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Yin ZN, Lai FL, Gao F. Unveiling human origins of replication using deep learning: accurate prediction and comprehensive analysis. Brief Bioinform 2023; 25:bbad432. [PMID: 38008420 PMCID: PMC10676776 DOI: 10.1093/bib/bbad432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/11/2023] [Accepted: 11/06/2023] [Indexed: 11/28/2023] Open
Abstract
Accurate identification of replication origins (ORIs) is crucial for a comprehensive investigation into the progression of human cell growth and cancer therapy. Here, we proposed a computational approach Ori-FinderH, which can efficiently and precisely predict the human ORIs of various lengths by combining the Z-curve method with deep learning approach. Compared with existing methods, Ori-FinderH exhibits superior performance, achieving an area under the receiver operating characteristic curve (AUC) of 0.9616 for K562 cell line in 10-fold cross-validation. In addition, we also established a cross-cell-line predictive model, which yielded a further improved AUC of 0.9706. The model was subsequently employed as a fitness function to support genetic algorithm for generating artificial ORIs. Sequence analysis through iORI-Euk revealed that a vast majority of the created sequences, specifically 98% or more, incorporate at least one ORI for three cell lines (Hela, MCF7 and K562). This innovative approach could provide more efficient, accurate and comprehensive information for experimental investigation, thereby further advancing the development of this field.
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Affiliation(s)
- Zhen-Ning Yin
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Fei-Liao Lai
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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Dong MJ, Luo H, Gao F. Ori-Finder 2022: A Comprehensive Web Server for Prediction and Analysis of Bacterial Replication Origins. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1207-1213. [PMID: 36257484 DOI: 10.1016/j.gpb.2022.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/21/2022] [Accepted: 10/11/2022] [Indexed: 12/26/2022]
Abstract
The replication of DNA is a complex biological process that is essential for life. Bacterial DNA replication is initiated at genomic loci referred to as replication origins (oriCs). Integrating the Z-curve method, DnaA box distribution, and comparative genomic analysis, we developed a web server to predict bacterial oriCs in 2008 called Ori-Finder, which contributes to clarify the characteristics of bacterial oriCs. The oriCs of hundreds of sequenced bacterial genomes have been annotated in the genome reports using Ori-Finder and the predicted results have been deposited in DoriC, a manually curated database of oriCs. This has facilitated large-scale data mining of functional elements in oriCs and strand-biased analysis. Here, we describe Ori-Finder 2022 with updated prediction framework, interactive visualization module, new analysis module, and user-friendly interface. More species-specific indicator genes and functional elements of oriCs are integrated into the updated framework, which has also been redesigned to predict oriCs in draft genomes. The interactive visualization module displays more genomic information related to oriCs and their functional elements. The analysis module includes regulatory protein annotation, repeat sequence discovery, homologous oriC search, and strand-biased analyses. The redesigned interface provides additional customization options for oriC prediction. Ori-Finder 2022 is freely available at http://tubic.tju.edu.cn/Ori-Finder/ and https://tubic.org/Ori-Finder/.
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Affiliation(s)
- Mei-Jing Dong
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China.
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Girdhar N, Kumari N, Krishnamachari A. Computational characterization and analysis of molecular sequence data of Elizabethkingia meningoseptica. BMC Res Notes 2022; 15:133. [PMID: 35397563 PMCID: PMC8994065 DOI: 10.1186/s13104-022-06011-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 03/17/2022] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Elizabethkingia meningoseptica is a multidrug resistance strain which primarily causes meningitis in neonates and immunocompromised patients. Being a nosocomial infection causing agent, less information is available in literature, specifically, about its genomic makeup and associated features. An attempt is made to study them through bioinformatics tools with respect to compositions, embedded periodicities, open reading frames, origin of replication, phylogeny, orthologous gene clusters analysis and pathways. RESULTS Complete DNA and protein sequence pertaining to E. meningoseptica were thoroughly analyzed as part of the study. E. meningoseptica G4076 genome showed 7593 ORFs it is GC rich. Fourier based analysis showed the presence of typical three base periodicity at the genome level. Putative origin of replication has been identified. Phylogenetically, E. meningoseptica is relatively closer to E. anophelis compared to other Elizabethkingia species. A total of 2606 COGs were shared by all five Elizabethkingia species. Out of 3391 annotated proteins, we could identify 18 unique ones involved in metabolic pathway of E. meningoseptica and this can be an initiation point for drug designing and development. Our study is novel in the aspect in characterizing and analyzing the whole genome data of E. meningoseptica.
