Identification, sequencing and molecular analysis of Chp4, a novel chlamydiaphage of Chlamydophila abortus belonging to the family Microviridae

Identification and characterization of multiple novel viruses in fecal samples of ruddy shelducks using viral metagenomics methods

The viral metagenomics approach is an effective technique for investigating and analysing both existing and emerging viruses in humans and diverse animal samples. The ruddy shelduck, a nationally protected secondary key species of wild animals, has become the predominant species among overwintering waterbirds in Qinghai Lake. Viruses carried by ruddy shelducks can potentially infect humans or other animals; however, limited research on the faecal virome of ruddy shelducks is currently available. In the present study, faecal samples of ruddy shelducks collected from Saga County, Shigatse City, Tibet, China, were subjected to viral metagenomic analysis. The predominant viral families identified in ruddy shelduck samples were Picornaviridae, Parvoviridae, Microviridae, Vilyaviridae, Astroviridae, and Caliciviridae. Among these, two picornavirus genomes have been identified as new strains of the genus Megrivirus in the family Parvoviridae. In addition, viruses that infect parasites and bacteria have been identified and characterised. The present study enhances our comprehension of the composition of the viral community in ruddy shelducks faeces and highlights the dynamic nature of viral evolution and the significance of continuous monitoring to assess potential risks to wildlife and public health.

The ΦCPG1 chlamydiaphage can infect Chlamydia trachomatis and significantly reduce its infectivity

Recent years have seen a significant increase in rates of persistent, antibiotic-resistant infection of Chlamydia trachomatis (CT) infections, representing an increasingly serious public health threat. At present there are no effective vaccines or antibodies available to treat CT, prompting the need for novel treatment strategies. One potential solution to this issue is the use of ΦCPG1, a chlamydia-specific lytic phage which has over 90% nucleotide sequence identity with other chlamydiaphages. Previous work has shown the Vp1 capsid protein of ΦCPG1 to exhibit broad inhibitory activity against all CT serotypes, inhibiting CT-mediated host cell toxicity. Patients with CT infections exhibit circulating antibodies against this Vp1 protein, suggesting that this or similar phages may be present in vivo in the context of CT infections, even though no phages have been specifically detected to date. Given these previous findings, we hypothesized that the ΦCPG1 chlamydiaphage may be able to infect CT, thereby inhibiting its growth and proliferation. To test this, we generated a recombinant pGFP-ΦCPG1 phage which we used to explore its effects on CT and chlamydia conjunctivitis of guinea pigs (GPIC). We found that pGFP insertion did not alter the packaging or infectivity of ΦCPG1, and that this recombinant phage was readily able to infect CT and GPIC and inhibit CT and GPIC in a dose-dependent fashion. This inhibition was most pronounced during the mid and late stages of the CT infection, disrupting the reticular body (RB) to EB transition, leading to the formation of enlarged RBs. These results indicate that ΦCPG1 is able to infect CT, highlighting this phage as a novel potential therapeutic agent for treating chlamydia infections. In addition, by engineering pGFP to express ΦCPG1, we have produced an valuable experimental tool useful for future studies of drug resistance, pathogenicity, and vaccine research aimed at improving CT treatment.

The smallest ssDNA phage infecting a marine bacterium

In the marine environment, only a few lytic single-stranded DNA (ssDNA) phages have been isolated and characterized, despite the fact that diverse ssDNA bacteriophages have been discovered via metagenomic studies. In this study, we isolated and characterized a new ssDNA phage, vB_RpoMi-Mini, which infects a marine bacterium Ruegeria pomeroyi DSS-3. With a genome size of 4248 bp and only four putative open reading frames (ORF), vB_RpoMi-Mini becomes the smallest ssDNA phage among the known ssDNA phage isolates and represents the DNA bacteriophage with the least number of ORFs. Genome-wide analysis reveals that bacteriophage Mini is distantly related to the known ssDNA phages and belongs to an unclassified ssDNA phage within the Microviridae family. The presence of peptidase in vB_RpoMi-Mini genome further implies that horizontal gene transfer could be an important driving force in the evolution of ssDNA phages. Bacteriophage Mini seems to have lost the spike protein commonly seen in ssDNA phages, suggesting that ssDNA phage can be more diverse than previously thought. Metagenomic analysis indicates that Mini-like phages are widely distributed in the environments. The discovery of vB_RpoMi-Mini expands our understanding of ssDNA phages in nature, and also indicates our dearth of knowledge regarding of ssDNA phages.

