1
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Vainstein S, Banta S. Engineering Candida boidinii formate dehydrogenase for activity with the non-canonical cofactor 3'-NADP(H). Protein Eng Des Sel 2023; 36:gzad009. [PMID: 37658768 DOI: 10.1093/protein/gzad009] [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: 07/07/2023] [Revised: 08/21/2023] [Indexed: 09/05/2023] Open
Abstract
Oxidoreductases catalyze essential redox reactions, and many require a diffusible cofactor for electron transport, such as NAD(H). Non-canonical cofactor analogs have been explored as a means to create enzymatic reactions that operate orthogonally to existing metabolism. Here, we aimed to engineer the formate dehydrogenase from Candid boidinii (CbFDH) for activity with the non-canonical cofactor nicotinamide adenine dinucleotide 3'-phosphate (3'-NADP(H)). We used PyRosetta, the Cofactor Specificity Reversal Structural Analysis and Library Design (CSR-SALAD), and structure-guided saturation mutagenesis to identify mutations that enable CbFDH to use 3'-NADP+. Two single mutants, D195A and D195G, had the highest activities with 3'-NADP+, while the double mutant D195G/Y196S exhibited the highest cofactor selectivity reversal behavior. Steady state kinetic analyses were performed; the D195A mutant exhibited the highest KTS value with 3'-NADP+. This work compares the utility of computational approaches for cofactor specificity engineering while demonstrating the engineering of an important enzyme for novel non-canonical cofactor selectivity.
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Affiliation(s)
- Salomon Vainstein
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Scott Banta
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
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2
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Abstract
The discovery of NAADP-evoked Ca2+ release in sea urchin eggs and then as a ubiquitous Ca2+ mobilizing messenger has introduced several novel paradigms to our understanding of Ca2+ signalling, not least in providing a link between cell stimulation and Ca2+ release from lysosomes and other acidic Ca2+ storage organelles. In addition, the hallmark concentration-response relationship of NAADP-mediated Ca2+ release, shaped by striking activation/desensitization mechanisms, influences its actions as an intracellular messenger. There has been recent progress in our understanding of the molecular mechanisms underlying NAADP-evoked Ca2+ release, such as the identification of the endo-lysosomal two-pore channel family of cation channels (TPCs) as their principal target and the identity of NAADP-binding proteins that complex with them. The NAADP/TPC signalling axis has gained recent prominence in pathophysiology for their roles in such disease processes as neurodegeneration, tumorigenesis and cellular viral entry.
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Affiliation(s)
- Antony Galione
- Department of Pharmacology, University of Oxford, Oxford, UK.
| | - Lianne C Davis
- Department of Pharmacology, University of Oxford, Oxford, UK
| | - Lora L Martucci
- Department of Pharmacology, University of Oxford, Oxford, UK
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3
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Liu H, Lu C, Li Y, Wu T, Zhang B, Liu B, Feng W, Xu Q, Dong H, He S, Chu Z, Ding X. The bacterial effector AvrRxo1 inhibits vitamin B6 biosynthesis to promote infection in rice. PLANT COMMUNICATIONS 2022; 3:100324. [PMID: 35576156 PMCID: PMC9251433 DOI: 10.1016/j.xplc.2022.100324] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 03/15/2022] [Accepted: 04/08/2022] [Indexed: 06/02/2023]
Abstract
Xanthomonas oryzae pv. oryzicola (Xoc), which causes rice bacterial leaf streak, invades leaves mainly through stomata, which are often closed as a plant immune response against pathogen invasion. How Xoc overcomes stomatal immunity is unclear. Here, we show that the effector protein AvrRxo1, an ATP-dependent protease, enhances Xoc virulence and inhibits stomatal immunity by targeting and degrading rice OsPDX1 (pyridoxal phosphate synthase), thereby reducing vitamin B6 (VB6) levels in rice. VB6 is required for the activity of aldehyde oxidase, which catalyzes the last step of abscisic acid (ABA) biosynthesis, and ABA positively regulates rice stomatal immunity against Xoc. Thus, we provide evidence supporting a model in which a major bacterial pathogen inhibits plant stomatal immunity by directly targeting VB6 biosynthesis and consequently inhibiting the biosynthesis of ABA in guard cells to open stomata. Moreover, AvrRxo1-mediated VB6 targeting also explains the poor nutritional quality, including low VB6 levels, of Xoc-infected rice grains.
