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Caban-Penix S, Ho K, Yang Z, Baral R, Bradshaw N. Docking interactions determine substrate specificity of members of a widespread family of protein phosphatases. J Biol Chem 2024:107700. [PMID: 39173947 DOI: 10.1016/j.jbc.2024.107700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 08/24/2024] Open
Abstract
How protein phosphatases achieve specificity for their substrates is a major outstanding question. PPM family serine/threonine phosphatases are widespread in bacteria and eukaryotes, where they dephosphorylate target proteins with a high degree of specificity. In bacteria, PPM phosphatases control diverse transcriptional responses by dephosphorylating anti-anti-sigma factors of the STAS domain family, exemplified by B. subtilis phosphatases SpoIIE, which controls cell-fate during endospore formation, and RsbU, which initiates the General Stress Response. Using a combination of forward genetics, biochemical reconstitution, and AlphaFold2 structure prediction, we identified a conserved, tripartite substrate docking interface comprised of three variable loops on the surface of the PPM phosphatase domains of SpoIIE and RsbU that recognize the three-dimensional structure of the substrate protein. Non-conserved amino acids in these loops facilitate the accommodation of the cognate substrate and prevent dephosphorylation of the non-cognate substrate. Together, single-amino acid substitutions in these three elements cause an over five-hundred fold change in specificity. Our data additionally suggest that substrate-docking interactions regulate phosphatase specificity through a conserved allosteric switch element that controls the catalytic efficiency of the phosphatase by positioning the metal cofactor and substrate. We hypothesize that this is a generalizable mechanistic model for PPM family phosphatase substrate specificity. Importantly, the substrate docking interface with the phosphatase is only partially overlapping with the much more extensive interface with the upstream kinase, suggesting the possibility that kinase and phosphatase specificity evolved independently.
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Affiliation(s)
- Suhaily Caban-Penix
- Molecular and Cell Biology Program, Brandeis University; Department of Biochemistry, Brandeis University
| | - Kristin Ho
- Department of Biochemistry, Brandeis University
| | - Zhewen Yang
- Department of Biochemistry, Brandeis University
| | - Rishika Baral
- Department of Biochemistry, Brandeis University; Biochemistry and Biophysics Program, Brandeis University
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Baral R, Ho K, Kumar RP, Hopkins JB, Watkins MB, LaRussa S, Caban-Penix S, Calderone LA, Bradshaw N. A General Mechanism for the General Stress Response in Bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580724. [PMID: 38405867 PMCID: PMC10889023 DOI: 10.1101/2024.02.16.580724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
The General Stress Response promotes survival of bacteria in adverse conditions, but how sensor proteins transduce species-specific signals to initiate the response is not known. The serine/threonine phosphatase RsbU initiates the General Stress Response in B. subtilis upon binding a partner protein (RsbT) that is released from sequestration by environmental stresses. We report that RsbT activates RsbU by inducing otherwise flexible linkers of RsbU to form a short coiled-coil that dimerizes and activates the phosphatase domains. Importantly, we present evidence that related coiled-coil linkers and phosphatase dimers transduce signals from diverse sensor domains to control the General Stress Response and other signaling across bacterial phyla. These results additionally resolve the mystery of how shared sensory domains control serine/threonine phosphatases, diguanylate cyclases and histidine kinases, revealing a common coiled-coil linker transduction mechanism. We propose that this provides bacteria with a modularly exchangeable toolkit for the evolution of diverse signaling pathways.
