Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea

Wu, Zhenfang; Liu, Hailong; Liu, Jingfang; Liu, Xiaoqing; Xiang, Hua

doi:10.1186/1471-2164-13-478

Cited by 33 publications

(102 citation statements)

References 55 publications

(116 reference statements)

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“…The upstream and downstream sequence up to 2 Kb length was scanned for AT richness and the same was investigated for the presence of consensus ORB's. As ORB sequences in archaea vary from species to species [14] and there are only few archaea for which the ORB sequences have been experimentally verified [12,15,16], we have used such sequences to find consensus ORB sequences in the closely related species using multiple sequence alignment. Presence of ORB sequence, cdc6 gene and AT rich region is a good indicator of Ori site in archaea.…”

Section: Methods and Resultsmentioning

confidence: 99%

ArchaeProfile: A Database of Archaea and their Origins of Replication

Kumar¹

2015

J Comput Sci Syst Biol 2015

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Archaea are single cell microorganisms having several unique characteristics which differentiate them from bacteria. One of the key features which make archaea distinct from bacteria is the replication process, which is very different and resembles that of the eukaryotes. In-vivo mapping of the ori site in Archae is a time consuming and tedious job due to complexity involved in the culture of archaeal colony, which puts challenges as well as opportunity to scientist to devise in-silico method to map the Ori site in archaeal genomes. Z-curve approach is a widely used insilico method to predict the Ori site in archaea, but it is not equally successful for all archaeal genomes. Several other parameters like copy number and location of the cdc6 gene, AT rich region with the presence of origin recognition boxes (ORB) provide a better estimate of the Ori site in archaea. The motivation behind development of Archae Profile database is to predict the location and the number of putative Ori sites in archaeal genomes based on purinepyrimidine(R-Y) and amino-keto(M-K) disparity curve along with the consensus ORB sequences, cdc6 gene copy number, their location and upstream AT richness. Quick update cycle and easy browser interface makes Archae Profile distinct from other databases. Another important feature is the integration of tools for plotting disparity plot of a given genome sequence and finding specific repeats with copy number and location in a sequence. ArchaeProfile will be updated timely and the emphasis will be to integrate other tools for genome analysis as well as new search features in the database. Presently Archaea Profile has Ori related data of 122 archeal genome which is likely to increase with time.Availability: ArchaeProfile can be accessed freely from http://www.bioinfommv.in/archaeprofile. Data available on the database could be used for further analysis and tutorial purpose. Furthermore a tool has also been incorporated within the database which can draw the nucleotide skew plot of the nucleotide sequence supplied by users. Another tool which is helpful in finding specific repeats and their position in nucleotide sequence, is also given in the database, this can be useful in detecting short and long repeats in the Ori site in archaeal genomes which are very common [10,11]. Genes associated with the origin of replication in archaea like cdc6 with the full description of the location and the copy number of the above genes is also available on the database, as the association of cdc6 gene with the change in sign of the of disparity curve is a good indicator to find Ori site in archaeal genomes. Further the location of Origin Recognition Boxes (ORB) is necessary as a confirmation of the detection of the Ori site in Archae [12]. In Archae Profile database we have given all experimentally verified ORB's as well as in-silico predicted consensus ORB sequences and their location. The consensus ORB sequences were generated by multiple sequence alignment of predicted Ori region of closely related arche...

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Section: Methods and Resultsmentioning

confidence: 99%

ArchaeProfile: A Database of Archaea and their Origins of Replication

Kumar¹

2015

J Comput Sci Syst Biol 2015

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“…Haloarchaea usually contain a main chromosome and several megaplasmids (176,177). More than 15 haloarchaeal genomes are available in public databases, along with a large number of genomes of haloarchaeal plasmids, most of which are obtained from genome sequencing projects (40). Haloarchaeal plasmids often exhibit dynamic interactions with chromosomes due to the presence of a large number of insertion sequence elements.…”

