scholarly journals Genome Assembly of the A-Group Wolbachia in Nasonia oneida Using Linked-Reads Technology

2019 ◽  
Vol 11 (10) ◽  
pp. 3008-3013 ◽  
Author(s):  
Xiaozhu Wang ◽  
Xiao Xiong ◽  
Wenqi Cao ◽  
Chao Zhang ◽  
John H Werren ◽  
...  
Keyword(s):  
Read Depth ◽  
Intracellular Bacteria ◽  
Bacterial Genomes ◽  
Wasp Species ◽  
Draft Assembly ◽  
Arthropod Species ◽  
Low Concentrations ◽  
Wolbachia Genome ◽  
Obligate Intracellular Bacteria ◽  
Laboratory Culturing

Abstract Wolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Genome sequences have been generated from arthropod samples following enrichment for the intracellular bacteria, and genomes have also been assembled from arthropod whole-genome sequencing projects. However, these methods remain challenging for infections that occur at low titers in hosts. Here we report the first Wolbachia genome assembled from host sequences using 10× Genomics linked-reads technology. The high read depth attainable by this method allows for recovery of intracellular bacteria that are at low concentrations. Based on the depth differences (714× for the insect and 59× for the bacterium), we assembled the genome of a Wolbachia in the parasitoid jewel wasp species Nasonia oneida. The final draft assembly consists of 1,293, 06 bp in 47 scaffolds with 1,114 coding genes and 97.01% genome completeness assessed by checkM. Comparisons of the five Multi Locus Sequence Typing genes revealed that the sequenced Wolbachia genome is the A1 strain (henceforth wOneA1) previously reported in N. oneida. Pyrosequencing confirms that the wasp strain lacks A2 and B types previously detected in this insect, which were likely lost during laboratory culturing. Assembling bacterial genomes from host genome projects can provide an effective method for sequencing bacterial genomes, even when the infections occur at low density in sampled tissues.

scholarly journals The Most Widespread Phage in Animals: Genomics and Taxonomic Classification of Phage WO

2021 ◽  
Author(s):  
Sarah R Bordenstein ◽  
Seth Bordenstein
Keyword(s):  
Taxonomic Classification ◽  
Aquatic Environments ◽  
Intracellular Bacteria ◽  
Obligate Intracellular ◽  
Host Interaction ◽  
Wolbachia Genome ◽  
Parasitism Genes ◽  
Obligate Intracellular Bacteria ◽  
Gene Island

Wolbachia are the most common obligate, intracellular bacteria in animals. They exist worldwide in arthropod and nematode hosts in which they commonly act as reproductive parasites or mutualists, respectively. Bacteriophage WO, the largest of Wolbachia's mobile elements, includes reproductive parasitism genes, serves as a hotspot for genetic divergence and genomic rearrangement of the bacterial chromosome, and uniquely encodes a Eukaryotic Association Module with eukaryotic-like genes and an ensemble of putative host interaction genes. Despite WO's relevance to genome evolution, selfish genetics, and symbiotic applications, relatively little is known about its origin, host range, diversification, and taxonomic classification. Here we analyze the most comprehensive set of 150 Wolbachia and phage WO assemblies to provide a framework for discretely organizing and naming integrated phage WO genomes. We demonstrate that WO is principally in arthropod Wolbachia with relatives in diverse endosymbionts and metagenomes, organized into four variants related by gene synteny, often oriented opposite the origin of replication in the Wolbachia chromosome, and the large serine recombinase is an ideal typing tool to assign taxonomic classification of the four variants. We identify a novel, putative lytic cassette and WO's association with a conserved eleven gene island, termed Undecim Cluster, that is enriched with virulence-like genes. Finally, we evaluate WO-like Islands in the Wolbachia genome and discuss a new model in which Octomom, a notable WO-like Island, arose from a split with WO. Together, these findings establish the first comprehensive Linnaean taxonomic classification of endosymbiont phages that includes distinguishable genera of phage WO, a family of non-Wolbachia phages from aquatic environments, and an order that captures the collective relatedness of these viruses.

scholarly journals Long-read whole genome sequencing and comparative analysis of six strains of the human pathogenOrientia tsutsugamushi

