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Role of alphasatellite in begomoviral disease complex.

Introduction

Geminiviruses are an emerging group of plant viruses infecting most of economically important crops and ornamental plants throughout the world (Mansoor et al., 2003). Based on the host range, genome organisation and the vector, die Geminiviruses ate classified into seven genera: Becurtovirus, Eragrovirus, Turncutovirus Topocuvirus, Curtovirus, Mastrevirus and Begomovirus (Adam et al., 2013; Brown et al., 2012). However, majority of the members of this family belongs to the genus Begomovirus and are spread by the whitefly, Bemisia tabaci (Briddon and Stanley, 2006). Viruses of tins genus are distributed into two subgroups; bipartite begomoviruses with DNA-A?B genomes and monopardte begomoviruses that have a single DNA chain homologous to the DNA-A of bipartite begomovirus. DNA-A component of bipartite and die single component of monopartite begomoviruses (homologues to die DNA-A) encodes all viral functions required for virus replication, control of gene expression and insect transmission All begomoviruses have a potential stem-loop structure containing die nono-nucleotide sequence TAA/TATT/AC, necessary for replication.

In the last few years alphasatellite, the member of monopartite betasatellite/begomoviruses complexes, with a monomer of approximately 1375 nucleotide sequences, has attracted much attention and has become, probably, the most attentive scientific topic in the study of single stranded DNA (ssDNA) viruses. After the discovery of this satellite in 1999, more than 150 alphasatellite sequences have been deposited in database to date, however, very little is known about their function(s) during begomovirus-satellites infections. Examples of stability and maintaining of the alphasatellite component in natural infection with several begomoviruses complex have been shown several times since its first discovery, but without gaining further insights on their function (Shahid et al., 2014: Amrao et al., 2010; Mubin el al., 2010). Certainly, alphasatellites are nonessential for vims infection and appear to play no major role in the etiology of the infections with which they are associated (Mansoor et al., 1999). However, recent reports showed that some alphasatellites can attenuate disease symptoms caused by begomovirus-betasatellite complexes in the early stages of infection (Idris et al., 2011: Nawazul-Rehman et al., 2010). An overview of the origin and evolution of alphasatellites including the recent advances in understanding their molecular structure and their applications for reverse genetics are discussed.

General characteristics of alphasatellites. Despite that alphasatellites were discovered virtually 15 years ago, very little information is available up til now about its functions). Alphasatellite molecules are mostly associated with monopartite begomovirus-betasatellite complex and also monopartite begomovirus can contain this component frequently (Shahid et al., 2014; Harimalala et al., 2013; Zhou, 2013; Zia-Ur-Rehman et al., 2013; Mubin et al., 2010; Dry et al., 1997). On the contrary, a few bipartite begomoviruses have been reported to be associated with alphasatellite (Satya et al., 2014; Paprotka et al., 2010).

Initially, alphasatellites were found in association with the begomovirus-betasatellite complex from the old world (OW). Nevertheless, some distinctive alphasatellites were recently discovered to be associated with the new world (NW) begomovirus complex (Fiallo-Olive et al., 2012). Alphasatellites are believed to have evolved from satellite-like, Rep-encoding components associated with nanoviruses (Wyant et al., 2012; Briddon and Stanley 2006; Saunders and Stanley, 1999), another family of plant ssDNA viruses. Alphasatellite was also found in association with a yellow vein disease in Ageratum conyzoides (weeds) (Saunders and Stanley, 1999).

