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John Stanley - One of the best experts on this subject based on the ideXlab platform.

  • chArActerisAtion of sri lAnkAn cAssAvA mosAic virus And indiAn cAssAvA mosAic virus evidence for Acquisition of A DNA b component by A monopArtite begomovirus
    Virology, 2002
    Co-Authors: Keith Saunders, N Salim, Vasant R Mali, V G Malathi, Rob W Briddon, P G Markham, John Stanley
    Abstract:

    AbstrAct Two bipArtite begomoviruses, IndiAn cAssAvA mosAic virus (ICMV) And Sri LAnkAn cAssAvA mosAic virus (SLCMV), hAve been isolAted from mosAic-diseAsed cAssAvA originAting from centrAl IndiA And Sri LAnkA, respectively. ICMV wAs trAnsmitted with low efficiency from cAssAvA to NicotiAnA benthAmiAnA by sAp inoculAtion to give leAf curl symptoms. SLCMV wAs much more virulent in this host, producing severe stunting, leAf curl, And chlorosis. These symptoms were reproduced when their cloned genomic components (DNAs A And B) were introduced into N. benthAmiAnA by either mechAnicAl or AgrobActerium -mediAted inoculAtion (AgroinoculAtion). SLCMV is more closely relAted to ICMV (DNA A, 84%; DNA B, 94% nucleotide identity) thAn AfricAn cAssAvA mosAic virus (ACMV) (DNA A, 74%; DNA B, 47% nucleotide identity). Sequence compArisons suggest thAt SLCMV DNA B originAted from ICMV DNA B by A recombinAtion event involving the SLCMV DNA A intergenic region. PseudorecombinAnts produced by reAssortment of the cloned components of ICMV And ACMV were not infectious in N. benthAmiAnA, emphAsising their stAtus As distinct virus species. In contrAst, A pseudorecombinAnt between ACMV DNA A And SLCMV DNA B wAs infectious. Consistent with these observAtions, iteron motifs locAted within the intergenic region thAt mAy be involved in the initiAtion of virAl DNA replicAtion Are conserved between SLCMV And ACMV but not ICMV. When introduced into N. benthAmiAnA by AgroinoculAtion, SLCMV DNA A Alone produced A severe upwArd leAf roll symptom, reminiscent of the phenotype AssociAted with some monopArtite begomoviruses. Furthermore, coinoculAtion of SLCMV DNA A And the sAtellite DNA β AssociAted with AgerAtum yellow vein virus (AYVV) produced severe downwArd leAf curl in N. glutinosA And yellow vein symptoms in AgerAtum conyzoides, resembling the phenotypes AssociAted with AYVV DNA A And DNA β infection in these hosts. Thus, SLCMV DNA A hAs biologicAl chArActeristics of A monopArtite begomovirus, And the virus probAbly evolved by Acquisition of A DNA B component from ICMV.

  • A nAnovirus like DNA component AssociAted with yellow vein diseAse of AgerAtum conyzoides evidence for interfAmiliAl recombinAtion between plAnt DNA viruses
    Virology, 1999
    Co-Authors: Keith Saunders, John Stanley
    Abstract:

    Yellow vein diseAse of AgerAtum conyzoides, A weed species thAt is widely distributed throughout AsiA, hAs been Attributed to infection by the geminivirus AgerAtum yellow vein virus (AYVV). In Addition to A single AYVV genomic component (DNA A), we hAve previously demonstrAted thAt infected plAnts contAin chimeric defective virAl components, comprising DNA A And nongeminivirAl sequences, thAt Act As defective interfering DNAs. A dAtAbAse seArch hAs reveAled thAt the nongeminivirAl sequences of one such defective component (def19) show significAnt homology with sequences of nAnovirus components thAt encode replicAtion-AssociAted proteins (Reps). Primers designed to hybridise to the nongeminivirAl DNA were used to PCR-Amplify A full-length nAnovirus-like component, referred to As DNA 1, from An extrAct of infected A. conyzoides. DNA 1 is unrelAted to AYVV DNA A but resembles nAnovirus components thAt encode Reps And is most closely relAted (73% identity) to A nAnovirus-like DNA recently isolAted from geminivirus-infected cotton. DNA 1 is dependent on AYVV DNA A for systemic infection of A. conyzoides And NicotiAnA benthAmiAnA And cAn systemicAlly infect N. benthAmiAnA in the presence of the bipArtite geminivirus AfricAn cAssAvA mosAic virus. A. conyzoides plAnts coinfected with AYVV DNA A And DNA 1 remAin AsymptomAtic, indicAting thAt AdditionAl fActors Are required to elicit yellow vein diseAse. Our results provide direct evidence for recombinAtion between distinct fAmilies of plAnt single-strAnded DNA viruses And suggest thAt coinfection by geminivirus And nAnovirus-like pAthogens mAy be A widespreAd phenomenon. The Ability of plAnt DNA viruses to recombine in this wAy mAy greAtly increAse their scope for diversificAtion.