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Affiliation(s)
- Haifeng Liu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong, PR China; College of Agronomy, Shandong Agricultural University, Tai an, 271018 Shandong, PR China
| | - Chongchong Lu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong, PR China
| | - Yang Li
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong, PR China
| | - Tao Wu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong, PR China
| | - Baogang Zhang
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong, PR China
| | - Baoyou Liu
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong, PR China
| | - Wenjie Feng
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong, PR China
| | - Qian Xu
- College of Agronomy, Shandong Agricultural University, Tai an, 271018 Shandong, PR China
| | - Hansong Dong
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong, PR China
| | - Shengyang He
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA; Department of Biology, Duke University, Durham, NC 27708, USA; Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Zhaohui Chu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072 Hubei, PR China.
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai an, 271018 Shandong, PR China.
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4
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Wu T, Zhang H, Bi Y, Yu Y, Liu H, Yang H, Yuan B, Ding X, Chu Z. Tal2c Activates the Expression of OsF3H04g to Promote Infection as a Redundant TALE of Tal2b in Xanthomonas oryzae pv. oryzicola. Int J Mol Sci 2021; 22:ijms222413628. [PMID: 34948428 PMCID: PMC8707247 DOI: 10.3390/ijms222413628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/11/2022] Open
Abstract
Xanthomonas oryzae delivers transcription activator-like effectors (TALEs) into plant cells to facilitate infection. Following economic principles, the redundant TALEs are rarely identified in Xanthomonas. Previously, we identified the Tal2b, which activates the expression of the rice 2-oxoglutarate-dependent dioxygenase gene OsF3H03g to promote infection in the highly virulent strain of X. oryzae pv. oryzicola HGA4. Here, we reveal that another clustered TALE, Tal2c, also functioned as a virulence factor to target rice OsF3H04g, a homologue of OsF3H03g. Transferring Tal2c into RS105 induced expression of OsF3H04g to coincide with increased susceptibility in rice. Overexpressing OsF3H04g caused higher susceptibility and less salicylic acid (SA) production compared to wild-type plants. Moreover, CRISPR–Cas9 system-mediated editing of the effector-binding element in the promoters of OsF3H03g or OsF3H04g was found to specifically enhance resistance to Tal2b- or Tal2c-transferring strains, but had no effect on resistance to either RS105 or HGA4. Furthermore, transcriptome analysis revealed that several reported SA-related and defense-related genes commonly altered expression in OsF3H04g overexpression line compared with those identified in OsF3H03g overexpression line. Overall, our results reveal a functional redundancy mechanism of pathogenic virulence in Xoc in which tandem Tal2b and Tal2c specifically target homologues of host genes to interfere with rice immunity by reducing SA.
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Affiliation(s)
- Tao Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan 430072, China;
| | - Haimiao Zhang
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
| | - Yunya Bi
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan 430072, China;
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China;
| | - Yue Yu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
| | - Haifeng Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
| | - Hong Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China;
| | - Bin Yuan
- Institute of Plant Protection and Soil Fertilizer, Hubei Academy of Agricultural Sciences, Wuhan 430064, China;
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
- Correspondence: (X.D.); (Z.C.); Tel.: +86-538-8245569 (X.D.); +86-27-68752095 (Z.C.)
| | - Zhaohui Chu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an 271018, China; (T.W.); (H.Z.); (Y.Y.); (H.L.)
