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DNA replication origins in archaea  [PDF]
Zhenfang Wu,Jingfang Liu,Haibo Yang,Hua Xiang
Frontiers in Microbiology , 2014, DOI: 10.3389/fmicb.2014.00179
Abstract: DNA replication initiation, which starts at specific chromosomal site (known as replication origins), is the key regulatory stage of chromosome replication. Archaea, the third domain of life, use a single or multiple origin(s) to initiate replication of their circular chromosomes. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several conserved repeats (origin recognition box, ORB) that are located adjacent to a replication initiator gene. Both the ORB sequence and the adjacent initiator gene are considerably diverse among different replication origins, while in silico and genetic analyses have indicated the specificity between the initiator genes and their cognate origins. These replicator–initiator pairings are reminiscent of the oriC-dnaA system in bacteria, and a model for the negative regulation of origin activity by a downstream cluster of ORB elements has been recently proposed in haloarchaea. Moreover, comparative genomic analyses have revealed that the mosaics of replicator-initiator pairings in archaeal chromosomes originated from the integration of extrachromosomal elements. This review summarizes the research progress in understanding of archaeal replication origins with particular focus on the utilization, control and evolution of multiple replication origins in haloarchaea.
Where does DNA replication start in archaea?
Amit Vas, Janet Leatherwood
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-3-reviews1020
Abstract: Use of genome sequences is a powerful art that goes beyond finding protein homologs: it has changed how we can approach basic biological questions. This is particularly apparent for the enigmatic archaebacteria. Here, more than for other organisms, available genome data far exceed traditional biological study. A recent striking example of the insights that can be gained from archaeal genomics is provided by a report in Science from Myllykallio et al. [1] showing the use of DNA strand compositional bias, or GC skew, to find the likely replication origin in three Pyrococcus species. One reason for widespread interest in archaeal replication origins is the similarity between the factors involved in DNA replication in archaea and eukaryotes. Archaeal homologs of eukaryotic replication factors and DNA polymerase suggest that archaebacteria could become an important model to aid understanding of eukaryotic DNA replication.Are archaea like humans or bacteria? This was the issue raised when archaeal genome sequencing revealed some areas of surprising similarity between these prokaryotes and eukaryotes. Though archaeal metabolism and operon gene organization is certainly most similar to prokaryotic eubacteria, the archaeal factors for transcription, translation and DNA replication seem more akin to those found in eukaryotes. Thus, the third kingdom, archaebacteria, might serve as a simple model for mechanisms of eukaryotic cell function. And we are left wondering just how much these prokaryotes resemble ourselves. (For more extensive reviews of this issue see [2,3,4,5,6]).Archaea (as exemplified by Pyrococcus sp.) replicate their circular genome from a single DNA replication origin as do bacteria, even though they may use eukaryotic-like proteins to do so (Figure 1; [1]). This single-origin replication is definitely un-human, as our DNA replication depends on initiation at thousands of different origins. The multiple sites of initiation are essential for timely replication o
Evolution of DNA Replication Protein Complexes in Eukaryotes and Archaea  [PDF]
Nicholas Chia,Isaac Cann,Gary J. Olsen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0010866
Abstract: The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA), replication factor C (RFC), and the minichromosome maintenance (MCM) complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best.
Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution  [PDF]
Anja Spang,Joran Martijn,Jimmy H. Saw,Anders E. Lind,Lionel Guy,Thijs J. G. Ettema
Archaea , 2013, DOI: 10.1155/2013/202358
Abstract: The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life. 1. Introduction The description of the three (cellular) domains of life—Eukarya, Bacteria, and Archaea—by Carl Woese and George Fox [1] represents a milestone in the modern era of microbiology. In particular, using phylogenetic reconstructions of the small-subunit (16S or 18S) ribosomal RNA gene, Woese discovered that microscopically indistinguishable prokaryotes are not a homogeneous assemblage but are comprised of two fundamentally different groups of organisms: Eubacteria (later Bacteria) on one side and an additional life form referred to as Archaebacteria (later Archaea) on the other side [1]. Though not immediately accepted by the scientific community, this finding was early on supported by Wolfram Zillig through his studies on DNA-dependent RNA polymerases, as well as by Otto Kandler investigating “bacterial” cell walls [2]. Indeed, a subset of prokaryotic organisms subsequently assigned to Archaea was found to harbor DNA-dependent RNA polymerases that bore more similarity to those of eukaryotes, and to contain proteinaceous cell walls that lack peptidoglycan as well as cell membranes composed of L-glycerol ether lipids with isoprenoid chains instead of D-glycerol ester lipids with fatty acid chains [3–6]. Since then, further investigation of cellular characteristics of archaea has revealed that this domain of life contains eukaryotic-like information-processing machineries [7–14]. These findings were later supported by genome sequences and comparative analyses of genes coding for replication, transcription, and translation machineries as well as by protein crystal structures [15–21]. Additionally, some archaeal lineages were shown to contain homologs of eukaryotic cell division and cytoskeleton genes as well as histones and seem to express a chromatin architecture similar to eukaryotes [22–28]. In contrast to information-processing and cell division genes, archaeal operational systems (energy metabolism, biosynthesis pathways, and regulation) often
Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation
Jonathan Berthon, Diego Cortez, Patrick Forterre
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-4-r71
Abstract: Two distinct sets of DNA replication genes frequently co-localize in archaeal genomes: the first includes the genes for PCNA, the small subunit of the DNA primase (PriS), and Gins15; the second comprises the genes for MCM and Gins23. Other genomic associations of genes encoding proteins involved in informational processes that may be functionally relevant at the cellular level have also been noted; in particular, the association between the genes for PCNA, transcription factor S, and NudF. Surprisingly, a conserved cluster of genes coding for proteins involved in translation or ribosome biogenesis (S27E, L44E, aIF-2 alpha, Nop10) is almost systematically contiguous to the group of genes coding for PCNA, PriS, and Gins15. The functional relevance of this cluster encoding proteins conserved in Archaea and Eukarya is strongly supported by statistical analysis. Interestingly, the gene encoding the S27E protein, also known as metallopanstimulin 1 (MPS-1) in human, is overexpressed in multiple cancer cell lines.Our genome context analysis suggests specific functional interactions for proteins involved in DNA replication between each other or with proteins involved in DNA repair or transcription. Furthermore, it suggests a previously unrecognized regulatory network coupling DNA replication and translation in Archaea that may also exist in Eukarya.Alignment of prokaryotic genomes revealed that synteny is globally weak, indicating that bacterial and archaeal chromosomes experience continuous remodeling [1-3]. A few operons encoding physically interacting proteins involved in fundamental processes have been preserved between Archaea and Bacteria in the course of evolution (for example, operons encoding ribosomal proteins, RNA polymerase subunits, or ATP synthase subunits) [1-3]. Most gene strings are only conserved in closely related genomes or exhibit a patchy distribution among genomes in one large group of organisms (for example, in Archaea). Therefore, gene associations t
Rapid progress on the vertebrate tree of life
Robert C Thomson, H Bradley Shaffer
BMC Biology , 2010, DOI: 10.1186/1741-7007-8-19
