Nucleotide sequence analysis of Jembrana disease virus: a bovine lentivirus associated with an acute disease syndrome

Chadwick, B. J.; Coelen, R.J.; Wilcox, G. E.; Sammels, Leanne M.; Kertayadnya, G.

doi:10.1099/0022-1317-76-7-1637

Cited by 60 publications

(56 citation statements)

References 46 publications

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“…We previously described a ''chameleon'' Tat peptide from Jembrana disease virus (JDV) (31,32) that is related to the BIV ARM and is able to bind not only to its cognate JDV TAR but also to HIV and BIV TARs (33). This ARM domain is particularly interestingly for two reasons: first, it behaves as a structural chameleon that binds to HIV and BIV TARs in the HIV Tat and BIV Tat respective binding modes and, second, it binds BIV TAR with even higher affinity than the cognate BIV peptide because of amino acid differences at its C terminus (33).…”

mentioning

confidence: 99%

A single intermolecular contact mediates intramolecular stabilization of both RNA and protein

Calabro

Daugherty

Frankel

2005

Proc. Natl. Acad. Sci. U.S.A.

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An arginine-rich peptide from the Jembrana disease virus (JDV) Tat protein is a structural ''chameleon'' that binds bovine immunodeficiency virus (BIV) or HIV TAR RNAs in two different binding modes, with an affinity for BIV TAR even higher than the cognate BIV peptide. We determined the NMR structure of the JDV Tat-BIV TAR high-affinity complex and found that the C-terminal tyrosine in JDV Tat forms a network of inter-and intramolecular hydrogen bonding and stacking interactions that simultaneously stabilize the ␤-hairpin conformation of the peptide and a base triple in the RNA. A neighboring histidine also appears to help stabilize the peptide conformation. Induced fit binding is recurrent in protein-protein and protein-nucleic acid interactions, and the JDV Tat complex demonstrates how high affinity can be achieved not only by optimization of the binding interface but also by inducing new intramolecular contacts that stabilize each binding partner. Comparison to the cognate BIV Tat peptide-TAR complex shows how such a costabilization mechanism can evolve with only small changes to the peptide sequence. In addition, the bound structure of BIV TAR in the chameleon peptide complex is strikingly similar to the bound conformation of HIV TAR, suggesting new strategies for the development of HIV TAR binding molecules.NMR ͉ RNA structure ͉ RNA-binding domain T he ability of macromolecules to interact with high affinity and specificity is often accompanied by conformational changes in the binding partners (1-4). Flexibility of one or both molecules can contribute to optimization of the binding surfaces and allow binding to multiple partners (5, 6). Numerous examples of conformational adaptability have been observed in protein-protein and protein-nucleic acid interactions, including Ig proteins, which can accommodate a remarkably wide range of binding partners, and the ribosome, where induced-fit binding helps direct its ordered assembly (7-9).In RNA-protein interactions, the arginine-rich motif (ARM) has served as a model system for examining structural mechanisms that underlie induced fit binding (10-12). Studies of ARM peptide-RNA complexes, including the Tat ARM-TAR RNA interactions of several lentiviruses, have shown that the unbound ARMs generally are unfolded and can adopt a variety of conformations upon RNA binding, often with a concomitant change in RNA structure. In the case of HIV Tat, a relatively weak binding ARM peptide remains in an extended conformational when bound to HIV TAR but causes a large conformational change in the RNA, inducing stacking between the two helical stems and formation of a U-A:U base triple (13-23). In the case of bovine immunodeficiency virus (BIV) Tat, a conformational change in BIV TAR also is observed upon binding, but the cognate ARM peptide undergoes a large conformational rearrangement, forming a ␤-hairpin structure that facilitates high-affinity binding through a large set of specific contacts to the RNA (24-29). Despite the striking difference in binding modes of these two...

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mentioning

confidence: 99%

A single intermolecular contact mediates intramolecular stabilization of both RNA and protein

Calabro

Daugherty

Frankel

2005

Proc. Natl. Acad. Sci. U.S.A.

