Metabolic Promiscuity of an Orphan Small Alarmone Hydrolase Facilitates Bacterial Environmental Adaptation

Fung, Danny Ka Chun; Bai, Kaihong; Yang, Jin; Xu, Xiaoli; Stevenson, David; Amador‐Noguez, Daniel; Luo, Laixin; Wang, Jue D.

doi:10.1128/mbio.02422-22

Cited by 6 publications

(6 citation statements)

References 60 publications

(107 reference statements)

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“…In this work, we discover that Aph1 and related proteins function as potent (p)ppApp hydrolases. Prior to our study, six other enzymes had been shown to hydrolyze (p)ppApp: SAH Mex , Dm MESH-1, Hs MESH-1, Pa SAH, ATFaRel, and Xcc SAH ( 13 , 24 – 26 ). Of these, only SAH Mex specifically hydrolyzes (p)ppApp but it does so at a much lower catalytic rate than Aph1.…”

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: Discussionmentioning

confidence: 99%

“…Similarly, dual activity was also observed for an SAH identified in Xanthomonas campestris pv. campestris , Xcc SAH ( 25 ). In addition to Pa SAH and Xcc SAH, the cognate antitoxin for FaRel, referred to as ATFaRel, degrades both (p)ppGpp and ppApp to protect against FaRel-mediated intoxication ( 13 ).…”

mentioning

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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show abstract

“…5a). Interestingly, recent 13 studies mention the ability of the Methylobacterium extorquens RSH, B. subtilis SasA and Treponema denticola SAS proteins to synthesize both (p)ppGpp and (p)ppApp [26][27][28].…”

Section: Discussionmentioning

confidence: 99%

Characterization of a (p)ppApp Synthetase Belonging to a New Family of Polymorphic Toxin Associated with Temperate Phages

Bartoli,

Tempier,

Guzzi

et al. 2023

Journal of Molecular Biology

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“…Interestingly, a recent paper from Wang lab has confirmed the NADPH phosphatase activities of SAH in phytopathogen Xanthomonas campestris pv. campestris ( Xcc ) and sah loss strongly reduced NADH, showing the evolutionary conservation of the NADPH phosphatase activities across multiple kingdoms [ 33 ].…”

Section: The Relevant Substrate Of Mesh1 Is Revealedmentioning

confidence: 99%

“…In addition, there is also an evolutionary acquisition of distinct substrates of SpoT versus MESH1. During evolution, enzymes may have altered substrate specificity for a new substrate or broader substrate specificity, as shown for the ability of Xcc SAH to hydrolyze both (p)ppGpp and NADPH [ 33 ]. Evolutionary changes in substrate preferences can coincide with the development of new signaling pathways.…”

Section: Implication For Our Understanding Of Stringent Response and ...mentioning

confidence: 99%