Masato Ikegami - One of the best experts on this subject based on the ideXlab platform.

  • Pepper yellow leAf curl IndonesiA virus, A new bipArtite begomovirus species thAt belongs to distinct clAde of Old World geminiviruses
    Nature Precedings, 2010
    Co-Authors: Pradeep Sharma, Yutaka Shibuya, J. Sakata, Masato Ikegami
    Abstract:

    Begomoviruses Are currently emerging As A mAjor threAt to vegetAble production in mAny tropicAl And subtropicAl regions worldwide. Pepper yellow leAf curl diseAse (PepYLCD) hAs been noticed in mAny CApsicum Annum L. producing regions from EAst AsiA especiAlly from IndonesiA And cAuses devAstAting dAmAge to pepper crop production since 2000. In this study we hAve cloned And sequenced complete nucleotide of begomoviruses from pepper exhibiting leAf curling And bright yellowing symptoms. Besides, we Also determined the occurrence of diseAse on tomAto evoking leAf curl symptoms And AgerAtum with yellow vein type of symptoms. On the bAsis of genome orgAnizAtion And sequence homology, these viruses were designAted As Pepper yellow leAf curl IndonesiA virus (PeYLCIV)- new species followed by its two new stArins i.e. PeYLCIV-TomAto And PeYLCIV-AgerAtum. These viruses hAve bipArtite genomes. Pepper virus DNAs from IndonesiA (PepYLCIV, PepYLCIV-TomAto And PepYLCIV-AgerAtum DNA-As) were noticeAbly distinct, forming A sepArAte brAnch from the other viruses infecting pepper. A considerAble divergence is observed in the common region (CR) of the genomic components of PeYLCIV (77%), PeYLCIV-TomAto (82%) And PeYLCIV-AgerAtum (75%). A stem-loop forming region And Rep-binding motif Are identicAl in CRs of three viruses. CR of PepYLCIV-AgerAtum DNA-A is ApproximAtely 10 nucleotides longer thAn those of PepYLCIV DNA-A And PepYLCIV-TomAto DNA-A. SimilAr insertion is Also found in the common region of PepYLCIV-AgerAtum DNA-B. PeYLCIV DNA-A Alone is infectious in pepper And N. benthAmiAnA plAnts And AssociAtion with DNA-B increAses symptom severity.

  • StrAins of A new bipArtite begomovirus, pepper yellow leAf curl IndonesiA virus, in leAf-curl-diseAsed tomAto And yellow-vein-diseAsed AgerAtum in IndonesiA
    Archives of Virology, 2008
    Co-Authors: Jyun-ji Sakata, Yutaka Shibuya, Pradeep Sharma, Masato Ikegami
    Abstract:

    The complete nucleotide sequences of begomoviruses from pepper with leAf curl And yellowing symptoms, tomAto with leAf curl symptoms, And AgerAtum with yellow vein in IndonesiA were determined. On the bAsis of genome orgAnizAtion And sequence homology, they were proposed to belong to A new species, Pepper yellow leAf curl IndonesiA virus (PepYLCIV), which includes the new strAins PepYLCIV-TomAto And PepYLCIV-AgerAtum. These viruses hAd bipArtite genomes. Pepper virus DNAs from IndonesiA (PepYLCIV, PepYLCIV-TomAto And PepYLCIV-AgerAtum DNA-As) were noticeAbly distinct, forming A sepArAte brAnch from the viruses infecting pepper. ConsiderAble divergence wAs observed in the common region (CR) of the genomic components of PepYLCIV (77%), PepYLCIV-TomAto (82%) And PeYLCIV-AgerAtum (75%). A stem-loop-forming region And A Rep-binding motif were identicAl in the CR of the three viruses. The CRs of PepYLCIV-AgerAtum DNA-A wAs ApproximAtely 10 nucleotides longer thAn thAt of PepYLCIV DNA-A And PepYLCIV-TomAto DNA-A. A similAr insertion wAs Also found in the CR of PepYLCIV-AgerAtum DNA-B. PepYLCIV DNA-A Alone wAs infectious in pepper And NicotiAnA benthAmiAnA plAnts, And AssociAtion with DNA-B increAsed symptom severity.

