BorreliaBase: a phylogeny-centered browser of Borrelia genomes

Di, Lia; Pagan, Pedro; Packer, Daniel; Martin, Che L.; Akther, Saymon; Ramrattan, Girish; Mongodin, Emmanuel F.; Fraser, Claire M.; Schutzer, Steven E.; Luft, Benjamin J.; Casjens, Sherwood; Qiu, Wei

doi:10.1186/1471-2105-15-233

Cited by 34 publications

(34 citation statements)

References 53 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…mayonii chromosomes using a progressive Mauve 2.4.0 alignment [28]. The Mauve alignment was compared to the Core Genome comparison tool available at www.borreliabase.org [29]. Ideograms of each annotated plasmid were generated using CViT 1.2.1 (linear) and Circos 0.69 (circular) [30, 31].…”

Section: Methodsmentioning

confidence: 99%

Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii

et al. 2016

View full text Add to dashboard Cite

Borrelia mayonii, a Borrelia burgdorferi sensu lato (Bbsl) genospecies, was recently identified as a cause of Lyme borreliosis (LB) among patients from the upper midwestern United States. By microscopy and PCR, spirochete/genome loads in infected patients were estimated at 105 to 106 per milliliter of blood. Here, we present the full chromosome and plasmid sequences of two B. mayonii isolates, MN14-1420 and MN14-1539, cultured from blood of two of these patients. Whole genome sequencing and assembly was conducted using PacBio long read sequencing (Pacific Biosciences RSII instrument) followed by hierarchical genome-assembly process (HGAP). The B. mayonii genome is ~1.31 Mbp in size (26.9% average GC content) and is comprised of a linear chromosome, 8 linear and 7 circular plasmids. Consistent with its taxonomic designation as a new Bbsl genospecies, the B. mayonii linear chromosome shares only 93.83% average nucleotide identity with other genospecies. Both B. mayonii genomes contain plasmids similar to B. burgdorferi sensu stricto lp54, lp36, lp28-3, lp28-4, lp25, lp17, lp5, 5 cp32s, cp26, and cp9. The vls locus present on lp28-10 of B. mayonii MN14-1420 is remarkably long, being comprised of 24 silent vls cassettes. Genetic differences between the two B. mayonii genomes are limited and include 15 single nucleotide variations as well as 7 fewer silent vls cassettes and a lack of the lp5 plasmid in MN14-1539. Notably, 68 homologs to proteins present in B. burgdorferi sensu stricto appear to be lacking from the B. mayonii genomes. These include the complement inhibitor, CspZ (BB_H06), the fibronectin binding protein, BB_K32, as well as multiple lipoproteins and proteins of unknown function. This study shows the utility of long read sequencing for full genome assembly of Bbsl genomes, identifies putative genome regions of B. mayonii that may be linked to clinical manifestation or tissue tropism, and provides a valuable resource for pathogenicity, diagnostic and vaccine studies.

show abstract

Section: Methodsmentioning

confidence: 99%

Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii

et al. 2016

View full text Add to dashboard Cite

show abstract

“…(e) Extremophiles: Many, if not all, of these organisms (Supplementary Material 2) live in various degrees of extreme habitats and often derive energy from the reduction of exotic substrates. For example, Desulfotalea psychrophila is a marine, sulfate-reducing, deltaproteobacterium that is ice-dwelling (sympagic) and can grow at subzero temperatures (Rabus et al 2004); Flavobacterium psychrophilum is a psychrotroph that infects diverse species of cold water salmon and trout (Duchaud et al 2007;Nematollahi et al 2003); Psychroflexus torquis represents a group of Antarctic ice-derived psychrophilic proteobacteria (Feng et al 2014); Borrelia hermsii, causative agent of tick-borne relapsing fever (Di et al 2014), must survive at the febrile temperature resulting from the host's response to the parasite. Lastly, nearly all Flavobacteria and many Spirochetes use a large variety of substrates and are also flexible in this behavior.…”