2018 ◽  
Author(s):  
Elizabeth M. Batty ◽  
Suwittra Chaemchuen ◽  
Stuart D. Blacksell ◽  
Daniel Paris ◽  
Rory Bowden ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Single Molecule ◽  
Genomic Variation ◽  
Intracellular Bacteria ◽  
Whole Genome ◽  
Orientia Tsutsugamushi ◽  
Bacterial Genomes ◽  
Obligate Intracellular ◽  
Long Read ◽  
Obligate Intracellular Bacteria

AbstractBackgroundOrientia tsutsugamushiis a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus. In contrast to the genome reduction seen in many obligate intracellular bacteria, early genetic studies ofOrientiahave revealed one of the most repetitive bacterial genomes sequenced to date. The dramatic expansion of mobile elements has hampered efforts to generate complete genome sequences using short read sequencing methodologies, and consequently there have been few studies of the comparative genomics of this neglected species.ResultsWe report new high-quality genomes ofOrientia tsutsugamushi,generated using PacBio single molecule long read sequencing, for six strains: Karp, Kato, Gilliam, TA686, UT76 and UT176. In comparative genomics analyses of these strains together with existing reference genomes from Ikeda and Boryong strains, we identify a relatively small core genome of 657 genes, grouped into core gene ‘islands’ and separated by repeat regions, and use the core genes to infer the first whole-genome phylogeny ofOrientia.ConclusionsComplete assemblies of multiple Orientia genomes verify initial suggestions that these are remarkable organisms. They have large genomes with widespread amplification of repeat elements and massive chromosomal rearrangements between strains. At the gene level, Orientia has a relatively small set of universally conserved genes, similar to other obligate intracellular bacteria, and the relative expansion in genome size can be accounted for by gene duplication and repeat amplification. Our study demonstrates the utility of long read sequencing to investigate complex bacterial genomes and characterise genomic variation.

scholarly journals Genome assembly of the A-group Wolbachia in Nasonia oneida and phylogenomic analysis of Wolbachia strains reveals patterns of genome evolution and lateral gene transfer

2018 ◽  
Author(s):  
Xiaozhu Wang ◽  
Xiao Xiong ◽  
Wenqi Cao ◽  
Chao Zhang ◽  
John H. Werren ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Intracellular Bacteria ◽  
Whole Genome ◽  
Gene Duplications ◽  
Strain Variation ◽  
Wasp Species ◽  
Arthropod Species

AbstractWolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Based on depth differences, we assembled the genome of Wolbachia in the parasitoid jewel wasp species Nasonia oneida (wOne), using 10X Genomics Chromium linked-read technology. The final draft assembly consists of 1,293,406 bp in 47 scaffolds with 1,114 coding genes and 97.01% genome completeness assessed by checkM. wOne is the A1 strain previously reported in N. oneida, and pyrosequencing confirms that the wasp strain lacks A2 and B types, which were likely lost during laboratory culturing. Polymorphisms identified in the wOneA1 genome have elevated read depths, indicating recent gene duplications rather that strain variation. These polymorphisms are enriched in nonsynonymous changes in 27 coding genes, including phase baseplate assembly proteins and transporter activity related genes. wOneA1 is more closely grouped with A-Wolbachia in the Drosophila simulans (wHa) than A-Wolbachia found in wasps. Genome variation was next evaluated in 34 published Wolbachia genomes for 211 single ortholog genes, and revealed six supergroup discordant trees, indicating recombination events not only between A and B supergroups, but also between A and E supergroups. Comparisons of strain divergence using the five genes of the Multi Locus Strain Typing (MLST) system show a high correlation (rho=0.98) between MLST and whole genome divergences, indicating that MLST is a reliable method for identifying related strains when whole genome data are not available. Assembling bacterial genomes from host genome projects can provide an effective method for sequencing Wolbachia genomes and characterizing their diversity.Author SummaryMore than half of the arthropod species are infected by the obligated intracellular bacteria Wolbachia. As one of the most widespread parasitic microbes, Wolbachia mediate important biological processes such as cytoplasmic incompatibility and lateral gene transfer in insects. Their evolutionary relationship has been characterize using five protein-coding and 16S rRNA genes. In this work, we identified 211 conserved single copies genes in 34 genome sequenced Wolbachia strains, and we discovered that they maintain the supergroup relationship classified previously based on selected genes. We constructed phylogenetic trees for individual genes and found only six genes display discordant tree structure between supergroups, due to lateral gene transfer and homologous recombination events. But these events are not common (3%) in Wolbachia genomes, at least in these conserved single copy genes. In addition to known lateral gene transfer events between A and B supergroups, we identified transfers between A and E supergroups for the first time. Selective maintenance of such transfers suggests possible roles in Wolbachia infection related functions. We also found enriched nonsynonymous polymorphisms in Nasonia oneida Wobachia genome, and their differences are more likely to result from gene duplications within the strain, rather than strain variation within the parasitoid.