Henryk Czosnek - One of the best experts on this subject based on the ideXlab platform.

  • tomAto leAf curl virus from bAngAlore tolcv bAn4 sequence compArison with indiAn tolcv isolAtes detection in plAnts And insects And vector relAtionships
    Archives of Virology, 2000
    Co-Authors: V Muniyappa, H M Venkatesh, H K Ramappa, R S Kulkarni, Muhammad Zeidan, C Y Tarba, Murad Ghanim, Henryk Czosnek
    Abstract:

    TomAto leAf curl virus (ToLCV) is A whitefly (BemisiA tAbAci) trAnsmitted geminivirus (fAmily GeminiviridAe, genus Begomovirus) cAusing A destructive diseAse of tomAto in mAny regions of IndiA, EAst AsiA And AustrAliA. While ToLCV isolAtes from AustrAliA And TAiwAn hAve A single genomic component (designAted DNA-A), those from Northern IndiA hAve two components (DNA-A And DNA-B). The ToLCV isolAtes from Southern IndiA (BAngAlore) previously cloned seem to hAve A DNA-A-like monopArtite genome. We hAve used degenerAte DNA-A-specific PCR primers to clone the genome of A ToLCV isolAte (nAmed ToLCV-BAn4) from field-infected tomAto plAnts growing in BAngAlore, IndiA, in 1997. DegenerAte DNA-B-specific PCR primers hAve not Allowed to Amplify A putAtive DNA-B from infected tomAto, At the time when DNA-B frAgments were Amplified from plAnts infected by known bipArtite begomoviruses. The full-length 2759 nucleotide-long DNA-A-like virAl genome wAs sequenced. SimilArly to other monopArtite ToLCV And TYLCV isolAtes, ToLCV-BAn4 contAins six open reAding frAmes, two on the virion strAnd And four on the complementAry strAnd. Sequence compArisons indicAted thAt ToLCV-BAn4 is similAr to the other three isolAtes from BAngAlore previously sequenced, And is closely relAted to ToLCV-BAn2 (ApproximAtely 91\% nucleotide sequence identity). Phylogenetic AnAlysis showed thAt the ToLCV isolAtes from BAngAlore constitute A group of viruses sepArAted from those of Northern IndiA. ToLCV-BAn4 wAs detected in tomAto And in its whitefly vector BemisiA tAbAci by one or by A combinAtion of ELISA, Southern blot hybridizAtion And PCR. PArAmeters of virus Acquisition, retention And trAnsmission by the whitefly vector were investigAted in the lAborAtory. Single whiteflies were Able to Acquire ToLCV-BAn4 from infected tomAto And to trAnsmit the virus to tomAto test plAnts, but five insects were necessAry to Achieve 100% trAnsmission. Minimum Acquisition Access And inoculAtion Access periods were 10 min And 20 min, respectively. A lAtent period of 6 h wAs required for B. tAbAci to efficiently infect tomAto test plAnts. Following A 24 h Acquisition Access period the insect retAined its Ability to infect tomAto test plAnts for 12 dAys, but not for its entire life. In one insect/one plAnt inoculAtion tests, femAle whiteflies were more efficient (∼95%) thAn mAles (∼25%) in trAnsmitting the virus.

Keith Saunders - One of the best experts on this subject based on the ideXlab platform.

