Plant virus studies involving VIGS do not customarily use a VIGS vector derived from the same virus being studied for fear that the potential trait observed following the VIGS vector inoculation could be due to plant responses to the silencing vector. However in the case of many non-model crops, such as cassava, they are not susceptible to any of the known viruses used for VIGS vectors. For geminivirus studies in cassava, a SACMV-VIGS vector has been previously constructed for functional gene studies (Mwaba 2010). The only other cassava virus vector tested is the ACMV VIGS vector (Fofana et al. 2004), and more recently east african cassava mosaic virus (EACMV) (Beyene et al. 2017). A VIGS study was performed to knock out myosins in N. benthamiana and to ascertain the effect on SACMV infectivity. Comparisons between two different silencing vectors, namely SACMV and TRV, were performed in order to determine if the silencing vectors would yield different silencing results. Furthermore, TRV or SACMV VIGS silenced plants were challenged with SACMV, and possible effects of the two VIGS vectors on subsequent SACMV pathogenicity/infectivity evaluated.
In plants not challenged with SACMV, inoculation of SACMV-VIGS constructs and TRV-VIGS constructs resulted in minimal to no symptom (figure 2-18 - figure 2-21) however TRV-VIGS constructs induced a stronger reduction in myosin silencing compared to SACMV-VIGS constructs (figure 2-10; appendix A1.3.1). Several factors have been shown to determine the efficiency of a VIGS vector system and because TRV-VIGS system has been extensively used, its protocol has been optimised in terms of the length of the insert, the method of inoculation and the timing at which silencing was measured. Although this experiment was not carried out at the optimum temperature established for TRV-VIGS system which is 18- 20◦C, the length of the insert, the method of inoculation and the timing at which silencing was measured (21 dpi post initiation of myosin silencing which is equivalent to 14 dpi in this study) was performed as suggested for TRV-VIGS (Senthil-Kumar and Mysore 2011b; Senthil- Kumar and Mysore 2014) and it is possible that those conditions whilst being optimum for
TRV-VIGS studies, aren’t for SACMV-VIGS and the SACMV-VIGS system requires more optimization to improve its silencing efficiency.
Despite TRV-VIGS being more efficient at SACMV-VIGS, in both system, the efficacy and efficiency of both VIGS system was better at 14 dpi than at 28 dpi (figure 2-10). At 14 dpi, both SACMV-VIGS and TRV-VIGS silenced more myosins than at 28 but in both system, silencing was stronger at 14 than at 28 dpi. The reduction in silencing efficiency observed at 28 dpi for TRV VIGS system could be due to the TRV genome being targeted by the host’s silencing machinery. DNA viruses have an advantage over RNA viruses for VIGS, because their genome is not a direct target of the host’s post-transcriptional gene silencing (PTGS) machinery unlike RNA based virus vectors which can be eliminated from the host (Ruiz et al. 1998; Robertson 2004). Although unlike PVX-VIGS and TMV-VIGS which can be cleared from the host, (Ruiz et al. 1998; Hiriart et al. 2003), there is no record of TRV-VIGS being eliminated, it requires a booster application to be maintained in the plants over time (Senthil-Kumar and Mysore 2014) and it’s possible that the decrease in silencing efficiency is due to a decrease in its genome accumulation in the plant. Given that SACMV-VIGS is a DNA virus, the decrease in efficiency of silencing for SACMV-VIGS is probably due to an increase in the VIGS vector “load” which results in an increase in the expression of RNA silencing suppressors encoded by the VIGS vector. An efficient VIGS vector must be able to suppress the host’s transcriptional PTGS machinery, enough to allow for its genome to carry on proliferating and at the same time allow for expression of the gene of interest to be suppressed and with time an increase in silencing suppressors activity allows SACMV-VIGS vector to proliferate in the host but negatively impacts its ability to induce silencing.
2.4.3
SACMV challenge of N. benthamiana relieves silencing by SACMV-
VIGS and TRV-VIGS constructs
Despite the silencing observed in SACMV-challenged/TRV::M11.K plants at 28 dpi, accumulation of DNA-A was not different to that in SACMV-challenged/TRV-VIGS vector (figure 2-16b). When viral load at 28 dpi was compared to viral load at 14 dpi, the fold increase in SACMV-challenged/TRV::M11.K was lower than SACMV-challenged/TRV-VIGS vector, indicating that reduction in M11.K expression slowed the spread of SACMV without affecting its replication. In N. benthamiana NbXI-K has been linked with organelles
movement, vesicle transport and movement of Golgi bodies (Avisar et al. 2008b; Avisar et al. 2012; Peremyslov et al. 2012) and members of the endomembrane system have been linked to movement of geminiviruses (Lewis and Lazarowitz 2010; Lozano-Durán et al. 2011). Besides its role in plants trafficking, NbXI-K has been linked to cell growth and expansion as well as gravitropism (Ojangu et al. 2007; Park and Nebenführ 2013; Ueda et al. 2015; Talts et al. 2016). The decrease in SACMV proliferation observed in plants with a reduced expression of M11.K suggests a role for the endomembrane system in SACMV movement. The decrease in SACMV proliferation over the two time points was however not mirrored with a decrease in viral load. Myosin XI-K is known to have redundant role with other myosins both in its involvement with endomembrane trafficking as well as in its role gravitropism and cell growth and expansion and it would be interesting to look into whether the lack of decrease in viral accumulation was masked by the redundancy in M11.K function by these other myosins.
