List of published studies reporting deletion mutants of monopartite begomoviruses
The geminiviruses are plant-infecting viruses with genomes consisting of circular, single-stranded DNA (ssDNA) geminate particles . Members of the family
2. Functions of effectors encoded by monopartite begomoviruses
The complementary-sense strand encodes the Rep proteins, also known as C1, AC1 and AL1, is a multifunctional protein and the only viral protein absolutely required for virus replication. Rep is encoded on the complementary sense strand (Fig. 1 DNA A). This protein is involved in several biological processes: initiation and termination of rolling circle replication (RCR) by nicking and religating the replication origin of viral DNA  and repression of its own gene transcription . The Rep proteins of geminiviruses are closely related and show substantial sequence conservation. Four functional domains have been delineated for begomovirus Rep : the N-terminal domain (amino acids 1 to 120), which is involved in initiation by geminiviruses , AC1 protein initiates rolling circle replication by a site-specific cleavage within the loop of the conserved nonamer sequence, TAATATTAC . The AC1 protein binding site is located between the TATA box and the transcription start site for the
The transcriptional activator protein (TrAP); is also known as AC2, C2 an AL2. AC2 is a ~15-KD a transcriptional activator protein unique to begomoviruses because it is absent in mastreviruses and a related protein in curtoviruses, AC2 protein, seems to play a different role. In mastreviruses, AC1 protein provide the functions of AC2 . TrAP is necessary for transactivation of late genes . Recently, several researchers have shown that the AC2 gene of
The replication enhancer protein (REn); also named as AC3/AL3. AC3 is a ~16 KD a protein in curtoviruses and in begomoviruses. The AC3 protein greatly enhances viral DNA accumulation of curtoviruses and begomoviruses [22, 92] by interacting with Rep . Experimental observations suggested that AC3 protein might increase the affinity of Rep for the origin. Complementation studies revealed that AC3 could act on heterologous viruses .
The C4 protein, for which the function remains unclear but for some viruses is a pathogenicity determinant and a suppressor of PTGS . AC4 is highly variable among begomoviruses, which is expressed from an open reading frame (ORF) embedded in the Rep ORF.
The virion-sense strand encodes the genes required for insect transmission and movement in plants, coat protein (CP) and V2 protein. Monopartite begomovirus capsids are composed of a single CP, encoded by the
In contrast to New World (NW) begomoviruses, Old World (OW) begomoviruses have AV2/V2 and this is involved in the movement of monopartite viruses. A recent report shown that the V2 (a homolog of AV2) of a monopartite begomovirus is involved in overcoming host defenses mediated by post-transcriptional gene silencing as well as in movement [114, 115]. V2 targets a step in the RNA silencing pathway which is subsequent to the Dicer-mediated cleavage of dsRNA [109, 70].
3. Role of effectors encoded by satellites
Recently, the majority of the begomoviruses originating from the OW have been shown to be monopartite and to associate with a class of ssDNA satellites known as betasatellites (earlier known as DNAβ) . Betasatellites are approximately half the size of their helper begomoviruses (approx.1.4 kb) and are required by the helper virus to induce typical disease symptoms in their original hosts. The success of begomovirus-betasatellite disease complexes appears to be due to the promiscuous nature of betasatellites that allows them to be
All the reported betasatellites  or defective betasatellites (half size of wild type betasatellite)  contain the A-rich region, the A-rich region may play biological role in betasatellites . A-rich region is not required for
In Arabidopsis, these pathways are affected by the DICER- like proteins (DCL1, DCL2, and DCL3) that are nuclear localized and are required for miRNA and siRNA biogenesis. Thus, βC1 protein may affect the activity of the DICER-like proteins in plants during nuclear activities that function in silencing suppression. The other possibilities are that βC1 protein could down-regulate transcription of a host protein that acts in the PTGS pathway in the cytoplasm or that βC1 protein could activate transcription of a host PTGS inhibitor .
