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The repeat structure of two paralogous genes, Yersinia ruckeri invasin (yrInv) and a “Y. ruckeri invasin-like molecule”, (yrIlm) sheds light on the evolution of adhesive capacities of a fish pathogen
Abstract
Inverse autotransporters comprise the recently identified type Ve secretion system and are exemplified by intimin from enterohaemorrhagic Escherichia coli and invasin from enteropathogenic Yersiniae. These proteins share a common domain architecture and promote bacterial adhesion to host cells. Here, we identified and characterized two putative inverse autotransporter genes in the fish pathogen Yersinia ruckeri NVH_3758, namely yrInv (for Y. ruckeri invasin) and yrIlm (for Y. ruckeri invasin-like molecule). When trying to clone the highly repetitive genes for structural and functional studies, we experienced problems in obtaining PCR products. PCR failures and the highly repetitive nature of inverse autotransporters prompted us to sequence the genome of Y. ruckeri NVH_3758 using PacBio sequencing, which produces some of the longest average read lengths available in the industry at this moment. According to our sequencing data, YrIlm is composed of 2603 amino acids (7812bp) and has a molecular mass of 256.4kDa. Based on the new genome information, we performed PCR analysis on four non-sequenced Y. ruckeri strains as well as the sequenced. Y. ruckeri type strain. We found that the genes are variably present in the strains, and that the length of yrIlm, when present, also varies. In addition, the length of the gene product for all strains, including the type strain, was much longer than expected based on deposited sequences. The internal repeats of the yrInv gene product are hig…
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“Deposited genomes based on short-read methods show underestimated repeat numbers (by a factor of 4 to 5).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [81]
In the citing paper
“As an example, Wrobel et al. (81) have shown that in the fish pathogen Yersinia ruckeri, a surface adhesin involved in biofilm formation called Ilm has >20 Ig-like domains repeated in tandem that are identical even on the DNA level (repeat length ∼300 bp).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [81]
In the citing paper
“Repeat numbers vary slightly from strain to strain, but in this case only PacBio-based genomes show the correct number of repeats (Figure 1).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [81]
In the citing paper
“Repeat numbers vary slightly from strain to strain, but in this case only PacBio-based genomes show the correct number of repeats (Figure 1).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [81]
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Tørresen, O. K., Star, B., Mier, P., Andrade-Navarro, M. A., Bateman, A., Jarnot, P., Gruca, A., Grynberg, M., Kajava, A. V., Promponas, V. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz841 · Cited by 347
Self-citation
Metadata
- Authors
- Wrobel, A., Ottoni, C., Leo, J. C., Gulla, S., & Linke, D.
- ORCID
- Linke, Dirk
- Venue
- Journal of Structural Biology
- Publisher
- Elsevier BV
- Published
- 2018-02
- Volume
- 201
- Issue
- 2
- Pages
- 171-183
- ISSN
- 1047-8477
- Cited by
- 20
- References
- 79
- Language
- en
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
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