- Comparative genome characterization of the periodontal pathogen Tannerella. - forsythia ATCC 43037 covering 99% of the genome in three sequences. - 80% of the strains analysed. - 2020 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - Full list of author information is available at the end of the article Zwickl et al. - forsythia have been reported in the context of the pathogenesis of the disease. - A multi-gene locus encoding the species-specific part of the T. - Following assembly of the glycoprotein in the bacterial periplasm, the S-layer glycoproteins are targeted via their conserved C-terminal domain (CTD) to a type IX secretion system (T9SS) for export across the outer membrane [12]. - The glycobiology repertoire of the T.. - Previous characterizations of the T. - forsythia virulence factors were mostly based on the American Type Culture Collection (ATCC) 43037 type strain employing wet-lab experimentation, whereas computational analyses of the virulence-related gene repertoire mostly used the genome sequence of strain FDC 92A2. - forsythia species, and (iii) explore features of the T. - forsythia ATCC 43037 type strain, which is based on sequences of the published draft assembly and, hence, is compatible with previous studies and gene anno- tations. - Improved assembly of the Tannerella forsythia type strain ATCC 43037. - The genome of the T. - The largest sequence was 487 kbp comprising about 15% of the total assembly size of 3.282 Megabase- pairs (Mbp). - We used both the published paired-end se- quencing reads downsampled to a coverage of 100-fold and the newly generated mate-pairs to build connections between the contigs of the ATCC 43037 genome assembly generated by Friedrich et al. - The three largest sequences (1.85 Mbp, 859 kbp, 532 kbp) encompassed 99.1% of the assembly. - We compared our ATCC 43037 assembly to a published 15 kbp-long genomic sequence (GenBank accession KP715369) of the same T. - About one half of the sequence pub- lished by Ksiazek et al. - While some parts of the 15-kbp sequence aligned also to other regions, a distinct split, as described above for ATCC 43037, could not be observed (Additional file 12: File S1). - Three of the assem- blies showed considerable fragmentation (strain UB4:. - Only a few contigs that could not be aligned to the 92A2 reference under these conditions exceeded 1000 bp (one, six, and seven contigs for UB4, UB20, and UB22, respectively), comprising only 2–8% of the total assembly lengths (Table 2). - One of these rearrangements disrupted the larger of the two KLIKK protease loci, which was con- tained within the 15-kbp sequence mentioned above.. - forsythia subtree was almost as large as the distance of the outgroup (Fig. - We found large differences to the genome structure of the putative periodontal health-associated isolate Tannerella sp.. - In contrast, the genome sequences of the putative peri- odontal health-associated phylotype Tannerella sp. - BU063 covered less than 1% of the 92A2 genome by alignments with a sequence identity of at least 80%. - Even when lowering the sequence identity cut-off to 70 and 50% the alignments covered only 24 and 38% of the 92A2 sequence, respectively.. - Al- though 55% of the genes encoded within the Tannerella sp. - 0.4 indi- cated absence in at least one of the pathogenic strains (forsi- lysin in strain 9610. - Table S1) providing evidence that re-evaluation of the. - forsythia strains for the surface anti- gen BspA, one of the most comprehensively described virulence factors of T. - is characteristic of the C-terminal extension in KLIKK proteases.. - BU063 assembly, in this case with 53% identity over the entire length of the gene. - Interestingly, a large fraction of the dissimilarity between T. - BU063 genome assem- bly was found in regions other than the catalytic domain of the protein (Additional file 13: File S2).. - out of the 45 potential virulence factors the 20 genes showing a BSR of 0.9 or larger in T.. - Analysis of the T. - The comparison of gene repertoires encoded within different genomes of the same species has indicated. - For a particular species, a certain set of genes will be found in all of the studied ge- nomes, while some genes will be restricted to just a subset thereof. - Therefore, criteria are specified which demand core genes to be present in at least 80% or 90% of the studied genomes, respectively. - ATCC KS16, UB4, UB20, UB22, 9610, WW11663, WW10960, and 92A2, we assessed a core genome of the species comprising 1864 genes, when requiring a core gene to be present in each strain without exception. - 90% of the strains contained 2043 genes. - Analysis of the number of genes after iterative addition of the ten strains revealed saturation of the gene number in the core genome, whereas the pan. - On the other hand, some of the pathogenic strains show reduced similarity to some predicted virulence factors. - genome of the species may still increase when analysing more strains (Fig. - Of the genes found in the T. - Searching for Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology terms overrepresented in this gene set turned out to be inconclusive, because such terms had been assigned to only about a quarter of the genes. - forsythia strain 92A2 that contained at least five consecutive genes, (i) which were part of the T. - Five of the island candi- dates contained more than ten such genes. - Notably, nine of the islands encode SusD/TonB/TolC- like