- State Key Laboratory of Hybrid Rice, Hubei Hongshan Laboratory, College of Life Sciences, Wuhan University, Wuhan 430072, China;
- Correspondence: (X.D.); (Z.C.); Tel.: +86-538-8245569 (X.D.); +86-27-68752095 (Z.C.)
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5
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Wang S, Li S, Wang J, Li Q, Xin XF, Zhou S, Wang Y, Li D, Xu J, Luo ZQ, He SY, Sun W. A bacterial kinase phosphorylates OSK1 to suppress stomatal immunity in rice. Nat Commun 2021; 12:5479. [PMID: 34531388 PMCID: PMC8445998 DOI: 10.1038/s41467-021-25748-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
The Xanthomonas outer protein C2 (XopC2) family of bacterial effectors is widely found in plant pathogens and Legionella species. However, the biochemical activity and host targets of these effectors remain enigmatic. Here we show that ectopic expression of XopC2 promotes jasmonate signaling and stomatal opening in transgenic rice plants, which are more susceptible to Xanthomonas oryzae pv. oryzicola infection. Guided by these phenotypes, we discover that XopC2 represents a family of atypical kinases that specifically phosphorylate OSK1, a universal adaptor protein of the Skp1-Cullin-F-box ubiquitin ligase complexes. Intriguingly, OSK1 phosphorylation at Ser53 by XopC2 exclusively increases the binding affinity of OSK1 to the jasmonate receptor OsCOI1b, and specifically enhances the ubiquitination and degradation of JAZ transcription repressors and plant disease susceptibility through inhibiting stomatal immunity. These results define XopC2 as a prototypic member of a family of pathogenic effector kinases and highlight a smart molecular mechanism to activate jasmonate signaling.
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Affiliation(s)
- Shanzhi Wang
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Shuai Li
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Jiyang Wang
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Qian Li
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Xiu-Fang Xin
- grid.17088.360000 0001 2150 1785DOE Plant Research Laboratory, Michigan State University, East Lansing, MI USA ,grid.9227.e0000000119573309National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences (CAS), CAS John Innes Centre of Excellence for Plant and Microbial Sciences (CEPAMS), Shanghai, China
| | - Shuang Zhou
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Yanping Wang
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Dayong Li
- grid.464353.30000 0000 9888 756XCollege of Plant Protection, Jilin Agricultural University, Changchun, Jilin China
| | - Jiaqing Xu
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China
| | - Zhao-Qing Luo
- grid.169077.e0000 0004 1937 2197Purdue Institute for Inflammation, Immunology and Infectious Disease and Department of Biological Sciences, Purdue University, West Lafayette, IN USA
| | - Sheng Yang He
- grid.17088.360000 0001 2150 1785DOE Plant Research Laboratory, Michigan State University, East Lansing, MI USA ,grid.17088.360000 0001 2150 1785Howard Hughes Medical Institute, Michigan State University, East Lansing, MI USA
| | - Wenxian Sun
- grid.22935.3f0000 0004 0530 8290Department of Plant Pathology, the Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing, China ,grid.464353.30000 0000 9888 756XCollege of Plant Protection, Jilin Agricultural University, Changchun, Jilin China
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6
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Schreiber KJ, Chau-Ly IJ, Lewis JD. What the Wild Things Do: Mechanisms of Plant Host Manipulation by Bacterial Type III-Secreted Effector Proteins. Microorganisms 2021; 9:1029. [PMID: 34064647 PMCID: PMC8150971 DOI: 10.3390/microorganisms9051029] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 01/05/2023] Open
Abstract
Phytopathogenic bacteria possess an arsenal of effector proteins that enable them to subvert host recognition and manipulate the host to promote pathogen fitness. The type III secretion system (T3SS) delivers type III-secreted effector proteins (T3SEs) from bacterial pathogens such as Pseudomonas syringae, Ralstonia solanacearum, and various Xanthomonas species. These T3SEs interact with and modify a range of intracellular host targets to alter their activity and thereby attenuate host immune signaling. Pathogens have evolved T3SEs with diverse biochemical activities, which can be difficult to predict in the absence of structural data. Interestingly, several T3SEs are activated following injection into the host cell. Here, we review T3SEs with documented enzymatic activities, as well as T3SEs that facilitate virulence-promoting processes either indirectly or through non-enzymatic mechanisms. We discuss the mechanisms by which T3SEs are activated in the cell, as well as how T3SEs modify host targets to promote virulence or trigger immunity. These mechanisms may suggest common enzymatic activities and convergent targets that could be manipulated to protect crop plants from infection.
