@article{peele_jordan_muangsan_turnage_egelkrout_eagle_hanley-bowdoin_robertson_2001, title={Silencing of a meristematic gene using geminivirus-derived vectors}, volume={27}, ISSN={["0960-7412"]}, DOI={10.1046/j.1365-313x.2001.01080.x}, abstractNote={Geminiviruses are DNA viruses that replicate and transcribe their genes in plant nuclei. They are ideal vectors for understanding plant gene function because of their ability to cause systemic silencing in new growth and ease of inoculation. We previously demonstrated DNA episome-mediated gene silencing from a bipartite geminivirus in Nicotiana benthamiana. Using an improved vector, we now show that extensive silencing of endogenous genes can be obtained using less than 100 bp of homologous sequence. Concomitant symptom development varied depending upon the target gene and insert size, with larger inserts producing milder symptoms. In situ hybridization of silenced tissue in attenuated infections demonstrated that silencing occurs in cells that lack detectable levels of viral DNA. A mutation confining the virus to vascular tissue produced extensive silencing in mesophyll tissue, further demonstrating that endogenous gene silencing can be separated from viral infection. We also show that two essential genes encoding a subunit of magnesium chelatase and proliferating cell nuclear antigen (PCNA) can be silenced simultaneously from different components of the same viral vector. Immunolocalization of silenced tissue showed that the PCNA protein was down-regulated throughout meristematic tissues. Our results demonstrate that geminivirus-derived vectors can be used to study genes involved in meristem function in intact plants.}, number={4}, journal={PLANT JOURNAL}, author={Peele, C and Jordan, CV and Muangsan, N and Turnage, M and Egelkrout, E and Eagle, P and Hanley-Bowdoin, L and Robertson, D}, year={2001}, month={Aug}, pages={357–366} }
 @article{orozco_gladfelter_settlage_eagle_gentry_hanley-bowdoin_1998, title={Multiple cis elements contribute to geminivirus origin function}, volume={242}, ISSN={["0042-6822"]}, DOI={10.1006/viro.1997.9013}, abstractNote={The genome of the geminivirus tomato golden mosaic virus (TGMV) consists of two circular DNA molecules which are dissimilar in sequence except for a highly conserved 200-bp common region that includes the origin for rolling circle replication. To better characterize the plus-strand origin, we analyzed the capacities of various TGMV common region sequences to support episomal replication in tobacco protoplasts when the viral replication proteins AL1 and AL3 were supplied in trans. These experiments demonstrated that the minimal origin is located in 89-bp common region fragment that includes the known AL1 binding motif and a hairpin structure containing the DNA cleavage site. Analyses of mutant origin sequences identified two additional cis elements--one that is required for origin activity and a second that greatly enhances replication. In contrast, a conserved partial copy of the AL1 binding site did not contribute to origin function. Mutational analysis of the functional AL1 binding site showed that both spacing and sequence of this motif are important for replication in vivo and AL1/DNA binding in vitro. Spacing changes between the AL1 binding site and hairpin also negatively impacted TGMV origin function in a position-dependent manner. Together, these results demonstrated that the organization of TGMV plus-strand origin is complex, involving multiple cis elements that are likely to interact with each other during initiation of replication.}, number={2}, journal={VIROLOGY}, author={Orozco, BM and Gladfelter, HJ and Settlage, SB and Eagle, PA and Gentry, RN and Hanley-Bowdoin, L}, year={1998}, month={Mar}, pages={346–356} }
 @article{eagle_hanley-bowdoin_1997, title={CIS elements that contribute to geminivirus transcriptional regulation and the efficiency of DNA replication}, volume={71}, number={9}, journal={Journal of Virology}, author={Eagle, P. A. and Hanley-Bowdoin, L. K.}, year={1997}, pages={6947–6955} }
 @article{gladfelter_eagle_fontes_batts_hanley-bowdoin_1997, title={Two domains of the AL1 protein mediate geminivirus origin recognition}, volume={239}, ISSN={["0042-6822"]}, DOI={10.1006/viro.1997.8869}, abstractNote={The geminiviruses tomato golden mosaic virus (TGMV) and bean golden mosaic virus (BGMV) have bipartite genomes. Their A and B DNA components contain cis -acting sequences that function as origins of replication, while their A components encode the trans -acting replication proteins—AL1 and AL3. Earlier experiments demonstrated that virus-specific interactions between the cis - and trans -acting functions are required for TGMV and BGMV replication and that the AL1 proteins of the two viruses specifically bind their respective origins. In the current study, characterization of AL1 and AL3 proteins produced from plant expression cassettes in transient replication assays revealed that interaction between AL1 and the origin is responsible for virus-specific replication. The AL3 protein does not contribute to specificity but can be preferred by its cognate AL1 protein when replication is impaired. Analysis of chimeric proteins showed that two regions of AL1 act as specificity determinants during replication. The first domain is located between amino acids 1 and 116 and recognizes the AL1 origin binding site. The second region, which is between amino acids 121 and 209, is not dependent on the known AL1 DNA binding site. Analysis of wild type and chimeric proteins in transient transcription assays showed that AL1 also represses its own promoter in a virus-specific manner. Transcriptional specificity is conferred primarily by AL1 amino acids 1–93 with amino acids 121–209 making a smaller contribution. Together, these results demonstrated that the virus-specific interactions of AL1 during replication and transcription are complex, involving at least two discreet domains of the protein.}, number={1}, journal={VIROLOGY}, author={Gladfelter, HJ and Eagle, PA and Fontes, EPB and Batts, L and Hanley-Bowdoin, L}, year={1997}, month={Dec}, pages={186–197} }
 @article{eagle_orozco_hanley-bowdoin_1994, title={A DNA sequence required for geminivirus replication also mediates transcriptional regulation}, volume={6}, number={8}, journal={Plant Cell}, author={Eagle, P. A. and Orozco, B. M. and Hanley-Bowdoin, L.}, year={1994}, pages={1157} }