51
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Hawkins M, Malla S, Blythe MJ, Nieduszynski CA, Allers T. Accelerated growth in the absence of DNA replication origins. Nature 2013; 503:544-547. [PMID: 24185008 PMCID: PMC3843117 DOI: 10.1038/nature12650] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Accepted: 09/12/2013] [Indexed: 11/09/2022]
Abstract
DNA replication initiates at defined sites called origins, which serve as binding sites for initiator proteins that recruit the replicative machinery. Origins differ in number and structure across the three domains of life and their properties determine the dynamics of chromosome replication. Bacteria and some archaea replicate from single origins, whereas most archaea and all eukaryotes replicate using multiple origins. Initiation mechanisms that rely on homologous recombination operate in some viruses. Here we show that such mechanisms also operate in archaea. We use deep sequencing to study replication in Haloferax volcanii and identify four chromosomal origins of differing activity. Deletion of individual origins results in perturbed replication dynamics and reduced growth. However, a strain lacking all origins has no apparent defects and grows significantly faster than wild type. Origin-less cells initiate replication at dispersed sites rather than at discrete origins and have an absolute requirement for the recombinase RadA, unlike strains lacking individual origins. Our results demonstrate that homologous recombination alone can efficiently initiate the replication of an entire cellular genome. This raises the question of what purpose replication origins serve and why they have evolved.
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Affiliation(s)
- Michelle Hawkins
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Sunir Malla
- DeepSeq, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Martin J Blythe
- DeepSeq, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Conrad A Nieduszynski
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Thorsten Allers
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
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52
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Affiliation(s)
- Joel A. Farkas
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Jonathan W. Picking
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
| | - Thomas J. Santangelo
- Department of Microbiology and Center for RNA Biology, Ohio State University, Columbus, Ohio 43210
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523;
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53
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Wu Z, Liu J, Yang H, Liu H, Xiang H. Multiple replication origins with diverse control mechanisms in Haloarcula hispanica. Nucleic Acids Res 2013; 42:2282-94. [PMID: 24271389 PMCID: PMC3936714 DOI: 10.1093/nar/gkt1214] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The use of multiple replication origins in archaea is not well understood. In particular, little is known about their specific control mechanisms. Here, we investigated the active replication origins in the three replicons of a halophilic archaeon, Haloarcula hispanica, by extensive gene deletion, DNA mutation and genome-wide marker frequency analyses. We revealed that individual origins are specifically dependent on their co-located cdc6 genes, and a single active origin/cdc6 pairing is essential and sufficient for each replicon. Notably, we demonstrated that the activities of oriC1 and oriC2, the two origins on the main chromosome, are differently controlled. A G-rich inverted repeat located in the internal region between the two inverted origin recognition boxes (ORBs) plays as an enhancer for oriC1, whereas the replication initiation at oriC2 is negatively regulated by an ORB-rich region located downstream of oriC2-cdc6E, likely via Cdc6E-titrating. The oriC2 placed on a plasmid is incompatible with the wild-type (but not the ΔoriC2) host strain, further indicating that strict control of the oriC2 activity is important for the cell. This is the first report revealing diverse control mechanisms of origins in haloarchaea, which has provided novel insights into the use and coordination of multiple replication origins in the domain of Archaea.
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Affiliation(s)
- Zhenfang Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China and University of Chinese Academy of Sciences, Beijing 100049, China
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54
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Characterization of the replication initiator Orc1/Cdc6 from the Archaeon Picrophilus torridus. J Bacteriol 2013; 196:276-86. [PMID: 24187082 DOI: 10.1128/jb.01020-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Eukaryotic DNA replication is preceded by the assembly of prereplication complexes (pre-RCs) at or very near origins in G1 phase, which licenses origin firing in S phase. The archaeal DNA replication machinery broadly resembles the eukaryal apparatus, though simpler in form. The eukaryotic replication initiator origin recognition complex (ORC), which serially recruits Cdc6 and other pre-RC proteins, comprises six components, Orc1-6. In archaea, a single gene encodes a protein similar to both the eukaryotic Cdc6 and the Orc1 subunit of the eukaryotic ORC, with most archaea possessing one to three Orc1/Cdc6 orthologs. Genome sequence analysis of the extreme acidophile Picrophilus torridus revealed a single Orc1/Cdc6 (PtOrc1/Cdc6). Biochemical analyses show MBP-tagged PtOrc1/Cdc6 to preferentially bind ORB (origin recognition box) sequences. The protein hydrolyzes ATP in a DNA-independent manner, though DNA inhibits MBP-PtOrc1/Cdc6-mediated ATP hydrolysis. PtOrc1/Cdc6 exists in stable complex with PCNA in Picrophilus extracts, and MBP-PtOrc1/Cdc6 interacts directly with PCNA through a PIP box near its C terminus. Furthermore, PCNA stimulates MBP-PtOrc1/Cdc6-mediated ATP hydrolysis in a DNA-dependent manner. This is the first study reporting a direct interaction between Orc1/Cdc6 and PCNA in archaea. The bacterial initiator DnaA is converted from an active to an inactive form by ATP hydrolysis, a process greatly facilitated by the bacterial ortholog of PCNA, the β subunit of Pol III. The stimulation of PtOrc1/Cdc6-mediated ATP hydrolysis by PCNA and the conservation of PCNA-interacting protein motifs in several archaeal PCNAs suggest the possibility of a similar mechanism of regulation existing in archaea. This mechanism may involve other yet to be identified archaeal proteins.
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55
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Hyrien O, Rappailles A, Guilbaud G, Baker A, Chen CL, Goldar A, Petryk N, Kahli M, Ma E, d'Aubenton-Carafa Y, Audit B, Thermes C, Arneodo A. From simple bacterial and archaeal replicons to replication N/U-domains. J Mol Biol 2013; 425:4673-89. [PMID: 24095859 DOI: 10.1016/j.jmb.2013.09.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Revised: 09/15/2013] [Accepted: 09/19/2013] [Indexed: 10/26/2022]
Abstract
The Replicon Theory proposed 50 years ago has proven to apply for replicons of the three domains of life. Here, we review our knowledge of genome organization into single and multiple replicons in bacteria, archaea and eukarya. Bacterial and archaeal replicator/initiator systems are quite specific and efficient, whereas eukaryotic replicons show degenerate specificity and efficiency, allowing for complex regulation of origin firing time. We expand on recent evidence that ~50% of the human genome is organized as ~1,500 megabase-sized replication domains with a characteristic parabolic (U-shaped) replication timing profile and linear (N-shaped) gradient of replication fork polarity. These N/U-domains correspond to self-interacting segments of the chromatin fiber bordered by open chromatin zones and replicate by cascades of origin firing initiating at their borders and propagating to their center, possibly by fork-stimulated initiation. The conserved occurrence of this replication pattern in the germline of mammals has resulted over evolutionary times in the formation of megabase-sized domains with an N-shaped nucleotide compositional skew profile due to replication-associated mutational asymmetries. Overall, these results reveal an evolutionarily conserved but developmentally plastic organization of replication that is driving mammalian genome evolution.
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Affiliation(s)
- Olivier Hyrien
- Ecole Normale Supérieure, IBENS UMR8197 U1024, Paris 75005, France.
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56
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Lestini R, Laptenok SP, Kühn J, Hink MA, Schanne-Klein MC, Liebl U, Myllykallio H. Intracellular dynamics of archaeal FANCM homologue Hef in response to halted DNA replication. Nucleic Acids Res 2013; 41:10358-70. [PMID: 24049073 PMCID: PMC3905845 DOI: 10.1093/nar/gkt816] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Hef is an archaeal member of the DNA repair endonuclease XPF (XPF)/Crossover junction endonuclease MUS81 (MUS81)/Fanconi anemia, complementation group M (FANCM) protein family that in eukaryotes participates in the restart of stalled DNA replication forks. To investigate the physiological roles of Hef in maintaining genome stability in living archaeal cells, we studied the localization of Hef–green fluorescent protein fusions by fluorescence microscopy. Our studies revealed that Haloferax volcanii Hef proteins formed specific localization foci under regular growth conditions, the number of which specifically increased in response to replication arrest. Purification of the full-length Hef protein from its native host revealed that it forms a stable homodimer in solution, with a peculiar elongated configuration. Altogether our data indicate that the shape of Hef, significant physicochemical constraints and/or interactions with DNA limit the apparent cytosolic diffusion of halophilic DNA replication/repair complexes, and demonstrate that Hef proteins are dynamically recruited to archaeal eukaryotic-like chromatin to counteract DNA replication stress. We suggest that the evolutionary conserved function of Hef/FANCM proteins is to enhance replication fork stability by directly interacting with collapsed replication forks.