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Affiliation(s)
- Karl J. Schreiber
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
| | - Ilea J. Chau-Ly
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
| | - Jennifer D. Lewis
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94710, USA; (K.J.S.); (I.J.C.-L.)
- Plant Gene Expression Center, United States Department of Agriculture, University of California, Berkeley, CA 94710, USA
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7
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Bayless AM, Nishimura MT. Enzymatic Functions for Toll/Interleukin-1 Receptor Domain Proteins in the Plant Immune System. Front Genet 2020; 11:539. [PMID: 32582284 PMCID: PMC7282519 DOI: 10.3389/fgene.2020.00539] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 05/04/2020] [Indexed: 01/09/2023] Open
Abstract
Rationally engineered improvements to crop plants will be needed to keep pace with increasing demands placed on agricultural systems by population growth and climate change. Engineering of plant immune systems provides an opportunity to increase yields by limiting losses to pathogens. Intracellular immune receptors are commonly used as agricultural disease resistance traits. Despite their importance, how intracellular immune receptors confer disease resistance is still unknown. One major class of immune receptors in dicots contains a Toll/Interleukin-1 Receptor (TIR) domain. The mechanisms of TIR-containing proteins during plant immunity have remained elusive. The TIR domain is an ancient module found in archaeal, bacterial and eukaryotic proteins. In animals, TIR domains serve a structural role by generating innate immune signaling complexes. The unusual animal TIR-protein, SARM1, was recently discovered to function instead as an enzyme that depletes cellular NAD+ (nicotinamide adenine dinucleotide) to trigger axonal cell death. Two recent reports have found that plant TIR proteins also have the ability to cleave NAD+. This presents a new paradigm from which to consider how plant TIR immune receptors function. Here, we will review recent reports of the structure and function of TIR-domain containing proteins. Intriguingly, it appears that TIR proteins in all kingdoms may use similar enzymatic mechanisms in a variety of cell death and immune pathways. We will also discuss TIR structure–function hypotheses in light of the recent publication of the ZAR1 resistosome structure. Finally, we will explore the evolutionary context of plant TIR-containing proteins and their downstream signaling components across phylogenies and the functional implications of these findings.
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Affiliation(s)
- Adam M Bayless
- Department of Biology, Colorado State University, Fort Collins, CO, United States
| | - Marc T Nishimura
- Department of Biology, Colorado State University, Fort Collins, CO, United States
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8
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The ng_ζ1 toxin of the gonococcal epsilon/zeta toxin/antitoxin system drains precursors for cell wall synthesis. Nat Commun 2018; 9:1686. [PMID: 29703974 PMCID: PMC5923241 DOI: 10.1038/s41467-018-03652-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 03/02/2018] [Indexed: 01/14/2023] Open
Abstract
Bacterial toxin–antitoxin complexes are emerging as key players modulating bacterial physiology as activation of toxins induces stasis or programmed cell death by interference with vital cellular processes. Zeta toxins, which are prevalent in many bacterial genomes, were shown to interfere with cell wall formation by perturbing peptidoglycan synthesis in Gram-positive bacteria. Here, we characterize the epsilon/zeta toxin–antitoxin (TA) homologue from the Gram-negative pathogen Neisseria gonorrhoeae termed ng_ɛ1 / ng_ζ1. Contrary to previously studied streptococcal epsilon/zeta TA systems, ng_ɛ1 has an epsilon-unrelated fold and ng_ζ1 displays broader substrate specificity and phosphorylates multiple UDP-activated sugars that are precursors of peptidoglycan and lipopolysaccharide synthesis. Moreover, the phosphorylation site is different from the streptococcal zeta toxins, resulting in a different interference with cell wall synthesis. This difference most likely reflects adaptation to the individual cell wall composition of Gram-negative and Gram-positive organisms but also the distinct involvement of cell wall components in virulence. Toxin–antitoxin (TA) systems are important modulators of bacterial physiology. Here, the authors structurally characterize the epsilon/zeta TA system from the Gram-negative pathogen Neisseria gonorrhoeae and show that the toxin interferes with peptidoglycan and lipopolysaccharide synthesis by phosphorylating the UDP-activated sugar-precursors.
