@article{arguello-astorga_ascencio-ibanez_dallas_orozco_hanley-bowdoin_2007, title={High-frequency reversion of geminivirus replication protein mutants during infection}, volume={81}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.00925-07}, abstractNote={ABSTRACT}, number={20}, journal={JOURNAL OF VIROLOGY}, author={Arguello-Astorga, Gerardo and Ascencio-Ibanez, J. Trinidad and Dallas, Mary Beth and Orozco, Beverly M. and Hanley-Bowdoin, Linda}, year={2007}, month={Oct}, pages={11005–11015} }
 @article{arguello-astorga_lopez-ochoa_kong_orozco_settlage_hanley-bowdoin_2004, title={A novel motif in geminivirus replication proteins interacts with the plant retinoblastoma-related protein}, volume={78}, ISSN={["1098-5514"]}, DOI={10.1128/JVI.78.9.4817-4826.2004}, abstractNote={ABSTRACT}, number={9}, journal={JOURNAL OF VIROLOGY}, author={Arguello-Astorga, G and Lopez-Ochoa, L and Kong, LJ and Orozco, BM and Settlage, SB and Hanley-Bowdoin, L}, year={2004}, month={May}, pages={4817–4826} }
 @misc{hanley-bowdoin_orozco_kong_gruissem_2004, title={Geminivirus resistant transgenic plants}, volume={6,800,793}, number={2004 Oct. 5}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Hanley-Bowdoin, L. and Orozco, B. M. and Kong, L. J. and Gruissem, W.}, year={2004} }
 @article{kong_orozco_roe_nagar_ou_feiler_durfee_miller_gruissem_robertson_et al._2000, title={A geminivirus replication protein interacts with the retinoblastoma protein through a novel domain to determine symptoms and tissue specificity of infection in plants}, volume={19}, ISSN={["0261-4189"]}, DOI={10.1093/emboj/19.13.3485}, abstractNote={Geminiviruses replicate in nuclei of mature plant cells after inducing the accumulation of host DNA replication machinery. Earlier studies showed that the viral replication factor, AL1, is sufficient for host induction and interacts with the cell cycle regulator, retinoblastoma (pRb). Unlike other DNA virus proteins, AL1 does not contain the pRb binding consensus, LXCXE, and interacts with plant pRb homo logues (pRBR) through a novel amino acid sequence. We mapped the pRBR binding domain of AL1 between amino acids 101 and 180 and identified two mutants that are differentially impacted for AL1–pRBR interactions. Plants infected with the E‐N140 mutant, which is wild‐type for pRBR binding, developed wild‐type symptoms and accumulated viral DNA and AL1 protein in epidermal, mesophyll and vascular cells of mature leaves. Plants inoculated with the KEE146 mutant, which retains 16% pRBR binding activity, only developed chlorosis along the veins, and viral DNA, AL1 protein and the host DNA synthesis factor, proliferating cell nuclear antigen, were localized to vascular tissue. These results established the importance of AL1–pRBR interactions during geminivirus infection of plants.}, number={13}, journal={EMBO JOURNAL}, author={Kong, LJ and Orozco, BM and Roe, JL and Nagar, S and Ou, S and Feiler, HS and Durfee, T and Miller, AB and Gruissem, W and Robertson, D and et al.}, year={2000}, month={Jul}, pages={3485–3495} }
 @article{hanley-bowdoin_settlage_orozco_nagar_robertson_2000, title={Geminiviruses - Models for plant DNA replication, transcription and cell cycle regulation ([correction to] vol 35, pg 105, 2000)}, volume={35}, number={4}, journal={Critical Reviews in Biochemistry and Molecular Biology}, author={Hanley-Bowdoin, L. and Settlage, S. B. and Orozco, B. M. and Nagar, S. and Robertson, D.}, year={2000}, pages={U4} }
 @article{hanley-bowdoin_settlage_orozco_nagar_robertson_2000, title={Geminiviruses: Models for plant DNA replication, transcription, and cell cycle regulation}, volume={35}, number={2}, journal={Critical Reviews in Biochemistry and Molecular Biology}, author={Hanley-Bowdoin, L. and Settlage, S. B. and Orozco, B. M. and Nagar, S. and Robertson, D.}, year={2000}, pages={105–140} }