Genome, genomic organization and replication mechanism. The size of alphasatellite is between 1,300 bp to 1,400 bp nucleotides in length and has three conserved domains: a hairpin structure, a rolling circle replication initiator protein (Rep) and a rich region (A-rich) (Fig. 1). The hairpin structure has a loop that includes a unique nono-nucleotide sequence, which usually varies from rest of the begomovirus components. TAG/TAT/IAC and differs from the TAA/TAT/TAC sequence of geminiviruses by one nucleotide (G instead of A on a third nucleotide). In both begomoviruses and nanoviruses this sequence contains the origin of replication (ori) and is nicked by the rolling circle replication initiator protein to initiate viral DNA replication. The Rep of alphasatellite is the only single large open reading frame in the virion-sense which is predicted to encode a 315 amino acid product similar to the replication associated protein of nanoviruses. An adenine-rich region (approximately 200 bp with 45-52% adenine content) is also present, which is hypothesised to be a stuffer sequence that serves to fulfill the size constrain imposed by helper virus-mediated movement or encapsidation (Shahid et al., 2014; Zhou, 2013). Alphasatellite can replicate autonomously and its replication is specifically mediated by its Rep (Tao et al., 2004), while the replication of other components including betasatellite, is specifically mediated by the begomovirus Rep. This would suggest a difference in the begomovirus and alphasatellite replication origins. Recently, an alphasatellite associated with Okra leaf curl disease from West Africa (Kon et al., 2009) is highly divergent molecule from previously characterized alphasatellites (Fiallo-Olive et al., 2012; Saunders et al., 2002) indicating geographically isolated evolution of a West African lineage of these satellites. The geographical distribution and the genetic diversity of these satellites are consistent with a long term association with monopartite begomoviruses (Briddon and Stanley, 2006).

[FIGURE 1 OMITTED]

Genetic variability. Most of the monopartite begomovirus-betasatellite complex associated with alphasatellites have been characterised in the OW. Previous studies have shown that cotton leaf curl Multan virus (CLCuMV), cotton leaf curl Burewala virus (CLCuBV), tobacco leaf curl Pusa virus (TbLCuPuV), Ageratum yellow vein virus (AYVV), tobacco curly shoot virus (TbCSV), tomato yellow leaf curl virus (TYLCV), East African cassava mosaic Kenya virus (EACMKnV) and mungbean yellow mosaic virus (MYMV) are usually associated with alphasatellite (Satya et al., 2014; Shahid et al., 2014; Harimalala el al., 2013; Kumar et al., 2011; Singh et al., 2011; Mubin et al., 2010; Xie et al., 2010; Mansoor et al., 1999) (Fig. 2). Recently, different alphasatellites such as cassava mosaic (virus) alphasatellite, Gossvpium darwinii symptomless alphasatellite, Vernonia yellow vein Fijian alphasatellite associated with EACMKnV, and CLCuBV, MYMV were isolated from different hosts i.e., cassava, cucurbits and legumes (Satya et al., 2014; Harimalala et al., 2013; Zia-Ur-Rehman et al., 2013). Interestingly, a strain of TYLCV originating from Oman has been shown to be associated with an unusual alphasatellite (Ageratun yellow vein Singapore alphasatellite), the only alphasatellite that was previously reported from Singapore back in 1999 (Idris et al., 2011; Saunders and Stanley, 1999). Recently, Sida yellow vein China alphasatellite (SiYVCNA) has been identified in association with TYLCW from main land Japan. However, the low levels of sequence divergence between all isolates of SiYVCNA suggests that this has only recently spread into Japan (Shahid et al., 2014).

[FIGURE 2 OMITTED]