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9
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Guse AH, Diercks BP. Integration of nicotinic acid adenine dinucleotide phosphate (NAADP)-dependent calcium signalling. J Physiol 2018; 596:2735-2743. [PMID: 29635794 DOI: 10.1113/jp275974] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 03/15/2018] [Indexed: 11/08/2022] Open
Abstract
Nicotinic acid adenine dinucleotide phosphate (NAADP) is currently the most potent endogenous Ca2+ mobilizing second messenger. Upon specific extracellular stimulation, rapid production of NAADP has been observed in different cell types from sea urchin eggs to mammalian cells. More than 20 years after the discovery of NAADP, there is still controversy surrounding its metabolism and target receptors/ion channels and organelles. This article briefly reviews recent developments in the NAADP field. Besides the metabolism of NAADP, this review focuses on assumed organelles and putative targets, e.g. ion channels, with special emphasis on ryanodine receptor type 1 (RyR1) and two-pore channels (TPCs). The role of NAADP as a Ca2+ trigger is also discussed and the importance of NAADP in the formation of initial Ca2+ microdomains is highlighted.
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Affiliation(s)
- Andreas H Guse
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Centre Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20246, Germany
| | - Björn-Philipp Diercks
- The Calcium Signalling Group, Department of Biochemistry and Molecular Cell Biology, University Medical Centre Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20246, Germany
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10
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Islam W, Noman A, Qasim M, Wang L. Plant Responses to Pathogen Attack: Small RNAs in Focus. Int J Mol Sci 2018; 19:E515. [PMID: 29419801 PMCID: PMC5855737 DOI: 10.3390/ijms19020515] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 02/04/2018] [Accepted: 02/05/2018] [Indexed: 12/25/2022] Open
Abstract
Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.
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Affiliation(s)
- Waqar Islam
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad 38040, Pakistan.
- College of Crop Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Muhammad Qasim
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Liande Wang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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11
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Jaén-Luchoro D, Aliaga-Lozano F, Gomila RM, Gomila M, Salvà-Serra F, Lalucat J, Bennasar-Figueras A. First insights into a type II toxin-antitoxin system from the clinical isolate Mycobacterium sp. MHSD3, similar to epsilon/zeta systems. PLoS One 2017; 12:e0189459. [PMID: 29236773 PMCID: PMC5728571 DOI: 10.1371/journal.pone.0189459] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/28/2017] [Indexed: 01/21/2023] Open
Abstract
A putative type II toxin-antitoxin (TA) system was found in the clinical isolate Mycobacterium sp. MHSD3, a strain closely related to Mycobacterium chelonae. Further analyses of the protein sequences of the two genes revealed the presence of domains related to a TA system. BLAST analyses indicated the presence of closely related proteins in the genomes of other recently published M. chelonae strains. The functionality of both elements of the TA system was demonstrated when expressed in Escherichia coli cells, and the predicted structure of the toxin is very similar to those of well-known zeta-toxins, leading to the definition of a type II TA system similar to epsilon/zeta TA systems in strains that are closely related to M. chelonae.
