Li et al. BMC Genomics 2014, 15:201 http://www.biomedcentral.com/1471-2164/15/201 RESEARCH ARTICLE Open Access Gene polymorphism analysis of Yersinia enterocolitica outer membrane protein A and putative outer membrane protein A family protein Kewei Li1†, Wenpeng Gu2†, Junrong Liang1†, Yuchun Xiao1, Haiyan Qiu1, Haoshu Yang1, Xin Wang1 and Huaiqi Jing1* Abstract Background: Yersinia enterocolitica outer membrane protein A (OmpA) is one of the major outer membrane proteins with high immunogenicity. We performed the polymorphism analysis for the outer membrane protein A and putative outer membrane protein A (p-ompA) family protein gene of 318 Y. enterocolitica strains. Results: The data showed all the pathogenic strains and biotype 1A strains harboring ystB gene carried both ompA and p-ompA genes; parts of the biotype 1A strains not harboring ystB gene carried either ompA or p-ompA gene. In non-pathogenic strains (biotype 1A), distribution of the two genes and ystB were highly correlated, showing genetic polymorphism. The pathogenic and non-pathogenic, highly and weakly pathogenic strains were divided into different groups based on sequence analysis of two genes. Although the variations of the sequences, the translated proteins and predicted secondary or tertiary structures of OmpA and P-OmpA were similar. Conclusions: OmpA and p-ompA gene were highly conserved for pathogenic Y. enterocolitica. The distributions of two genes were correlated with ystB for biotype 1A strains. The polymorphism analysis results of the two genes probably due to different bio-serotypes of the strains, and reflected the dissemination of different bio-serotype clones of Y. enterocolitica. Keywords: Yersinia enterocolitica, ompA, p-ompA, ystB Background are mainly referred to type III secretion system (TTSS) Y. enterocolitica is spread primarily through contami- encoded by 70-kb plasmid pYV [3,5], Yersinia adhesin nated food or water [1] and causes a wide range of intes- A (YadA), the virulence genes involved inv (invasion gene), tinal diseases, including enteritis, mesenteric lymphadenitis, ail (attachment and invasion locus gene), yst (Yersinia and sepsis in some severe cases; and also cause some stable toxin gene), myfA (mucoid Yersinia factor gene) and complications such as erythema nodosum and reactive the pathogenic island (HPI), etc. [6]. Biotype 1A strains are arthritis [2]. Currently, Y. enterocolitica is divided into traditionally considered non-pathogenic, however in recent six biotypes (1A, 1B, and 2–5) and more than 50 sero- studies have confirmed that a portion of them can cause types [3]. The biotypes of Y. enterocolitica are divided clinical symptoms similar to pathogenic strains [7]. into three groups according to the bacterial pathogenic Bacterial outer membrane proteins primarily contain properties: non-pathogenic biotype 1A, weakly patho- outer membrane protein A, porin C and F, being the genic biotypes 2–5, and highly pathogenic biotype 1B major immunogenic proteins, and widely present in [4]. At present, the virulent factors of Y. enterocolitica Gram-negative Enterobacteriaceae [8]. Recently, multi- function of outer membrane protein A of intestinal bacteria has been demonstrated [9-12], but seldom re- * Correspondence: [email protected] †Equal contributors ferred to Y. enterocolitica. In our previous study [13], 1National Institute for Communicable Disease Control and Prevention, OmpA was the major immunogenic protein of both Chinese Center for Disease Control and Prevention, State Key Laboratory for highly and weakly pathogenic Y. enterocolitica incu- Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, 102206 Beijing, China bated at different temperatures. To further identify the Full list of author information is available at the end of the article © 2014 Li et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. Li et al. BMC Genomics 2014, 15:201 Page 2 of 8 http://www.biomedcentral.com/1471-2164/15/201 characteristics of ompA for Y. enterocolitica,wese- Table 2 Distribution of ompA and ystB gene in biotype quenced and analyzed the polymorphism of ompA (and 1A strains p-ompA) genes of Y. enterocolitica. ompA ystB Total + − Results +84791 ompA p ompA Distribution of and - genes − 05757 The ompA and p-ompA genes were detected in 318 Total 84 64 148 Y. enterocolitica strains. The data showed 170 of all the − pathogenic strains carried both ompA and p-ompA;91 +: positive; : negative. biotype 1A strains carried ompA, and 106 carried p-ompA (Table 1). The ompA and p-ompA genes were both existed strains carried the ystB gene were clustered into pattern for biotype 1A strains carried ystB gene. However, the iso- F-T; Eight strains (except one) without ystB gene