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Affiliation(s)
- Roxane Lestini
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645-INSERM U696, 91128 Palaiseau Cedex, France and Section of Molecular Cytology, Swammerdam Institute for Life Sciences, van Leeuwenhoek Centre for Advanced Microscopy, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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57
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Pelve EA, Martens-Habbena W, Stahl DA, Bernander R. Mapping of active replication origins in vivo in thaum- and euryarchaeal replicons. Mol Microbiol 2013; 90:538-50. [PMID: 23991938 DOI: 10.1111/mmi.12382] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2013] [Indexed: 02/03/2023]
Abstract
We report mapping of active replication origins in thaum- and euryarchaeal replicons using high-throughput sequencing-based marker frequency analysis. The chromosome of the thaumarchaeon Nitrosopumilus maritimus is shown to contain a single origin of replication, whereas the main chromosome in the halophilic euryarchaea Haloferax mediterranei and Haloferax volcanii each contains two origins. All replication origins specified bidirectional replication, and the two origins in the halophiles were initiated in synchrony. The pHM500 plasmid of H. mediterranei is shown to contain a single origin, and the copy numbers of five plasmid replicons in the two halophiles were inferred to be close to that of the main chromosome. Origin recognition boxes (ORBs) that provide binding sites for Orc1/Cdc6 replication initiator proteins are identified at all chromosomal origins, as well as in a range of additional thaumarchaeal species. An annotation update is provided for all three species.
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Affiliation(s)
- Erik A Pelve
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
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58
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Abstract
DNA replication plays an essential role in all life forms. Research on archaeal DNA replication began approximately 20 years ago. Progress was hindered, however, by the lack of genetic tools to supplement the biochemical and structural studies. This has changed, however, and genetic approaches are now available for several archaeal species. One of these organisms is the thermophilic euryarchaeon Thermococcus kodakarensis. In the present paper, the recent developments in the biochemical, structural and genetic studies on the replication machinery of T. kodakarensis are summarized.
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59
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Abstract
Growth and proliferation of all cell types require intricate regulation and coordination of chromosome replication, genome segregation, cell division and the systems that determine cell shape. Recent findings have provided insight into the cell cycle of archaea, including the multiple-origin mode of DNA replication, the initial characterization of a genome segregation machinery and the discovery of a novel cell division system. The first archaeal cytoskeletal protein, crenactin, was also recently described and shown to function in cell shape determination. Here, we outline the current understanding of the archaeal cell cycle and cytoskeleton, with an emphasis on species in the genus Sulfolobus, and consider the major outstanding questions in the field.
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Affiliation(s)
- Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
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60
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Maier LK, Lange SJ, Stoll B, Haas KA, Fischer S, Fischer E, Duchardt-Ferner E, Wöhnert J, Backofen R, Marchfelder A. Essential requirements for the detection and degradation of invaders by the Haloferax volcanii CRISPR/Cas system I-B. RNA Biol 2013; 10:865-74. [PMID: 23594992 PMCID: PMC3737343 DOI: 10.4161/rna.24282] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
To fend off foreign genetic elements, prokaryotes have developed several defense systems. The most recently discovered defense system, CRISPR/Cas, is sequence-specific, adaptive and heritable. The two central components of this system are the Cas proteins and the CRISPR RNA. The latter consists of repeat sequences that are interspersed with spacer sequences. The CRISPR locus is transcribed into a precursor RNA that is subsequently processed into short crRNAs. CRISPR/Cas systems have been identified in bacteria and archaea, and data show that many variations of this system exist. We analyzed the requirements for a successful defense reaction in the halophilic archaeon Haloferax volcanii. Haloferax encodes a CRISPR/Cas system of the I-B subtype, about which very little is known. Analysis of the mature crRNAs revealed that they contain a spacer as their central element, which is preceded by an eight-nucleotide-long 5′ handle that originates from the upstream repeat. The repeat sequences have the potential to fold into a minimal stem loop. Sequencing of the crRNA population indicated that not all of the spacers that are encoded by the three CRISPR loci are present in the same abundance. By challenging Haloferax with an invader plasmid, we demonstrated that the interaction of the crRNA with the invader DNA requires a 10-nucleotide-long seed sequence. In addition, we found that not all of the crRNAs from the three CRISPR loci are effective at triggering the degradation of invader plasmids. The interference does not seem to be influenced by the copy number of the invader plasmid.
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61
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Samson RY, Xu Y, Gadelha C, Stone TA, Faqiri JN, Li D, Qin N, Pu F, Liang YX, She Q, Bell SD. Specificity and function of archaeal DNA replication initiator proteins. Cell Rep 2013; 3:485-96. [PMID: 23375370 PMCID: PMC3607249 DOI: 10.1016/j.celrep.2013.01.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 10/09/2012] [Accepted: 01/03/2013] [Indexed: 01/09/2023] Open
Abstract
Chromosomes with multiple DNA replication origins are a hallmark of Eukaryotes and some Archaea. All eukaryal nuclear replication origins are defined by the origin recognition complex (ORC) that recruits the replicative helicase MCM(2-7) via Cdc6 and Cdt1. We find that the three origins in the single chromosome of the archaeon Sulfolobus islandicus are specified by distinct initiation factors. While two origins are dependent on archaeal homologs of eukaryal Orc1 and Cdc6, the third origin is instead reliant on an archaeal Cdt1 homolog. We exploit the nonessential nature of the orc1-1 gene to investigate the role of ATP binding and hydrolysis in initiator function in vivo and in vitro. We find that the ATP-bound form of Orc1-1 is proficient for replication and implicates hydrolysis of ATP in downregulation of origin activity. Finally, we reveal that ATP and DNA binding by Orc1-1 remodels the protein’s structure rather than that of the DNA template.
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Affiliation(s)
- Rachel Y Samson
- Sir William Dunn School of Pathology, Oxford University, South Parks Road, Oxford OX1 3RE, UK
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62
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Abstract
The initiation of DNA replication represents a committing step to cell proliferation. Appropriate replication onset depends on multiprotein complexes that help properly distinguish origin regions, generate nascent replication bubbles, and promote replisome formation. This review describes initiation systems employed by bacteria, archaea, and eukaryotes, with a focus on comparing and contrasting molecular mechanisms among organisms. Although commonalities can be found in the functional domains and strategies used to carry out and regulate initiation, many key participants have markedly different activities and appear to have evolved convergently. Despite significant advances in the field, major questions still persist in understanding how initiation programs are executed at the molecular level.
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Affiliation(s)
- Alessandro Costa
- Clare Hall Laboratories, London Research Institute, Cancer Research UK, Hertfordshire, EN6 3LD United Kingdom
| | - Iris V. Hood
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
| | - James M. Berger
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, California 94720
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63
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Liu X, Miao D, Zhang F, Wu Z, Liu J, Xiang H. Characterization of the minimal replicon of pHM300 and independent copy number control of major and minor chromosomes of Haloferax mediterranei. FEMS Microbiol Lett 2012; 339:66-74. [PMID: 23173581 DOI: 10.1111/1574-6968.12052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Accepted: 11/19/2012] [Indexed: 11/28/2022] Open
Abstract
The presence of minichromosomes is very common in haloarchaea, but little is known about the coordination of replication between the major and minor chromosomes. In this study, we analyzed the replication of pHM300, a 321,908-bp minichromosome, which encodes versatile metabolism pathways in Haloferax mediterranei. The replication origin of pHM300 was predicted in the 699-bp intergenic region between the cdc6K and tbp4 gene, and the minimal replicon, consisting of an AT-rich region flanked by putative origin recognition boxes (ORBs) and the adjacent cdc6K gene, was determined by assaying for its ability to replicate autonomously in Haloarcula hispanica. Southern blot analysis indicated that the ratio of pHM300 to chromosome increased from the early exponential to middle stationary phase. The copy numbers of these minor and major chromosomes were then evaluated by real-time PCR and showed that both decreased in stationary phase. However, the decrease in the copy number of the major chromosome was a little earlier and much greater than that of pHM300, revealing that the copy number control of the minichromosome pHM300 is independent from that of the major chromosome in H. mediterranei.