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Affiliation(s)
- Rishika Baral
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
- Graduate program in Biochemistry and Biophysics, Brandeis University, Waltham, Massachusetts, USA
| | - Kristin Ho
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Ramasamy P. Kumar
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
| | - Jesse B Hopkins
- Biophysics Collaborative Access Team (BioCAT), Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Maxwell B. Watkins
- Biophysics Collaborative Access Team (BioCAT), Department of Biology, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Salvatore LaRussa
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
- Graduate program in Biochemistry and Biophysics, Brandeis University, Waltham, Massachusetts, USA
| | - Suhaily Caban-Penix
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
- Graduate program in Molecular and Cell Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Logan A. Calderone
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
- Graduate program in Biochemistry and Biophysics, Brandeis University, Waltham, Massachusetts, USA
| | - Niels Bradshaw
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts, USA
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Kurttila M, Rumfeldt J, Takala H, Ihalainen JA. The interconnecting hairpin extension "arm": An essential allosteric element of phytochrome activity. Structure 2023; 31:1100-1108.e4. [PMID: 37392739 DOI: 10.1016/j.str.2023.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/23/2023] [Accepted: 06/06/2023] [Indexed: 07/03/2023]
Abstract
In red-light sensing phytochromes, isomerization of the bilin chromophore triggers structural and dynamic changes across multiple domains, ultimately leading to control of the output module (OPM) activity. In between, a hairpin structure, "arm", extends from an interconnecting domain to the chromophore region. Here, by removing this protein segment in a bacteriophytochrome from Deinococcus radiodurans (DrBphP), we show that the arm is crucial for signal transduction. Crystallographic, spectroscopic, and biochemical data indicate that this variant maintains the properties of DrBphP in the resting state. Spectroscopic data also reveal that the armless systems maintain the ability to respond to light. However, there is no subsequent regulation of OPM activity without the arms. Thermal denaturation reveals that the arms stabilize the DrBphP structure. Our results underline the importance of the structurally flexible interconnecting hairpin extensions and describe their central role in the allosteric coupling of phytochromes.
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Affiliation(s)
- Moona Kurttila
- University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyvaskyla, Finland
| | - Jessica Rumfeldt
- University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyvaskyla, Finland
| | - Heikki Takala
- University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyvaskyla, Finland.
| | - Janne A Ihalainen
- University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Science, 40014 Jyvaskyla, Finland.
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Sisi C, Jieru D, Peidong C, Zhaolong Z, Yihang W, Shuwen C, Yan T, Tianyu W, Guiyan Y. Transcriptome-wide identification of walnut PP2C family genes in response to external stimulus. BMC Genomics 2022; 23:640. [PMID: 36076184 PMCID: PMC9461273 DOI: 10.1186/s12864-022-08856-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/23/2022] [Indexed: 11/11/2022] Open
Abstract
Walnut is an important economic tree species while confronting with global environmental stress, resulting in decline in quality and yield. Therefore, it is urgent to elucidate the molecular mechanism for the regulation of walnut response to adversity. The protein phosphatase 2C (PP2C) gene family participates in cellular processes in eukaryotes through reversible phosphorylation of proteins and signal transduction regulation. However, the stress response function of PP2C genes was far to be clarified. Therefore, to understand the stress response mechanism of walnut tree, in this study, a total of 41 PP2C genes with complete ORFs were identified from Juglans regia, whose basic bio-information and expression patterns in response to multiple stresses and ABA were confirmed. The results showed that the ORFs of JrPP2Cs were 495 ~ 3231 bp in length, the predicted JrPP2C proteins contained 164 to 1076 amino acids and the molecular weights were 18,581.96 ~ 118,853.34 Da, the pI was 4.55 ~ 9.58. These JrPP2C genes were unevenly distributed on 14 chromosomes, among which Chr11 and Chr13 contained the most genes. Phylogenetic analysis found that these JrPP2C proteins were classed into 9 subfamilies, among which group F covered most JrPP2Cs. The JrPP2Cs in the same subfamily exhibited similarities in the composition of conserved domains, amino acid sequences of motifs and exon/intron organization in DNA sequences. Each JrPP2C includes 4 ~ 10 motifs and each motif contained 15 ~ 37 amino acids. Among the motifs, motif1, motif2, motif3 and motif8 were most abundant. Most of the JrPP2C genes diversely response to osmotic, cadmium, and Colletotrichum gloeosporioide stress as well as ABA treatments, among which JrPP2C28, JrPP2C17, JrPP2C09, JrPP2C36 were more obvious and deserves further attention. All these results indicated that JrPP2C genes play potential vital roles in plant response to multiple stimulus, and are possibly involved in ABA-dependent signaling pathway.
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Affiliation(s)
- Chen Sisi
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Deng Jieru
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Cheng Peidong
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Zhang Zhaolong
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Wang Yihang
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Chen Shuwen
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Tang Yan
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Wang Tianyu
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Yang Guiyan
- Labortory of Walnut Research Center, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China. .,Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F University, Yangling, 712100, Shaanxi, China.
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