickettsia sibirica

The effect of tetracycline and rifampicin on R. prowazekii, strain Breinl and R. sibirica, strain X1 was studied in the experiments with chick embryos exposed to the antibiotic mixture with the infection material. It was shown that tetracycline in doses of 0.1 and 1 mg/embryo had the rickettsiostatic and rickettsiocidic effects respectively on R. sibirica. Rifampicin had only the rickettsiostatic effect in a dose of 0.1 mg/embryo and no rickettsiocidic effect even in a dose of 2 mg/embryo. Higher doses were toxic for 100 per cent of the embryos. The rickettsiostatic and rickettsiocidic effects of tetracycline on R. prowazekii were evident in doses of 0.05 and 0.1 mg/embryo, respectively. Rifampicin in a dose of 0.05 mg/embryo had both the rickettsiostatic and the rickettsiocidic effects on R. prowazekii. Therefore, rifampicin was more active with respect to R. prowazekii and tetracycline was more active with respect to R. sibirica. In addition, R. sibirica was more resistant to both tetracycline and rifampicin as compared to R. prowazekii.