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Affiliation(s)
- Xiaoqing Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
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64
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Delmas S, Duggin IG, Allers T. DNA damage induces nucleoid compaction via the Mre11-Rad50 complex in the archaeon Haloferax volcanii. Mol Microbiol 2012; 87:168-79. [PMID: 23145964 PMCID: PMC3565448 DOI: 10.1111/mmi.12091] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2012] [Indexed: 11/30/2022]
Abstract
In prokaryotes the genome is organized in a dynamic structure called the nucleoid, which is embedded in the cytoplasm. We show here that in the archaeon Haloferax volcanii, compaction and reorganization of the nucleoid is induced by stresses that damage the genome or interfere with its replication. The fraction of cells exhibiting nucleoid compaction was proportional to the dose of the DNA damaging agent, and results obtained in cells defective for nucleotide excision repair suggest that breakage of DNA strands triggers reorganization of the nucleoid. We observed that compaction depends on the Mre11-Rad50 complex, suggesting a link to DNA double-strand break repair. However, compaction was observed in a radA mutant, indicating that the role of Mre11-Rad50 in nucleoid reorganisation is independent of homologous recombination. We therefore propose that nucleoid compaction is part of a DNA damage response that accelerates cell recovery by helping DNA repair proteins to locate their targets, and facilitating the search for intact DNA sequences during homologous recombination.
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Affiliation(s)
- Stéphane Delmas
- School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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65
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Gao F, Luo H, Zhang CT. DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes. Nucleic Acids Res 2012; 41:D90-3. [PMID: 23093601 PMCID: PMC3531139 DOI: 10.1093/nar/gks990] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Replication of chromosomes is one of the central events in the cell cycle. Chromosome replication begins at specific sites, called origins of replication (oriCs), for all three domains of life. However, the origins of replication still remain unknown in a considerably large number of bacterial and archaeal genomes completely sequenced so far. The availability of increasing complete bacterial and archaeal genomes has created challenges and opportunities for identification of their oriCs in silico, as well as in vivo. Based on the Z-curve theory, we have developed a web-based system Ori-Finder to predict oriCs in bacterial genomes with high accuracy and reliability by taking advantage of comparative genomics, and the predicted oriC regions have been organized into an online database DoriC, which is publicly available at http://tubic.tju.edu.cn/doric/ since 2007. Five years after we constructed DoriC, the database has significant advances over the number of bacterial genomes, increasing about 4-fold. Additionally, oriC regions in archaeal genomes identified by in vivo experiments, as well as in silico analyses, have also been added to the database. Consequently, the latest release of DoriC contains oriCs for >1500 bacterial genomes and 81 archaeal genomes, respectively.
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Affiliation(s)
- Feng Gao
- Department of Physics, Tianjin University, Tianjin 300072, China.
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66
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Spang A, Poehlein A, Offre P, Zumbrägel S, Haider S, Rychlik N, Nowka B, Schmeisser C, Lebedeva EV, Rattei T, Böhm C, Schmid M, Galushko A, Hatzenpichler R, Weinmaier T, Daniel R, Schleper C, Spieck E, Streit W, Wagner M. The genome of the ammonia-oxidizing Candidatus Nitrososphaera gargensis: insights into metabolic versatility and environmental adaptations. Environ Microbiol 2012; 14:3122-45. [PMID: 23057602 DOI: 10.1111/j.1462-2920.2012.02893.x] [Citation(s) in RCA: 217] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 09/01/2012] [Indexed: 01/21/2023]
Abstract
The cohort of the ammonia-oxidizing archaea (AOA) of the phylum Thaumarchaeota is a diverse, widespread and functionally important group of microorganisms in many ecosystems. However, our understanding of their biology is still very rudimentary in part because all available genome sequences of this phylum are from members of the Nitrosopumilus cluster. Here we report on the complete genome sequence of Candidatus Nitrososphaera gargensis obtained from an enrichment culture, representing a different evolutionary lineage of AOA frequently found in high numbers in many terrestrial environments. With its 2.83 Mb the genome is much larger than that of other AOA. The presence of a high number of (active) IS elements/transposases, genomic islands, gene duplications and a complete CRISPR/Cas defence system testifies to its dynamic evolution consistent with low degree of synteny with other thaumarchaeal genomes. As expected, the repertoire of conserved enzymes proposed to be required for archaeal ammonia oxidation is encoded by N. gargensis, but it can also use urea and possibly cyanate as alternative ammonia sources. Furthermore, its carbon metabolism is more flexible at the central pyruvate switch point, encompasses the ability to take up small organic compounds and might even include an oxidative pentose phosphate pathway. Furthermore, we show that thaumarchaeota produce cofactor F420 as well as polyhydroxyalkanoates. Lateral gene transfer from bacteria and euryarchaeota has contributed to the metabolic versatility of N. gargensis. This organisms is well adapted to its niche in a heavy metal-containing thermal spring by encoding a multitude of heavy metal resistance genes, chaperones and mannosylglycerate as compatible solute and has the genetic ability to respond to environmental changes by signal transduction via a large number of two-component systems, by chemotaxis and flagella-mediated motility and possibly even by gas vacuole formation. These findings extend our understanding of thaumarchaeal evolution and physiology and offer many testable hypotheses for future experimental research on these nitrifiers.
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Affiliation(s)
- Anja Spang
- Department of Genetics in Ecology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
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67
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Wu Z, Liu H, Liu J, Liu X, Xiang H. Diversity and evolution of multiple orc/cdc6-adjacent replication origins in haloarchaea. BMC Genomics 2012; 13:478. [PMID: 22978470 PMCID: PMC3528665 DOI: 10.1186/1471-2164-13-478] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 08/28/2012] [Indexed: 11/10/2022] Open
Abstract
Background While multiple replication origins have been observed in archaea, considerably less is known about their evolutionary processes. Here, we performed a comparative analysis of the predicted (proved in part) orc/cdc6-associated replication origins in 15 completely sequenced haloarchaeal genomes to investigate the diversity and evolution of replication origins in halophilic Archaea. Results Multiple orc/cdc6-associated replication origins were predicted in all of the analyzed haloarchaeal genomes following the identification of putative ORBs (origin recognition boxes) that are associated with orc/cdc6 genes. Five of these predicted replication origins in Haloarcula hispanica were experimentally confirmed via autonomous replication activities. Strikingly, several predicted replication origins in H. hispanica and Haloarcula marismortui are located in the distinct regions of their highly homologous chromosomes, suggesting that these replication origins might have been introduced as parts of new genomic content. A comparison of the origin-associated Orc/Cdc6 homologs and the corresponding predicted ORB elements revealed that the replication origins in a given haloarchaeon are quite diverse, while different haloarchaea can share a few conserved origins. Phylogenetic and genomic context analyses suggested that there is an original replication origin (oriC1) that was inherited from the ancestor of archaea, and several other origins were likely evolved and/or translocated within the haloarchaeal species. Conclusion This study provides detailed information about the diversity of multiple orc/cdc6-associated replication origins in haloarchaeal genomes, and provides novel insight into the evolution of multiple replication origins in Archaea.