Many begomovirus betasatellite complexes are also associated with a third ssDNA component for which the collective term alphasatellite (earlier known as DNA 1; R.W. Briddon, manuscript in preparation). However, alphasatellites are dispensable for virus infection and appear to play no significant role in the etiology of the diseases with which they are associated . Alphasatellite components are satellite-like, circular ssDNA molecules approx.1375 nucleotides in length (Fig.1 alphasatellite). They encode a single gene, a rolling circle replication initiator protein (Rep), and are capable of autonomous replication in plant cells. Closely related to the replication associated protein encoding components of nanoviruses (a second family of plant infecting ssDNA viruses), from which they are believed to have evolved, they require a helper begomovirus for movement within and between plants [56, 80].
Several alphasatellites are capable of replicating and systemically infecting their plant host in the presence of a helper begomovirus without a visible effect on symptom development or virulence [6, 40]. However AYVSGA a different type of ‘DNA-2’-class alphasatellite that ameliorates symptom severity in an infected host and also capable of reducing virulence and the relative accumulation of its associated Tomato leaf curl betasatellite (ToLCB) . Alphasatellites have been acquired by helper begomoviruses to restrain virulence to achieve increased viral fitness [76, 105].
Recently, two ‘DNA-1-type’ alphasatellites Gossypium mustelinium symptomless alphasatellite (GMusSLA) and Gossypium darwinii symptomless alphasatellite (GDarSLA) phylogenetically divergent from the DNA-2-type alphasatellite have each been shown to attenuate symptoms caused by their helper begomovirus . However  hypothesize that symptom attenuation and a relative reduction in betasatellite accumulation might result from DNA-2-mediated modulation of betasatellite activity. Possibly alphasatellite modulates begomovirus-betasatellite pathogenicity by interfering with βC1, a key virulence factor . Also alphasatellite rep can interact with C4 of CLCuRaV that might be providing an additional possible mechanism for symptom amelioration by alphasatellites. Furthermore alpha-Rep down regulate betasatellite replication (In the field), and thus down- regulation of the manifestation of the pathogenicity determinant βC1 , moreover alpha-Rep proteins GMusSLA and GDarSLA can act as a strong suppression of posttranscriptional gene silencing (PTGS) .
5. Post-transcriptional gene silencing (PTGS)
Post-transcriptional gene silencing (PTGS) which is initiated by double stranded RNA (dsRNA) is common in plant–virus interactions and is an evolutionarily conserved mechanism that protects host cells against invasive nucleic acids, such as viruses, transposons and transgenes . As a counter to this host defense, most plant viruses encode proteins which act as suppressors of PTGS . Viral suppressors of PTGS interfere with various steps of this pathway including initiation, maintenance or systemic silencing which are mainly downstream of dsRNA production [52, 57].
RNA silencing in plants operates as an antiviral defense response; to establish infection, viruses must suppress RNA silencing by the host . Begomoviruses have been shown to induce PTGS in infected plants by producing virus specific siRNAs (21, 22 and 24 nt) . To counteract this host defence, geminiviruses encode RNA silencing suppressors . However, depending on each intrinsic virus and its interaction with plant host factors, the efficacy of virus-induced PTGS may vary . At least three RNA-silencing suppressors have been reported in TYLCD-associated or related begomoviruses. Thus, the V2 protein of TYLCV functions as an RNA-silencing suppressor; it counteracts the innate immune response of the host plant by interacting with SISGS3, the tomato homolog of the Arabidopsis SGS3 protein involved in the RNA-silencing pathway. The TrAP protein of the related monopartite begomovirus.
