C-Terminal Region of Sulfite Reductase Is Important to Localize to Chloroplast Nucleoids in Land Plants

Abstract

Chloroplast (cp) DNA is compacted into cpDNA-protein complexes, called cp nucleoids. An abundant and extensively studied component of cp nucleoids is the bifunctional protein sulfite reductase (SiR). The preconceived role of SiR as the core cp nucleoid protein, however, is becoming less likely because of the recent findings that SiRs do not associate with cp nucleoids in some plant species, such as Zea mays and Arabidopsis thaliana. To address this discrepancy, we have performed a detailed phylogenetic analysis of SiRs, which shows that cp nucleoid-type SiRs share conserved C-terminally encoded peptides (CEPs). The CEPs are likely to form a bacterial ribbon–helix–helix DNA-binding motif, implying a potential role in attaching SiRs onto cp nucleoids. A proof-of-concept experiment was conducted by fusing the nonnucleoid-type SiR from A. thaliana (AtSiR) with the CEP from the cp nucleoid-type SiR of Phaseolus vulgaris. The addition of the CEP drastically altered the intra-cp localization of AtSiR to cp nucleoids. Our analysis supports the possible functions of CEPs in determining the localization of SiRs to cp nucleoids and illuminates a possible evolutionary scenario for SiR as a cp nucleoid protein.

WHIRLY1 of Barley and Maize Share a PRAPP Motif Conferring Nucleoid Compaction

“…SIR like WHIRLY1 binds to ssDNA and dsDNA without any sequence specificity (25,64). The compacting activity of SIR is mediated by a C-terminally encoded peptide (CEP) (65). This CEP is predicted to form a bacterial ribbon-helix-helix DNA binding motif that could facilitate interaction with plastid nucleoids (65).…”

“…The compacting activity of SIR is mediated by a C-terminally encoded peptide (CEP) (65). This CEP is predicted to form a bacterial ribbon-helix-helix DNA binding motif that could facilitate interaction with plastid nucleoids (65). SIR of Nicotiana tabacum (NbSIR), Pisum sativum (PsSIR) and Glycine max (GmSIR) can act as nucleoid compacting proteins.…”

“…Furthermore maize and pea SIR also differ in their ability to compact chloroplast DNA in vitro indicating that SIR proteins need the CEP for nucleoid compaction. Indeed, several members of the Brassicaceae and the Poaceae such as maize and Arabidopsis possess SIR without a CEP (65). Although CEP was found to be necessary for nucleoid localization and compaction, the addition of CEP at the C-terminus to the Arabidopsis SIR (AtSIR) merely resulted in a co-localization of AtSIR+CEP with plastid nucleoids but did not affect the compaction of plastid DNA (65).…”

The Maize Sulfite Reductase Is Involved in Cold and Oxidative Stress Responses

“…For example, Nicotiana benthamiana SiR (NbSiR) protein has been evidenced to act as a chloroplast (cp) nucleoid protein with cp DNA-compacting and transcription-regulatory activities ( Sekine et al, 2007 ; Kang et al, 2010 ). Furthermore, the conserved C-terminally encoded peptides of the SiR are important to localize to the cp nucleoids in plants ( Kobayashi et al, 2016 ). NbSiR silencing differentially affected expression of plastid-encoded genes and ultimately resulted in chloroplast ablation ( Kang et al, 2010 ), indicating that plant SiR functions in cp-nucleoid metabolism, plastid gene expression, and chloroplast development.…”

Identification of Holliday junction resolvases crucial for the chloroplast nucleoid morphology and segregation

“…(Allen 2003, Timmis et al 2004, Stern et al 2010 DNA 100 DNA (Kuroiwa 1991) DNA (Kuroiwa 1991, Sato et al 1999, Kobayashi et al 2002, Sakai et al 2004, Karcher et al 2009 DAPI SYBR Green I DNA 1980 (Kuroiwa 1991) DNA (Pfalz et al 2006, Krupinska et al 2013, Pfalz and (Sato 2001, Kobayashi et al 2016a, Kobayashi et al 2016b) , Kuroiwa 1991 5 10 (Ehara et al 1990, Kamimura et al 2018 Iwasaki et al 1991, Ip et al 2008, Wyatt et al 2013…”