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Affiliation(s)
- Zhenfang Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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68
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Xia X. DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes. Curr Genomics 2012; 13:16-27. [PMID: 22942672 PMCID: PMC3269012 DOI: 10.2174/138920212799034776] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 09/26/2011] [Accepted: 10/02/2011] [Indexed: 11/22/2022] Open
Abstract
Different patterns of strand asymmetry have been documented in a variety of prokaryotic genomes as well as mitochondrial genomes. Because different replication mechanisms often lead to different patterns of strand asymmetry, much can be learned of replication mechanisms by examining strand asymmetry. Here I summarize the diverse patterns of strand asymmetry among different taxonomic groups to suggest that (1) the single-origin replication may not be universal among bacterial species as the endosymbionts Wigglesworthia glossinidia, Wolbachia species, cyanobacterium Synechocystis 6803 and Mycoplasma pulmonis genomes all exhibit strand asymmetry patterns consistent with the multiple origins of replication, (2) different replication origins in some archaeal genomes leave quite different patterns of strand asymmetry, suggesting that different replication origins in the same genome may be differentially used, (3) mitochondrial genomes from representative vertebrate species share one strand asymmetry pattern consistent with the strand-displacement replication documented in mammalian mtDNA, suggesting that the mtDNA replication mechanism in mammals may be shared among all vertebrate species, and (4) mitochondrial genomes from primitive forms of metazoans such as the sponge and hydra (representing Porifera and Cnidaria, respectively), as well as those from plants, have strand asymmetry patterns similar to single-origin or multi-origin replications observed in prokaryotes and are drastically different from mitochondrial genomes from other metazoans. This may explain why sponge and hydra mitochondrial genomes, as well as plant mitochondrial genomes, evolves much slower than those from other metazoans.
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Affiliation(s)
- Xuhua Xia
- Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, P.O. Box 450, Station A, Ottawa, Ontario, Canada
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69
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Retkute R, Nieduszynski CA, de Moura A. Mathematical modeling of genome replication. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:031916. [PMID: 23030953 PMCID: PMC3671344 DOI: 10.1103/physreve.86.031916] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 08/15/2012] [Indexed: 06/01/2023]
Abstract
Eukaryotic DNA replication is initiated from multiple sites on the chromosome, but little is known about the global and local regulation of replication. We present a mathematical model for the spatial dynamics of DNA replication, which offers insight into the kinetics of replication in different types of organisms. Most biological experiments involve average quantities over large cell populations (typically >10(7) cells) and therefore can mask the cell-to-cell variability present in the system. Although the model is formulated in terms of a population of cells, using mathematical analysis we show that one can obtain signatures of stochasticity in individual cells from averaged quantities. This work generalizes the result by Retkute et al. [Phys. Rev. Lett. 107, 068103 (2011)] to a broader set of parameter regimes.
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Affiliation(s)
- Renata Retkute
- Centre for Genetics and Genomics, University of Nottingham, Nottingham NG7 2UH, United Kingdom
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70
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Pelve EA, Lindås AC, Knöppel A, Mira A, Bernander R. Four chromosome replication origins in the archaeonPyrobaculum calidifontis. Mol Microbiol 2012; 85:986-95. [DOI: 10.1111/j.1365-2958.2012.08155.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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71
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Ishino Y, Ishino S. Rapid progress of DNA replication studies in Archaea, the third domain of life. SCIENCE CHINA-LIFE SCIENCES 2012; 55:386-403. [PMID: 22645083 DOI: 10.1007/s11427-012-4324-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 04/20/2012] [Indexed: 02/04/2023]
Abstract
Archaea, the third domain of life, are interesting organisms to study from the aspects of molecular and evolutionary biology. Archaeal cells have a unicellular ultrastructure without a nucleus, resembling bacterial cells, but the proteins involved in genetic information processing pathways, including DNA replication, transcription, and translation, share strong similarities with those of Eukaryota. Therefore, archaea provide useful model systems to understand the more complex mechanisms of genetic information processing in eukaryotic cells. Moreover, the hyperthermophilic archaea provide very stable proteins, which are especially useful for the isolation of replisomal multicomplexes, to analyze their structures and functions. This review focuses on the history, current status, and future directions of archaeal DNA replication studies.
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Affiliation(s)
- Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan.
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72
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Siddaramappa S, Challacombe JF, DeCastro RE, Pfeiffer F, Sastre DE, Giménez MI, Paggi RA, Detter JC, Davenport KW, Goodwin LA, Kyrpides N, Tapia R, Pitluck S, Lucas S, Woyke T, Maupin-Furlow JA. A comparative genomics perspective on the genetic content of the alkaliphilic haloarchaeon Natrialba magadii ATCC 43099T. BMC Genomics 2012; 13:165. [PMID: 22559199 PMCID: PMC3403918 DOI: 10.1186/1471-2164-13-165] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 05/04/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Natrialba magadii is an aerobic chemoorganotrophic member of the Euryarchaeota and is a dual extremophile requiring alkaline conditions and hypersalinity for optimal growth. The genome sequence of Nab. magadii type strain ATCC 43099 was deciphered to obtain a comprehensive insight into the genetic content of this haloarchaeon and to understand the basis of some of the cellular functions necessary for its survival. RESULTS The genome of Nab. magadii consists of four replicons with a total sequence of 4,443,643 bp and encodes 4,212 putative proteins, some of which contain peptide repeats of various lengths. Comparative genome analyses facilitated the identification of genes encoding putative proteins involved in adaptation to hypersalinity, stress response, glycosylation, and polysaccharide biosynthesis. A proton-driven ATP synthase and a variety of putative cytochromes and other proteins supporting aerobic respiration and electron transfer were encoded by one or more of Nab. magadii replicons. The genome encodes a number of putative proteases/peptidases as well as protein secretion functions. Genes encoding putative transcriptional regulators, basal transcription factors, signal perception/transduction proteins, and chemotaxis/phototaxis proteins were abundant in the genome. Pathways for the biosynthesis of thiamine, riboflavin, heme, cobalamin, coenzyme F420 and other essential co-factors were deduced by in depth sequence analyses. However, approximately 36% of Nab. magadii protein coding genes could not be assigned a function based on Blast analysis and have been annotated as encoding hypothetical or conserved hypothetical proteins. Furthermore, despite extensive comparative genomic analyses, genes necessary for survival in alkaline conditions could not be identified in Nab. magadii. CONCLUSIONS Based on genomic analyses, Nab. magadii is predicted to be metabolically versatile and it could use different carbon and energy sources to sustain growth. Nab. magadii has the genetic potential to adapt to its milieu by intracellular accumulation of inorganic cations and/or neutral organic compounds. The identification of Nab. magadii genes involved in coenzyme biosynthesis is a necessary step toward further reconstruction of the metabolic pathways in halophilic archaea and other extremophiles. The knowledge gained from the genome sequence of this haloalkaliphilic archaeon is highly valuable in advancing the applications of extremophiles and their enzymes.
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Affiliation(s)
| | - Jean F Challacombe
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Rosana E DeCastro
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250 4to Nivel, Mar del Plata, 7600, Argentina
| | - Friedhelm Pfeiffer
- Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152, Martinsried, Germany
| | - Diego E Sastre
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250 4to Nivel, Mar del Plata, 7600, Argentina
| | - María I Giménez
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250 4to Nivel, Mar del Plata, 7600, Argentina
| | - Roberto A Paggi
- Instituto de Investigaciones Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Funes 3250 4to Nivel, Mar del Plata, 7600, Argentina
| | - John C Detter
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Karen W Davenport
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Lynne A Goodwin
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Nikos Kyrpides
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Roxanne Tapia
- DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Samuel Pitluck
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Bldg. 981, Museum Rd., P.O. Box 110700, Gainesville, FL, 32611-0700, USA
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Timpson LM, Liliensiek AK, Alsafadi D, Cassidy J, Sharkey MA, Liddell S, Allers T, Paradisi F. A comparison of two novel alcohol dehydrogenase enzymes (ADH1 and ADH2) from the extreme halophile Haloferax volcanii. Appl Microbiol Biotechnol 2012; 97:195-203. [PMID: 22526808 DOI: 10.1007/s00253-012-4074-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 03/28/2012] [Accepted: 03/31/2012] [Indexed: 11/25/2022]
Abstract
Haloarchaeal alcohol dehydrogenases are exciting biocatalysts with potential industrial applications. In this study, two alcohol dehydrogenase enzymes from the extremely halophilic archaeon Haloferax volcanii (HvADH1 and HvADH2) were homologously expressed and subsequently purified by immobilized metal-affinity chromatography. The proteins appeared to copurify with endogenous alcohol dehydrogenases, and a double Δadh2 Δadh1 gene deletion strain was constructed to prevent this occurrence. Purified HvADH1 and HvADH2 were compared in terms of stability and enzymatic activity over a range of pH values, salt concentrations, and temperatures. Both enzymes were haloalkaliphilic and thermoactive for the oxidative reaction and catalyzed the reductive reaction at a slightly acidic pH. While the NAD(+)-dependent HvADH1 showed a preference for short-chain alcohols and was inherently unstable, HvADH2 exhibited dual cofactor specificity, accepted a broad range of substrates, and, with respect to HvADH1, was remarkably stable. Furthermore, HvADH2 exhibited tolerance to organic solvents. HvADH2 therefore displays much greater potential as an industrially useful biocatalyst than HvADH1.