6. Mutagenesis of effectors encoded by monopartite begomoviruses
Little is known about gene function in monopartite begomoviruses. However, gene function has been studied extensively in other types of geminiviruses which share organization and nucleotide sequence similarities with TYLCV. Mutational analysis of few monopartite begomoviruses like TYLCV define similarities and differences between this single component geminivirus and bipartite geminiviruses in functions essential for systemic spread and infectivity . The CP appeared to be required for systemic movement of TYLCV in
TYLCV ORF V1 truncated either 133 nt upstream or 19 nt downstream of the initiation codon of ORF V2 would altered the viral DNA forms, it suggested that the V1 protein may participate in the switch from dsDNA to ssDNA synthesis. Indeed, interaction between V1 and the CP has already been proposed, in view of the concerted evolution of these two protein sequences following a geo-graphical gradient of similarity , and the synergistic reduction in ssDNA levels of a TYLCV V1-V2 double mutant compared to single mutants . Although TYLCV V1 mutants did not greatly overproduce dsDNA, the similarity of phenotype between BCTV V2 and TYLCV V1 mutants may indicated that the two corresponding gene products serve a related function. It has shown  (Table 1) has shown that disruption of the V1 gene in the monopartite Australian isolate of TLCV did not affect its ability to spread in tomato, although the infection was asymptomatic and the DNA levels reduced.
|Accession number||Type of|
|TLCV-[AU]||AF084006||V1||N-terminal/||frameshift||Rigden et al., 1993|
|deletion||Rigden et al., 1993|
|C4||N-terminal (at 2457&2463)||revertion|
|TYLCV-Sar[ES:Psp95:93]||Z25751||C4||C"/>T at 2432||point||Jupin et al., 1994|
|C4||C"/>T at 2423|
|TYLCV-Sar[ES:Psp95:93]||Z25751||C2||∆CC2"/>31||deletion||Noris et al., 1996|
|TYLCV-Sar[FR:98]||X61153||C2||1523+GATC||frameshift||Wartig et al.,1997|
|TYLCV-Sic[IT:pSic36:95]||Z28390||CP||H134||substitution||Noris et al., 1998|
|TYLCV-Sar[ES:Psp95:93]||Z25751||CP||Q134H||site-directed||Noris et al., 1998|
|TYLCV-DO[DO:99]||AF024715||CP||∆NCP"/>180||deletion||Rojas et al., 2001|
|AYVV-[SG:pHN419:97]||X74516||C4||A"/>T at 2419 C4mut||substitution||Saunders et al., 2004|
|PaLCuV-[PK:02]||AJ436992||V2||N-terminal (1-32)||deletion||Mubin et al., 2010|
|TYLCV-IL[IL:89]||X15656||CP||Lys-Thr CPmut3||substitution||Yaakov et al., 2011|
|TYLCV-Mld[ES:72:97]||AF071228||C4||C"/>G at 9 C4mut||substitution||Tomas et al., 2011|
|ToLCJV-A[ID]||AB100304||CP||CPΔ191-257||deletion||Sharma et al.,|
|ToLCJV-A[ID]||AB100304||V2||N-terminal (58aa)||Sharma et al., 2010|
|ToLCJV-A[ID]||AB100304||V2||pGEMV2ΔC||Sharma et al., 2011|
For example Noris et al.  suggested that the region of the CP between amino acids 129 and 134 is essential for both the correct assembly of virions and transmission by the insect vector. The genome of the SicRcv (infectious) had the same size as the original Sic DNA 9 (non-infectious) differed by only 2 nt. One change was at nt 2025 (A instead of T in the plus strand), determining a CAC-to-CUC codon change in the RepC1 mRNA and an H198L replacement in the RepC1 protein. The other mutation located at nt 708 (C instead of G), determining a CAG-to-CAC codon change in the CP mRNA and a Q134H replacement in the CP. This indicated that the Q134H mutation changed a viral DNA, only capable of replicating in single cells (Sic), into one that was systemically infectious, but not insect transmissible (SicRcv). Comparative analysis of Sic, SicRcv, and the hybrid genomes and showed that the mutation in the CP gene, not in the Rep gene, was responsible for restoring infectivity in SicRcv; however, it still did not result in a whitefly-transmissible TYLCV. In TYLCV-Sar, the two capsid protein alterations resulted in the same either non-infectious or non-transmissible phenotype. Mutants containing the combinations QQ, QH, and PH at positions 129 and 134 were infectious in plants, whereas those with PQ are not. The PQ mutants can replicate and accumulate CP and V2 protein in leaf discs, but appear unable to produce virus particles. Mutants having the PH combination at positions 129 and 134 infect plants and form apparently normal virions, but are not transmissible by whiteflies. Changing the amino acid at position 152 (D or E) does not influence the phenotype. Requirement of the CP for infection has been demonstrated previously  suggested that accurate particle assembly is also necessary. In fact, the PQ mutants, which are unable to assemble virions, accumulate CP in leaf discs, showing that its expression and stability were not altered. Another TYLCV protein, V2, for which a role in virus assembly has recently been, suggested .