Potential alphasatellite functions. Alphasatellites have no obvious contribution to symptoms induced by begomovirus-betasatellite disease complexes and appear to affect betasatellite replication but do not affect helper virus replication. However, some alphasatellites can attenuate disease symptoms caused by begomovirus-betasatellite complex in the early stages of infection. For example, Nawaz-ul-Rehman et al. (2010) have shown the alphasatellite Rep proteins encoded by two non-pathogenic alphasatellites, Gossvpium darwinii symptomless alphasatellite (GDarSLA) and Gossvpium mustelinium symptomless alphasatellite (GMusSLA). They can interact with Cotton leaf curl Rajasthan vims (CLCuRaV) Rep proteins (Table 1). Betasatellites depend solely for replication on the Rep proteins encoded by their helper begomoviruses: binding between alphasatellite-Rep and helper virus Rep proteins may inhibit betasatellite replication and results in down regulated expression of [beta]C1 and correspondent symptom amelioration. Also GDarSLA and GMusSLA alphasatellite-Reps have strong gene silencing suppressor activities (Nawaz-ul-Rehman et al., 2010). Although further investigations are required to prove whether alphasatellite-Reps encoded by other alphasatellites also have silencing suppressor activities. Recently, alphasatellites have been found in association with bipartite begomoviruses in Venezuela and Brazil (Zia-Ur-Rehman et al., 2013; Romay et al., 2010), respectively. The DNA-2 type alphasatellite, a different alphasatellite (only two members) of this alphasatellite are found until now, one from. Ageratum in Singapore and the other from tomato from Oman (Idris et al., 2011; Saunders et al., 2002). Although all these members contain conserved alphasatellite genome features, the DNA-2 type molecules are less homogeneous and have less than 50% nucleotide sequence identity with each other. The DNA-2 type alphasatellite identified in Oman can attenuate begomovirus symptoms and reduce accumulations of betasatellites (Idris et al., 2011). Further studies are needed to confirm whether these satellite molecules are replicated by their helper virus (es) and whether they have role in pathogenesis similar to those of betasatellites and some alphasatellites. New technologies like vector-enabled metagenomics and the recent circular DNA genomics (Ng et al., 2011) are anticipated to soon provide additional information about the field distributions of these novel satellites and their associated begomoviruses. The promising study about the function of this satellite indicate that the alphasatellite is most likely a molecular parasite of the helper begomovirus (Kon et al., 2009).

Viral vectors based on alphasatellites. Many plant viruses have been adapted into expression and VIGS vectors for external protein expression (Gleba et al., 2007) and silencing (Purkayastha and Dasgupta. 2009) of target genes in main crop plants. Recently, tobacco curly shoot alphasatellite (TbCSA) was successfully used to silence [beta]-glucuronidase and the sulphur desatinase genes in different Nictoiana tabacum cultivare (Purkayastha and Dasgupta, 2009). Among that it can be used to investigate gene expression (or as an expression vector) on the entire host range of the begomoviruses/curtoviruses. Alphasatellite has some unique properties that make this component distinctive among other molecules. For example, it has Rep gene which makes the alphasatellite autonomous in replication, secondly it has a-rich region if deleted cannot effect on its replication, lastly this molecule is quiet small and easy to manipulate. Shahid et al. (2009) have shown by agroinoculation studies with a-rich deleted cotton leaf curl Multan alphasatellite (CLCuMA) that this sequence is not required for the infectivity or maintenance of CLCuMA. Also CLCuMA has a wider host range and can successfully be maintained by a large number of diverse Begomovirus species. The ability to amplify itself is useful in a vector since it will increase the copy number (and thus also expression) of inserted sequences, deletion of a-rich region to increase the insert size and wider host range makes it a potentially useful vector (Tao and Zhou, 2004). The a-rich deleted CLCuMA was maintained in plants in the presence of a begomovirus. Although little is yet known about the maintenance of alphasatellites by begomoviruses, it is likely that high-level replication of these molecules is required for their maintenance, which depends upon its own Rep. There is no evidence for a (strong) selection mechanism for maintenance of alphasatellites. Maintenance of alphasatellites can simply be a selection of numbers; plants containing high levels of the satellite allow cell-to-cell movement by the virus encoded movement proteins or infection to the next plant by the vector of the helper begomovirus. Tao and Zhou (2004) used modified CLCuMA for virus induced gene silencing vector in plants. The same vector was used to successfully silence the chelates gene (ChlI). One of the advantages of an alphasatellite vector, over many of the other vectors, is that it can, at least in theory, be used with different Begomovirus or even Curtovirus (Saunders et al. 2002).