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Affiliation(s)
- Leanne M Timpson
- Centre for Synthesis and Chemical Biology, UCD School of Chemistry and Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
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74
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Chemnitz Galal W, Pan M, Kelman Z, Hurwitz J. Characterization of DNA primase complex isolated from the archaeon, Thermococcus kodakaraensis. J Biol Chem 2012; 287:16209-19. [PMID: 22351771 DOI: 10.1074/jbc.m111.338145] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In most organisms, DNA replication is initiated by DNA primases, which synthesize primers that are elongated by DNA polymerases. In this study, we describe the isolation and biochemical characterization of the DNA primase complex and its subunits from the archaeon Thermococcus kodakaraensis. The T. kodakaraensis DNA primase complex is a heterodimer containing stoichiometric levels of the p41 and p46 subunits. The catalytic activity of the complex resides within the p41 subunit. We show that the complex supports both DNA and RNA synthesis, whereas the p41 subunit alone marginally produces RNA and synthesizes DNA chains that are longer than those formed by the complex. We report that the T. kodakaraensis primase complex preferentially interacts with dNTP rather than ribonucleoside triphosphates and initiates RNA as well as DNA chains de novo. The latter findings indicate that the archaeal primase complex, in contrast to the eukaryote homolog, can initiate DNA chain synthesis in the absence of ribonucleoside triphosphates. DNA primers formed by the archaeal complex can be elongated extensively by the T. kodakaraensis DNA polymerase (Pol) B, whereas DNA primers formed by the p41 catalytic subunit alone were not. Supplementation of reactions containing the p41 subunit with the p46 subunit leads to PolB-catalyzed DNA synthesis. We also established a rolling circle reaction using a primed 200-nucleotide circle as the substrate. In the presence of the T. kodakaraensis minichromosome maintenance (MCM) 3' → 5' DNA helicase, PolB, replication factor C, and proliferating cell nuclear antigen, long leading strands (>10 kb) are produced. Supplementation of such reactions with the DNA primase complex supported lagging strand formation as well.
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Affiliation(s)
- Wiebke Chemnitz Galal
- Program of Molecular Biology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
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75
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Abstract
The initiation of DNA replication in most archaeal genomes is mediated by proteins related to eukaryotic Orc1 and Cdc6. Archaeal replication origins have been mapped and their interactions with Orc1/Cdc6 proteins have been characterized at the biochemical level. Structural and biophysical studies have revealed the basic rules of sequence recognition by archaeal initiators.
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76
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Functional genomic and advanced genetic studies reveal novel insights into the metabolism, regulation, and biology of Haloferax volcanii. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2011; 2011:602408. [PMID: 22190865 PMCID: PMC3235422 DOI: 10.1155/2011/602408] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Revised: 07/04/2011] [Accepted: 09/06/2011] [Indexed: 11/18/2022]
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.
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77
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Rajewska M, Wegrzyn K, Konieczny I. AT-rich region and repeated sequences - the essential elements of replication origins of bacterial replicons. FEMS Microbiol Rev 2011; 36:408-34. [PMID: 22092310 DOI: 10.1111/j.1574-6976.2011.00300.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 07/07/2011] [Indexed: 11/27/2022] Open
Abstract
Repeated sequences are commonly present in the sites for DNA replication initiation in bacterial, archaeal, and eukaryotic replicons. Those motifs are usually the binding places for replication initiation proteins or replication regulatory factors. In prokaryotic replication origins, the most abundant repeated sequences are DnaA boxes which are the binding sites for chromosomal replication initiation protein DnaA, iterons which bind plasmid or phage DNA replication initiators, defined motifs for site-specific DNA methylation, and 13-nucleotide-long motifs of a not too well-characterized function, which are present within a specific region of replication origin containing higher than average content of adenine and thymine residues. In this review, we specify methods allowing identification of a replication origin, basing on the localization of an AT-rich region and the arrangement of the origin's structural elements. We describe the regularity of the position and structure of the AT-rich regions in bacterial chromosomes and plasmids. The importance of 13-nucleotide-long repeats present at the AT-rich region, as well as other motifs overlapping them, was pointed out to be essential for DNA replication initiation including origin opening, helicase loading and replication complex assembly. We also summarize the role of AT-rich region repeated sequences for DNA replication regulation.
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Affiliation(s)
- Magdalena Rajewska
- Department of Molecular and Cellular Biology, Intercollegiate Faculty of Biotechnology, University of Gdansk, Gdansk, Poland
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78
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Dyall-Smith ML, Pfeiffer F, Klee K, Palm P, Gross K, Schuster SC, Rampp M, Oesterhelt D. Haloquadratum walsbyi: limited diversity in a global pond. PLoS One 2011; 6:e20968. [PMID: 21701686 PMCID: PMC3119063 DOI: 10.1371/journal.pone.0020968] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 05/14/2011] [Indexed: 12/03/2022] Open
Abstract
Background Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared. Principal Findings Both chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4–20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23T but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23T carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea. Conclusions Deletion-coupled insertions show that Hqr. walsbyi evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.
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Affiliation(s)
- Mike L Dyall-Smith
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany.
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79
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Samson RY, Bell SD. Cell cycles and cell division in the archaea. Curr Opin Microbiol 2011; 14:350-6. [PMID: 21543251 DOI: 10.1016/j.mib.2011.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/25/2011] [Accepted: 04/07/2011] [Indexed: 10/18/2022]
Abstract
Until recently little was known about the cell cycle parameters and division mechanisms of archaeal organisms. Although this is still the case for the majority of archaea, significant advances have been made in some model species. The information that has been gleaned thus far points to a remarkable degree of diversity within the archaeal domain of life. More specifically, members of distinct phyla have very different chromosome copy numbers, replication control systems and even employ distinct machineries for cell division.
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Affiliation(s)
- Rachel Y Samson
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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80
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Abstract
Most of the core components of the archaeal chromosomal DNA replication apparatus share significant protein sequence similarity with eukaryotic replication factors, making the Archaea an excellent model system for understanding the biology of chromosome replication in eukaryotes. The present review summarizes current knowledge of how the core components of the archaeal chromosome replication apparatus interact with one another to perform their essential functions.
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81
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Leigh JA, Albers SV, Atomi H, Allers T. Model organisms for genetics in the domain Archaea: methanogens, halophiles, Thermococcales and Sulfolobales. FEMS Microbiol Rev 2011; 35:577-608. [PMID: 21265868 DOI: 10.1111/j.1574-6976.2011.00265.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The tree of life is split into three main branches: eukaryotes, bacteria, and archaea. Our knowledge of eukaryotic and bacteria cell biology has been built on a foundation of studies in model organisms, using the complementary approaches of genetics and biochemistry. Archaea have led to some exciting discoveries in the field of biochemistry, but archaeal genetics has been slow to get off the ground, not least because these organisms inhabit some of the more inhospitable places on earth and are therefore believed to be difficult to culture. In fact, many species can be cultivated with relative ease and there has been tremendous progress in the development of genetic tools for both major archaeal phyla, the Euryarchaeota and the Crenarchaeota. There are several model organisms available for methanogens, halophiles, and thermophiles; in the latter group, there are genetic systems for Sulfolobales and Thermococcales. In this review, we present the advantages and disadvantages of working with each archaeal group, give an overview of their different genetic systems, and direct the neophyte archaeologist to the most appropriate model organism.