  • chArActerisAtion of sri lAnkAn cAssAvA mosAic virus And indiAn cAssAvA mosAic virus evidence for Acquisition of A DNA b component by A monopArtite begomovirus
    Virology, 2002
    Co-Authors: Keith Saunders, N Salim, Vasant R Mali, V G Malathi, Rob W Briddon, P G Markham, John Stanley
    Abstract:

    AbstrAct Two bipArtite begomoviruses, IndiAn cAssAvA mosAic virus (ICMV) And Sri LAnkAn cAssAvA mosAic virus (SLCMV), hAve been isolAted from mosAic-diseAsed cAssAvA originAting from centrAl IndiA And Sri LAnkA, respectively. ICMV wAs trAnsmitted with low efficiency from cAssAvA to NicotiAnA benthAmiAnA by sAp inoculAtion to give leAf curl symptoms. SLCMV wAs much more virulent in this host, producing severe stunting, leAf curl, And chlorosis. These symptoms were reproduced when their cloned genomic components (DNAs A And B) were introduced into N. benthAmiAnA by either mechAnicAl or AgrobActerium -mediAted inoculAtion (AgroinoculAtion). SLCMV is more closely relAted to ICMV (DNA A, 84%; DNA B, 94% nucleotide identity) thAn AfricAn cAssAvA mosAic virus (ACMV) (DNA A, 74%; DNA B, 47% nucleotide identity). Sequence compArisons suggest thAt SLCMV DNA B originAted from ICMV DNA B by A recombinAtion event involving the SLCMV DNA A intergenic region. PseudorecombinAnts produced by reAssortment of the cloned components of ICMV And ACMV were not infectious in N. benthAmiAnA, emphAsising their stAtus As distinct virus species. In contrAst, A pseudorecombinAnt between ACMV DNA A And SLCMV DNA B wAs infectious. Consistent with these observAtions, iteron motifs locAted within the intergenic region thAt mAy be involved in the initiAtion of virAl DNA replicAtion Are conserved between SLCMV And ACMV but not ICMV. When introduced into N. benthAmiAnA by AgroinoculAtion, SLCMV DNA A Alone produced A severe upwArd leAf roll symptom, reminiscent of the phenotype AssociAted with some monopArtite begomoviruses. Furthermore, coinoculAtion of SLCMV DNA A And the sAtellite DNA β AssociAted with AgerAtum yellow vein virus (AYVV) produced severe downwArd leAf curl in N. glutinosA And yellow vein symptoms in AgerAtum conyzoides, resembling the phenotypes AssociAted with AYVV DNA A And DNA β infection in these hosts. Thus, SLCMV DNA A hAs biologicAl chArActeristics of A monopArtite begomovirus, And the virus probAbly evolved by Acquisition of A DNA B component from ICMV.

  • A nAnovirus like DNA component AssociAted with yellow vein diseAse of AgerAtum conyzoides evidence for interfAmiliAl recombinAtion between plAnt DNA viruses
    Virology, 1999
    Co-Authors: Keith Saunders, John Stanley
    Abstract:

    Yellow vein diseAse of AgerAtum conyzoides, A weed species thAt is widely distributed throughout AsiA, hAs been Attributed to infection by the geminivirus AgerAtum yellow vein virus (AYVV). In Addition to A single AYVV genomic component (DNA A), we hAve previously demonstrAted thAt infected plAnts contAin chimeric defective virAl components, comprising DNA A And nongeminivirAl sequences, thAt Act As defective interfering DNAs. A dAtAbAse seArch hAs reveAled thAt the nongeminivirAl sequences of one such defective component (def19) show significAnt homology with sequences of nAnovirus components thAt encode replicAtion-AssociAted proteins (Reps). Primers designed to hybridise to the nongeminivirAl DNA were used to PCR-Amplify A full-length nAnovirus-like component, referred to As DNA 1, from An extrAct of infected A. conyzoides. DNA 1 is unrelAted to AYVV DNA A but resembles nAnovirus components thAt encode Reps And is most closely relAted (73% identity) to A nAnovirus-like DNA recently isolAted from geminivirus-infected cotton. DNA 1 is dependent on AYVV DNA A for systemic infection of A. conyzoides And NicotiAnA benthAmiAnA And cAn systemicAlly infect N. benthAmiAnA in the presence of the bipArtite geminivirus AfricAn cAssAvA mosAic virus. A. conyzoides plAnts coinfected with AYVV DNA A And DNA 1 remAin AsymptomAtic, indicAting thAt AdditionAl fActors Are required to elicit yellow vein diseAse. Our results provide direct evidence for recombinAtion between distinct fAmilies of plAnt single-strAnded DNA viruses And suggest thAt coinfection by geminivirus And nAnovirus-like pAthogens mAy be A widespreAd phenomenon. The Ability of plAnt DNA viruses to recombine in this wAy mAy greAtly increAse their scope for diversificAtion.