Capsid protein Vp1 from chlamydiaphage φCPG1 effectively alleviates cytotoxicity induced by Chlamydia trachomatis

Chlamydia trachomatis is the leading cause of sexually transmitted bacterial infections. C. trachomatis genital infection may lead to pelvic inflammatory disease, ectopic pregnancy and tubal infertility, which are major public health problems. However, the pathogenic mechanisms of this bacterium remain unclear, and the efficacy of clinical therapeutics is unsatisfactory. In the current study, whether Vp1 can alleviate the cytotoxicity induced by Chlamydia trachomatis infection was investigated. C. trachomatis was pre-treated with BSA or purified Vp1 protein and used to infect HeLa cells. It was observed that Vp1 significantly inhibited the infectivity of C. trachomatis in cell cultures. In addition, the Vp1 pretreatment reduced the chlamydial Hsp60 protein levels and decreased the C. trachomatis inclusion number. The Vp1 pretreatment also prevented C. trachomatis-induced cytotoxicity in host cells. Furthermore, the chlamydial suppression of host cell proapoptotic p53 protein and the induction of antiapoptotic cIAP-2 and Mcl-1 gene expression were reversed by the Vp1 pretreatment. These observations suggest that Vp1 has a clear inhibitory effect on C. trachomatis growth in vitro.

PmpI antibody reduces the inhibitory effect of Vp1 on Chlamydia trachomatis infectivity

Chlamydia trachomatis is the most common cause of bacterial sexually transmitted infections. The effect of antibiotic treatment is not satisfactory, and there is currently no vaccine to prevent C. trachomatis infection. Our results showed that Chlamydia virus CPG1 capsid protein Vp1 treatment significantly inhibited C. trachomatis growth in cell culture, and the inclusion numbers of different C. trachomatis serotypes were decreased. In addition, we conducted a preliminary investigation of the possible mechanisms behind the Vp1 inhibition effects and the C. trachomatis molecules targeted by Vp1. Using far-western blot and GST pull-down assay, we found that purified Vp1 can bind to the C. trachomatis outer membrane protein PmpI. PmpI polyclonal antibody treatment markedly reduced the inhibitory effect of Vp1 on C. trachomatis infectivity. On the basis of these experimental results, we infer that PmpI participates in the inhibitory effect of Vp1 and may be a potential receptor of Vp1 in the outer membrane of C. trachomatis. Our research provides clues regarding the molecular mechanisms underlying the interactions between chlamydia virus and chlamydia.

Identification of proteins differentially expressed by Chlamydia trachomatis treated with chlamydiaphage capsid protein VP1 during intracellular growth

Chlamydia trachomatis infection is one of the most prevalent sexually transmitted diseases. Our research pertains to the inhibitory effect and molecular mechanism of the chlamydiaphage capsid protein VP1 on the growth of Chlamydia trachomatis. In this research, the capsid protein VP1 of the guinea-pig conjunctivitis chlamydiaphage phiCPG1 was expressed, purified and identified, and then, it was applied to the cultivation of different serovars of Chlamydia trachomatis and Chlamydia psittaci. The inhibitory effect was observed in each serovar of Chlamydia trachomatis (D, E, F, G, H, I, K, and L2) and Chlamydia psittaci inoculated with VP1 protein. The inhibition affection of VP1 on the growth of Chlamydia trachomatis was caused by the changes of expressions of some related proteins including 36 proteins up-regulated and 81 proteins down-regulated in the development cycle of Ct through the label-free test, and the transcription levels of these proteins, including Hc1, pmpD, and MOMP, were confirmed by RT-PCR. It provides information that is essential for understanding the mechanism of chlamydiaphage capsid protein VP1 on chlamydia and a new direction for further clinical treatment of chlamydial infection.

Emancipating Chlamydia: Advances in the Genetic Manipulation of a Recalcitrant Intracellular Pathogen

Chlamydia species infect millions of individuals worldwide and are important etiological agents of sexually transmitted disease, infertility, and blinding trachoma. Historically, the genetic intractability of this intracellular pathogen has hindered the molecular dissection of virulence factors contributing to its pathogenesis. The obligate intracellular life cycle of Chlamydia and restrictions on the use of antibiotics as selectable markers have impeded the development of molecular tools to genetically manipulate these pathogens. However, recent developments in the field have resulted in significant gains in our ability to alter the genome of Chlamydia, which will expedite the elucidation of virulence mechanisms. In this review, we discuss the challenges affecting the development of molecular genetic tools for Chlamydia and the work that laid the foundation for recent advancements in the genetic analysis of this recalcitrant pathogen.