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Affiliation(s)
- John A Leigh
- Department of Microbiology, University of Washington, Seattle, WA, USA
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82
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Jarrell KF, Walters AD, Bochiwal C, Borgia JM, Dickinson T, Chong JPJ. Major players on the microbial stage: why archaea are important. MICROBIOLOGY-SGM 2011; 157:919-936. [PMID: 21330437 DOI: 10.1099/mic.0.047837-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
As microbiology undergoes a renaissance, fuelled in part by developments in new sequencing technologies, the massive diversity and abundance of microbes becomes yet more obvious. The Archaea have traditionally been perceived as a minor group of organisms forced to evolve into environmental niches not occupied by their more 'successful' and 'vigorous' counterparts, the bacteria. Here we outline some of the evidence gathered by an increasingly large and productive group of scientists that demonstrates not only that the Archaea contribute significantly to global nutrient cycling, but also that they compete successfully in 'mainstream' environments. Recent data suggest that the Archaea provide the major routes for ammonia oxidation in the environment. Archaea also have huge economic potential that to date has only been fully realized in the production of thermostable polymerases. Archaea have furnished us with key paradigms for understanding fundamentally conserved processes across all domains of life. In addition, they have provided numerous exemplars of novel biological mechanisms that provide us with a much broader view of the forms that life can take and the way in which micro-organisms can interact with other species. That this information has been garnered in a relatively short period of time, and appears to represent only a small proportion of what the Archaea have to offer, should provide further incentives to microbiologists to investigate the underlying biology of this fascinating domain.
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Affiliation(s)
- Ken F Jarrell
- Department of Microbiology and Immunology, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Alison D Walters
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Chitvan Bochiwal
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Juliet M Borgia
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
| | - Thomas Dickinson
- Sheffield Hallam University, City Campus, Howard Street, Sheffield S1 1WB, UK
| | - James P J Chong
- Department of Biology, University of York, Wentworth Way, Heslington, York YO10 5DD, UK
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83
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Naor A, Lazary R, Barzel A, Papke RT, Gophna U. In vivo characterization of the homing endonuclease within the polB gene in the halophilic archaeon Haloferax volcanii. PLoS One 2011; 6:e15833. [PMID: 21283796 PMCID: PMC3024317 DOI: 10.1371/journal.pone.0015833] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 11/26/2010] [Indexed: 12/28/2022] Open
Abstract
Inteins are parasitic genetic elements, analogous to introns that excise themselves at the protein level by self-splicing, allowing the formation of functional non-disrupted proteins. Many inteins contain a homing endonuclease (HEN) gene, and rely on its activity for horizontal propagation. In the halophilic archaeon, Haloferax volcanii, the gene encoding DNA polymerase B (polB) contains an intein with an annotated but uncharacterized HEN. Here we examine the activity of the polB HEN in vivo, within its natural archaeal host. We show that this HEN is highly active, and able to insert the intein into both a chromosomal target and an extra-chromosomal plasmid target, by gene conversion. We also demonstrate that the frequency of its incorporation depends on the length of the flanking homologous sequences around the target site, reflecting its dependence on the homologous recombination machinery. Although several evolutionary models predict that the presence of an intein involves a change in the fitness of the host organism, our results show that a strain deleted for the intein sequence shows no significant changes in growth rate compared to the wild type.
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Affiliation(s)
- Adit Naor
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rona Lazary
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Adi Barzel
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - R. Thane Papke
- Department of Molecular Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Uri Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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84
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Capes MD, Coker JA, Gessler R, Grinblat-Huse V, DasSarma SL, Jacob CG, Kim JM, DasSarma P, DasSarma S. The information transfer system of halophilic archaea. Plasmid 2010; 65:77-101. [PMID: 21094181 DOI: 10.1016/j.plasmid.2010.11.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2010] [Revised: 11/08/2010] [Accepted: 11/15/2010] [Indexed: 10/18/2022]
Abstract
Information transfer is fundamental to all life forms. In the third domain of life, the archaea, many of the genes functioning in these processes are similar to their eukaryotic counterparts, including DNA replication and repair, basal transcription, and translation genes, while many transcriptional regulators and the overall genome structure are more bacterial-like. Among halophilic (salt-loving) archaea, the genomes commonly include extrachromosomal elements, many of which are large megaplasmids or minichromosomes. With the sequencing of genomes representing ten different genera of halophilic archaea and the availability of genetic systems in two diverse models, Halobacterium sp. NRC-1 and Haloferax volcanii, a large number of genes have now been annotated, classified, and studied. Here, we review the comparative genomic, genetic, and biochemical work primarily aimed at the information transfer system of halophilic archaea, highlighting gene conservation and differences in the chromosomes and the large extrachromosomal elements among these organisms.
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Affiliation(s)
- Melinda D Capes
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
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85
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Ojha KK, Swati D. Mapping of origin of replication in Themococcales. Bioinformation 2010; 5:213-8. [PMID: 21364800 PMCID: PMC3041001 DOI: 10.6026/97320630005213] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Accepted: 09/24/2010] [Indexed: 11/23/2022] Open
Abstract
Genome replication is a crucial and essential process for the continuity of life.In all organisms it starts at a specific region of the genome known as origin of replication (Ori) site. The number of Ori sites varies in prokaryotes and eukaryotes. Replication starts at a single Ori site in bacteria, but in eukaryotes multiple Ori sites are used for fast copying across all chromosomes. The situation becomes complex in archaea, where some groups have single and others have multiple origins of replication. Themococcales, are a hyperthermophilic order of archaea. They are anaerobes and heterotrophs-peptide fermenters, sulphate reducers, methanogens being some of the examples of metabolic types. In this paper we have applied a combination of multiple in silico approaches - Z curve, the cell division cycle (cdc6) gene location and location of consensus origin recognition box (ORB) sequences for location of origin of replication in Thermococcus onnurineus, Thermococcus gammatolerans and other Themococcales and compared the results to that of the well-documented case of Pyrococcus abyssi. The motivation behind this study is to find the number of Ori sites based on the data available for members of this order. Results from this in silico analysis show that the Themococcales have a single origin of replication.
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Affiliation(s)
- Krishna K Ojha
- Department of Bioinformatics, MMV, Banaras Hindu University, India
| | - D Swati
- Department of Bioinformatics, MMV, Banaras Hindu University, India
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86
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Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA. The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One 2010; 5:e9605. [PMID: 20333302 PMCID: PMC2841640 DOI: 10.1371/journal.pone.0009605] [Citation(s) in RCA: 199] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Accepted: 02/11/2010] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. METHODOLOGY/PRINCIPAL FINDINGS We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studies of Hfx. volcanii.
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Affiliation(s)
- Amber L. Hartman
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, United States of America
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
| | - Cédric Norais
- Institut de Génétique et Microbiologie, Université Paris-Sud, Paris, France
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Jonathan H. Badger
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Stéphane Delmas
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Sam Haldenby
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Ramana Madupu
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Jeffrey Robinson
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Hoda Khouri
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Qinghu Ren
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
| | - Todd M. Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Julie Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida, United States of America
| | - Mecky Pohlschroder
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Charles Daniels
- Department of Microbiology, Ohio State University, Columbus, Ohio, United States of America
| | - Friedhelm Pfeiffer
- Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany
| | - Thorsten Allers
- Institute of Genetics, University of Nottingham, Nottingham, United Kingdom
| | - Jonathan A. Eisen
- The Institute for Genomic Research (J. Craig Venter Institute), Rockville, Maryland, United States of America
- UC Davis Genome Center, University of California Davis, Davis, California, United States of America
- Department of Medical Microbiology and Immunology, University of California Davis, Davis, California, United States of America
- Department of Evolution and Ecology, University of California Davis, Davis, California, United States of America
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87
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Allers T. Overexpression and purification of halophilic proteins in Haloferax volcanii. Bioeng Bugs 2010; 1:288-90. [PMID: 21327063 DOI: 10.4161/bbug.1.4.11794] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 03/17/2010] [Indexed: 11/19/2022] Open
Abstract
Halophilic enzymes function optimally at high salt concentrations and are active at low water availability. Such conditions are encountered at elevated concentrations of solutes such as salts and sugars, and at high concentrations of organic solvents. However, expression in heterologous hosts such as Escherichia coli can cause problems, since halophilic proteins typically misfold and aggregate in conditions of low ionic strength. We have harnessed the sophisticated genetic tools available for the haloarchaeon Haloferax volcanii, to develop a system for the overexpression and purification of halophilic proteins under native conditions.