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Affiliation(s)
- Daniel Jaén-Luchoro
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
- * E-mail:
| | - Francisco Aliaga-Lozano
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Laboratorio de Biología Molecular, Clínica Rotger, Palma de Mallorca, Spain
| | - Rosa Maria Gomila
- Serveis Cientifico-Tècnics, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Francisco Salvà-Serra
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Department of Infectious Diseases, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
| | - Jorge Lalucat
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Institut Mediterrani d’Estudis Avançats (IMEDEA, CSIC-UIB), Esporles, Spain
| | - Antoni Bennasar-Figueras
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
- Area de Enfermedades Infecciosas, Instituto Universitario de Investigaciones en Ciencias de la Salud (IUNICS-UIB), Universitat de les Illes Balears, Palma de Mallorca, Spain
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12
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Harms A, Liesch M, Körner J, Québatte M, Engel P, Dehio C. A bacterial toxin-antitoxin module is the origin of inter-bacterial and inter-kingdom effectors of Bartonella. PLoS Genet 2017; 13:e1007077. [PMID: 29073136 PMCID: PMC5675462 DOI: 10.1371/journal.pgen.1007077] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 11/07/2017] [Accepted: 10/16/2017] [Indexed: 12/22/2022] Open
Abstract
Host-targeting type IV secretion systems (T4SS) evolved from conjugative T4SS machineries that mediate interbacterial plasmid transfer. However, the origins of effectors secreted by these virulence devices have remained largely elusive. Previous work showed that some effectors exhibit homology to toxins of bacterial toxin-antitoxin modules, but the evolutionary trajectories underlying these ties had not been resolved. We previously reported that FicT toxins of FicTA toxin-antitoxin modules disrupt cellular DNA topology via their enzymatic FIC (filamentation induced by cAMP) domain. Intriguingly, the FIC domain of the FicT toxin VbhT of Bartonella schoenbuchensis is fused to a type IV secretion signal–the BID (Bep intracellular delivery) domain—similar to the Bartonella effector proteins (Beps) that are secreted into eukaryotic host cells via the host-targeting VirB T4SS. In this study, we show that the VbhT toxin is an interbacterial effector protein secreted via the conjugative Vbh T4SS that is closely related to the VirB T4SS and encoded by plasmid pVbh of B. schoenbuchensis. We therefore propose that the Vbh T4SS together with its effector VbhT represent an evolutionary missing link on a path that leads from a regular conjugation system and FicTA toxin-antitoxin modules to the VirB T4SS and the Beps. Intriguingly, phylogenetic analyses revealed that the fusion of FIC and BID domains has probably occurred independently in VbhT and the common ancestor of the Beps, suggesting parallel evolutionary paths. Moreover, several other examples of TA module toxins that are bona fide substrates of conjugative T4SS indicate that their recruitment as interbacterial effectors is prevalent and serves yet unknown biological functions in the context of bacterial conjugation. We propose that the adaptation for interbacterial transfer favors the exaptation of FicT and other TA module toxins as inter-kingdom effectors and may thus constitute an important stepping stone in the evolution of host-targeted effector proteins. Many bacterial pathogens use secretion systems to translocate effector proteins into host cells where they manipulate cell functions in favor of the pathogen. It is well-known that these secretion systems evolved from ancestors with functions in genuine bacterial contexts, but the origins of their secreted effectors have largely remained elusive. In this article we studied the evolutionary history of a host-targeting effector secretion system of the mammalian pathogen Bartonella that belongs to a group of machineries descended from secretion systems originally mediating DNA transfer between bacterial cells. Intriguingly, we found that such a DNA transfer machinery closely related to the host-targeting secretion system of Bartonella has recruited a bacterial protein involved in modulating DNA topology as an interbacterial effector protein that is translocated together with the DNA into recipient cells. The overall setup of this interbacterial effector is remarkably similar to the host-targeted effectors of Bartonella, and we propose that it represents an evolutionary missing link on the path from a genuine bacterial protein to effectors that manipulates host cell functioning. Further analyses showed that interbacterial effectors in DNA transfer may be a more common phenomenon and represent an important reservoir for the evolution of new host-targeted effectors.
