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DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids

Hao Luo, Feng Gao
2018 Nucleic Acids Research  
DoriC, a database of replication origins, was initially created to present the bacterial oriCs predicted by Ori-Finder or determined by experiments in 2007.  ...  Now, DoriC becomes the most complete and scalable database of replication origins in prokaryotic genomes, and facilitates the studies in large-scale oriC data mining, strand-biased analyses and replication  ...  Chun-Ting Zhang for the invaluable assistance and inspiring discussions. FUNDING  ... 
doi:10.1093/nar/gky1014 pmid:30364951 fatcat:tldou2mcaba4xllk5tfvuac46m

Choosing a suitable method for the identification of replication origins in microbial genomes

Chengcheng Song, Shaocun Zhang, He Huang
2015 Frontiers in Microbiology  
Using various in silico approaches such as Ori-Finder, and databases such as DoriC, researchers have predicted the locations of replication origins sites for thousands of bacterial chromosomes and archaeal  ...  A number of computational tools based on various skew types have been developed to predict replication origins.  ...  Acknowledgments The present work was partially supported by National High Technology Research and Development Program of China (Grant No. 2015AA020701) and National Natural Science Foundation of China  ... 
doi:10.3389/fmicb.2015.01049 pmid:26483774 pmcid:PMC4588119 fatcat:lhv3taujqvdfjnenvsjsxrorfe

The Complete Genome Sequence of the Murine Pathobiont Helicobacter typhlonius

Jeroen Frank, Celia Dingemanse, Arnoud M. Schmitz, Rolf H. A. M. Vossen, Gert-Jan B. van Ommen, Johan T. den Dunnen, Els C. Robanus-Maandag, Seyed Yahya Anvar
2016 Frontiers in Microbiology  
Follow-up studies are necessary to evaluate the true nature of its pathogenic capabilities. We found many methylated sites and a plethora of restriction-modification systems.  ...  Determination of the global methylation state revealed eight distinct recognition motifs for adenine and cytosine methylation. H. typhlonius shares four of its recognition motifs with H. pylori.  ...  Subsequently, we estimated the location of the origin of replication (oriC) using Ori-Finder in conjunction with the DoriC database (Gao and Zhang, 2008; Gao et al., 2013) .  ... 
doi:10.3389/fmicb.2015.01549 pmid:26779178 pmcid:PMC4705304 fatcat:zuqethatkjfg7fg3dyrq47l6hm

A systematic strategy for the investigation of vaccines and drugs targeting bacteria

Fangfang Yan, Feng Gao
2020 Computational and Structural Biotechnology Journal  
, replication-related proteins, transcriptomics and riboswitches, which plays a significant part in the treatment of infectious and pandemic diseases.  ...  Currently, target discovery, target analysis and MD analysis are integrated into a systematic set of drug and vaccine analysis strategy for bacteria.  ...  Meanwhile, we have massively updated the information about the oriC of pathogenic bacteria in the online DoriC 10.0 [72] database based on the predicted results of Ori-Finder [73, 74] , which can provide  ... 
doi:10.1016/j.csbj.2020.06.008 pmid:32637049 pmcid:PMC7327267 fatcat:lznperlwgjav7amumkbjqryudu

Exploring the Roles of DNA Methylation in the Metal-Reducing Bacterium Shewanella oneidensis MR-1

M. L. Bendall, K. Luong, K. M. Wetmore, M. Blow, J. Korlach, A. Deutschbauer, R. R. Malmstrom
2013 Journal of Bacteriology  
However, the developing systems-level view of Shewanella does not yet 86 incorporate DNA methylation and its potential regulatory roles.  ...  The enrichment 28 of methylated GATC motifs in the origin of replication indicate DNA methylation 29 may regulate genome replication in a manner similar to that seen in Escherichia 30 coli.  ...  For the small 440 number of genomes missing from DoriC, the origin was found using Ori-Finder 441 (http://tubic.tju.edu.cn/Ori-Finder) [67].  ... 
doi:10.1128/jb.00935-13 pmid:23995632 pmcid:PMC3807482 fatcat:bmqhis3mvjd5xgotax52n7n2gy

Colicin Z, a structurally and functionally novel colicin type that selectively kills enteroinvasive Escherichia coli and Shigella strains

Lenka Micenková, Juraj Bosák, Jiri Kucera, Matěj Hrala, Tereza Dolejšová, Ondrej Šedo, Dirk Linke, Radovan Fišer, David Šmajs
2019 Scientific Reports  
The cza and czi genes are transcribed in opposite directions and encode for 237 and 151 amino acid-long proteins, respectively.  ...  A novel colicin type, colicin Z (26.3 kDa), was described as a product of an original producer, extraintestinal E. coli B1356 strain, isolated from the anorectal abscess of a 17 years-old man.  ...  Acknowledgements This work was supported by the Grant Agency of the Czech Republic (16-21649S) and MUNI/A/1087/2018 to DS, and by a project of the Grant Agency of Charles University (390115) to TD.  ... 
doi:10.1038/s41598-019-47488-8 pmid:31366939 pmcid:PMC6668396 fatcat:w4hs2lizgbgpjdoilmf7c6f4qa

Genome Analysis of Streptococcus pyogenes Associated with Pharyngitis and Skin Infections

Joe Ibrahim, Jonathan A. Eisen, Guillaume Jospin, David A. Coil, Georges Khazen, Sima Tokajian, Feng Gao
2016 PLoS ONE  
The genomes were found to also house a multitude of features including gene regulation systems, virulence factors and antimicrobial resistance mechanisms.  ...  Karaky et al. in a more recent study detected 33 emm types and subtypes with the dominant being emm1, emm22, emm28, emm88 and emm4 and with 10% of the isolates being resistant to erythromycin and 3% resistant  ...  For our purpose, we used the web-based Ori-Finder system as described by Gao & Zhang [50] to identify oriCs and DNA boxes in our assembled genomes and the results subsequently BLASTed against the DoriC  ... 
doi:10.1371/journal.pone.0168177 pmid:27977735 pmcid:PMC5158041 fatcat:bxd5cxx5drfblgxw6nph2vopqq

Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade

Huei-Mien Ke, Anuphap Prachumwat, Chun-Ping Yu, Yi-Ting Yang, Sutitcha Promsri, Kuan-Fu Liu, Chu-Fang Lo, Mei-Yeh Jade Lu, Mei-Chin Lai, Isheng J. Tsai, Wen-Hsiung Li
2017 Scientific Reports  
A recent study of V. harveyi compared the genome of this species with those of three other  ...  Our study revealed the characteristics of V. campbellii in the Harveyi clade and the genetic basis for their wide-spread pathogenicity.  ...  AP and SP acknowledged the support from Mahidol University and the National Center for Genetic Engineering and Biotechnology (BIOTEC) of the Thai National Science and Technology Development Agency (NSTDA  ... 
doi:10.1038/srep41394 pmid:28145490 pmcid:PMC5286417 fatcat:wr5n4e5auzf5nb3o2gxvjra55m