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Affiliation(s)
- Thorsten Allers
- Institute of Genetics, School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, UK.
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88
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Improved strains and plasmid vectors for conditional overexpression of His-tagged proteins in Haloferax volcanii. Appl Environ Microbiol 2010; 76:1759-69. [PMID: 20097827 DOI: 10.1128/aem.02670-09] [Citation(s) in RCA: 141] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Research into archaea will not achieve its full potential until systems are in place to carry out genetics and biochemistry in the same species. Haloferax volcanii is widely regarded as the best-equipped organism for archaeal genetics, but the development of tools for the expression and purification of H. volcanii proteins has been neglected. We have developed a series of plasmid vectors and host strains for conditional overexpression of halophilic proteins in H. volcanii. The plasmids feature the tryptophan-inducible p.tnaA promoter and a 6xHis tag for protein purification by metal affinity chromatography. Purification is facilitated by host strains, where pitA is replaced by the ortholog from Natronomonas pharaonis. The latter lacks the histidine-rich linker region found in H. volcanii PitA and does not copurify with His-tagged recombinant proteins. We also deleted the mrr restriction endonuclease gene, thereby allowing direct transformation without the need to passage DNA through an Escherichia coli dam mutant.
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89
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LccA, an archaeal laccase secreted as a highly stable glycoprotein into the extracellular medium by Haloferax volcanii. Appl Environ Microbiol 2009; 76:733-43. [PMID: 19966030 DOI: 10.1128/aem.01757-09] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Laccases couple the oxidation of phenolic compounds to the reduction of molecular oxygen and thus span a wide variety of applications. While laccases of eukaryotes and bacteria are well characterized, these enzymes have not been described in archaea. Here, we report the purification and characterization of a laccase (LccA) from the halophilic archaeon Haloferax volcanii. LccA was secreted at high levels into the culture supernatant of a recombinant H. volcanii strain, with peak activity (170 +/- 10 mU.ml(-)(1)) at stationary phase (72 to 80 h). LccA was purified 13-fold to an overall yield of 72% and a specific activity of 29.4 U.mg(-)(1) with an absorbance spectrum typical of blue multicopper oxidases. The mature LccA was processed to expose an N-terminal Ala after the removal of 31 amino acid residues and was glycosylated to 6.9% carbohydrate content. Purified LccA oxidized a variety of organic substrates, including bilirubin, syringaldazine (SGZ), 2,2,-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS), and dimethoxyphenol (DMP), with DMP oxidation requiring the addition of CuSO(4). Optimal oxidation of ABTS and SGZ was at 45 degrees C and pH 6 and pH 8.4, respectively. The apparent K(m) values for SGZ, bilirubin, and ABTS were 35, 236, and 670 muM, with corresponding k(cat) values of 22, 29, and 10 s(-)(1), respectively. The purified LccA was tolerant of high salt, mixed organosolvents, and high temperatures, with a half-life of inactivation at 50 degrees C of 31.5 h.
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90
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Delmas S, Shunburne L, Ngo HP, Allers T. Mre11-Rad50 promotes rapid repair of DNA damage in the polyploid archaeon Haloferax volcanii by restraining homologous recombination. PLoS Genet 2009; 5:e1000552. [PMID: 19593371 PMCID: PMC2700283 DOI: 10.1371/journal.pgen.1000552] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2008] [Accepted: 06/09/2009] [Indexed: 11/18/2022] Open
Abstract
Polyploidy is frequent in nature and is a hallmark of cancer cells, but little is known about the strategy of DNA repair in polyploid organisms. We have studied DNA repair in the polyploid archaeon Haloferax volcanii, which contains up to 20 genome copies. We have focused on the role of Mre11 and Rad50 proteins, which are found in all domains of life and which form a complex that binds to and coordinates the repair of DNA double-strand breaks (DSBs). Surprisingly, mre11 rad50 mutants are more resistant to DNA damage than the wild-type. However, wild-type cells recover faster from DNA damage, and pulsed-field gel electrophoresis shows that DNA double-strand breaks are repaired more slowly in mre11 rad50 mutants. Using a plasmid repair assay, we show that wild-type and mre11 rad50 cells use different strategies of DSB repair. In the wild-type, Mre11-Rad50 appears to prevent the repair of DSBs by homologous recombination (HR), allowing microhomology-mediated end-joining to act as the primary repair pathway. However, genetic analysis of recombination-defective radA mutants suggests that DNA repair in wild-type cells ultimately requires HR, therefore Mre11-Rad50 merely delays this mode of repair. In polyploid organisms, DSB repair by HR is potentially hazardous, since each DNA end will have multiple partners. We show that in the polyploid archaeon H. volcanii the repair of DSBs by HR is restrained by Mre11-Rad50. The unrestrained use of HR in mre11 rad50 mutants enhances cell survival but leads to slow recovery from DNA damage, presumably due to difficulties in the resolution of DNA repair intermediates. Our results suggest that recombination might be similarly repressed in other polyploid organisms and at repetitive sequences in haploid and diploid species.
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Affiliation(s)
- Stéphane Delmas
- Institute of Genetics, School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Lee Shunburne
- Institute of Genetics, School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Hien-Ping Ngo
- Institute of Genetics, School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Thorsten Allers
- Institute of Genetics, School of Biology, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
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91
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Multiple replication origins of Halobacterium sp. strain NRC-1: properties of the conserved orc7-dependent oriC1. J Bacteriol 2009; 191:5253-61. [PMID: 19502403 DOI: 10.1128/jb.00210-09] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The eukaryote-like DNA replication system of the model haloarchaeon Halobacterium NRC-1 is encoded within a circular chromosome and two large megaplasmids or minichromosomes, pNRC100 and pNRC200. We previously showed by genetic analysis that 2 (orc2 and orc10) of the 10 genes coding for Orc-Cdc6 replication initiator proteins were essential, while a third (orc7), located near a highly conserved autonomously replicating sequence, oriC1, was nonessential for cell viability. Here we used whole-genome marker frequency analysis (MFA) and found multiple peaks, indicative of multiple replication origins. The largest chromosomal peaks were located proximal to orc7 (oriC1) and orc10 (oriC2), and the largest peaks on the extrachromosomal elements were near orc9 (oriP1) in both pNRC100 and -200 and near orc4 (oriP2) in pNRC200. MFA of deletion strains containing different combinations of chromosomal orc genes showed that replication initiation at oriC1 requires orc7 but not orc6 and orc8. The initiation sites at oriC1 were determined by replication initiation point analysis and found to map divergently within and near an AT-rich element flanked by likely Orc binding sites. The oriC1 region, Orc binding sites, and orc7 gene orthologs were conserved in all sequenced haloarchaea. Serial deletion of orc genes resulted in the construction of a minimal strain containing not only orc2 and orc10 but also orc9. Our results suggest that replication in this model system is intriguing and more complex than previously thought. We discuss these results from the perspective of the replication strategy and evolution of haloarchaeal genomes.