scholarly journals The growing repertoire of genetic tools for dissecting chlamydial pathogenesis

2021 ◽  
Author(s):  
Arkaprabha Banerjee ◽  
David E Nelson
Keyword(s):  
Genetic Engineering ◽  
Intracellular Bacteria ◽  
Human Pathogens ◽  
Pathogenic Potential ◽  
Host Preferences ◽  
Genetic Tools ◽  
Obligate Intracellular ◽  
Obligate Intracellular Bacteria ◽  
Multiple Species

Abstract Multiple species of obligate intracellular bacteria in the genus Chlamydia are important veterinary and/or human pathogens. These pathogens all share similar biphasic developmental cycles and transition between intracellular vegetative reticulate bodies and infectious elementary forms, but vary substantially in their host preferences and pathogenic potential. A lack of tools for genetic engineering of these organisms has long been an impediment to the study of their biology and pathogenesis. However, the refinement of approaches developed in C. trachomatis over the last ten years, and adaptation of some of these approaches to other Chlamydia spp. in just the last few years, has opened exciting new possibilities for studying this ubiquitous group of important pathogens.

scholarly journals Initial Characterization of the Two ClpP Paralogs ofChlamydia trachomatisSuggests Unique Functionality for Each

2018 ◽  
Vol 201 (2) ◽  
Author(s):  
Nicholas A. Wood ◽  
Krystal Y. Chung ◽  
Amanda M. Blocker ◽  
Nathalia Rodrigues de Almeida ◽  
Martin Conda-Sheridan ◽  
...  
Keyword(s):  
Host Cells ◽  
Developmental Cycle ◽  
Intracellular Bacteria ◽  
Clp Protease ◽  
Content Type ◽  
Sexually Transmitted ◽  
Obligate Intracellular ◽  
Developmental Form ◽  
Obligate Intracellular Bacteria

ABSTRACTMembers ofChlamydiaare obligate intracellular bacteria that differentiate between two distinct functional and morphological forms during their developmental cycle, elementary bodies (EBs) and reticulate bodies (RBs). EBs are nondividing small electron-dense forms that infect host cells. RBs are larger noninfectious replicative forms that develop within a membrane-bound vesicle, termed an inclusion. Given the unique properties of each developmental form of this bacterium, we hypothesized that the Clp protease system plays an integral role in proteomic turnover by degrading specific proteins from one developmental form or the other.Chlamydiaspp. have five uncharacterizedclpgenes,clpX,clpC, twoclpPparalogs, andclpB. In other bacteria, ClpC and ClpX are ATPases that unfold and feed proteins into the ClpP protease to be degraded, and ClpB is a deaggregase. Here, we focused on characterizing the ClpP paralogs. Transcriptional analyses and immunoblotting determined that these genes are expressed midcycle. Bioinformatic analyses of these proteins identified key residues important for activity. Overexpression of inactiveclpPmutants inChlamydiaspp. suggested independent function of each ClpP paralog. To further probe these differences, we determined interactions between the ClpP proteins using bacterial two-hybrid assays and native gel analysis of recombinant proteins. Homotypic interactions of the ClpP proteins, but not heterotypic interactions between the ClpP paralogs, were detected. Interestingly, protease activity of ClpP2, but not ClpP1, was detectedin vitro. This activity was stimulated by antibiotics known to activate ClpP, which also blocked chlamydial growth. Our data suggest the chlamydial ClpP paralogs likely serve distinct and critical roles in this important pathogen.IMPORTANCEChlamydia trachomatisis the leading cause of preventable infectious blindness and of bacterial sexually transmitted infections worldwide. Chlamydiae are developmentally regulated obligate intracellular pathogens that alternate between two functional and morphologic forms, with distinct repertoires of proteins. We hypothesize that protein degradation is a critical aspect to the developmental cycle. A key system involved in protein turnover in bacteria is the Clp protease system. Here, we characterized the two chlamydial ClpP paralogs by examining their expression inChlamydiaspp., their ability to oligomerize, and their proteolytic activity. This work will help understand the evolutionarily diverse Clp proteases in the context of intracellular organisms, which may aid in the study of other clinically relevant intracellular bacteria.