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“…The most downstream region is the U5 region which is 53 nucleotides long and 42 nucleotides shorter than BIV U5 region. The terminal 7 nucleotides repeat (see above) and the tetranucleotide sequence which is supposed to be implicated with transcription termination, are found both in BIV and JDV genomes (Chadwick et al, 1995b).…”

Section: Long Terminal Repeats (Ltr)mentioning

confidence: 99%

“…Within this region, the poly (A) signal and the termination transcription signal are conserved with regards to the BIV ones. The putative 5'-terminus of the viral RNA genome has been identified as the trans-activating response (TAR) region (Chadwick et al, 1995b) to which the trans-activator of transcription (Tat) protein binds for its activity (Carpenter et al, 1992). JDV TAR region has the potential to form a secondary structure, i.e.…”

Section: Long Terminal Repeats (Ltr)mentioning

confidence: 99%

“…Sequence alignment has also enabled the identification of putative features in JDV genome. It contains the structural genes gag, pol and env which encode structural and enzymatic proteins that make up infectious viral particles and flanking long terminal repeats (LTR) that characterize all retroviruses and finally a number of accessory genes, including tat, rev and vif that are typical of lentiviruses and which are required for the production of The Structure and Function of Jembrana Disease Virus Genome regulatory proteins (Chadwick et al, 1995b). Products of most accessory genes have been shown to play important roles in viral replication and pathogenesis (Kirchhoff et al, 1999).…”

Section: Genome Of Jdvmentioning

confidence: 99%

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The Structure and Function of Jembrana Disease Virus Genome

Kusumawati¹,

Wanahari²,

Tampubolon³

2014

J. Inf. Mol. Biol.

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“…no. U21603; version U21603.1 GI: 733067; www.ncbi.nlm.nih.gov/nucleotide/) [2,3] and synthetized by ''1st Base Custom Oligos'' (Singapore).…”

Section: Lamp Primers and Probementioning

confidence: 99%

Use of reverse transcription loop-mediated isothermal amplification combined with lateral flow dipstick for an easy and rapid detection of Jembrana disease virus

et al. 2015

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Jembrana disease virus (JDV) is a viral pathogen that causes Jembrana disease in Bali cattle (Bos javanicus) with high mortality rate. An easy and rapid diagnostic method is essential for further control this disease. We used a reverse transcription loop-mediated isothermal amplification (RT-LAMP) combined with lateral flow dipstick (LFD), based on conserved tm subunit of Jembrana disease virus env gene. The RT-LAMP conditions were optimized by varying the concentration of MgSO 4 , betaine, dNTP, and temperature as well as the time and duration of reaction. The primers sensitivity for JDV was confirmed. The method was able to detect env-tm gene dilution which contained 2 9 10 -15 g of template. Comparatively, the sensitivity of RT-LAMP/LFD was 100-fold more sensitive than reverse transcription-polymerase chain reaction. The primers specificity for JDV was also confirmed using positive and negative controls. This work also showed that virus detection could be done not only on total RNA extracted from blood but various organs could also be analyzed for the presence of JDV using RT-LAMP/LFD method. The whole process, including the LAMP reaction and the LFD hybridization step only lasts approximately 75 min. Results of analysis can be easily observed with naked eyes without addition of any chemical or further analysis. The combination of RT-LAMP with LFD makes the method a more suitable diagnostic tool in conditions where sophisticated and expensive equipments are not available for field investigations on Jembrana disease in Bali cattle.

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Nucleotide sequence analysis of Jembrana disease virus: a bovine lentivirus associated with an acute disease syndrome

Cited by 60 publications

References 46 publications

A single intermolecular contact mediates intramolecular stabilization of both RNA and protein

A single intermolecular contact mediates intramolecular stabilization of both RNA and protein

The Structure and Function of Jembrana Disease Virus Genome

Use of reverse transcription loop-mediated isothermal amplification combined with lateral flow dipstick for an easy and rapid detection of Jembrana disease virus

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