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Affiliation(s)
- Neha Girdhar
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Jaipur, 304022, Rajasthan, India
| | - Nilima Kumari
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Jaipur, 304022, Rajasthan, India
| | - A Krishnamachari
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Abstract
While the model bacteria Escherichia coli and Bacillus subtilis harbor single chromosomes, which is known as monoploidy, some freshwater cyanobacteria contain multiple chromosome copies per cell throughout their cell cycle, which is known as polyploidy. In the model cyanobacteria Synechococcus elongatus PCC 7942 and Synechocystis sp. PCC 6803, chromosome copy number (ploidy) is regulated in response to growth phase and environmental factors. In S. elongatus 7942, chromosome replication is asynchronous both among cells and chromosomes. Comparative analysis of S. elongatus 7942 and S. sp. 6803 revealed a variety of DNA replication mechanisms. In this review, the current knowledge of ploidy and DNA replication mechanisms in cyanobacteria is summarized together with information on the features common with plant chloroplasts. It is worth noting that the occurrence of polyploidy and its regulation are correlated with certain cyanobacterial lifestyles and are shared between some cyanobacteria and chloroplasts. ABBREVIATIONS NGS: next-generation sequencing; Repli-seq: replication sequencing; BrdU: 5-bromo-2'-deoxyuridine; TK: thymidine kinase; GCSI: GC skew index; PET: photosynthetic electron transport; RET: respiration electron transport; Cyt b6f complex: cytochrome b6f complex; PQ: plastoquinone; PC: plastocyanin.
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Affiliation(s)
- Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture , Tokyo, Japan
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Quan CL, Gao F. Quantitative analysis and assessment of base composition asymmetry and gene orientation bias in bacterial genomes. FEBS Lett 2019; 593:918-925. [PMID: 30941752 DOI: 10.1002/1873-3468.13374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/28/2019] [Accepted: 03/31/2019] [Indexed: 11/10/2022]
Abstract
Base composition asymmetry and gene orientation bias are two common genomic structures in bacterial genomes. Here, correlation coefficients between nucleotide disparities and coding sequence (CDS) skew have been calculated, which provides insights into their relationship from an individual genome perspective. Consequently, we find GC and RY disparities correlate significantly with CDS skew, since around 60% of the bacterial genomes under study have correlation coefficients > 0.9. Then, we present a model for quantitative assessment of nucleotide disparity and CDS skew in which a numerical index R2 is used for evaluation. We find that skew curves with higher R2 perform better on the prediction of replication origins in bacteria.
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Affiliation(s)
- Chun-Lan Quan
- Department of Physics, School of Science, Tianjin University, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), China
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Luo H, Quan CL, Peng C, Gao F. Recent development of Ori-Finder system and DoriC database for microbial replication origins. Brief Bioinform 2018; 20:1114-1124. [DOI: 10.1093/bib/bbx174] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Indexed: 01/28/2023] Open
Abstract
Abstract
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes.
Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.
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Phylogenomic proximity and metabolic discrepancy of Methanosarcina mazei Go1 across methanosarcinal genomes. Biosystems 2017; 155:20-28. [DOI: 10.1016/j.biosystems.2017.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Revised: 03/15/2017] [Accepted: 03/20/2017] [Indexed: 02/04/2023]
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Quantitative analysis of correlation between AT and GC biases among bacterial genomes. PLoS One 2017; 12:e0171408. [PMID: 28158313 PMCID: PMC5291525 DOI: 10.1371/journal.pone.0171408] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 01/20/2017] [Indexed: 01/03/2023] Open
Abstract
Due to different replication mechanisms between the leading and lagging strands, nucleotide composition asymmetries widely exist in bacterial genomes. A general consideration reveals that the leading strand is enriched in Guanine (G) and Thymine (T), and the lagging strand shows richness in Adenine (A) and Cytosine (C). However, some bacteria like Bacillus subtilis have been discovered composing more A than T in the leading strand. To investigate the difference, we analyze the nucleotide asymmetry from the aspect of AT and GC bias correlations. In this study, we propose a windowless method, the Z-curve Correlation Coefficient (ZCC) index, based on the Z-curve method, and analyzed more than 2000 bacterial genomes. We find that the majority of bacteria reveal negative correlations between AT and GC biases, while most genomes in Firmicutes and Tenericutes have positive ZCC indexes. The presence of PolC, purine asymmetry and stronger genes preference in the leading strand are not confined to Firmicutes, but also likely to happen in other phyla dominated by positive ZCC indexes. This method also provides a new insight into other relevant features like aerobism, and can be applied to analyze the correlation between RY (Purine and Pyrimidine) and MK (Amino and Keto) bias and so on.