Recent research advances. Recent progresses in research comprises of the construction of the alphasatellite-based vectors, the development of the first VIGS system for different agricultural crops, the description of new alphasatellites, improvement in diagnostics, and new information on the begomovirus-satellite complex.

Conclusion

The role that alphasatellites play in begomovirus-satellite disease complex is still generally unidentified. The recent advancement and emerging potential of Next Generation Sequencing approaches will undoubtedly contribute considerably to the elucidation of the aetiology of many of these alphasatellite associated diseases. The fairly recent discovery of alphasatellite in Japan (Shahid et al., 2014) and its presence in papaya gardens in Nepal (Shahid et al., 2013) suggest that its occurrence and possible role in disease in other agricultural-producing regions need to be investigated. What effect the presence of an alphasatellite and the defective allied component may have on future begomovirus-betasatellite complex is not clear.

Whereas outdated research focused on the detection and characterisation of prevailing and new begomovirus-satellite complexes, we believe research on (i) the elucidation of the etiology of these disease complexes (ii) the development of resistance using non-transgenic approaches, and (iii) studies on the molecular interaction of alphasatellites and their helper viruses with their original host. As efficient tools are being developed now, future research with begomoviruses, as well as with all other whitefly-vectoring viruses, has to move from typical (model) plants like Nicotiana benthamiana towards other host plants to allow the study of symptomology, pathogenicity, host-plant response and viral determinants of vector transmission in their natural host.

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Muhammad Shafiq Shahid (a) *, Mehmoona Ilyas (b), Abdul Waheed (a) and Rajarshi Kumar Gaur (c)

(a) Department of Biosciences, COMSATS Institute of Information Technology, Sahiwal 57000, Pakistan

(b) Department of Biotechnology, University of Sargodha, Sargodha, Pakistan

(c) Department of Science, Faculty of Arts, Science and Commerce, Mody Institute of Technology and Science, Lakshmangarh, Sikar-332311, Rajasthan, India

(received April 29, 2015; revised June 17, 2015; accepted August 19, 2015)

* Author for correspondence; E-mail: shafiqinayat@gmail.com.
Table 1. Alphasatellite associated with monopartite-betasatellite
complex

Alphasatellite              Acc. no.   Associated Virus

Ageratum yellow vein        AJ238493   Ageratum yellow vein
  alphasatellite                         virus (AYVV)
Ageratum yellow vein        JX570736   Tomato leaf curl
  India alphasatellite                   Karnataka virus
Ageratum yellow vein        AJ512960   Diversity of
  Kenya alphasatellite                   alphasatellite
Ageratum yellow vein        FR772085   Cotton leaf curl
  Pakistan                               Burewala virus
  alphasatellite
Ageratum yellow vein        AJ416153   AYVV
  Singapore
  alphasatellite
Cassava mosaic              HE984148   East African cassava
  Madagascar                             mosaic Kenya virus
  alphasatellite
Cleome leaf crumple         FN436007   Cleome leaf crumple
  alphasatellite                         virus
Cotton leaf curl Dabwali    AJ512957   Diversity of
  alphasatellite                         alphasatellite
Cotton leaf curl Gezira     FM164740   AYVV
  alphasatellite
Croton yellow vein          FN658711   Croton yellow vein
  mosaic alphasatellite                  mosaic virus
Euphorbia yellow mosaic     FN436008   Euphorbia yellow mosaic
  alphasatellite                         virus
Gossypium darwinii          EU384606   Cototn leaf curl
  symptomless                            Rajasthan virus
  alphasatellite
Hibiscus leaf curl          AJ512950   Diversity of
  alphasatellite                         alphasatellite
Hollyhock yellow vein       FR772086   Hollyhock yellow vein
  symptomless                            virus
  alphasatellite
Lantana yellow vein         KC206075   Lantana yellow vein
  alphasatellite                         virus
Malvastrum yellow mosaic    AM050734   Malvastrum yellow mosaic
  alphasatellite                         virus
Malvastrum yellow mosaic    FN675297   Tomato yellow leaf curl
  Cameroon                               China virus (ToLCCNV)
  alphasatellite
Melon chlorotic mosaic      FM163578   Melonchlorotic leaf curl
  virus alphasatellite                   virus
Mesta yellow vein mosaic    JX183090   Mesta yellow vein mosaic
  alphasatellite                         virus
Okra leaf curl              AJ512954   Diversity of
  alphasatellite                         alphasatellite
Sida yellow vein Vietnam    DQ641718   Sida yellow vein Vietnam
  alphasatellite                         virus
Tobacco curly shoot         AJ579361   Tomato yellow leaf curl
  alphasatellite                         China virus (ToLCCNV)
Tomato yellow leaf curl     AJ579358   ToLCCNV
  China alphasatellite
Verbesina encelioides       HQ631431   Hollyhock yellow vein
  leaf curl                              virus
  alphasatellite
Vemonia yellow vein         JF733780   Vemonia yellow vein
  Fujian alphasatellite                  Fujian virus
Vinca yellow vein           KC206076   Vinca yellow vein virus
  alphasatellite

