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The PII protein-protein interaction network in Azospirillum brasilense reveals a novel role of PII in the control of c-di-GMP homeostasis

ABSTRACT: The PII family comprises a group of widely distributed signal transduction proteins ubiquitous present in prokaryotes and in the chloroplast of plants. The PII proteins sense the levels of key metabolites ATP, ADP and 2-oxoglutarate which affect the PII structure and the ability of PII to interact with a range of target proteins. Here we performed multiple PII ligand fishing assays to identify proteins that are likely to be part of the PII protein interaction network in plant-growth promoting nitrogen-fixing bacterium Azospirillum brasilense. Among the PII targets identified were enzymes related to nitrogen and fatty acid metabolism, signaling, co-enzyme synthesis, RNA catabolism and transcription. Direct binary PII-target complex was confirmed for xx protein complex using pull-down assays with recombinant proteins. Untargeted metabolome showed that PII is required to proper maintenance of Coenzyme A, panthotenate, PRPP and SAICAR levels. Two enzymes involved in c-di-GMP metabolism were among the identified PII targets. A PII minus strain showed reduced c-di-GMP levels and swimming behavior. These data support that PII acts as a major metabolic hub controlling key metabolic enzymes and c-di-GMP homeostasis accordingly to the prevailing nutritional status.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Azospirillum Brasilense Sp245

SUBMITTER: Gustavo De Souza

LAB HEAD: Luciano Huergo

PROVIDER: PXD018530 | Pride | 2020-10-23

REPOSITORIES: Pride

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Transcription profiling by array of adenylylation of mycobacterial Glnk (PII) protein induced by nitrogen limitation

Project description:PII proteins are pivotal regulators of nitrogen metabolism in most prokaryotes, controlling the activities of many targets, including nitrogen assimilation enzymes, two component regulatory systems and ammonium transport proteins. Escherichia coli contains two PII-like proteins, PII (product of glnB) and GlnK, both of which are uridylylated under nitrogen limitation at a conserved Tyrosine-51 residue by GlnD (a uridylyl transferase). PII-uridylylation in E. coli controls glutamine synthetase (GS) adenylylation by GlnE and mediates the NtrB/C transcriptomic response. Mycobacteria contain only one PII protein (GlnK) which in environmental Actinomycetales is adenylylated by GlnD under nitrogen limitation. However in mycobacteria, neither the type of GlnK (PII) covalent modification nor its precise role under nitrogen limitation is known. In this study, we used LC-Tandem MS to analyse the modification state of mycobacterial GlnK (PII), and demonstrate that during nitrogen limitation GlnK from both non-pathogenic Mycobacterium smegmatis and pathogenic Mycobacterium tuberculosis is adenylylated at the Tyrosine-51 residue; we also show that GlnD is the adenylyl transferase enzyme responsible. Further analysis shows that in contrast to E. coli, GlnK (PII) adenylylation in M. tuberculosis does not regulate GS adenylylation, nor does it mediate the transcriptomic response to nitrogen limitation. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-135]

2013-05-10 | E-BUGS-135 | biostudies-arrayexpress

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Project description:Although the ubiquitous bacterial secondary messenger cyclic diguanylate (c-di-GMP) plays important roles in various cellular functions including the formation of biofilm in a wide range of bacteria, its function in model plant pathogen Pseudomonas syringae is largely elusive. In order to test this in P. syringae, we overexpressed a diguanylate cyclase (YedQ) and a phosphodiesterase (YhjH) that are originally from Escherichia coli, resulting in high and low c-di-GMP levels in P. syringae, respectively. Through performing genome-wide RNA sequencing of these two strains, we found that c-di-GMP regulates (i) fliN, fliE and flhA genes, which are associated with flagellar assembly, (ii) alg8 and alg44, which are related to exopolysaccaride biosynthesis pathway, (iii) pvdE, pvdP and pvsA genes, related to siderophore biosynthesis pathway, and (iv) sodA, which is a superoxide dismutase. In particular, we identified five genes sensitive to elevated c-di-GMP level and constructed five luciferase-based reporters that effectively respond to intracellular level of c-di-GMP in P. syringae, which can be used to measure c-di-GMP levels in vivo in the future. Based on the RNA-seq results, phenotypic assays confirmed that c-di-GMP regulated many important biological pathways in P. syringae, such as negative regulation of type III secretion system (T3SS) and motility as well as positive regulation of EPS production, siderophore production and oxidative stress resistance. Taken together, the present study demonstrated that c-di-GMP is closely related to virulence and stress response in P. syringae, suggesting that tuning its level can be a new strategy to protect plants from the attack of this pathogen in the future.

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2023-08-21 | GSE233207 | GEO

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