 @article{orozco_kong_batts_elledge_hanley-bowdoin_2000, title={The multifunctional character of a geminivirus replication protein is reflected by its complex oligomerization properties}, volume={275}, ISSN={["0021-9258"]}, DOI={10.1074/jbc.275.9.6114}, abstractNote={Tomato golden mosaic virus (TGMV), a member of the geminivirus family, encodes one essential replication protein, AL1, and recruits the rest of the DNA replication apparatus from its plant host. TGMV AL1 is an oligomeric protein that binds double-stranded DNA and catalyzes cleavage and ligation of single-stranded DNA. The oligomerization domain, which is required for DNA binding, maps to a region that displays strong sequence and structural homology to other geminivirus Rep proteins. To assess the importance of conserved residues, we generated a series of site-directed mutations and analyzed their impact on AL1 function in vitro and in vivo. Two-hybrid experiments revealed that mutation of amino acids 157–159 inhibited AL1-AL1 interactions, whereas mutations at nearby residues reduced complex stability. Changes at positions 157–159 also disrupted interaction between the full-length mutant protein and a glutathione S-transferase-AL1 oligomerization domain fusion in insect cells. The mutations had no detectable effect on oligomerization when both proteins contained full-length AL1 sequences, indicating that AL1 complexes can be stabilized by amino acids outside of the oligomerization domain. Nearly all of the oligomerization domain mutants were inhibited or severely attenuated in their ability to support AL1-directed viral DNA replication. In contrast, the same mutants were enhanced for AL1-mediated transcriptional repression. The replication-defective AL1 mutants also interfered with replication of a TGMV A DNA encoding wild type AL1. Full-length mutant AL1 was more effective in the interference assays than truncated proteins containing the oligomerization domain. Together, these results suggested that different AL1 complexes mediate viral replication and transcriptional regulation and that replication interference involves multiple domains of the AL1 protein.}, number={9}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Orozco, BM and Kong, LJ and Batts, LA and Elledge, S and Hanley-Bowdoin, L}, year={2000}, month={Mar}, pages={6114–6122} }
 @article{hanley-bowdoin_settlage_orozco_nagar_robertson_1999, title={Geminiviruses: Models for plant DNA replication, transcription, and cell cycle regulation {review}}, volume={18}, DOI={10.1080/07352689991309162}, abstractNote={Geminiviruses have small, single-stranded DNA genomes that replicate through double-stranded intermediates in the nuclei of infected plant cells. Viral double-stranded DNA also assembles into minichromosomes and is transcribed in infected cells. Geminiviruses encode only a few proteins for their replication and transcription and rely on host enzymes for these processes. However, most plant cells, which have exited the cell cycle and undergone differentiation, do not contain the replicative enzymes necessary for viral DNA synthesis. To overcome this barrier, geminiviruses induce the accumulation of DNA replication machinery in mature plant cells, most likely by modifying cell cycle and transcriptional controls. In animals, several DNA viruses depend on host replication and transcription machinery and can alter their hosts to create an environment that facilitates efficient viral replication. Analysis of these viruses and their proteins has contributed significantly to our understanding of DNA replication, transcription, and cell cycle regulation in mammalian cells. Geminiviruses have the same potential for plant systems. Plants offer many advantages for these types of studies, including ease of transformation, well-defined cell populations and developmental programs, and greater tolerance of cell cycle perturbation and polyploidy. Our knowledge of the molecular and cellular events that mediate geminivirus infection has increased significantly during recent years. The goal of this review is to summarize recent research addressing geminivirus DNA replication and its integration with transcriptional and cell cycle regulatory processes.}, number={1}, journal={Critical Reviews in Plant Sciences}, author={Hanley-Bowdoin, L. and Settlage, S. B. and Orozco, B. M. and Nagar, S. and Robertson, D.}, year={1999}, pages={71–106} }