Challenging N. benthamiana with SACMV affected the silencing efficacy and efficiency of each vector as TRV::myosin failed to induce any silencing at 14 dpi and SACMV-VIGS constructs resulted in downregulation of M11.F at 14 dpi. At 28 dpi TRV::myosin reduced the expression of M11.F and M11.K and SACMV::myosin reduced the expression of M11.F. Silencing of M11.F in SACMV::M11.F was not different to silencing SACMV-challenged/ SACMV::M11.F however silencing induced by TRV::M11.F and TRV::M11.K was improved upon the introduction of SACMV.
Although the silencing of M11.F by TRV-silencing construct and SACMV-silencing construct was not affected by the presence of SACMV, this isn’t true for the other myosins that failed to be silenced in the presence of SACMV. The reversal of silencing induced by the TRV-VIGS system was unexpected as functional genomic studies that combined the use of TRV-VIGS and geminiviruses infection have shown that co-infection of TRV-VIGS constructs and tomato yellow leaf curl Sardinia virus (TYLCSV) doesn’t affect the silencing induced by TRV (Luna et al. 2006; Lozano-Durán et al. 2011; Czosnek et al. 2013). The reversal of silencing by SACMV-VIGS in the presence of SACMV however was expected as co-infection of SACMV VIGS vector with wild type SACMV in our laboratory has previously been reported to reverse downregulation of the magnesium chelatase gene (su-gene) induced by SACMV VIGS in N. benthamiana (figure 2-24; Mwaba 2010).
Silencing induced by VIGS can be uneven or patchy (Senthil-Kumar and Mysore 2011a), and the resulting RNA pool used for detection of myosin expression by qPCR has a mixture of both silenced and non-silenced tissue, which can affect the efficiency of silencing. Unlike silencing in su-gene expression which can be visually evaluated, silencing of myosin doesn’t result in visual cues, and it is difficult to know if the lack of silencing detected was due to a complete loss in silencing or an increase in unevenness of myosin suppression.
A B
Figure 2-24: Silencing of su-gene from N. benthamiana a. SACMV-VIGS construct su; b. SACMV-A::su infected N. benthamiana with delayed SACMV inoculation at 7 dpi
(Mwaba 2010)
There reversal of silencing by SACMV introduction could be to the effect that the virus on its own, or in partnership with the VIGS construct has on the expression of the gene being investigated. Loss of silencing has been suggested to be due to in-planta partial or full deletion of the insert (Senthil-Kumar and Mysore 2011a; Senthil-Kumar and Mysore 2014) and it is possible that the interaction of SACMV with either TRV-VIGS constructs and SACMV-VIGS constructs resulted in loss of the silencing insert. Furthermore the delayed introduction of SACMV brings with it the expression of SACMV encoded suppressors of RNA silencing such as the Transactivating protein (TrAP or AC2) and AC4 which work in synergy to supress RNA silencing for the benefit of the invading challenger (Nawaz-ul-rehman and Fauquet 2009) but with the consequence of negatively affecting silencing induced by the VIGS vectors. Although SACMV-VIGS vector is derived from SACMV, it accumulates at lower level than wildtype SACMV (Mwaba 2010), therefore the expression of silencing suppressors encoded by SACMV-VIGS vector and constructs is lower as well as its capacity to supress RNA-silencing.
Understanding the mechanism behind the reversal of silencing by SACMV-challenge would further explain whether VIGS silencing of M11.F in the presence of SACMV was preserved due to its involvement in SACMV pathogenicity. The expression of M11.F was upregulated by SACMV-challenge in N. benthamiana (figure 2-15) and the expression of the other myosins were not and M11.F is the only myosin that was positively silenced by both SACMV::myosin and TRV::myosin.
2.4.4
2.6.3 Downregulation of NbXI-F and NbX-K and its effect on SACMV
pathogenicity
In this study, suppression of M11.F expression by TRV-VIGS at 28 dpi led to a decrease in SACMV-A accumulation however the suppression of M11.F expression by SACMV-VIGS at 14 and 28 dpi did not and resulted in an increased viral accumulation (figure 2-16a). There was no significant increase in viral load at 28 dpi, from viral at 14 dpi and fold change in viral load over the two time points was lower for SACMV-challenged/TRV::M11.F than for SACMV-challenged/TRV-VIGS, suggesting that virus proliferation in SACMV- challenged/TRV::M11.F was impeded. These results together with the fact that expression of M11.F in SACMV-challenged/NO-VIGS was upregulated at 28 dpi provide strong evidence that NbXI-F is involved in SACMV responses in N. benthamiana.
Myosin NbXI-F have been shown to bind to chloroplasts and stromules and are believed to aid in their cellular movement (Sattarzadeh et al. 2009). Stromules or stroma filled tubules are extension of plastidial membrane allowing an increase in the surface area of plastids. Formation of stromules can be induced by sucrose and glucose, salicylic acid (SA) and reactive oxygen species like hydrogen peroxide (H202) but not nitric oxide (NO) (Schattat and
Klösgen 2011; Brunkard et al. 2015; Caplan et al. 2015). During plant defence responses, stromules extend to the nucleus and they have been shown to transport pro-defence proteins and signalling molecules from the chloroplast during defence responses to TMV (Caplan et al. 2015; Ho and Theg 2016). In Arabidopsis, the geminivirus abutilon mosaic virus (AbMV) induces stromules formation, which could provide a way along which viral particles travel through the plasmodesmata to neighbouring cells (Krenz et al. 2012). Inhibition of myosin activity has been shown to interfere with stromules formation (Natesan et al. 2009) and interfering with expression of M11.F using a VIGS approach, could therefore affect the
stability of the stromule network and should SACMV employ stromules as a mean of transport like it has been suggested of AbMV, SACMV movement would be consequently disturbed.