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Affiliation(s)
- Alexander Harms
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Marius Liesch
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Jonas Körner
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Maxime Québatte
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
- * E-mail:
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13
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Díaz-Orejas R, Espinosa M, Yeo CC. The Importance of the Expendable: Toxin-Antitoxin Genes in Plasmids and Chromosomes. Front Microbiol 2017; 8:1479. [PMID: 28824602 PMCID: PMC5543033 DOI: 10.3389/fmicb.2017.01479] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/24/2017] [Indexed: 02/01/2023] Open
Abstract
Toxin–antitoxin (TA) genes were first reported in plasmids and were considered expendable genetic cassettes involved in the stable maintenance of the plasmid replicon by interfering with growth and/or viability of bacteria in which the plasmid was lost. TAs were later found in bacterial chromosomes and also in integrated mobile genetic elements; they were proposed to be involved in the bacterial response to stressful situations. At present, 100s of TAs have been identified and classified in up to six families (I to VI), with those belonging to the type II (constituted by two protein components) being the most studied. Based on well-characterized examples of several type II TAs, we discuss in this review that irrespective of their locations in plasmids or chromosomes, TAs functionally overlap as indicated by: (i) in both locations they can mediate the maintenance of genetic elements to which they are physical linked, and (ii) they can induce persistence or virulence in response to stress situations. Examples of functional confluences in homologous TA systems with different locations are also given. We also consider whether the physiological role of TAs is due to their genetic organization as operons or to their inherent properties, like the short lifespan of the antitoxin component.
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Affiliation(s)
- Ramón Díaz-Orejas
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC)Madrid, Spain
| | - Manuel Espinosa
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC)Madrid, Spain
| | - Chew Chieng Yeo
- Faculty of Medicine, Biomedical Research Centre, Universiti Sultan Zainal AbidinKuala Terengganu, Malaysia
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14
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Michelmore R, Coaker G, Bart R, Beattie G, Bent A, Bruce T, Cameron D, Dangl J, Dinesh-Kumar S, Edwards R, Eves-van den Akker S, Gassmann W, Greenberg JT, Hanley-Bowdoin L, Harrison RJ, Harvey J, He P, Huffaker A, Hulbert S, Innes R, Jones JDG, Kaloshian I, Kamoun S, Katagiri F, Leach J, Ma W, McDowell J, Medford J, Meyers B, Nelson R, Oliver R, Qi Y, Saunders D, Shaw M, Smart C, Subudhi P, Torrance L, Tyler B, Valent B, Walsh J. Foundational and Translational Research Opportunities to Improve Plant Health. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:515-516. [PMID: 28398839 PMCID: PMC5810936 DOI: 10.1094/mpmi-01-17-0010-cr] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Reader Comments | Submit a Comment The white paper reports the deliberations of a workshop focused on biotic challenges to plant health held in Washington, D.C. in September 2016. Ensuring health of food plants is critical to maintaining the quality and productivity of crops and for sustenance of the rapidly growing human population. There is a close linkage between food security and societal stability; however, global food security is threatened by the vulnerability of our agricultural systems to numerous pests, pathogens, weeds, and environmental stresses. These threats are aggravated by climate change, the globalization of agriculture, and an over-reliance on nonsustainable inputs. New analytical and computational technologies are providing unprecedented resolution at a variety of molecular, cellular, organismal, and population scales for crop plants as well as pathogens, pests, beneficial microbes, and weeds. It is now possible to both characterize useful or deleterious variation as well as precisely manipulate it. Data-driven, informed decisions based on knowledge of the variation of biotic challenges and of natural and synthetic variation in crop plants will enable deployment of durable interventions throughout the world. These should be integral, dynamic components of agricultural strategies for sustainable agriculture.