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Singh VK, Krishnamachari A. Context based computational analysis and characterization of ARS consensus sequences (ACS) of Saccharomyces cerevisiae genome. GENOMICS DATA 2016; 9:130-6. [PMID: 27508123 PMCID: PMC4971157 DOI: 10.1016/j.gdata.2016.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/27/2016] [Accepted: 07/06/2016] [Indexed: 01/08/2023]
Abstract
Genome-wide experimental studies in Saccharomyces cerevisiae reveal that autonomous replicating sequence (ARS) requires an essential consensus sequence (ACS) for replication activity. Computational studies identified thousands of ACS like patterns in the genome. However, only a few hundreds of these sites act as replicating sites and the rest are considered as dormant or evolving sites. In a bid to understand the sequence makeup of replication sites, a content and context-based analysis was performed on a set of replicating ACS sequences that binds to origin-recognition complex (ORC) denoted as ORC-ACS and non-replicating ACS sequences (nrACS), that are not bound by ORC. In this study, DNA properties such as base composition, correlation, sequence dependent thermodynamic and DNA structural profiles, and their positions have been considered for characterizing ORC-ACS and nrACS. Analysis reveals that ORC-ACS depict marked differences in nucleotide composition and context features in its vicinity compared to nrACS. Interestingly, an A-rich motif was also discovered in ORC-ACS sequences within its nucleosome-free region. Profound changes in the conformational features, such as DNA helical twist, inclination angle and stacking energy between ORC-ACS and nrACS were observed. Distribution of ACS motifs in the non-coding segments points to the locations of ORC-ACS which are found far away from the adjacent gene start position compared to nrACS thereby enabling an accessible environment for ORC-proteins. Our attempt is novel in considering the contextual view of ACS and its flanking region along with nucleosome positioning in the S. cerevisiae genome and may be useful for any computational prediction scheme.
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Abstract
The omnipresence of Arthrobacter species in polluted and toxic soils indicates their great potential in environmental biotechnologies, but practical applications of these bacteria are scarce mainly due to the availability of useful genetic engineering tools. Although many fully sequenced Arthrobacter genomes have been deposited in GenBank, little is known about the biology of their plasmids, especially the core functions: replication and partition. In this study the available Arthrobacter plasmid sequences were analyzed in order to identify their putative replication origin. At least the oris from the cryptic plasmids pXZ10142, pCG1, and pBL1 appear to work in this genus. Based on ParA homolog sequences, the Arthrobacter specific plasmids were classified into 4 clades. Iteron-like sequences were identified on most of the plasmids, indicating the position of the putative Arthrobacter specific oris. Although attempts were made to identify the core gene set required for plasmid replication in this genus, it was not possible. The plasmid proteomes showed a rather low similarity.
