Ori-Finder: A web-based system for finding oriC s in unannotated bacterial genomes

Gao, Feng; Zhang, Chun‐Ting

doi:10.1186/1471-2105-9-79

Cited by 249 publications

(230 citation statements)

References 12 publications

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“…The first region extends from 62.7 to 67.5 kb and contains genes for tRNAs, while the second is found between kb 116.5 and kb 118.8. In an effort to determine whether this region served as the replication origin, we used Ori Finder analysis (19), but it failed to define the Ori sequence of this virus. The low GϩC content of the phage may result in problems of codon usage during phage infection (59).…”

Section: Resultsmentioning

confidence: 99%

Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus

Santos

Kropinski

Ceyssens

et al. 2011

J Virol

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(Bacterio)phage PVP-SE1, isolated from a German wastewater plant, presents a high potential value as a biocontrol agent and as a diagnostic tool, even compared to the well-studied typing phage Felix 01, due to its broad lytic spectrum against different Salmonella strains. Sequence analysis of its genome (145,964 bp) shows it to be terminally redundant and circularly permuted. Its G؉C content, 45.6 mol%, is lower than that of its hosts (50 to 54 mol%). We found a total of 244 open reading frames (ORFs), representing 91.6% of the coding capacity of the genome. Approximately 46% of encoded proteins are unique to this phage, and 22.1% of the proteins could be functionally assigned. This myovirus encodes a large number of tRNAs (n ‫؍‬ 24), reflecting its lytic capacity and evolution through different hosts. Tandem mass spectrometric analysis using electron spray ionization revealed 25 structural proteins as part of the mature phage particle. The genome sequence was found to share homology with 140 proteins of the Escherichia coli bacteriophage rV5. Both phages are unrelated to any other known virus, which suggests that an "rV5-like virus" genus should be created within the Myoviridae to contain these two phages.

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Section: Resultsmentioning

confidence: 99%

Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus

Santos

Kropinski

Ceyssens

et al. 2011

J Virol

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“…The genome contains 2877 predicted protein-coding genes; a functional prediction could be assigned for 2248 genes (B78%), whereas 629 genes had no functional prediction of any kind. The putative origin of replication (OriC) was identified via DNA-BoxComplex using OriFinder (Gao and Zhang, 2008) and was in the vicinity of the GC skew minimum and adjacent to recF (CCALI_ 01940). The genome contained one complete rRNA operon (16S, 5S and 23S) and one additional copy of the 16S rRNA gene; both 16S rRNA genes (1416 bp) had identical nucleotide sequences.…”

Section: Resultsmentioning

confidence: 99%

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

et al. 2014

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Most of the lineages of bacteria have remained unknown beyond environmental surveys using molecular markers. Until the recent characterisation of several strains, the phylum Armatimonadetes (formerly known as 'candidate division OP10') was a dominant and globally-distributed lineage within this 'uncultured majority'. Here we report the first Armatimonadetes genome from the thermophile Chthonomonas calidirosea T49 T and its role as a saccharide scavenger in a geothermal steam-affected soil environment. Phylogenomic analysis indicates T49 T to be related closely to the phylum Chloroflexi. The predicted genes encoding for carbohydrate transporters (27 carbohydrate ATP-binding cassette transporter-related genes) and carbohydrate-metabolising enzymes (including at least 55 putative enzymes with glycosyl hydrolase domains) within the 3.43 Mb genome help explain its ability to utilise a wide range of carbohydrates as well as its inability to break down extracellular cellulose. The presence of only a single class of branched amino acid transporter appears to be the causative step for the requirement of isoleucine for growth. The genome lacks many commonly conserved operons (for example, lac and trp). Potential causes for this, such as dispersion of functionally related genes via horizontal gene transfer from distant taxa or recent genome recombination, were rejected. Evidence suggests T49 T relies on the relatively abundant r-factors, instead of operonic organisation, as the primary means of transcriptional regulation. Examination of the genome with physiological data and environmental dynamics (including interspecific interactions) reveals ecological factors behind the apparent elusiveness of T49 T to cultivation and, by extension, the remaining 'uncultured majority' that have so far evaded conventional microbiological techniques.

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“…To improve the stability of the plasmid and the efficiency of target gene expression in the bacteria [30], the native chromosomal DNA replication origin (OriC) in H. campaniensis LS21 genome was screened for plasmid construction. Ori-Finder (http://tubic.tju.edu.cn/Ori-Finder), an online system, has been used for finding oriC H. campaniensis LS21 genome (with the kind assistance from Professor Zhang Chunting and Dr Gao Feng of Tianjin University, China), which is based on an integrated method comprising the analysis of base composition asymmetry using the Z-curve method, distribution of DnaA boxes, and the occurrence of genes frequently close to OriC.…”

Section: Oric Sequence Screeningmentioning

confidence: 99%

A seawater-based open and continuous process for polyhydroxyalkanoates production by recombinant Halomonas campaniensis LS21 grown in mixed substrates

Yue

Chen

Yang

et al. 2014

Biotechnol Biofuels

148

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Background: High-cost production of bioplastics polyhydroxyalkanoates (PHA) is a major concern for their large scale application. In order to produce PHA economically, new technology must be developed to reduce costs on energy consumption, fresh water and substrate usages. It is also important to conduct the PHA production process in a continuous way rather than in a batch process. Results: A halophile Halomonas campaniensis strain LS21 was isolated to allow the development of a sea water based open and continuous process for PHA production utilizing mixed substrates consisting of mostly cellulose, starch, lipids and proteins. To study the feasibilities of open and long-term cultivation as well as genetic manipulation of this strain, polyhydroxybutyrate (PHB), the first member of the diverse PHA family, was taken as an example for the application of H. campaniensis LS21 in a robust and long lasting fermentation process. Wild type and recombinant H. campaniensis LS21 containing a PHB synthesis genes phbCAB were allowed respectively to grow in artificial seawater containing mixed substrates similar to kitchen wastes, including soluble and insoluble cellulose, proteins, fats, fatty acids and starch for 65 days without interruption. In the presence of 27 g/L NaCl under a pH around 10 at 37°C, the recombinant produced approximately 70% PHB and the wild type 26% during the 65 days fermentation process without infection. H. campaniensis LS21 secreted extracellular amylase, lipase, protease and cellulase simultaneously during the whole process to allow consumption of the mixed substrates. The recombinant was also found to stably maintain the phbCAB plasmid over the entire 65 days process. Conclusions:The seawater based open and continuous process based on halophilic Halomonas campaniensis LS21 allowed the applications of kitchen wastes like mixed substrates as nutrients for production of bioplastic PHB. This study demonstrates the advantages of this technology in terms of energy saving (non-sterilization), seawater based (not fresh water needed), long-lasting and continuous open processing (against batch process), and low cost substrates (non-food mixed substrates). Combined with its ease of genetic manipulation, Halomonas campaniensis LS21 could be developed into a platform for low cost production of chemicals, materials and biofuels.

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Ori-Finder: A web-based system for finding oriC s in unannotated bacterial genomes

Cited by 249 publications

References 12 publications

Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus

Genomic and Proteomic Characterization of the Broad-Host-Range Salmonella Phage PVP-SE1: Creation of a New Phage Genus

Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

A seawater-based open and continuous process for polyhydroxyalkanoates production by recombinant Halomonas campaniensis LS21 grown in mixed substrates

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