Identification of the nicking tyrosine of geminivirus Rep protein

Laufs, Jürgen; Schumacher, S.; Geisler, Norbert; Jupin, Isabelle; Gronenborn, Bruno

doi:10.1016/0014-5793(95)01355-5

Cited by 69 publications

(44 citation statements)

References 50 publications

(63 reference statements)

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“…This common region contains the origin of viral DNA replication and is immediately upstream of the two, bidirectional promoters of each DNA component, which are involved in viral and complementary gene expression. The viral AL1 protein nicks double-stranded DNA to initiate replicational release of a single-stranded viral DNA molecule (Laufs et al, 1995). Host DNA replication machinery is required for both single-and double-stranded DNA synthesis and it is the singlestranded form that is encapsidated into viral particles that remain in the nucleus.…”

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confidence: 99%

Geminivirus-Mediated Gene Silencing fromCotton Leaf Crumple VirusIs Enhanced by Low Temperature in Cotton

et al. 2008

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A silencing vector for cotton (Gossypium hirsutum) was developed from the geminivirus Cotton leaf crumple virus (CLCrV). The CLCrV coat protein gene was replaced by up to 500 bp of DNA homologous to one of two endogenous genes, the magnesium chelatase subunit I gene (ChlI) or the phytoene desaturase gene (PDS). Cotyledons of cotton cultivar 'Deltapine 5415' bombarded with the modified viral vectors manifested chlorosis due to silencing of either ChlI or PDS in approximately 70% of inoculated plants after 2 to 3 weeks. Use of the green fluorescence protein gene showed that replication of viral DNA was restricted to vascular tissue and that the viral vector could transmit to leaves, roots, and the ovule integument from which fibers originate. Temperature had profound effects on vector DNA accumulation and the spread of endogenous gene silencing. Consistent with reports that silencing against viruses increases at higher temperatures, plants grown at a 30°C/26°C day/night cycle had a greater than 10-fold reduction in viral DNA accumulation compared to plants grown at 22°C/18°C. However, endogenous gene silencing decreased at 30°C/26°C. There was an approximately 7 d delay in the onset of gene silencing at 22°C/18°C, but silencing was extensive and persisted throughout the life of the plant. The extent of silencing in new growth could be increased or decreased by changing temperature regimes at various times following the onset of silencing. Our experiments establish the use of the CLCrV silencing vector to study gene function in cotton and show that temperature can have a major impact on the extent of geminivirus-induced gene silencing.

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Geminivirus-Mediated Gene Silencing fromCotton Leaf Crumple VirusIs Enhanced by Low Temperature in Cotton

et al. 2008

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“…However, it is more likely that this gene encodes a replication initiator protein (Rep) based on the presence of other motifs conserved within this protein and the lack of any similarity with known polymerases. Rep proteins have been found to be associated with a variety of plasmids of Gram-positive (Koepsel et al, 1985 ;te Riele et al, 1986 ;Gros et al, 1987 ;Gruss & Ehrlich, 1989) and Gramnegative bacteria (Yasukawa et al, 1991), ss and dsDNA phages (Baas & Jansz, 1988) and viruses, including the geminiviruses (Laufs et al, 1995 a), all of which replicate via a rolling-circle mechanism. These proteins generally have multifunctional roles and are involved in both initiation and termination of rolling-circle replication.…”

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confidence: 99%

“…In the geminiviruses, the Rep protein is the only gene product essential for virus replication (reviewed by Laufs et al, 1995 a). Laufs et al (1995 c) have shown that the Rep protein of tomato yellow leaf curl geminivirus (TYLCV) initiates viralstrand DNA synthesis by introducing a nick within the conserved nonanucleotide loop sequence of the virion-sense strand.…”

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confidence: 99%

“…Covalently linked protein-DNA complexes are typical of other nicking-joining enzymes such as the Rep proteins of the geminivirus TYLCV and RC-plasmid pT181, the gene A product of φX174, the Tra protein of RP4 and the Mob protein of RSF1010 (Pansegrau et al, 1990 ;Thomas et al, 1990 ;Rasooly & Novick, 1993 ;Scherzinger et al, 1993 ;Laufs et al, 1995 b). However, other Rep proteins such as Rep B of pMV158 (Moscoso et al, 1995) and the gene II product of coliphage fd (Meyer & Geider, 1979) effect protein-DNA interactions through transient phosphodiester bonds or through non-covalent binding.…”

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Nicking and joining activity of banana bunchy top virus replication protein in vitro.