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92
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Glycerol-mediated repression of glucose metabolism and glycerol kinase as the sole route of glycerol catabolism in the haloarchaeon Haloferax volcanii. J Bacteriol 2009; 191:4307-15. [PMID: 19411322 DOI: 10.1128/jb.00131-09] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although glycerol is the primary carbon source available to halophilic heterotrophic communities, little is known regarding haloarchaeal glycerol metabolism. In this study, a gene encoding a glycerol kinase homolog (glpK; HVO_1541) was deleted from the genome of the haloarchaeon Haloferax volcanii by a markerless knockout strategy. The glpK mutant, KS4, readily grew on yeast extract-peptone complex medium and glucose minimal medium but was incapable of growth on glycerol. Glycerol kinase activity was dependent on the glpK gene and readily detected in cells grown on glucose and/or glycerol, with the activity level higher in medium supplemented with glycerol (with or without glucose) than in medium with glucose alone. An analysis of carbon utilization revealed that glycerol suppressed the metabolism of glucose in both the parent H26 and glpK mutant strains, with catabolite repression more pronounced in the glycerol kinase mutant. Transcripts specific for glpK and an upstream gene, gpdA, encoding a homolog of glycerol-3-phosphate dehydrogenase subunit A, were upregulated (8- and 74-fold, respectively) in the presence of glycerol and glucose compared to those in the presence of glucose alone. Furthermore, glpK was transcriptionally linked to the gpdC gene of the putative glycerol-3-phosphate dehydrogenase operon (gpdABC), based on the findings of reverse transcriptase PCR analysis. The results presented here provide genetic and biochemical evidence that glycerol metabolism proceeds through a glycerol kinase encoded by glpK and suggest that a glycerol-3-phosphate dehydrogenase encoded by the upstream gpdABC operon is also involved in this pathway. Furthermore, our findings reveal a unique example of glycerol-induced repression of glucose metabolism in H. volcanii.
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93
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Wigley DB. ORC proteins: marking the start. Curr Opin Struct Biol 2009; 19:72-8. [PMID: 19217277 DOI: 10.1016/j.sbi.2008.12.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 12/19/2008] [Indexed: 11/27/2022]
Abstract
The DNA replication apparatus of archaea is more closely related to that of eukaryotes than eubacteria. Furthermore, recent work has shown that archaea, like eukaryotes, have multiple replication origins. Biochemical data are starting to reveal how archaeal origin binding proteins recognise and remodel origin DNA sequences. Crystal structures of archaeal replication origin binding proteins complexed with their DNA targets revealed details of how they interact with origins and showed that they introduce significant deformations of the DNA. Although these recent advances provide insight about the initial interactions of proteins at archaeal replication origins, the molecular mechanisms of origin assembly and firing still remain elusive.
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Affiliation(s)
- Dale B Wigley
- Cancer Research UK Clare Hall Laboratories, The London Research Institute, Blanche Lane, South Mimms, Potters Bar, Herts, UK.
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94
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How is the archaeal MCM helicase assembled at the origin? Possible mechanisms. Biochem Soc Trans 2009; 37:7-11. [PMID: 19143593 DOI: 10.1042/bst0370007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In order for any organism to replicate its DNA, a helicase must unwind the duplex DNA in front of the replication fork. In archaea, the replicative helicase is the MCM (minichromosome maintenance) helicase. Although much is known about the biochemical properties of the MCM helicase, the mechanism of assembly at the origin of replication is unknown. In the present paper, several possible mechanisms for the loading process are described.
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95
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Abstract
Many bacterial cellular processes interact intimately with the chromosome. Such interplay is the major driving force of genome structure or organization. Interactions take place at different scales-local for gene expression, global for replication-and lead to the differentiation of the chromosome into organizational units such as operons, replichores, or macrodomains. These processes are intermingled in the cell and create complex higher-level organizational features that are adaptive because they favor the interplay between the processes. The surprising result of selection for genome organization is that gene repertoires change much more quickly than chromosomal structure. Comparative genomics and experimental genomic manipulations are untangling the different cellular and evolutionary mechanisms causing such resilience to change. Since organization results from cellular processes, a better understanding of chromosome organization will help unravel the underlying cellular processes and their diversity.
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Affiliation(s)
- Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, F-75015 Paris, France.
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96
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Abstract
The powerful combination of genetic and biochemical analysis has provided many key insights into the structure and function of the chromosomal DNA replication machineries of bacterial and eukaryotic cells. In contrast, in the archaea, biochemical studies have dominated, mainly due to the absence of efficient genetic systems for these organisms. This situation is changing, however, and, in this regard, the genetically tractable haloarchaea Haloferax volcanii and Halobacterium sp. NRC-1 are emerging as key models. In the present review, I give an overview of the components of the replication machinery in the haloarchaea, with particular emphasis on the protein factors presumed to travel with the replication fork.
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97
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Duderstadt KE, Berger JM. AAA+ ATPases in the initiation of DNA replication. Crit Rev Biochem Mol Biol 2008; 43:163-87. [PMID: 18568846 DOI: 10.1080/10409230802058296] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
All cellular organisms and many viruses rely on large, multi-subunit molecular machines, termed replisomes, to ensure that genetic material is accurately duplicated for transmission from one generation to the next. Replisome assembly is facilitated by dedicated initiator proteins, which serve to both recognize replication origins and recruit requisite replisomal components to the DNA in a cell-cycle coordinated manner. Exactly how imitators accomplish this task, and the extent to which initiator mechanisms are conserved among different organisms have remained outstanding issues. Recent structural and biochemical findings have revealed that all cellular initiators, as well as the initiators of certain classes of double-stranded DNA viruses, possess a common adenine nucleotide-binding fold belonging to the ATPases Associated with various cellular Activities (AAA+) family. This review focuses on how the AAA+ domain has been recruited and adapted to control the initiation of DNA replication, and how the use of this ATPase module underlies a common set of initiator assembly states and functions. How biochemical and structural properties correlate with initiator activity, and how species-specific modifications give rise to unique initiator functions, are also discussed.
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Affiliation(s)
- Karl E Duderstadt
- Department Molecular and Cell Biology and Biophysics Graduate Group, California Institute for Quantitative Biology, University of California, Berkeley, California 94720-3220, USA.
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98
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Sernova NV, Gelfand MS. Identification of replication origins in prokaryotic genomes. Brief Bioinform 2008; 9:376-91. [PMID: 18660512 DOI: 10.1093/bib/bbn031] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The availability of hundreds of complete bacterial genomes has created new challenges and simultaneously opportunities for bioinformatics. In the area of statistical analysis of genomic sequences, the studies of nucleotide compositional bias and gene bias between strands and replichores paved way to the development of tools for prediction of bacterial replication origins. Only a few (about 20) origin regions for eubacteria and archaea have been proven experimentally. One reason for that may be that this is now considered as an essentially bioinformatics problem, where predictions are sufficiently reliable not to run labor-intensive experiments, unless specifically needed. Here we describe the main existing approaches to the identification of replication origin (oriC) and termination (terC) loci in prokaryotic chromosomes and characterize a number of computational tools based on various skew types and other types of evidence. We also classify the eubacterial and archaeal chromosomes by predictability of their replication origins using skew plots. Finally, we discuss possible combined approaches to the identification of the oriC sites that may be used to improve the prediction tools, in particular, the analysis of DnaA binding sites using the comparative genomic methods.
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Affiliation(s)
- Natalia V Sernova
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetny pereulok, 19, Moscow, 127994, Russia
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99
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Berkner S, Lipps G. Genetic tools for Sulfolobus spp.: vectors and first applications. Arch Microbiol 2008; 190:217-30. [PMID: 18542925 DOI: 10.1007/s00203-008-0392-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 05/14/2008] [Accepted: 05/19/2008] [Indexed: 10/22/2022]
Abstract
Sulfolobus species belong to the best-studied archaeal organisms but have lacked powerful genetic methods. Recently, there has been considerable progress in the field of Sulfolobus genetics. Urgently needed basic genetic tools, such as targeted gene knockout techniques and shuttle vectors are being developed at an increasing pace. For S. solfataricus knockout systems as well as different shuttle vectors are available. For the genetically more stable S. acidocaldarius shuttle vectors have been recently developed. In this review we summarize the currently available genetic tools and methods for the genus Sulfolobus. Different transformation protocols are discussed, as well as all so far developed knockout systems and Sulfolobus-Escherichia coli shuttle vectors are summarized. Special emphasis is put on the important vector components, i.e., selectable markers and Sulfolobus replicons. Additionally, the information gathered on different Sulfolobus strains with respect to their use as recipient strains is reviewed. The advantages and disadvantages of the different systems are discussed and aims for further improvement of genetic systems are identified.
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Affiliation(s)
- Silvia Berkner
- Department of Biochemistry, University of Bayreuth, Universitätsstr. 30, 95447 Bayreuth, Germany
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100
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Extra-chromosomal elements and the evolution of cellular DNA replication machineries. Nat Rev Mol Cell Biol 2008; 9:569-74. [DOI: 10.1038/nrm2426] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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