For example Rojas et al.  has shown that C4, V1, and CP gene may function in TYLCV-DO movement. The CP localized to nuclei and nucleoli and was found to act as a nuclear shuttle, mediating the import and export of DNA . It was consistent with results obtained for the TYLCV CP in heterologous experimental systems [43, 68]. Recently, Liu et al  also showed the same behavior for the CP of the monopartite mastrevirus, MSV. TYLCV CP was found to accumulate in the nucleolus and the absence of the N-and C-terminal CP mutants from the nucleolus implicates CP motifs in this localization. As the nucleolus is the site of rRNA synthesis and packaging of ribosomal proteins, it may also serve as the site of geminiviral replication/gene expression . The TYLCV C4 targeted to the cell periphery and/or cell wall, consistent with a role in cell-to-cell movement of viral DNA [65, 75, 101].
Disruption of the AYVV C4 ORF (A>T at position 2419nt) alters the phenotype in agroinoculated
For example Stanley and Latham  have shown that V2 protein of
The first 30 N-terminal amino acids of the TYLCV-IL CP are needed for nuclear import of the protein into the plant cell, suggesting the CP’s involvement in nuclear shuttling of the virus genome . This was confirmed by the finding of a strong interaction between the CP and the plant nuclear import receptor karyopherin α1 (Kap α1) . The TYLCV CP has been found to inter act with itself (CP–CP or homotypic interaction) which may be important for capsule assembly as it is made up solely of CP units serving as building blocks. Mutations in the TYLCV-IL V1 gene coding for the TYLCV-IL CP by replacing Lys with Thr, Arg with Pro, and Arg with Leu, according to the positions of amino acids mutated . TYLCV CP mutated failed to interact with the w.t. CP, while the w.t. protein showed strong homo typic interaction. As the CP has been suggested to be a shuttle protein for the viral genome into the plant cell nucleus [43, 70], its interaction with the nuclear-transport mediator Kap α1 is an important step and has been shown to occur at high affinity . A mutation in the NLS domain, in particular at Arg19, disrupts the CP’s interaction with proteins that are known to interact with the w.t. CP [106.]. Earlier Sharma et al. [113-115] demonstrated by the constructed a series of single and double deletions into the coding sequence of
|AYVB-[SG:pBS-beta:99]||AJ252072||AT"/>TA at 547/|
|Saunders et al., 2004|
|G"/>T at 486 βC1mut2|
|site-derected||Cui et al., 2004|
|ATG (2) "/>ATC (2)|
|TYLCCNB-[CN:Y10:01]||AJ421621||742-952||deletation||Xiaorong et al., 2004|
|TYLCCNB-[CN:Y10:01]||AJ421621||∆C1β||truncation||Qian and Zhou 2005|
|CLCuVβ-[PK:00]||AJ298903||195-484||site-derected||Saeed et al., 2005|
|BYVMB-[IN:Muth:01]||AJ308425||51-140 ∆NβC1||deletation||Kumar et al., 2006|
|TYLCV-satDNA-[AU:96]||U74627||∆nt 35-146 (112nt)||deletation||Li et al., 2007|
|∆nt 146-296 (151nt)||deletation|
|∆nt 35-296 (262nt)||deletation|
|∆nt 296-420 (1251nt)||deletation|
|∆nt 296-492 (197nt)||deletation|
|∆nt 492-540 (49nt)||deletation|
|∆nt 540-641 (105nt)||deletation|
|AYVJB-[ID:04]||AB162142||4"/>ATGtga||stop||Kont et al., 2007|
|AYVB-[SG:pBS-beta:99]||AJ252072||794-795||deletation||Saunders et al., 2008|
|TbCSVB-[CN:Y35:01]||AJ420318||DNA∆C1β||Qian et al., 2008|
|CLCuMA-[PK:2:99]||AJ132345||915-1117||deletation||Shahid et al., 2009|
|CLCuMuB-[PK:09]||FJ607041||∆150-840||deletation||Nawaz-ul-Rehman et al., 2009|
|CLCuMB-[PK:00]||AJ298903||∆C1β||deletation||Kharazmi et al., 2012|