Abstract: Using an automated phylogenetic approach, we analyse all available molecular data for a large sample of vertebrate diversity, comprising nearly 12,000 species and 210,000 sequences. Our results indicate that progress has been rapid, increasing polynomially during the age of molecular systematics. It is also skewed, with birds and mammals receiving the most attention and marine organisms accumulating far fewer data and a slower rate of increase in phylogenetic resolution than terrestrial taxa. We analyse the contributors to this phylogenetic progress and make recommendations for future work.Our analyses suggest that a large majority of the vertebrate tree of life will: (1) be resolved within the next few decades; (2) identify specific data collection strategies that may help to spur future progress; and (3) identify branches of the vertebrate tree of life in need of increased research effort.Resolution of a well-resolved phylogeny for all species is a central goal for biology in the 21st century. Inference of this 'tree of life' has far-reaching implications for nearly all fields of biology, from human health to conservation [1]. As efforts have shifted from primarily morphological to molecular approaches, a number of complex methodological issues central to the reconstruction of large phylogenies containing hundreds to thousands of species have been identified and, in some cases, solved [2-4]. At the most basic level, however, progress on the tree of life is limited by data. Both the rates at which DNA sequences are gathered and species are sampled have increased at a dramatic pace, leading to the now well-known exponential accumulation of basepairs in GenBank (Figure 1a) [5]. At the same time, the number of studies that infer and/or apply phylogenies has also grown rapidly (Figure 1b) [6]. While these indications of progress on the tree of life are encouraging, they are indirect and fall short of quantifying the growth of phylogenetic knowledge.GenBank is composed
The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes
Kira S Makarova, Eugene V Koonin, Zvi Kelman
Biology Direct , 2012, DOI: 10.1186/1745-6150-7-7
Abstract: We confirm and extend the recent hypothesis that CDC45 is the eukaryotic ortholog of the bacterial and archaeal RecJ family nucleases. At least one RecJ homolog was identified in all sequenced archaeal genomes, with the single exception of Caldivirga maquilingensis. These proteins include previously unnoticed remote RecJ homologs with inactivated DHH domain in Thermoproteales. Combined with phylogenetic tree reconstruction of diverse eukaryotic, archaeal and bacterial DHH subfamilies, this analysis yields a complex scenario of RecJ family evolution in Archaea which includes independent inactivation of the nuclease domain in Crenarchaeota and Halobacteria, and loss of this domain in Methanococcales.The archaeal complex of a CDC45/RecJ homolog, MCM and GINS is homologous and most likely functionally analogous to the eukaryotic CMG complex, and appears to be a key component of the DNA replication machinery in all Archaea. It is inferred that the last common archaeo-eukaryotic ancestor encoded a CMG complex that contained an active nuclease of the RecJ family. The inactivated RecJ homologs in several archaeal lineages most likely are dedicated structural components of replication complexes.This article was reviewed by Prof. Patrick Forterre, Dr. Stephen John Aves (nominated by Dr. Purificacion Lopez-Garcia) and Prof. Martijn Huynen.For the full reviews, see the Reviewers' Comments section.The eukaryotic minichromosome maintenance (MCM) complex consists of six paralogous proteins (MCM2-7) which belong to a distinct family within the AAA+ superfamily of ATPases. All MCM complex subunits are essential for cell viability and are required for the initiation of DNA replication and replication fork progression. Genetic, biochemical and structural studies have shown that the MCM complex is the replicative helicase that is responsible for the separation of the DNA strands during chromosomal replication [1,2]. However, in vitro and in vivo experiments have demonstrated that the M
Functional Genomic and Advanced Genetic Studies Reveal Novel Insights into the Metabolism, Regulation, and Biology of Haloferax volcanii  [PDF]
J?rg Soppa
Archaea , 2011, DOI: 10.1155/2011/602408
Abstract: The genome sequence of Haloferax volcanii is available and several comparative genomic in silico studies were performed that yielded novel insight for example into protein export, RNA modifications, small non-coding RNAs, and ubiquitin-like Small Archaeal Modifier Proteins. The full range of functional genomic methods has been established and results from transcriptomic, proteomic and metabolomic studies are discussed. Notably, Hfx. volcanii is together with Halobacterium salinarum the only prokaryotic species for which a translatome analysis has been performed. The results revealed that the fraction of translationally-regulated genes in haloarchaea is as high as in eukaryotes. A highly efficient genetic system has been established that enables the application of libraries as well as the parallel generation of genomic deletion mutants. Facile mutant generation is complemented by the possibility to culture Hfx. volcanii in microtiter plates, allowing the phenotyping of mutant collections. Genetic approaches are currently used to study diverse biological questions–from replication to posttranslational modification—and selected results are discussed. Taken together, the wealth of functional genomic and genetic tools make Hfx. volcanii a bona fide archaeal model species, which has enabled the generation of important results in recent years and will most likely generate further breakthroughs in the future. 