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Gao F. Editorial: DNA Replication Origins in Microbial Genomes. Front Microbiol 2016; 6:1545. [PMID: 26779176 PMCID: PMC4705448 DOI: 10.3389/fmicb.2015.01545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 12/21/2015] [Indexed: 11/30/2022] Open
Affiliation(s)
- Feng Gao
- Department of Physics, Tianjin UniversityTianjin, China; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
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Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods. J Virol 2016; 90:3458-68. [PMID: 26763997 DOI: 10.1128/jvi.03098-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/07/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The field of viral metagenomics has expanded our understanding of viral diversity from all three domains of life (Archaea, Bacteria, and Eukarya). Traditionally, viral metagenomic studies provide information about viral gene content but rarely provide knowledge about virion morphology and/or cellular host identity. Here we describe a new virus, Acidianus tailed spindle virus (ATSV), initially identified by bioinformatic analysis of viral metagenomic data sets from a high-temperature (80°C) acidic (pH 2) hot spring located in Yellowstone National Park, followed by more detailed characterization using only environmental samples without dependency on culturing. Characterization included the identification of the large tailed spindle virion morphology, determination of the complete 70.8-kb circular double-stranded DNA (dsDNA) viral genome content, and identification of its cellular host. Annotation of the ATSV genome revealed a potential three-domain gene product containing an N-terminal leucine-rich repeat domain, followed by a likely posttranslation regulatory region consisting of high serine and threonine content, and a C-terminal ESCRT-III domain, suggesting interplay with the host ESCRT system. The host of ATSV, which is most closely related to Acidianus hospitalis, was determined by a combination of analysis of cellular clustered regularly interspaced short palindromic repeat (CRISPR)/Cas loci and dual viral and cellular fluorescence in situ hybridization (viral FISH) analysis of environmental samples and confirmed by culture-based infection studies. This work provides an expanded pathway for the discovery, isolation, and characterization of new viruses using culture-independent approaches and provides a platform for predicting and confirming virus hosts. IMPORTANCE Virus discovery and characterization have been traditionally accomplished by using culture-based methods. While a valuable approach, it is limited by the availability of culturable hosts. In this research, we report a virus-centered approach to virus discovery and characterization, linking viral metagenomic sequences to a virus particle, its sequenced genome, and its host directly in environmental samples, without using culture-dependent methods. This approach provides a pathway for the discovery, isolation, and characterization of new viruses. While this study used an acidic hot spring environment to characterize a new archaeal virus, Acidianus tailed spindle virus (ATSV), the approach can be generally applied to any environment to expand knowledge of virus diversity in all three domains of life.
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Huang H, Song CC, Yang ZL, Dong Y, Hu YZ, Gao F. Identification of the Replication Origins from Cyanothece ATCC 51142 and Their Interactions with the DnaA Protein: From In Silico to In Vitro Studies. Front Microbiol 2015; 6:1370. [PMID: 26696980 PMCID: PMC4674748 DOI: 10.3389/fmicb.2015.01370] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/17/2015] [Indexed: 11/30/2022] Open
Abstract
Based on the complete genome of Cyanothece ATCC 51142, the oriCs of both the circular and linear chromosomes in Cyanothece ATCC 51142 have been predicted by utilizing a web-based system Ori-Finder. Here, we provide experimental support for the results of Ori-Finder to identify the replication origins of Cyanothece ATCC 51142 and their interactions with the initiator protein, DnaA. The two replication origins are composed of three characteristically arranged DnaA boxes and an AT-rich stretch, and the oriC in the circular chromosome is followed by the dnaN gene. The dnaA gene is located downstream of the origin of the circular chromosome and it expresses a typical DnaA protein that is divided into four domains (I, II, III, IV), as with other members of the DnaA protein family. We purify DnaA (IV) and characterize the interaction of the purified protein with the replication origins, so as to offer experimental support for the prediction. The results of the electrophoretic mobility shift assay and DNase I footprint assay demonstrate that the C-terminal domain of the DnaA protein from Cyanothece ATCC 51142 specifically binds the oriCs of both the circular and linear chromosomes, and the DNase I footprint assay demonstrates that DnaA (IV) exhibits hypersensitive affinity with DnaA boxes in both oriCs.