|TYLCCNB-[CN:Y10:01]||AJ421621||N-terminal (NTG)||deletation||Cheng et al., 2011|
7. Mutational analysis of effectors encoded by satellites
Betasatellite molecules have been associated with numerous monopartite begomoviruses in China, including
ToLCJAV alone can cause infection and displayed leaf curl symptoms. But, symptom expression of ToLCJAV in the presence of ToLCJAB is enhanced. In contrast, ToLCJAV and AYVB (mutated βC1) restored mild symptoms. It suggested that the βC1 protein was required for symptom induction and is a determinant of pathogenicity, βC1 protein expression in
For example Li et al.  have shown the deletion mutant of TYLCV sat-DNA (from 296-641nt) lacked the ability to replicate or replicated poorly by deleting of (region nt 35-296). Also sequence from nt 296-35 is to be essential for sat-DNA replication. The deletion of a 112 nt region downstream of the stem-loop from nt 35-146 and 151nt from 146-296 cannot effect on the replication of sat-DNA but reduced significantly. However, the deletion from nt 35-296 regions diminished sat-DNA replication these deletions loss of genomic sequences required for replication or due to changes in genome size. Heterologous non-viral DNA fragments can restore the wild-type 682 nt sat-DNA size and of replication when the replacement occurred in the region between nt 35 and 296. However, the sequence replacements in the region nt 35 to 296 of the sat-DNA improved the accumulation of sat-DNA considerably relative to the deleted constructs in this region. The sequence elements distributed within the entire sat-DNA molecule contribute to replication activity, but that sequence elements within the region from nt 35 to 296 are dispensable for replication.
For example Saeed et al.  used mutagenesis study of CLCuMB and tobacco was used as the host plant rather that cotton, the natural host of CLCuB. Few studies showed that it was symptomless when inoculated with
In recent studies Saunders et al.  have proved that disruption of the βC1 ORF prevented infection of the AYVB complex in ageratum and altered their phenotype in
Disruption of the βC1 ORF of AYVB by introducing an internal in-frame nonsense codon (G>T) did not prevent transreplication and systemic movement of the βC1 mutant by AYVV in lab host (
For example  have demonstrated that the region of AYVB between the introduced nt 114 and 1047 sites is not required for betasatellite replication. This region includes the βC1 open reading frame (ORF), which encodes a gene essential for pathogenicity  and an A-rich region that may serve to maintain the size integrity of the satellite . For example  found that the entire ORF is dispensable and is consistent with the findings of  for the betasatellite associated with TYLCCNV. In addition, removal of the A-rich region from TYLCCNB was tolerated, although the deletion mutant was associated with milder infection than those produced by the wild-type satellite . In contrast, deletion of this region in AYVB did not affect the phenotype, at least in
SCR is highly conserved nature between distinct satellites [typically above 65% sequence identity with blocks of absolutely conserved sequence  strongly suggests that it also plays an important role in the virus replication cycle. In addition, the adjacent stem-loop and conserved nonanucleotide sequence would be expected to participate in replication. Approximately the 386 nt upstream of the stem–loop structure in ToLCV sat-DNA, as well as the stem–loop structure itself, are essential for replication .