1. Introduction On the one hand, biology tries to represent the biodiversity that is found in nature; in contrast to other natural sciences such as physics, this makes it nearly impossible to derive general rules. On the other hand, biology has profited tremendously from studies of so-called “model species,” for example, Escherichia coli and Bacillus subtilis for Gram-negative and gram-positive bacteria, Saccharomyces cerevisiae and Schizosaccharomyces pombe for fungi, Drosophila melanogaster for developmental biology, and, increasingly, the mouse for higher eukaryotes. Therefore, it is desirable to have a few model species for the third domain of life, the Archaea, and Haloferax volcanii has already been discussed as a suitable candidate [1]. There has been rapid progress in understanding the biology of Hfx. volcanii in the last five years. Therefore, results obtained in recent years will be reviewed here, with attention to (1) “functional genomics,” that is, the bioinformatic analysis of the genome sequence, transcriptomics, translatomics, proteomics, and metabolomics and (2) the genetic system of Hfx. volcanii and its application in characterizing a
Two new families of the FtsZ-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea
Kira S Makarova, Eugene V Koonin
Biology Direct , 2010, DOI: 10.1186/1745-6150-5-33
Abstract: This article was reviewed by Purificación López-García and Gáspár Jékely; for complete reviews, see the Reviewers Reports section.Proteins of the actin and tubulin superfamilies are major components of the cytoskeleton in all 3 domains of life, archaea, bacteria and eukaryotes [1,2]. FtsZ, the prokaryotic homolog of the eukaryotic cytoskeletal protein tubulin, is an essential protein that plays a central role in cell division of most bacteria and archaea [2-4]. Both FtsZ and tubulin undergo GTP- hydrolysis-dependent cycles of polymerization and depolymerization. Structural and biochemical analysis of both FtsZ and tubulin revealed mechanisms and structural determinants of GTP-binding and polymerization [5-7]. Recent progress in genome sequencing revealed numerous FtsZ paralogs, especially in archaea; some of these proteins lack the sequence motifs known to be important for the FtsZ-tubulin function, so their biological roles in the respective organisms remain obscure [8]. Furthermore, highly diverged FtsZ homologs were discovered on plasmids in several Bacillus species. These proteins, RepX from the pXO1 plasmid of Bacillus anthracis and TubZ from the Bacillus thuringiensis virulence plasmid pBtoxis, are required for plasmid replication and stability [9,10]. The diversity and functional flexibility of the FtsZ/tubulin superfamily suggests that additional families might surface when more genomic sequences become available. Here we report two new FtsZ-like protein families found in archaea and bacteria. One of these families is associated with a set of genes that can be predicted to encode multiple components of a novel molecular machinery for membrane remodeling.Analysis of the gene context of cell division related genes in archaea, including serine/threonine protein kinases (PK) implicated in FtsZ phosphorylation, revealed a locus in Halorhabdus utahensis (Huta_2050-Huta_2056) that, along with 3 PK genes, encompassed 3 additional "hypothetical genes" which we furthe
Rapid Titration of Measles and Other Viruses: Optimization with Determination of Replication Cycle Length  [PDF]
Boyan Grigorov, Jessica Rabilloud, Philip Lawrence, Denis Gerlier
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0024135
Abstract: Background Measles virus (MV) is a member of the Paramyxoviridae family and an important human pathogen causing strong immunosuppression in affected individuals and a considerable number of deaths worldwide. Currently, measles is a re-emerging disease in developed countries. MV is usually quantified in infectious units as determined by limiting dilution and counting of plaque forming unit either directly (PFU method) or indirectly from random distribution in microwells (TCID50 method). Both methods are time-consuming (up to several days), cumbersome and, in the case of the PFU assay, possibly operator dependent. Methods/Findings A rapid, optimized, accurate, and reliable technique for titration of measles virus was developed based on the detection of virus infected cells by flow cytometry, single round of infection and titer calculation according to the Poisson's law. The kinetics follow up of the number of infected cells after infection with serial dilutions of a virus allowed estimation of the duration of the replication cycle, and consequently, the optimal infection time. The assay was set up to quantify measles virus, vesicular stomatitis virus (VSV), and human immunodeficiency virus type 1 (HIV-1) using antibody labeling of viral glycoprotein, virus encoded fluorescent reporter protein and an inducible fluorescent-reporter cell line, respectively. Conclusion Overall, performing the assay takes only 24–30 hours for MV strains, 12 hours for VSV, and 52 hours for HIV-1. The step-by-step procedure we have set up can be, in principle, applicable to accurately quantify any virus including lentiviral vectors, provided that a virus encoded gene product can be detected by flow cytometry.
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