Structural variations between small alarmone hydrolase dimers support different modes of regulation of the stringent response

Bisiak, Francesco; Chrenková, Adriana; Zhang, Sheng-Da; Pedersen, Jannik Nedergaard; Otzen, Daniel E.; Zhang, Yong E.; Brodersen, D.E.

doi:10.1016/j.jbc.2022.102142

Cited by 4 publications

(9 citation statements)

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“…4 E ). Additionally, the structures of other previously characterized SAHs and long RSHs including MESH-1, Cg SAH, Ll SAH, Tt Rel, and Bs Rel show that these enzymes all contain at least nine α-helices ( 21 – 23 , 34 , 35 ). However, unlike tetrameric Aph1, the majority of characterized SAHs adopt a dimeric arrangement, which may not require each promoter to be as structurally compact as Aph1.…”

Section: Resultsmentioning

confidence: 88%

“…Our structure of Aph1 reveals that it is an SAH enzyme that adopts a tetrameric arrangement and that the formation of this unique oligomeric state is made possible by the absence of two α-helices commonly found in (p)ppGpp hydrolases. While the biological significance of Aph1’s oligomeric state is a subject for future investigation, one possibility is that the additional α-helices found in other alarmone hydrolases are important for their allosteric regulation as has been proposed for Cg SAH and Ll SAH whereas such regulation may not exist for Aph1 ( 35 ). This prediction is consistent with our proposed role of Aph1 as a detoxifying enzyme for the Apk2 (p)ppApp synthetase toxin, which differs substantially from the role of SAHs involved in the stringent response.…”

Section: Discussionmentioning

confidence: 99%

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Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp

Ahmad

Gordon

Tsang

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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Bacteria produce a variety of nucleotide second messengers to adapt to their surroundings. Although chemically similar, the nucleotides guanosine penta- and tetraphosphate [(p)ppGpp] and adenosine penta- and tetraphosphate [(p)ppApp] have distinct functions in bacteria. (p)ppGpp mediates survival under nutrient-limiting conditions and its intracellular levels are regulated by synthetases and hydrolases belonging to the RelA-SpoT homolog (RSH) family of enzymes. By contrast, (p)ppApp is not known to be involved in nutrient stress responses and is synthesized by RSH-resembling toxins that inhibit the growth of bacterial cells. However, it remains unclear whether there exists a family of hydrolases that specifically act on (p)ppApp to reverse its toxic effects. Here, we present the structure and biochemical characterization of adenosine 3′-pyrophosphohydrolase 1 (Aph1), the founding member of a monofunctional (p)ppApp hydrolase family of enzymes. Our work reveals that Aph1 adopts a histidine-aspartate (HD)-domain fold characteristic of phosphohydrolase metalloenzymes and its activity mitigates the growth inhibitory effects of (p)ppApp-synthesizing toxins. Using an informatic approach, we identify over 2,000 putative (p)ppApp hydrolases that are widely distributed across bacterial phyla and found in diverse genomic contexts, and we demonstrate that 12 representative members hydrolyze ppApp. In addition, our in silico analyses reveal a unique molecular signature that is specific to (p)ppApp hydrolases, and we show that mutation of two residues within this signature broadens the specificity of Aph1 to promiscuously hydrolyze (p)ppGpp in vitro. Overall, our findings indicate that like (p)ppGpp hydrolases, (p)ppApp hydrolases are widespread in bacteria and may play important and underappreciated role(s) in bacterial physiology.

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Section: Resultsmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 99%

Identification of a broadly conserved family of enzymes that hydrolyze (p)ppApp

Ahmad

Gordon

Tsang

et al. 2023

Proc. Natl. Acad. Sci. U.S.A.

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“…6B . This includes the C. glutamicum RelH (CgSAH; RelH Cg ; Protein Data Bank [PDB] entry 7QOD ) ( 36 , 39 ), Listeria monocytogenes Lmo0812 (LmSAH; PDB entry 4YF1), Pseudomonas aeruginosa PA0431 (PaSAH; PDB entry 6YVC ) ( 38 ), Methylorubrum ( Methylobacterium ) extorquens SAH Mex (MexSAH) ( 50 ), Cellulomonas marina ATFaRel (CmarSAH, WP_090034991) ( 31 ), human MESH1 (HsMESH1) ( 65 ), and the recently described Leptospira levettii SAH (LlevSAH; RelH Ll ; PDB entry 7QOE ) ( 39 ) proteins. The locations of six highly conserved “hydrolase domain motifs” (HD1 to HD6) are indicated ( 27 ).…”

Section: Resultsmentioning

confidence: 99%

“…SASs contain a SYNTH domain, catalyze only alarmone synthesis, and are typically ~200 to 230 aa in length ( 28 – 36 ). SAHs contain an HD domain, are typically 180 to 210 aa in length, and catalyze alarmone hydrolysis ( 37 – 39 ).…”

Section: Introductionmentioning

confidence: 99%

Functional Characterization of Small Alarmone Synthetase and Small Alarmone Hydrolase Proteins from Treponema denticola

et al. 2023

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“…1B ), which may also influence substrate specificity. Given the recent report that subtle structural variations between SAHs can lead to marked differences in hydrolysis properties ( 46 ), it is possible that Xcc SAH may have evolved unique features to achieve different degrees of substrate promiscuity and hydrolysis activities.…”

Section: Discussionmentioning

confidence: 99%