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Affiliation(s)
- Richard Michelmore
- 1 The Genome Center and Departments of Plant Sciences, Molecular & Cellular Biology, and Medical Microbiology & Immunology, University of California, Davis, CA, U.S.A
| | - Gitta Coaker
- 2 Department of Plant Pathology, University of California, Davis, CA, U.S.A
| | | | | | - Andrew Bent
- 5 University of Wisconsin, Madison, WI, U.S.A
| | | | | | - Jeffery Dangl
- 8 University of North Carolina, Chapel Hill, NC, U.S.A
| | | | - Rob Edwards
- 10 University of Newcastle, Newcastle upon Tyne, U.K
| | | | | | | | | | | | | | - Ping He
- 17 Texas A&M University, College Station, TX, U.S.A
| | | | - Scot Hulbert
- 19 Washington State University, Pullman, WA, U.S.A
| | - Roger Innes
- 20 Indiana University, Bloomigton, IN, U.S.A
| | | | | | | | | | - Jan Leach
- 24 Colorado State University, Fort Collins, CO, U.S.A
| | - Wenbo Ma
- 22 University of California, Riverside, CA, U.S.A
| | | | | | | | | | | | - Yiping Qi
- 29 East Carolina University, Greenville, NC, U.S.A
| | | | | | | | | | - Lesley Torrance
- 33 University of St. Andrews and James Hutton Institute, Fife, U.K
| | - Bret Tyler
- 34 Oregon State University, Corvallis, OR, U.S.A.; and
| | | | - John Walsh
- 35 University of Warwick, Wellesbourne, U.K
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15
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Shidore T, Broeckling CD, Kirkwood JS, Long JJ, Miao J, Zhao B, Leach JE, Triplett LR. The effector AvrRxo1 phosphorylates NAD in planta. PLoS Pathog 2017; 13:e1006442. [PMID: 28628666 PMCID: PMC5491322 DOI: 10.1371/journal.ppat.1006442] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 06/29/2017] [Accepted: 06/02/2017] [Indexed: 12/14/2022] Open
Abstract
Gram-negative bacterial pathogens of plants and animals employ type III secreted effectors to suppress innate immunity. Most characterized effectors work through modification of host proteins or transcriptional regulators, although a few are known to modify small molecule targets. The Xanthomonas type III secreted avirulence factor AvrRxo1 is a structural homolog of the zeta toxin family of sugar-nucleotide kinases that suppresses bacterial growth. AvrRxo1 was recently reported to phosphorylate the central metabolite and signaling molecule NAD in vitro, suggesting that the effector might enhance bacterial virulence on plants through manipulation of primary metabolic pathways. In this study, we determine that AvrRxo1 phosphorylates NAD in planta, and that its kinase catalytic sites are necessary for its toxic and resistance-triggering phenotypes. A global metabolomics approach was used to independently identify 3'-NADP as the sole detectable product of AvrRxo1 expression in yeast and bacteria, and NAD kinase activity was confirmed in vitro. 3'-NADP accumulated upon transient expression of AvrRxo1 in Nicotiana benthamiana and in rice leaves infected with avrRxo1-expressing strains of X. oryzae. Mutation of the catalytic aspartic acid residue D193 abolished AvrRxo1 kinase activity and several phenotypes of AvrRxo1, including toxicity in yeast, bacteria, and plants, suppression of the flg22-triggered ROS burst, and ability to trigger an R gene-mediated hypersensitive response. A mutation in the Walker A ATP-binding motif abolished the toxicity of AvrRxo1, but did not abolish the 3'-NADP production, virulence enhancement, ROS suppression, or HR-triggering phenotypes of AvrRxo1. These results demonstrate that a type III effector targets the central metabolite and redox carrier NAD in planta, and that this catalytic activity is required for toxicity and suppression of the ROS burst.
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Affiliation(s)
- Teja Shidore
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States of America
| | - Corey D. Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States of America
| | - Jay S. Kirkwood
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, CO, United States of America
| | - John J. Long
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Jiamin Miao
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Bingyu Zhao
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, United States of America
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Lindsay R. Triplett
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United States of America
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