Section: Dfi Genes Occur In Select Microorganisms Onlymentioning

confidence: 99%

On the role, ecology, phylogeny, and structure of dual-family immunophilins

Barik¹

2017

Cell Stress and Chaperones

View full text Add to dashboard Cite

The novel class of dual-family immunophilins (henceforth abbreviated as DFI) represents naturally occurring chimera of classical FK506-binding protein (FKBP) and cyclophilin (CYN), connected by a flexible linker that may include a three-unit tetratricopeptide (TPR) repeat. Here, I report a comprehensive analysis of all current DFI sequences and their host organisms. DFIs are of two kinds: CFBP (cyclosporin-and FK506-binding protein) and FCBP (FK506-and cyclosporin-binding protein), found in eukaryotes. The CFBP type occurs in select bacteria that are mostly extremophiles, such as psychrophilic, thermophilic, halophilic, and sulfur-reducing. Essentially all DFI organisms are unicellular. I suggest that DFIs are specialized bifunctional chaperones that use their flexible interdomain linker to associate with large polypeptides or multisubunit megacomplexes to promote simultaneous folding or renaturation of two clients in proximity, essential in stressful and denaturing environments. Analysis of sequence homology and predicted 3D structures of the FKBP and CYN domains as well as the TPR linkers upheld the modular nature of the DFIs and revealed the uniqueness of their TPR domain. The CFBP and FCBP genes appear to have evolved in parallel pathways with no obvious single common ancestor. The occurrence of both types of DFI in multiple unrelated phylogenetic clades supported their selection in metabolic and environmental niche roles rather than a traditional taxonomic relationship.Nonetheless, organisms with these rare immunophilins may define an operational taxonomic unit (OTU) bound by the commonality of chaperone function.

show abstract

“…Interestingly, while B. burgdorferi and B. afzelii have been shown to express FH binding proteins, previous studies have shown that most strains of B. garinii are serum sensitive and that orthologs of the major FH binding proteins, which are all encoded on plasmids, are not found in the majority of B. garinii strains (36,54). However, all borrelial isolates sequenced thus far encode orthologs of chromosomally encoded BB0405 and BB0406, irrespective of their serum resistance or sensitivity phenotype (55). Consistent with the finding that all serum-sensitive strains identified to date also contain orthologs of BB0405 and BB0406, we did not observe a role for BB0405, BB0406, BG0407, or BAPKO_0422 in FH binding.…”

Section: Discussionmentioning

confidence: 90%

Outer Membrane Proteins BB0405 and BB0406 Are Immunogenic, but Only BB0405 Is Required for Borrelia burgdorferi Infection

2017

View full text Add to dashboard Cite

We recently identified the Borrelia burgdorferi outer membrane protein (OMP) BB0406 and found that the gene encoding this OMP was cotranscribed with the gene encoding the OMP BB0405. Interestingly, BB0405 and BB0406 share 59% similarity and are grouped into the same B. burgdorferi paralogous gene family. Given their overall similarity, it is plausible that both OMPs have similar or overlapping functions in this pathogenic spirochete. BB0405 was recently shown to be required for mammalian infection despite the observations that BB0405 is poorly immunogenic and not recognized during mouse or human infection. BB0405 orthologs have also been shown to bind the complement regulator protein factor H. Therefore, to better elucidate the role of BB0405 and its paralog BB0406 during infection and in serum resistance, we examined both proteins in animal infection, factor H binding, and serum sensitivity assays. Our combined results suggest that BB0405-and BB0406-specific antibodies are borreliacidal and that both OMPs are immunogenic during nonhuman primate infection. Additionally, while BB0405 was found to be required for establishing mouse infection, BB0406 was not found to be essential for infectivity. In contrast to data from previous reports, however, neither OMP was found to bind human factor H or to be required for enhancing serum resistance of B. burgdorferi in vitro.KEYWORDS Borrelia burgdorferi, Lyme disease, outer membrane proteins, spirochete L yme disease is a multisystem infection caused by pathogenic spirochetes belonging to the Borrelia burgdorferi sensu lato complex (1, 2). It is the most prevalent arthropod-borne disease in the United States and has become a major public health concern (3, 4). The enzootic life cycle of the spirochete is complex and involves tick vectors of the Ixodes genus that transmit the spirochete to a wide range of mammalian host reservoirs in nature. Humans are accidental hosts and play no significant role in the spirochete life cycle (5). The primary manifestations of Lyme disease are a localized rash, termed erythema migrans, and flu-like symptoms (6). In the absence of antibiotic treatment, spirochetes can disseminate to multiple organs, including the heart, joints, skin, and nervous system (7). To disseminate to these distant sites, the spirochete must evade serum-mediated killing and the subsequent adaptive immune response that ensues in the mammalian host (5,6,8).Given that B. burgdorferi is an extracellular pathogen, the outer membrane (OM) of this organism is the interface between the spirochete and the host during infection. The two major classes of proteins present in the borrelial OM are (i) outer surface lipoproteins (Osps) that are anchored to the outer leaflet of the OM bilayer by their N-terminal lipid moieties and (ii) integral outer membrane proteins (OMPs) that contain membrane-spanning domains. Membrane-anchored Osps have been well studied be-

show abstract

BorreliaBase: a phylogeny-centered browser of Borrelia genomes

Cited by 34 publications

References 53 publications

Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii

Whole Genome Sequence and Comparative Genomics of the Novel Lyme Borreliosis Causing Pathogen, Borrelia mayonii

On the role, ecology, phylogeny, and structure of dual-family immunophilins

Outer Membrane Proteins BB0405 and BB0406 Are Immunogenic, but Only BB0405 Is Required for Borrelia burgdorferi Infection

Contact Info

Product

Resources

About