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Within and Beyond the Stringent Response-RSH and (P)Ppgpp In Planta (2017) 246:817–842 DOI 10.1007/s00425-017-2780-y REVIEW Within and beyond the stringent response‑RSH and (p)ppGpp in plants Justyna Boniecka1 · Justyna Prusińska2 · Grażyna B. Dąbrowska1 · Anna Goc1 Received: 25 May 2017 / Accepted: 17 September 2017 / Published online: 25 September 2017 © The Author(s) 2017. This article is an open access publication Abstract chloroplasts, in plants, unlike in bacteria, (p)ppGpp promote Main conclusion Plant RSH proteins are able to synthetize chloroplast DNA replication and division. Next, (p)ppGpp and/or hydrolyze unusual nucleotides called (p)ppGpp or may also perform their functions in cytoplasm, where they alarmones. These molecules regulate nuclear and chloroplast would promote plant growth inhibition. Furthermore, (p) transcription, chloroplast translation and plant development ppGpp accumulation also afects nuclear gene expression, and stress response. i.a., decreases the level of Arabidopsis defense gene tran- scripts, and promotes plants susceptibility towards Turnip Homologs of bacterial RelA/SpoT proteins, designated RSH, mosaic virus. In this review, we summarize recent fndings and products of their activity, (p)ppGpp—guanosine tetra— that show the importance of RSH and (p)ppGpp in plant and pentaphosphates, have been found in algae and higher growth and development, and open an area of research aim- plants. (p)ppGpp were frst identifed in bacteria as the efec- ing to understand the function of plant RSH in response to tors of the stringent response, a mechanism that orchestrates stress. pleiotropic adaptations to nutritional deprivation and vari- ous stress conditions. (p)ppGpp accumulation in bacteria Keywords RelA/SpoT homologs · Alarmones · decreases transcription—with exception to genes that help Plant growth and development · Stress response · to withstand or overcome current stressful situations, which Photosynthesis · Senescence are upregulated—and translation as well as DNA replication and eventually reduces metabolism and growth but promotes Abbreviations adaptive responses. In plants, RSH are nuclei-encoded and CTD C-terminal domain function in chloroplasts, where alarmones are produced (p)ppGpp Guanosine tetra- and pentaphosphates and decrease transcription, translation, hormone, lipid and RelA Escherichia coli (p)ppGpp synthetase metabolites accumulation and afect photosynthetic ef- RNAP RNA polymerase ciency and eventually plant growth and development. During RSH RelA/SpoT homolog senescence, alarmones coordinate nutrient remobilization SAH Small alarmone hydrolase and relocation from vegetative tissues into seeds. Despite SpoT Escherichia coli (p)ppGpp synthetase and the high conservancy of RSH protein domains among hydrolase bacteria and plants as well as the bacterial origin of plant TuMV Turnip mosaic virus WT Wild type * Grażyna B. Dąbrowska [email protected] Introduction 1 Department of Genetics, Nicolaus Copernicus University in Toruń, Lwowska 1, 87‑100 Toruń, Poland Prokaryotes have developed different types of stress 2 School of Life Sciences, University of Warwick, responses, including chemotaxis, the SOS response and the Coventry CV4 7AL, UK stringent response (Dabrowska et al. 2006b). The latter was Vol.:(0123456789)1 3 818 Planta (2017) 246:817–842 frst identifed in Escherichia coli as a reaction to amino probably act in a specifc manner (Ooga et al. 2009; Ito et al. acid deprivation (Cashel and Gallant 1969). Further experi- 2012; Mechold et al. 2013; Gaca et al. 2015). ments showed that it also takes place under limitation of The accumulation of (p)ppGpp results in decreased levels other nutrients, e.g., carbon (Flardh et al. 1994; Gentry and of ribosomal RNA (rRNA) and transfer RNA (tRNA), due Cashel 1996), iron (Vinella et al. 2005), fatty acid (Sey- to inhibition of transcription of corresponding genes, and fzadeh et al. 1993; Battesti and Bouveret 2006), phosphate increased expression of stress responsive genes to ensure (Spira et al. 1995) as well as during various environmental proper cell adaptation and survival. Alarmones are required stresses such as temperature change (Gallant et al. 1977; for production and function of alternative sigma factors, i.a., English et al. 2011). sigma factor S, which is responsible for bacterial entrance Under amino acid limitation, in E. coli, attachment of into a stationary phase and survival in stress conditions uncharged tRNA in the ribosome acceptor site activates the (Gentry et al. 1993; Kvint et al. 2000; Dabrowska et al. ribosome-associated RelA protein to synthesize pppGpp 2006b). The regulation of transcription occurs either via (p) and ppGpp nucleotides [hereafter referred to as (p)ppGpp] ppGpp-dependent inhibition of RNA polymerase (RNAP) via the transfer of pyrophosphate from ATP to the 3′ site (Ross et al. 2013; Zuo et al. 2013) or indirectly via the of GTP or GDP, respectively (reviewed in Hauryliuk et al. regulation of GTP pool via GDP/GTP consumption during 2015). According to other model, RelA is rather recruited (p)ppGpp synthesis and inhibition