 @article{orozco_hanley-bowdoin_1998, title={Conserved sequence and structural motifs contribute to the DNA binding and cleavage activities of a geminivirus replication protein}, volume={273}, ISSN={["0021-9258"]}, DOI={10.1074/jbc.273.38.24448}, abstractNote={Tomato golden mosaic virus (TGMV), a member of the geminivirus family, has a single-stranded DNA genome that replicates through a rolling circle mechanism in nuclei of infected plant cells. TGMV encodes one essential replication protein, AL1, and recruits the rest of the DNA replication apparatus from its host. AL1 is a multifunctional protein that binds double-stranded DNA, catalyzes cleavage and ligation of single-stranded DNA, and forms oligomers. Earlier experiments showed that the region of TGMV AL1 necessary for DNA binding maps to the N-terminal 181 amino acids of the protein and overlaps the DNA cleavage (amino acids 1–120) and oligomerization (amino acids 134–181) domains. In this study, we generated a series of site-directed mutations in conserved sequence and structural motifs in the overlapping DNA binding and cleavage domains and analyzed their impact on AL1 function in vivo and in vitro. Only two of the fifteen mutant proteins were capable of supporting viral DNA synthesis in tobacco protoplasts. In vitroexperiments demonstrated that a pair of predicted α-helices with highly conserved charged residues are essential for DNA binding and cleavage. Three sequence motifs conserved among geminivirus AL1 proteins and initiator proteins from other rolling circle systems are also required for both activities. We used truncated AL1 proteins fused to a heterologous dimerization domain to show that the DNA binding domain is located between amino acids 1 and 130 and that binding is dependent on protein dimerization. In contrast, AL1 monomers were sufficient for DNA cleavage and ligation. Together, these results established that the conserved motifs in the AL1 N terminus contribute to DNA binding and cleavage with both activities displaying nearly identical amino acid requirements. However, DNA binding was readily distinguished from cleavage and ligation by its dependence on AL1/AL1 interactions.}, number={38}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Orozco, BM and Hanley-Bowdoin, L}, year={1998}, month={Sep}, pages={24448–24456} }
 @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{orozco_miller_settlage_hanley-bowdoin_1997, title={Functional domains of a geminivirus replication protein}, volume={272}, DOI={10.1074/jbc.272.15.9840}, abstractNote={Tomato golden mosaic virus, a member of the geminivirus family, has a single-stranded DNA genome that is replicated and transcribed in infected plant cells through the concerted action of viral and host factors. One viral protein, AL1, contributes to both processes by binding to a directly repeated, double-stranded DNA sequence located in the overlapping (+) strand origin of replication and AL1 promoter. The AL1 protein, which occurs as a multimeric complex in solution, also catalyzes DNA cleavage during initiation of rolling circle replication. To identify the tomato golden mosaic virus AL1 domains that mediate protein oligomerization, DNA binding, and DNA cleavage, a series of truncated AL1 proteins were produced in a baculovirus expression system and assayed for each activity. These experiments localized the AL1 oligomerization domain between amino acids 121 and 181, the DNA binding domain between amino acids 1 and 181, and the DNA cleavage domain between amino acids 1 and 120. Deletion of the first 29 amino acids of AL1 abolished DNA binding and DNA cleavage, demonstrating that an intact N terminus is required for both activities. The observation that the DNA binding domain includes the oligomerization domain suggested that AL1-AL1 protein interaction may be a prerequisite for DNA binding but not for DNA cleavage. The significance of these results for AL1 function during geminivirus replication and transcription is discussed.}, number={15}, journal={Journal of Biological Chemistry}, author={Orozco, B. M. and Miller, A. B. and Settlage, S. B. and Hanley-Bowdoin, Linda}, year={1997}, pages={9840–9846} }
 @article{orozco_hanley-bowdoin_1996, title={A DNA structure is required for geminivirus replication origin function}, volume={70}, number={1}, journal={Journal of Virology}, author={Orozco, B. M. and Hanley-Bowdoin, L.}, year={1996}, pages={148} }