βC1 is a multi-functional protein encoded by betasatellites that are associated with the majority of monopartite begomoviruses . For example Cheng et al.  proved by deletion mutants of Y10βC1 that multimerization was mediated by amino acids between positions 60 and 100. Previous studies say that the C-terminal sequences of BYVMB-βC1 were interact with karyopherin α, a transport receptor involved in nuclear import . A myristoylation-like motif (GMDVNE) located at the C-terminal of CLCuMB-βC1 (103-108aa) interacted with a ubiquitin-conjugating enzyme involved in targeting proteins for degradation by the 26S proteasome . It also seems to indicate interference with a functionality associated with the C terminus of Y10βC1. βC1 protein of AYVB, CLCuMB or BYVMB with GFP fused at the N-terminus also presented as granular spots in the cytoplasm and around the nucleus [42, 84].
TYLCCNB presumably has one or more
The position and size of the βC1 gene of the betasatellite molecules are conserved in all betasatellite molecules, and the mutation of the start codon of C1 gene in TYLCCNB showed that it’s a pathogenicity determinant [108, 6]. Few studies has been also shown that the βC1 protein of betasatellite associated with TYLCCNV or AYVV is an essential pathogenicity determinant [17, 79], it may act as suppressors of post-transcriptional gene silencing that interfering the host defense system, thus, the presence of C1 protein facilitates efficient infection of the virus in hosts . For example Tau and Zhou  showed that
βC1of BYVMB have a nuclear export or peripheral localization function and βC1 interacts with itself, also with CP and the tomato protein karyopherin α. Mutagenesis of βC1 protein showed that the domain of βC1 interacting with CP is at the N terminal half whereas the domain(s) of βC1interacting with itself and karyopherin α are at the C terminal half and the role of BYVMD βC1 as a suppressor of posttranscriptional gene silencing was explored . Karyopherins are soluble transport receptors that interact with basic NLS sequences and help in nuclear import . Full length betasatellite of CLCuMB can substitute for the movement function of the DNA B of a bipartite begomovirus
8. Potential of mutated satellites using a virus induced gene silencing vectors
Betasatellites have about 200nt sequences (known as a-Rich region) conserved among all that indicating may be these sequences have some biological roles in satellites. The role of A-Rich sequence may be to increase the required size of the molecule that is essential for encapsidation or systemic movement by the coat protein or movement protein encoded by begomovirus. TYLCCNB-Y10 could be infectious and mutant betasatellite (deleted a-rich region) could be encapsidated in the coat protein encoded by DNA-A that suggested may be A-Rich region is not required for trans-replication of TYLCCNB but only for size maintaining . For example  reported that only a small region of the nucleotide sequence of CLCuMB upstream of the start codon of βC1 (a 68-nt fragment), which contains a G-box, was important for βC1 promoter activity. In addition to βC1 ORF of CLCuMB delete a larger region (complete βC1) to make it a gene delivery vector for plants. It can potentially tolerate the insertion of larger foreign sequences without affecting promoter activity . Putative promoter and TATA box are located upstream of the
Evidence has been shown that TYLCCNB modified by deletion of its
Also alphasatellite is a small molecule and easy to manipulate and have a wide host range and can apparently be maintained by a large number of distinct Begomovirus species. It has some sequences (A-rich approx.200 nt.), similar to betasatellite which can, potentially, be removed and still it can replicate autonomous. The A-rich deleted sequences of CLCuMA can not affect its ability to replicate autonomously and move, in trans, by a helper begomovirus that provide a space suitable for insertion of foreign sequences to increase its capacity to accept and maintain foreign gene sequences  (Table 2). This ability to amplify itself is useful for construction of VIGS vectors it will increase the copy number (and thus also expression) of inserted sequences . Rolling-circle replication initiator protein of GmusSA and GDarSLA act as a strong suppressor of PTGS.
The monopartite begomovirus associated with DNA-satellites (Betasatellite and Alphasatellite ) complex is in the norm throughout the Old World, particularly in South Asian countries. The epidemiology and evolution of this complex has been extensively analyzed since its first description. Monopartite begomovirus encoded all the genes needed to cause a successful infection. Many of these genes are coding for multifunctional proteins, adding another level of complexity in their interaction with host proteins, and their de novo creation. This shows the ability of begomoviruses and their associated satellites to rapidly evolve in response to selection pressures such as host plant resistance.
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