Section: Genomic Featuresmentioning

confidence: 99%

“…Therefore, some large plasmids (megaplasmids) carry genes essential for cell viability. For this reason, these plasmids are also termed the second chromosome in some haloarchaea in the literature (40,180). Minimal replicons have been determined for two large haloarchaeal plasmids, pHH1 and pNRC100 (181,182), both of which are involved in gas vacuole synthesis.…”

Section: Genomic Featuresmentioning

confidence: 99%

“…Further analyses led to the identification of a putative replication protein, RepH (haloarchaeal replication protein homolog), a protein that does not show any sequence similarity to replication proteins of plasmids of bacterial origin or those obtained from nonhalophilic archaea. While it has been shown that some small haloarchaeal plasmids replicate in an RCR or a unidirectional mode, other haloarchaeal plasmids may replicate by using a mechanism involving a RepH or an ORC (origin recognition complex) homolog, although none of the putative replication proteins has been characterized so far (40).…”

Section: Genomic Featuresmentioning

confidence: 99%

“…Among 15 haloarchaea for which complete genomes have been determined, only one lacks a plasmid (40). Systematic screening for plasmids has also been conducted for two families of thermophilic archaea, the Sulfolobaceae and Thermococcaceae.…”

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Archaeal Extrachromosomal Genetic Elements

Wang

Peng

Shah

et al. 2015

Microbiol Mol Biol Rev

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SUMMARY Research on archaeal extrachromosomal genetic elements (ECEs) has progressed rapidly in the past decade. To date, over 60 archaeal viruses and 60 plasmids have been isolated. These archaeal viruses exhibit an exceptional diversity in morphology, with a wide array of shapes, such as spindles, rods, filaments, spheres, head-tails, bottles, and droplets, and some of these new viruses have been classified into one order, 10 families, and 16 genera. Investigation of model archaeal viruses has yielded important insights into mechanisms underlining various steps in the viral life cycle, including infection, DNA replication and transcription, and virion egression. Many of these mechanisms are unprecedented for any known bacterial or eukaryal viruses. Studies of plasmids isolated from different archaeal hosts have also revealed a striking diversity in gene content and innovation in replication strategies. Highly divergent replication proteins are identified in both viral and plasmid genomes. Genomic studies of archaeal ECEs have revealed a modular sequence structure in which modules of DNA sequence are exchangeable within, as well as among, plasmid families and probably also between viruses and plasmids. In particular, it has been suggested that ECE-host interactions have shaped the coevolution of ECEs and their archaeal hosts. Furthermore, archaeal hosts have developed defense systems, including the innate restriction-modification (R-M) system and the adaptive CRISPR (clustered regularly interspaced short palindromic repeats) system, to restrict invasive plasmids and viruses. Together, these interactions permit a delicate balance between ECEs and their hosts, which is vitally important for maintaining an innovative gene reservoir carried by ECEs. In conclusion, while research on archaeal ECEs has just started to unravel the molecular biology of these genetic entities and their interactions with archaeal hosts, it is expected to accelerate in the next decade.

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Chromosome replication origins: Do we really need them?

Michel

Bernander

2014

BioEssays

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Replication of the main chromosome in the halophilic archaeon Haloferax volcanii was recently reported to continue despite deletion of all active replication origins. Equally surprising, the deletion strain grew faster than the parent strain. It was proposed that origin-less H. volcanii duplicate their chromosomes via recombination-dependent replication. Here, we recall our present knowledge of this mode of chromosome replication in different organisms. We consider the likelihood that it accounts for the viability of H. volcanii deleted for its main specific replication origins, as well as possible alternative interpretations of the results. The selective advantages of having defined chromosome replication origins are discussed from a functional and evolutionary perspective.

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Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea

Cited by 33 publications

References 55 publications

ArchaeProfile: A Database of Archaea and their Origins of Replication

ArchaeProfile: A Database of Archaea and their Origins of Replication

Archaeal Extrachromosomal Genetic Elements

Chromosome replication origins: Do we really need them?

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