Averages of three biological replicates are shown +/2 SE. Refer to Table

Averages of three biological replicates are shown +/2 SE. Refer to Table 1. ER = endosperm rupture and radicle emergence (completion of germination). Note that the Yaxis for the RNA data is in log-scale. (JPG) Figure S2 Expression analyses and histone H3 methylation pattern changes of markers of seed maturation/(DOC)AcknowledgmentsWe thank Preeti Goyal, Dr. Matthew Lorincz, Dr. Matyas Medzhiradszky and Dr. Kengo Morohashi for their help with establishing the seed nChIP protocol.Author ContributionsConceived and designed the experiments: KM ARK. Performed the experiments: KM. Analyzed the data: KM DB AS ARK. Wrote the paper: KM DB AS ARK.
The retroviral nucleocapsid (NC) corresponds to the C-terminal domain of the Gag polyprotein precursor and found as mature protein upon Gag processing by the viral protease (PR) during virus formation and budding. NC has nucleic acid chaperone Title Loaded From File activities supported by its basic residues and the zinc finger (ZF) motif (for review, [1,2]). The basic residues and the ZF domain mediate tight nucleic acid binding in vitro [3,4]. While NC of betaretroviruses (i.e. Mason-Pfizer Monkey Virus, MPMV), alpharetroviruses (i.e. Rous Sarcoma Virus, RSV) and lentiviruses (i.e. Human Immunodeficiency Virus; HIV) have two ZFs, gammaretroviruses, such as the prototypic Murine Leukemia Virus (MuLV), have only one NC ZF. This unique ZF and the basic residues on its N-terminal side are required for MuLV infectivity [5,6,7,8]. This region plays critical roles in the late phase of MuLV replication since mutating the ZF or deleting the N-terminal basic residues of NC impair packaging of the genomic RNA (gRNA) and virion formation [7,9,10,11,12,13]. Dimeriza-tion of the gRNA induces a structural RNA switch that exposes conserved UCUG elements that bind NC with high affinity [14,15,16]. Such genome recognition by NC promotes the specific packaging of the gRNA in a 1531364 dimeric form into newly made viral particles [17,18]. Early after virus infection of target cells, the gRNA is copied by the viral Reverse Transcriptase (RT) to Title Loaded From File generate the viral DNA in a process called Reverse Transcription (RTion). It is a multistep process initiated from a cellular tRNA annealed to the 59 end PBS (Primer Binding Site) of the gRNA and subsequently requires two DNA strand transfers to synthesize the complete double-stranded viral DNA flanked by the two long terminal repeats (LTR). Several steps of RTion require nucleic acids remodeling reactions that are chaperoned by NC, notably primer tRNA annealing to the PBS and the two obligatory DNA strand transfers (for review see [19,20,21]. Viral DNA synthesis can occur during retrovirus assembly as shown for RSV, MuLV and HIV-1, but at low level ([22,23,24]. Recently, mutations in the NC basic residues and ZFs were found to cause extensive RTion in the course of virusRoles of the NC in HIV-1 and MuLV Replicationsassembly in HIV-1 producing cells [25,26]. Similarly to HBV and foamy viruses, we called this process “late RTion”. Thus, our data further support a role for NC in the control of RTion and its timing throughout the HIV-1 replication cycle [27,28]. Yet it is not known whether the involvement of NC in the timing of RTion is specific for HIV-1 or is also valid for other retroviruses, such as alpha- and gammaretroviruses with diverse NCs. Late RTion was maximal when HIV-1 NC contained only the proximal ZF (ZF1) without ZF2 (DZF2), indicating that the two ZFs of HIV-1 are not functionally equivalent [26.Averages of three biological replicates are shown +/2 SE. Refer to Table 1. ER = endosperm rupture and radicle emergence (completion of germination). Note that the Yaxis for the RNA data is in log-scale. (JPG) Figure S2 Expression analyses and histone H3 methylation pattern changes of markers of seed maturation/(DOC)AcknowledgmentsWe thank Preeti Goyal, Dr. Matthew Lorincz, Dr. Matyas Medzhiradszky and Dr. Kengo Morohashi for their help with establishing the seed nChIP protocol.Author ContributionsConceived and designed the experiments: KM ARK. Performed the experiments: KM. Analyzed the data: KM DB AS ARK. Wrote the paper: KM DB AS ARK.
The retroviral nucleocapsid (NC) corresponds to the C-terminal domain of the Gag polyprotein precursor and found as mature protein upon Gag processing by the viral protease (PR) during virus formation and budding. NC has nucleic acid chaperone activities supported by its basic residues and the zinc finger (ZF) motif (for review, [1,2]). The basic residues and the ZF domain mediate tight nucleic acid binding in vitro [3,4]. While NC of betaretroviruses (i.e. Mason-Pfizer Monkey Virus, MPMV), alpharetroviruses (i.e. Rous Sarcoma Virus, RSV) and lentiviruses (i.e. Human Immunodeficiency Virus; HIV) have two ZFs, gammaretroviruses, such as the prototypic Murine Leukemia Virus (MuLV), have only one NC ZF. This unique ZF and the basic residues on its N-terminal side are required for MuLV infectivity [5,6,7,8]. This region plays critical roles in the late phase of MuLV replication since mutating the ZF or deleting the N-terminal basic residues of NC impair packaging of the genomic RNA (gRNA) and virion formation [7,9,10,11,12,13]. Dimeriza-tion of the gRNA induces a structural RNA switch that exposes conserved UCUG elements that bind NC with high affinity [14,15,16]. Such genome recognition by NC promotes the specific packaging of the gRNA in a 1531364 dimeric form into newly made viral particles [17,18]. Early after virus infection of target cells, the gRNA is copied by the viral Reverse Transcriptase (RT) to generate the viral DNA in a process called Reverse Transcription (RTion). It is a multistep process initiated from a cellular tRNA annealed to the 59 end PBS (Primer Binding Site) of the gRNA and subsequently requires two DNA strand transfers to synthesize the complete double-stranded viral DNA flanked by the two long terminal repeats (LTR). Several steps of RTion require nucleic acids remodeling reactions that are chaperoned by NC, notably primer tRNA annealing to the PBS and the two obligatory DNA strand transfers (for review see [19,20,21]. Viral DNA synthesis can occur during retrovirus assembly as shown for RSV, MuLV and HIV-1, but at low level ([22,23,24]. Recently, mutations in the NC basic residues and ZFs were found to cause extensive RTion in the course of virusRoles of the NC in HIV-1 and MuLV Replicationsassembly in HIV-1 producing cells [25,26]. Similarly to HBV and foamy viruses, we called this process “late RTion”. Thus, our data further support a role for NC in the control of RTion and its timing throughout the HIV-1 replication cycle [27,28]. Yet it is not known whether the involvement of NC in the timing of RTion is specific for HIV-1 or is also valid for other retroviruses, such as alpha- and gammaretroviruses with diverse NCs. Late RTion was maximal when HIV-1 NC contained only the proximal ZF (ZF1) without ZF2 (DZF2), indicating that the two ZFs of HIV-1 are not functionally equivalent [26.