Hafner

Stafford

Wolter

et al. 1997

Journal of General Virology

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The major open reading frame of banana bunchy top virus (BBTV) DNA-1 encodes a putative replication initiation protein (Rep). In vitro, a fusion protein of BBTV Rep linked to a maltose-binding protein exhibited both site-specific nicking and joining activities. These activities were dependent on the presence of Mg 2M or Mn 2M , but did not require ATP. The fusion protein specifically cleaved ssDNA between bases M 7 and M 8 of a conserved nonanucleotide loop sequence which is present in the virion-strand of the stem-loop common region of each BBTV component. During this reaction, the fusion protein became covalently attached to the 5h end of the 3h cleavage product. After the nicking reactions, the fusion protein was also capable of catalysing the joining of two nicked ssDNA fragments in a site-specific manner. Based on these activities, BBTV Rep would appear to be very similar to the Rep proteins of the geminiviruses.

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“…The N-terminal RCRE domain contains well-conserved motifs I, II and III. The putative α3-helix contains the motif III (YxxK) active-site tyrosine [134][135][136][137]. The S3H domain also contains wellconserved Walker-A, Walker-B, B' and C motifs [138][139][140][141].…”

Section: Genomic Configurationmentioning

confidence: 99%

The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem

Diemer¹

2000

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Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National Park, USA. BSL supports a purely microbial ecosystem comprised largely of Archaea and Bacteria, however, the lower temperature regions permit the growth of acid-and thermotolerant Eukarya. This distinctive feature of the BSL microbial ecosystem ensures that virus types infecting all domains of life will be present. The metagenomic sequence data was used to characterize the types of viruses present within the microbial ecosystem, to ascertain the extent of genetic diversity and novelty comprising the BSL virus assemblage, and to explore the genomic and structural modalities of virus evolution. New sequence data from metagenomic surveys of natural virus assemblages was also used to better characterize and define known virus protein families, as some of the viruses found in the BSL environment represent distant relatives of well-characterized isolates. By comparing viral genes and protein sequences from these highly divergent species, it is possible to better understand the dynamics of adaptation and evolution in the virosphere. Additionally, as structures of virus proteins continue to be experimentally determined by X-ray crystallography and cryo-electron microscopy, a merger of structural and metagenomic sequence data allows the opportunity to observe the structural dynamics underlying virus protein evolution.Capsid (structural) proteins from two distinct Microviridae strains; a globally ubiquitous and highly sequence-diverse virus family, were identified in, and isolated from the BSL metagenomic DNA sample. These BSL capsid protein sequences, along with several other homologous sequences derived from metagenomic surveys and laboratory isolates, were mapped to the solved structure of a closely related capsid protein from the Spiroplasma phage-4 microvirus. Patterns of amino acid sequence conservation, unveiled by structure-based homology modeling analysis, revealed that the iii protein sequences within this family exhibit a remarkable level of plasticity, while remaining structurally and functionally congruent.Lateral gene transfer is thought to have had a significant impact on the genomic evolution and adaptation of virus families. Genomic context analysis was also utilized to identify interviral gene transfer within the BSL virus assemblage. An ostensibly rare interviral gene transfer event, having transpired between single-stranded RNA ...

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Identification of the nicking tyrosine of geminivirus Rep protein

Cited by 69 publications

References 50 publications

Geminivirus-Mediated Gene Silencing fromCotton Leaf Crumple VirusIs Enhanced by Low Temperature in Cotton

Geminivirus-Mediated Gene Silencing fromCotton Leaf Crumple VirusIs Enhanced by Low Temperature in Cotton

Nicking and joining activity of banana bunchy top virus replication protein in vitro.

The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem

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