Evidence for horizontal gene transfer between Chlamydophila pneumoniae and Chlamydia phage

Chlamydia-infecting bacteriophages, members of the Microviridae family, specifically the Gokushovirinae subfamily, are small (4.5–5 kb) single-stranded circles with 8–10 open-reading frames similar to E. coli phage ϕX174. Using sequence information found in GenBank, we examined related genes in Chlamydophila pneumoniae and Chlamydia-infecting bacteriophages. The 5 completely sequenced C. pneumoniae strains contain a gene orthologous to a phage gene annotated as the putative replication initiation protein (PRIP, also called VP4), which is not found in any other members of the Chlamydiaceae family sequenced to date. The C. pneumoniae strain infecting koalas, LPCoLN, in addition contains another region orthologous to phage sequences derived from the minor capsid protein gene, VP3. Phylogenetically, the phage PRIP sequences are more diverse than the bacterial PRIP sequences; nevertheless, the bacterial sequences and the phage sequences each cluster together in their own clade. Finally, we found evidence for another Microviridae phage-related gene, the major capsid protein gene, VP1 in a number of other bacterial species and 2 eukaryotes, the woodland strawberry and a nematode. Thus, we find considerable evidence for DNA sequences related to genes found in bacteriophages of the Microviridae family not only in a variety of prokaryotic but also eukaryotic species.

Evolution, phylogeny, and molecular epidemiology of Chlamydia

The Chlamydiaceae are a family of obligate intracellular bacteria characterized by a unique biphasic developmental cycle. It encompasses the single genus Chlamydia, which involves nine species that affect a wide range of vertebral hosts, causing infections with serious impact on human health (mainly due to Chlamydia trachomatis infections) and on farming and veterinary industries. It is believed that Chlamydiales originated ∼700mya, whereas C. trachomatis likely split from the other Chlamydiaceae during the last 6mya. This corresponds to the emergence of modern human lineages, with the first descriptions of chlamydial infections as ancient as four millennia. Chlamydiaceae have undergone a massive genome reduction, on behalf of the deletional bias "use it or lose it", stabilizing at 1-1.2Mb and keeping a striking genome synteny. Their phylogeny reveals species segregation according to biological properties, with huge differences in terms of host range, tissue tropism, and disease outcomes. Genome differences rely on the occurrence of mutations in the >700 orthologous genes, as well as on events of recombination, gene loss, inversion, and paralogous expansion, affecting both a hypervariable region named the plasticity zone, and genes essentially encoding polymorphic and transmembrane head membrane proteins, type III secretion effectors and some metabolic pathways. Procedures for molecular typing are still not consensual but have allowed the knowledge of molecular epidemiology patterns for some species as well as the identification of outbreaks and emergence of successful clones for C. trachomatis. This manuscript intends to provide a comprehensive review on the evolution, phylogeny, and molecular epidemiology of Chlamydia.

Genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere

Prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet Earth with human beings (among others). However, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. An understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. The vast majority of characterized prokaryotic viruses belong to the order Caudovirales, double-stranded DNA (dsDNA) bacteriophages with tails. Consequently, these viruses have been studied (and reviewed) extensively from both genomic and functional perspectives. However, albeit numerous, tailed phages represent only a minor fraction of the prokaryotic virus diversity. Therefore, the knowledge which has been generated for this viral system does not offer a comprehensive view of the prokaryotic virosphere. In this review, we discuss all families of bacterial and archaeal viruses that contain more than one characterized member and for which evolutionary conclusions can be attempted by use of comparative genomic analysis. We focus on the molecular mechanisms of their genome evolution as well as on the relationships between different viral groups and plasmids. It becomes clear that evolutionary mechanisms shaping the genomes of prokaryotic viruses vary between different families and depend on the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the life cycle. We also point out that horizontal gene transfer is not equally prevalent in different virus families and is not uniformly unrestricted for diverse viral functions.

The complete genome sequence and genetic analysis of ΦCA82 a novel uncultured microphage from the turkey gastrointestinal system

The genomic DNA sequence of a novel enteric uncultured microphage, ΦCA82 from a turkey gastrointestinal system was determined utilizing metagenomics techniques. The entire circular, single-stranded nucleotide sequence of the genome was 5,514 nucleotides. The ΦCA82 genome is quite different from other microviruses as indicated by comparisons of nucleotide similarity, predicted protein similarity, and functional classifications. Only three genes showed significant similarity to microviral proteins as determined by local alignments using BLAST analysis. ORF1 encoded a predicted phage F capsid protein that was phylogenetically most similar to the Microviridae ΦMH2K member's major coat protein. The ΦCA82 genome also encoded a predicted minor capsid protein (ORF2) and putative replication initiation protein (ORF3) most similar to the microviral bacteriophage SpV4. The distant evolutionary relationship of ΦCA82 suggests that the divergence of this novel turkey microvirus from other microviruses may reflect unique evolutionary pressures encountered within the turkey gastrointestinal system.