components indicative of polysaccharide utilization loci (PULs). - forsythia strain 92A2 (misclassified as ATCC 43037) were consid- ered, whereas we focused on genes of the T. - However, the genes required for the initiation of the glycan synthesis have yet to be determined. - BU063 may explain pathogenicity of the former and association with periodontal health of the latter. - forsythia, the scnRCA method was able to remove the influence of the GC3s bias on the analysis as indicated by a content criterion value of 0.56 (Additional file 6: Table S6, Additional file 8: Table S8). - Whether transla- tional optimization is also a factor shaping the biases in one or both of the genomes remains to be elucidated.. - We were able to assemble 99% of the T. - In comparative analyses we provided an assessment of the presence or absence of currently known as well as suggested virulence factors in all presently available T.. - We may have missed orthologs in a given strain if genes were located in a re- gion of the genome that was not covered by its assembly.. - The deviation, however, is to be expected as only three of the 19 T. - How many and which of the reported candidate regions represent true pathogenicity islands, in the sense of the common definition, has yet to be discovered and will require experimental verification. - We provide an improved genome assembly of the reference type strain T.. - forsythia ATCC 43037, and we define a soft-core genome and an accessory genome of the species. - Comprehensive characterization of the T. - The quality of the genomic DNA was checked on a 0.6% standard agarose gel stained with ethidium bromide, and using a NanoDrop ND-1000 spectrophotometer (ThermoFisher, Waltham, MA, USA). - Briefly, the protocol consists of tagmentation, strand displacement, AMPure purification of the strand displacement reaction, and circularization. - ligation of Illumina adapters to the ends of the DNA frag- ments. - After PCR clean-up, 1 μl of the library was taken for valid- ation using a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). - Results were assessed using QUAST v3.2 [50], additionally, critical links were validated by manual inspection of the mate-pairs supporting these links in IGV . - forsythia core and accessory genomes were com- piled using components of the GET_HOMOLOGUES pipeline [59]. - Additional thresholds for two genes to be allowed to group in the same cluster were: sequence identity of at least 30% (−S 30), sequence coverage of the. - Clusters were allowed to contain genes from any number of the included genomes (−t 0).. - The intersection of the cluster sets generated by the two different algorithms was extracted using com- pare_clusters.pl and used for further analysis. - In an additional run, orthologs were required to be present in at least 80% of the T. - forsythia genomes to become part of a relaxed form of the core genome, sometimes referred to as “soft core genome”. - All these Perl scripts are part of the GET_HO- MOLOGUES pipeline.. - Based on the results of the pan-genome analysis, puta- tive pathogenicity islands were detected as follows:. - Genes that were found to be present in at least eight of the ten T. - The script takes a file containing all annotated genes of the genome in tabular form (as can be downloaded from https://www.ncbi.nlm.nih.gov/. - the split region of the circular gen- ome in the assembly was checked manually. - Additional analysis on the presence or absence of the detected puta- tive glycosylation loci in other members of the Bacteroi- dales order was performed using Gecko 3.1 [67].. - Organisms included in this analysis were chosen based on previous work [11], the RefSeq assembly versions of the corresponding genomes were downloaded from the NCBI ftp server as GenBank flat files (Additional file 4:. - Whether a putative glycosylation locus or parts of it can be found in one of the included genomes apart from T. - The value for the latter parameter was decreased by one in each subse- quent run either until parts of the cluster were found in a non-T. - Span size distribution of the mate-pair library prepared from DNA of T. - The peak of the distribution is at 1759 bp, indicated by the red line.. - Alignments of the sequence KP715369 to T.. - Part of the Illumina sequencing data used in this study were generated at the VBCF NGS Unit (www.viennabiocenter.org/. - The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.. - HH is a member of the editorial board of BMC Genomics.. - Identification and characterization of the genes encoding a unique surface (S-) layer of Tannerella forsythia. - Glycobiology aspects of the periodontal pathogen Tannerella forsythia.. - Nonulosonic acids contribute to the pathogenicity of the oral bacterium Tannerella forsythia.. - Potential of the Tannerella forsythia S-layer to delay the immune response. - A general protein O-glycosylation gene cluster encodes the species-specific glycan of the oral pathogen Tannerella forsythia: O-glycan biosynthesis and immunological implications. - Phylum-wide general protein O-glycosylation system of the. - Beta- hexosaminidase activity of the oral pathogen Tannerella forsythia influences biofilm formation on glycoprotein substrates. - Genomics of the Uncultivated, Periodontitis-Associated Bacterium Tannerella sp. - Genetics and evolution of the Salmonella galactose-initiated set of o antigens
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