Comparative analysis of prophages in Streptococcus mutans genomes

Tiwei Fu; Xiangyu Fan; Quanxin Long; Wanyan Deng; Jinlin Song; Enyi Huang

doi:10.7717/peerj.4057

Comparative analysis of prophages in Streptococcus mutans genomes

PeerJ. 2017 Nov 17:5:e4057. doi: 10.7717/peerj.4057. eCollection 2017.

Authors

Tiwei Fu¹, Xiangyu Fan², Quanxin Long³, Wanyan Deng⁴, Jinlin Song¹, Enyi Huang¹

Affiliations

¹ College of Stomatology, Chongqing Medical University, Chongqing Key Laboratory for Oral Diseases and Biomedical Sciences, Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China.
² School of Biological Science and Technology, University of Jinan, Jinan, China.
³ Key Laboratory of Molecular Biology for Infectious Diseases of Ministry of Education, Chongqing Medical University, Chongqing, China.
⁴ Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.

Abstract

Prophages have been considered genetic units that have an intimate association with novel phenotypic properties of bacterial hosts, such as pathogenicity and genomic variation. Little is known about the genetic information of prophages in the genome of Streptococcus mutans, a major pathogen of human dental caries. In this study, we identified 35 prophage-like elements in S. mutans genomes and performed a comparative genomic analysis. Comparative genomic and phylogenetic analyses of prophage sequences revealed that the prophages could be classified into three main large clusters: Cluster A, Cluster B, and Cluster C. The S. mutans prophages in each cluster were compared. The genomic sequences of phismuN66-1, phismuNLML9-1, and phismu24-1 all shared similarities with the previously reported S. mutans phages M102, M102AD, and ϕAPCM01. The genomes were organized into seven major gene clusters according to the putative functions of the predicted open reading frames: packaging and structural modules, integrase, host lysis modules, DNA replication/recombination modules, transcriptional regulatory modules, other protein modules, and hypothetical protein modules. Moreover, an integrase gene was only identified in phismuNLML9-1 prophages.

Keywords: Comparative genomics; Prophages; Streptococcus mutans.

Grants and funding

This work was supported by the Program for Innovation Team Building at Institutions of Higher Education in Chongqing in 2016 (Project No. CXTDG201602006), the Project Supported by Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, the National Natural Science Foundation of China (Project No. 31600148), the Shandong Excellent Young Scientist Award Fund (BS2014YY031), and the Foundation of University of Jinan (XBS1519, XKY1633). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.