scholarly journals Characterization of an ATP Translocase Identified in the Destructive Plant Pathogen “Candidatus Liberibacter asiaticus”

2009 ◽  
Vol 192 (3) ◽  
pp. 834-840 ◽  
Author(s):  
Cheryl M. Vahling ◽  
Yongping Duan ◽  
Hong Lin
Keyword(s):  
Plant Pathogen ◽  
Bioinformatic Analysis ◽  
Intracellular Bacteria ◽  
Cell Competition ◽  
Candidatus Liberibacter ◽  
Citrus Huanglongbing ◽  
Liberibacter Asiaticus ◽  
High Concentrations ◽  
Obligate Intracellular Bacteria

ABSTRACT ATP/ADP translocases transport ATP across a lipid bilayer, which is normally impermeable to this molecule due to its size and charge. These transport proteins appear to be unique to mitochondria, plant plastids, and obligate intracellular bacteria. All bacterial ATP/ADP translocases characterized thus far have been found in endosymbionts of protozoa or pathogens of higher-order animals, including humans. A putative ATP/ADP translocase was uncovered during the genomic sequencing of the intracellular plant pathogen “Candidatus Liberibacter asiaticus,” the causal agent of citrus huanglongbing. Bioinformatic analysis of the protein revealed 12 transmembrane helices and predicted an isoelectric point of 9.4, both of which are characteristic of this family of proteins. The “Ca. Liberibacter asiaticus” gene (nttA) encoding the translocase was subsequently expressed in Escherichia coli and shown to enable E. coli to import ATP directly into the cell. Competition assays with the heterologous E. coli system demonstrated that the translocase was highly specific for ATP and ADP but that other nucleotides, if present in high concentrations, could also be taken up and/or block the ability of the translocase to import ATP. In addition, a protein homologous to NttA was identified in “Ca. Liberibacter solanacearum,” the bacterium associated with potato zebra chip disease. This is the first reported characterization of an ATP translocase from “Ca. Liberibacter asiaticus,” indicating that some intracellular bacteria of plants also have the potential to import ATP directly from their environment.

Infections caused by obligate intracellular bacteria

2017 ◽  
Author(s):  
Philippa C. Matthews
Keyword(s):  
Clinical Significance ◽  
Classification System ◽  
Q Fever ◽  
Intracellular Bacteria ◽  
Rickettsial Infection ◽  
Obligate Intracellular ◽  
Treatment And Prevention ◽  
Clinical Syndromes ◽  
Obligate Intracellular Bacteria ◽  
The Tropics

This chapter consists of short notes, diagrams, and tables to summarize infections caused by obligate intracellular bacteria. The chapter begins with a classification system to divide these organisms into Rickettsia, Anaplasma, Chlamydia, Coxiella, and Bartonella species. Separate sections then follow on the infections of most clinical significance for the tropics and subtropics, including the typhus group (caused by rickettsial infection) and Q fever. For ease of reference, each topic is broken down into sections, including classification, epidemiology, microbiology, pathophysiology, clinical syndromes, diagnosis, treatment, and prevention.

scholarly journals Vaccine Design and Vaccination Strategies against Rickettsiae

Vaccines ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. 896
Author(s):  
Anke Osterloh
Keyword(s):  
Protective Immunity ◽  
Vaccine Development ◽  
Intracellular Bacteria ◽  
Obligate Intracellular ◽  
Vaccination Strategies ◽  
The Past ◽  
Rickettsial Infections ◽  
Causative Agents ◽  
Prophylactic Vaccines ◽  
Obligate Intracellular Bacteria