formed lates only had one of the two genes for biotype 1A strains pattern U-W (Figure 1A). without ystB gene. The distribution of the two genes was There were nucleotide fragment insertions and dele- associated with ystB, especially for ompA (Tables 2 and 3). tions for ompA gene sequences. The nucleotide fragment The correlation analysis (P < 0.05) showed correlation insertion was found for pattern C. The insertion site lo- coefficient (r) was 0.67 between ompA and ystB and cated at 659–664 nt of the ORF with the “-CTCCAG-” 0.58 between p-ompA and ystB. compared with pattern A (Figure 3I), this made an ala- nine (A) and a proline (P) inserted at position 220 and Polymorphism analysis of the two genes 221 in the amino acid sequence of the OmpA. For bio- ompA: The Open Reading Frame (ORF) of ompA was type 1A strains, sequence type diversities were found 1,074 bp encoding 357 amino acids (Genbank: YP_00 compared with pathogenic strains, and the nucleotide 1005874.1). The ompA gene of 261 strains formed 23 se- fragment deletions were observed for pattern U to W. quence types. The pathogenic group contained five 15 nucleotides deletions located at 140–154 nt with types, Pattern A-E (Figure 1A). 155 pathogenic strains “-TCTATGGCGACCAAG-”, and 6 nucleotides deletions (76 bio-serotype 3/O: 3, two 4/O: 3, 68 2/O: 9, one 4/O: located at 409–414 nt with “-GACGCA-” of ompA were 9 and eight 3/O: 9) were clustered into Pattern A, and found (Figure 3D). Eventually, this led to a change of the accounted for 91.2% of all of the pathogenic strains. amino acid of the OmpA at sites 39–52, 94–98,133-146, Therefore, pattern A was an absolute primary type in all included amino acid deletions or translation into other pathogenic isolates. Other nine pathogenic strains were amino acids. clustered into pattern B and C, seven (two bio-serotype Although some predicted amino acid differences were 2/O: 3, four 4/O: 3 and one 3/O: 9) were clustered into found for ompA of Y. enterocolitica, the primary proteins Pattern C, two pathogenic bio-serotype 2/O: 5, 27 clus- and its functions were the same, even if the insertions of tered into pattern B. Few nucleotide differences were the pathogenic or deletions of the non-pathogenic strains found between pattern A and B (Figure 2); while the nu- occurred. For all the Y. enterocolitica possessed ompA in cleotide insertion was found compared with pattern A and this study, the translated proteins were identical. The pre- C (Figure 3). Six highly pathogenic bio-serotype 1B/O: 8 dicted secondary structure of OmpA for all the strains strains were clustered into Patterns D and E (Figure 1A), were almost the same, and the predicted tertiary structure and the nucleotide differences were shown with red bases of OmpA for all the isolates were similar as well. It was compared with pattern A and B (Figure 2). highly conserved for the structure and function of OmpA The non-pathogenic group contained 91 biotype 1A for Y. enterocolitica, no matter the pathogenic ability and strains, formed 18 sequence types, Pattern F-W; all the 83 other characteristics. p-ompA: The Open Reading Frame (ORF) of p-ompA ompA p ompA Table 1 Distribution of and - gene in was 1,377 bp encoding 458 amino acids (GenBank: all strains ompA+ ompA− Total Table 3 Distribution of p-ompA and ystB gene in biotype p-ompA+ p-ompA− p-ompA+ p-ompA− 1A strains Pathogenic strains 170 0 0 0 170 p-ompA ystB Total Biotype 1A 84 0 0 0 84 + − strains ystB+ + 84 22 106 Biotype 1A 0 7 22 35 64 strains ystB− − 04242 Total 254 7 22 35 318 Total 84 64 148 +: positive; −: negative. +: positive; −: negative. Li et al. BMC Genomics 2014, 15:201 Page 3 of 8 http://www.biomedcentral.com/1471-2164/15/201 Figure 1 Cluster tree of ompA and p-ompA gene sequences. A: Cluster tree of ompA gene sequences from 261 strains; B: Cluster tree of p-ompA gene sequences from 275 strains; red: pathogenic strains; green: non-pathogenic strains. Figure 2 Sequence polymorphisms of ompA gene for pathogenic strains. The number above bases represented the position of bases in the ORF; figure in brackets represented strain number; red represented mutant bases; yellow area represented sense mutations, and others were nonsense mutations. Li et al. BMC Genomics 2014, 15:201 Page 4 of 8 http://www.biomedcentral.com/1471-2164/15/201 Figure 3 ompA nucleotide insertions and deletions. N: the ORF of pattern A for ompA; D: the deletion ORF of pattern U-W for ompA; I: the insertion ORF of pattern C for ompA; blue: nucleotide differences concentrated area; yellow: nucleotide deletion position; green: nucleotide insertion position. YP_001006877.1). P-ompA genes were existed among 276 pathogenic strains, 67 bio-serotype 2/O: 9, eight 3/O: 9, Y.