Robert B Macgregor - One of the best experts on this subject based on the ideXlab platform.

  • volumetric properties of the formAtion of double strAnded DNA A neArest neighbor AnAlysis
    Biopolymers, 2004
    Co-Authors: David N Dubins, Robert B Macgregor
    Abstract:

    The kinetics of the helix-coil trAnsition hAve been studied by performing UV-monitored melting And reAnneAling curves of DNA And AnAlyzing the resultAnt hysteresis between these curves. The AnAlysis Assumes A single-step bimoleculAr trAnsition with duplex formAtion defined As the forwArd reAction. Volume pArAmeters of the helix-coil trAnsition were obtAined by meAsuring the pressure dependence of the rAte constAnts from 5–200 MPA. The dAtA were interpreted in terms of severAl possible neArest-neighbor models, rAnging from one to eleven pArAmeters. Twenty-four oligonucleotide duplexes 22 bAse pAirs in length were used to solve for individuAl neArest-neighbor ActivAtion volumes And trAnsition volumes. StAtisticAlly, the most vAlid fit of the volumetric dAtA wAs obtAined with A six-pArAmeter model in which the directionAlity of the dinucleotide steps is not considered, for exAmple, 5′AG/CT is the sAme As 5′GA/TC. The resultAnt trAnsition volumes At 48°C rAnged from −7.1 ± 0.8 mL/mol (GC/CG) to +2.9 ± 0.3 mL/mol (AA/TT). The success of the six-pArAmeter model suggests thAt the relAtive size of the neArest-neighbor dinucleotides is the most importAnt fActor determining the mAgnitude of the volumetric pArAmeters. The finding thAt the mAgnitude of the volumetric pArAmeters correlAtes with the chAnge in the solvent Accessible surfAce AreA of the bAses during the helix-coil trAnsition corroborAtes this hypothesis. © 2003 Wiley PeriodicAls, Inc. Biopolymers 73: 242–257, 2004

  • Volumetric properties of the formAtion of double strAnded DNA: A neArest‐neighbor AnAlysis
    Biopolymers, 2004
    Co-Authors: David N Dubins, Robert B Macgregor
    Abstract:

    The kinetics of the helix-coil trAnsition hAve been studied by performing UV-monitored melting And reAnneAling curves of DNA And AnAlyzing the resultAnt hysteresis between these curves. The AnAlysis Assumes A single-step bimoleculAr trAnsition with duplex formAtion defined As the forwArd reAction. Volume pArAmeters of the helix-coil trAnsition were obtAined by meAsuring the pressure dependence of the rAte constAnts from 5–200 MPA. The dAtA were interpreted in terms of severAl possible neArest-neighbor models, rAnging from one to eleven pArAmeters. Twenty-four oligonucleotide duplexes 22 bAse pAirs in length were used to solve for individuAl neArest-neighbor ActivAtion volumes And trAnsition volumes. StAtisticAlly, the most vAlid fit of the volumetric dAtA wAs obtAined with A six-pArAmeter model in which the directionAlity of the dinucleotide steps is not considered, for exAmple, 5′AG/CT is the sAme As 5′GA/TC. The resultAnt trAnsition volumes At 48°C rAnged from −7.1 ± 0.8 mL/mol (GC/CG) to +2.9 ± 0.3 mL/mol (AA/TT). The success of the six-pArAmeter model suggests thAt the relAtive size of the neArest-neighbor dinucleotides is the most importAnt fActor determining the mAgnitude of the volumetric pArAmeters. The finding thAt the mAgnitude of the volumetric pArAmeters correlAtes with the chAnge in the solvent Accessible surfAce AreA of the bAses during the helix-coil trAnsition corroborAtes this hypothesis. © 2003 Wiley PeriodicAls, Inc. Biopolymers 73: 242–257, 2004