of enzymes involved in to ribosomes when uncharged tRNA is already bound in the guanosine nucleotide biosynthesis, such as guanylate kinase ribosome acceptor site, then activated to produce (p)ppGpp (Krasny and Gourse 2004; Kriel et al. 2012; Liu et al. 2015a, (Wendrich et al. 2002; Brown et al. 2016), and afterwards b). dissociates to fnd another ribosome-uncharged tRNA com- In bacteria, (p)ppGpp also regulate translation, DNA rep- plex (Wendrich et al. 2002). According to some research- lication, nucleotide metabolism and other targets. The indi- ers, RelA dissociates from the ribosome to perform several rect way to regulate translation is via the already mentioned rounds of (p)ppGpp synthesis in the ribosome-unattached transcriptional inhibition of rRNA and tRNA genes. Another state (English et al. 2011). On the other hand, other scientists way to inhibit translation is by competition between GTP and stated that RelA is actively displaced from ribosome during (p)ppGpp binding to translational guanosine triphosphatase translation but not during its working times. RelA conforma- initiation factor If2 and elongation factor Ef-G (Milon et al. tion required for (p)ppGpp synthesis is stabilized when the 2006; Mitkevich et al. 2010). (p)ppGpp also bind to DNA protein is bound to uncharged tRNA on ribosome (Loveland primase and thus downregulate bacterial DNA replication et al. 2016), undermining the aforementioned RelA “hop (Wang et al. 2007b). (p)ppGpp modify other targets as well, on-hop of” model (English et al. 2011). such as guanosine triphosphatases involved in the assembly (p)ppGpp act swiftly and robustly to regulate molecular of ribosomal small and large subunits (i.e., Obg, BipA) or targets, such as transcription (Traxler et al. 2011), transla- lysine decarboxylase LdcI to counteract low pH. All of these tion (Milon et al. 2006; Mitkevich et al. 2010), chromosomal mechanisms are described in recent reviews (Hauryliuk et al. and various plasmid DNA replication (Levine et al. 1991; 2015; Steinchen and Bange 2016). Wegrzyn 1999; Wang et al. 2007b; Maciag et al. 2010), The E. coli RelA and SpoT (p)ppGpp metabolizing and eventually afect growth (Potrykus and Cashel 2008) enzymes are typical for γ- and β-proteobacteria. Both RelA as well as bacterial virulence (Dalebroux et al. 2010). The and SpoT carry the synthetase domain (SYNTH domain) and changes invoked by alarmones are hallmarks of the stringent thus are able to produce (p)ppGpp. However, RelA is con- response, whose aim is to prevent excessive energy usage sidered as the major (p)ppGpp synthetase, since SpoT shows during unfavorable conditions. However, basal (p)ppGpp only weak synthetic activity. Both RelA and SpoT also carry levels are also efective and modulate bacterial growth, per- the metal-dependent hydrolysis domain (HD domain), which form housekeeping functions that regulate general metabo- appears to be involved in nucleic acid metabolism and signal lism and are even responsible for bacterial antibiotic survival transduction. However, only SpoT is able to hydrolyze (p) (Potrykus et al. 2011; Kriel et al. 2012; Gaca et al. 2013). ppGpp, since RelA lacks the highly conserved histidine and In E. coli, (p)ppGpp are hydrolyzed by SpoT, which aspartate residues in the catalytic part of the HD domain removes 3′ site pyrophosphate from pppGpp or ppGpp and (Xiao et al. 1991; Gentry and Cashel 1996; Aravind and generates GTP or GDP, respectively. SpoT is actually a Koonin 1998). Since the HD domain in RelA does not per- bifunctional protein that is capable of (p)ppGpp degrada- form the (p)ppGpp hydrolysis function but is not entirely tion and synthesis (Xiao et al. 1991). Other studies show lost, it was proposed to be involved in maintaining the sta- the existence of non-RelA/SpoT enzymes metabolizing bility of the SYNTH domain, signal transduction from the (p)ppGpp (reviewed in Hauryliuk et al. 2015; Steinchen C-terminal domain (CTD) and/or intermolecular interactions and Bange 2016) as well as of other alarmones (i.e., pGp, (Atkinson et al. 2011). The SYNTH and HD domains are ppGp, pGpp). Each of them, along with pppGpp and ppGpp, localized in the N-terminal part of RSH proteins, and their 1 3 Planta (2017) 246:817–842 819 activity in Streptococcus equisimilis was shown to be regu- Synthetases (SAS) or Small Alarmone Hydrolases (SAH), lated by the CTD of the protein (Mechold et al. 2002). respectively (Atkinson et al. 2011). One of such SAH ani- An SMG medium that contains only one carbon amino mal examples is Drosophila melanogaster, Caenorhabditis acid invokes metabolic imbalance and results in isoleucine elegans and human metazoan SpoT homologue 1 (MESH1). starvation that in wild-type (WT) strains promotes (p)ppGpp In bacteria, SAS and SAH accompany the long RSH and production what helps to overcome the amino acid shortage. were proposed to fne-tune bacterial sensitivity and to bolster Since in E. coli, RelA is the major (p)ppGpp synthase, its responses to the stringent response-inducing stimuli (Sun mutation (relA−) prevents alarmones production and sub- et al. 2010; Atkinson et al.
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