Alphasatellite              Source

Ageratum yellow vein        Saunders etal, 1997
  alphasatellite
Ageratum yellow vein        Chatchawankanphanich and
  India alphasatellite        Maxwell, 2002
Ageratum yellow vein        Briddon et al, 2004
  Kenya alphasatellite
Ageratum yellow vein        Iqbal et al, 2013
  Pakistan
  alphasatellite
Ageratum yellow vein        Saunders, 1999
  Singapore
  alphasatellite
Cassava mosaic              Harimalala et al, 2013
  Madagascar
  alphasatellite
Cleome leaf crumple         Paprotka et al, 2010
  alphasatellite
Cotton leaf curl Dabwali    Briddon et al, 2004
  alphasatellite
Cotton leaf curl Gezira     Leke et al, 2013
  alphasatellite
Croton yellow vein          Zaffalon et al, 2011
  mosaic alphasatellite
Euphorbia yellow mosaic     Fernanda et al, 2011
  alphasatellite
Gossypium darwinii          Nawazul-Rehman et al,
  symptomless                 2010
  alphasatellite
Hibiscus leaf curl          Briddon et al, 2004
  alphasatellite
Hollyhock yellow vein       Saunders et al, 2000
  symptomless
  alphasatellite
Lantana yellow vein         Marwal et al, 2013a
  alphasatellite
Malvastrum yellow mosaic    Guo et al, 2006
  alphasatellite
Malvastrum yellow mosaic    Leke et al, 2011
  Cameroon
  alphasatellite
Melon chlorotic mosaic      Romay et al, 2010
  virus alphasatellite
Mesta yellow vein mosaic    Chatterjee et al, 2005
  alphasatellite
Okra leaf curl              Briddon et al, 2004
  alphasatellite
Sida yellow vein Vietnam    Ha et al, 2006
  alphasatellite
Tobacco curly shoot         Xie et al, 2010
  alphasatellite
Tomato yellow leaf curl     Xie et al, 2010
  China alphasatellite
Verbesina encelioides       Prajapat et al, 2011
  leaf curl
  alphasatellite
Vemonia yellow vein         Zulfiqar et al, 2012
  Fujian alphasatellite
Vinca yellow vein           Marwal et al, 2013b
  alphasatellite
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Author:Shahid, Muhammad Shafiq; Ilyas, Mehmoona; Waheed, Abdul; Gaur, Rajarshi Kumar
Publication:Pakistan Journal of Scientific and Industrial Research Series B: Biological Sciences
Article Type:Report
Date:Mar 1, 2016
Words:4169
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