Rickettsioses are febrile, potentially lethal infectious diseases that are a serious health threat, especially in poor income countries. The causative agents are small obligate intracellular bacteria, rickettsiae. Rickettsial infections are emerging worldwide with increasing incidence and geographic distribution. Nonetheless, these infections are clearly underdiagnosed because methods of diagnosis are still limited and often not available. Another problem is that the bacteria respond to only a few antibiotics, so delayed or wrong antibiotic treatment often leads to a more severe outcome of the disease. In addition to that, the development of antibiotic resistance is a serious threat because alternative antibiotics are missing. For these reasons, prophylactic vaccines against rickettsiae are urgently needed. In the past years, knowledge about protective immunity against rickettsiae and immunogenic determinants has been increasing and provides a basis for vaccine development against these bacterial pathogens. This review provides an overview of experimental vaccination approaches against rickettsial infections and perspectives on vaccination strategies.

scholarly journals Wolbachia endosymbionts subvert the endoplasmic reticulum to acquire host membranes without triggering ER stress

2018 ◽  
Author(s):  
Nour Fattouh ◽  
Chantal Cazevieille ◽  
Frédéric Landmann
Keyword(s):  
Endoplasmic Reticulum ◽  
Golgi Apparatus ◽  
Host Cell ◽  
Pathogenic Bacteria ◽  
Secretory Pathway ◽  
Immune Surveillance ◽  
Lipid Synthesis ◽  
Time Lapse ◽  
Intracellular Bacteria ◽  
Arthropod Species

AbstractThe reproductive parasite Wolbachia are the most common endosymbionts on earth, present in a plethora of arthropod species. They have been introduced into mosquitos to successfully prevent the spread of vector-borne diseases, yet the strategies of host cell subversion underlying their obligate intracellular lifestyle remain to be explored in depth in order to gain insights into the mechanisms of pathogen-blocking. Like some other intracellular bacteria, Wolbachia reside in a host-derived vacuole in order to replicate and escape the immune surveillance. Using here the pathogen-blocking Wolbachia strain from Drosophila melanogaster, introduced into two different Drosophila cell lines, we show that Wolbachia subvert the endoplasmic reticulum to acquire their vacuolar membrane and colonize the host cell at high density. Wolbachia redistribute the endoplasmic reticulum to increase contact sites, and time lapse experiments reveal tight coupled dynamics suggesting important signalling events or nutrient uptake. They however do not affect the tubular or cisternal morphologies. A fraction of endoplasmic reticulum becomes clustered, allowing the endosymbionts to reside in between the endoplasmic reticulum and the Golgi apparatus, possibly modulating the traffic between these two organelles. Gene expression analyses and immunostaining studies suggest that Wolbachia achieve persistent infections at very high titers without triggering endoplasmic reticulum stress or enhanced ERAD-driven proteolysis, suggesting that amino acid salvage is achieved through modulation of other signalling pathways.Author summaryWolbachia are a genus of intracellular bacteria living in symbiosis with millions of arthropod species. They have the ability to block the transmission of arboviruses when introduced into mosquito vectors, by interfering with the cellular resources exploited by these viruses. Despite the biomedical interest of this symbiosis, little is known about the mechanisms by which Wolbachia survive and replicate in the host cell. We show here that the membrane composing the Wolbachia vacuole is acquired from the endoplasmic reticulum, a central organelle required for protein and lipid synthesis, and from which originates a vesicular trafficking toward the Golgi apparatus and the secretory pathway. Wolbachia modify the distribution of this organelle to increase their interactions with this source of membrane and likely of nutrients as well. In contrast to some intracellular pathogenic bacteria, the effect of Wolbachia on the cell homeostasis does not induce a stress on the endoplasmic reticulum. One of the consequences of such a stress would be an increased proteolysis used to relieve the cell from an excess of misfolded proteins. Incidentally, this shows that Wolbachia do not acquire amino acids from the host cell through this strategy.

Sign in / Sign up

Export Citation Format

Share Document