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Affiliation(s)
- He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering Tianjin, China
| | - Cheng-Cheng Song
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering Tianjin, China
| | - Zhi-Liang Yang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering Tianjin, China
| | - Yan Dong
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering Tianjin, China
| | - Yao-Zhong Hu
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering Tianjin, China
| | - Feng Gao
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University Tianjin, China ; Collaborative Innovation Center of Chemical Science and Engineering Tianjin, China ; Department of Physics, Tianjin University Tianjin, China
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Diversification of DnaA dependency for DNA replication in cyanobacterial evolution. ISME JOURNAL 2015; 10:1113-21. [PMID: 26517699 DOI: 10.1038/ismej.2015.194] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 09/01/2015] [Accepted: 09/27/2015] [Indexed: 11/08/2022]
Abstract
Regulating DNA replication is essential for all living cells. The DNA replication initiation factor DnaA is highly conserved in prokaryotes and is required for accurate initiation of chromosomal replication at oriC. DnaA-independent free-living bacteria have not been identified. The dnaA gene is absent in plastids and some symbiotic bacteria, although it is not known when or how DnaA-independent mechanisms were acquired. Here, we show that the degree of dependency of DNA replication on DnaA varies among cyanobacterial species. Deletion of the dnaA gene in Synechococcus elongatus PCC 7942 shifted DNA replication from oriC to a different site as a result of the integration of an episomal plasmid. Moreover, viability during the stationary phase was higher in dnaA disruptants than in wild-type cells. Deletion of dnaA did not affect DNA replication or cell growth in Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120, indicating that functional dependency on DnaA was already lost in some nonsymbiotic cyanobacterial lineages during diversification. Therefore, we proposed that cyanobacteria acquired DnaA-independent replication mechanisms before symbiosis and such an ancestral cyanobacterium was the sole primary endosymbiont to form a plastid precursor.
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Song C, Zhang S, Huang H. Choosing a suitable method for the identification of replication origins in microbial genomes. Front Microbiol 2015; 6:1049. [PMID: 26483774 PMCID: PMC4588119 DOI: 10.3389/fmicb.2015.01049] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 09/14/2015] [Indexed: 12/19/2022] Open
Abstract
As the replication of genomic DNA is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. Making sense of DNA replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. Thus, clearly comprehending the positions and sequences of replication origins which are fundamental to chromosome organization and duplication is the first priority of all. In view of such important roles of replication origins, tremendous work has been aimed at identifying and testing the specificity of replication origins. A number of computational tools based on various skew types have been developed to predict replication origins. 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 genomes. Based on the predicted results, we should choose an effective method for identifying and confirming the interactions at origins of replication. Here we describe the main existing experimental methods that aimed to determine the replication origin regions and list some of the many the practical applications of these methods.
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Affiliation(s)
- Chengcheng Song
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - Shaocun Zhang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin UniversityTianjin, China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin UniversityTianjin, China
- Collaborative Innovation Center of Chemical Science and EngineeringTianjin, China
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16
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Gao F. Bacteria may have multiple replication origins. Front Microbiol 2015; 6:324. [PMID: 25941523 PMCID: PMC4403523 DOI: 10.3389/fmicb.2015.00324] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/31/2015] [Indexed: 01/15/2023] Open
Affiliation(s)
- Feng Gao
- Department of Physics, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering Tianjin, China
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Luo H, Zhang CT, Gao F. Ori-Finder 2, an integrated tool to predict replication origins in the archaeal genomes. Front Microbiol 2014; 5:482. [PMID: 25309521 PMCID: PMC4164010 DOI: 10.3389/fmicb.2014.00482] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 08/27/2014] [Indexed: 11/13/2022] Open
Abstract
DNA replication is one of the most basic processes in all three domains of cellular life. With the advent of the post-genomic era, the increasing number of complete archaeal genomes has created an opportunity for exploration of the molecular mechanisms for initiating cellular DNA replication by in vivo experiments as well as in silico analysis. However, the location of replication origins (oriCs) in many sequenced archaeal genomes remains unknown. We present a web-based tool Ori-Finder 2 to predict oriCs in the archaeal genomes automatically, based on the integrated method comprising the analysis of base composition asymmetry using the Z-curve method, the distribution of origin recognition boxes identified by FIMO tool, and the occurrence of genes frequently close to oriCs. The web server is also able to analyze the unannotated genome sequences by integrating with gene prediction pipelines and BLAST software for gene identification and function annotation. The result of the predicted oriCs is displayed as an HTML table, which offers an intuitive way to browse the result in graphical and tabular form. The software presented here is accurate for the genomes with single oriC, but it does not necessarily find all the origins of replication for the genomes with multiple oriCs. Ori-Finder 2 aims to become a useful platform for the identification and analysis of oriCs in the archaeal genomes, which would provide insight into the replication mechanisms in archaea. The web server is freely available at http://tubic.tju.edu.cn/Ori-Finder2/.
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Affiliation(s)
- Hao Luo
- Department of Physics, Tianjin University Tianjin, China
| | | | - Feng Gao
- Department of Physics, Tianjin University Tianjin, China ; Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University Tianjin, China ; SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering Tianjin, China
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