Global Analysis of Arabidopsis Gene Expression Uncovers a Complex Array of Changes Impacting Pathogen Response and Cell Cycle during Geminivirus Infection  

Abstract

Geminiviruses are small DNA viruses that use plant replication machinery to amplify their genomes. Microarray analysis of the Arabidopsis (Arabidopsis thaliana) transcriptome in response to cabbage leaf curl virus (CaLCuV) infection uncovered 5,365 genes (false discovery rate ,0.005) differentially expressed in infected rosette leaves at 12 d postinoculation. Data mining revealed that CaLCuV triggers a pathogen response via the salicylic acid pathway and induces expression of genes involved in programmed cell death, genotoxic stress, and DNA repair. CaLCuV also altered expression of cell cycle-associated genes, preferentially activating genes expressed during S and G2 and inhibiting genes active in G1 and M. A limited set of core cell cycle genes associated with cell cycle reentry, late G1, S, and early G2 had increased RNA levels, while core cell cycle genes linked to early G1 and late G2 had reduced transcripts. Fluorescence-activated cell sorting of nuclei from infected leaves revealed a depletion of the 4C population and an increase in 8C, 16C, and 32C nuclei. Infectivity studies of transgenic Arabidopsis showed that overexpression of CYCD3;1 or E2FB, both of which promote the mitotic cell cycle, strongly impaired CaLCuV infection. In contrast, overexpression of E2FA or E2FC, which can facilitate the endocycle, had no apparent effect. These results showed that geminiviruses and RNA viruses interface with the host pathogen response via a common mechanism, and that geminiviruses modulate plant cell cycle status by differentially impacting the CYCD/retinoblastomarelated protein/E2F regulatory network and facilitating progression into the endocycle.

The Paralogous GenesRADICAL-INDUCED CELL DEATH1andSIMILAR TO RCD ONE1Have Partially Redundant Functions during Arabidopsis Development

“…These genes have been implicated in DNA repair (Doucet-Chabeaud et al, 2001;De Block et al, 2005) and have been shown to be associated with chromosomes through their N-terminal zinc fingers (Babiychuk et al, 2001). AtPARP1 and AtPARP2 are up-regulated during geminivirus infection, most likely in response to accumulation of nicked viral DNA forms (Ascencio-Ibanez et al, 2008), and also accumulate under conditions of DNA stress (Culligan et al, 2006). The finding that two putative transcriptional coactivators can bind to the zinc fingers of AtPARP1 suggests that, like mammalian PARP-1, this protein may also be involved in regulation of gene expression in addition to its role in DNA repair (Storozhenko et al, 2001).…”

Geminiviruses Subvert Ubiquitination by Altering CSN-Mediated Derubylation of SCF E3 Ligase Complexes and Inhibit Jasmonate Signaling inArabidopsis thaliana

“…Among them, the jasmonate response, dependent on the SCF COI1 complex, plays a crucial role in pathogen defenses. Not much information about the role of jasmonates on viral infection is currently available, but recent works revealed jasmonate signaling as an emerging topic in plant-virus interaction research (Vigliocco et al, 2002;Liu et al, 2004;Agudelo-Romero et al, 2008;Ascencio-Ibá ñ ez et al, 2008;Yang et al, 2008;Kovac et al, 2009).…”

Horizontal gene transfer is more frequent with increased heterotrophy and contributes to parasite adaptation

“…Table S10) (58,59). Orthogroup 1685 encodes a cysteine-rich receptor-like protein kinase, and the ortholog in Arabidopsis (AT1G70520) is up-regulated during pathogen infection and rapid cell death (51).…”