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Huang W, Wang D, Zhang XX, Zhao M, Sun L, Zhou Y, Guan X, Xie Z. Regulatory roles of the second messenger c-di-GMP in beneficial plant-bacteria interactions. Microbiol Res 2024; 285:127748. [PMID: 38735241 DOI: 10.1016/j.micres.2024.127748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/14/2024]
Abstract
The rhizosphere system of plants hosts a diverse consortium of bacteria that confer beneficial effects on plant, such as plant growth-promoting rhizobacteria (PGPR), biocontrol agents with disease-suppression activities, and symbiotic nitrogen fixing bacteria with the formation of root nodule. Efficient colonization in planta is of fundamental importance for promoting of these beneficial activities. However, the process of root colonization is complex, consisting of multiple stages, including chemotaxis, adhesion, aggregation, and biofilm formation. The secondary messenger, c-di-GMP (cyclic bis-(3'-5') dimeric guanosine monophosphate), plays a key regulatory role in a variety of physiological processes. This paper reviews recent progress on the actions of c-di-GMP in plant beneficial bacteria, with a specific focus on its role in chemotaxis, biofilm formation, and nodulation.
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Affiliation(s)
- Weiwei Huang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Dandan Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Xue-Xian Zhang
- School of Natural Sciences, Massey University at Albany, Auckland 0745, New Zealand
| | - Mengguang Zhao
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Li Sun
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Yanan Zhou
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Xin Guan
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment, Shandong Agricultural University, Taian, Shandong Province 271018, China.
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2
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Muok AR, Kurniyati K, Cassidy CK, Olsthoorn FA, Ortega DR, Mabrouk AS, Li C, Briegel A. A new class of protein sensor links spirochete pleomorphism, persistence, and chemotaxis. mBio 2023; 14:e0159823. [PMID: 37607060 PMCID: PMC10653840 DOI: 10.1128/mbio.01598-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 07/14/2023] [Indexed: 08/24/2023] Open
Abstract
IMPORTANCE A new class of bacterial protein sensors monitors intracellular levels of S-adenosylmethionine to modulate cell morphology, chemotaxis, and biofilm formation. Simultaneous regulation of these behaviors enables bacterial pathogens to survive within their niche. This sensor, exemplified by Treponema denticola CheWS, is anchored to the chemotaxis array and its sensor domain is located below the chemotaxis rings. This position may allow the sensor to directly interact with the chemotaxis histidine kinase CheA. Collectively, these data establish a critical role of CheWS in pathogenesis and further illustrate the impact of studying non-canonical chemotaxis proteins.
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Affiliation(s)
- A. R. Muok
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - K. Kurniyati
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, Virginia, USA
| | - C. K. Cassidy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, United Kingdom
| | - F. A. Olsthoorn
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - D. R. Ortega
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - A. Sidi Mabrouk
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
| | - C. Li
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, Virginia, USA
| | - A. Briegel
- Institute of Biology, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
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3
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Espinosa-Urgel M, Ramos-González MI. Becoming settlers: Elements and mechanisms for surface colonization by Pseudomonas putida. Environ Microbiol 2023; 25:1575-1593. [PMID: 37045787 DOI: 10.1111/1462-2920.16385] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023]
Abstract
Pseudomonads are considered to be among the most widespread culturable bacteria in mesophilic environments. The evolutive success of Pseudomonas species can be attributed to their metabolic versatility, in combination with a set of additional functions that enhance their ability to colonize different niches. These include the production of secondary metabolites involved in iron acquisition or having a detrimental effect on potential competitors, different types of motility, and the capacity to establish and persist within biofilms. Although biofilm formation has been extensively studied using the opportunistic pathogen Pseudomonas aeruginosa as a model organism, a significant body of knowledge is also becoming available for non-pathogenic Pseudomonas. In this review, we focus on the mechanisms that allow Pseudomonas putida to colonize biotic and abiotic surfaces and adapt to sessile life, as a relevant persistence strategy in the environment. This species is of particular interest because it includes plant-beneficial strains, in which colonization of plant surfaces may be relevant, and strains used for environmental and biotechnological applications, where the design and functionality of biofilm-based bioreactors, for example, also have to take into account the efficiency of bacterial colonization of solid surfaces. This work reviews the current knowledge of mechanistic and regulatory aspects of biofilm formation by P. putida and pinpoints the prospects in this field.
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Affiliation(s)
- Manuel Espinosa-Urgel
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Granada, Spain
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4
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Tagua VG, Molina‐Henares MA, Travieso ML, Nisa‐Martínez R, Quesada JM, Espinosa‐Urgel M, Ramos‐González MI. C‐di‐GMP
and biofilm are regulated in
Pseudomonas putida
by the
CfcA
/
CfcR
two‐component system in response to salts. Environ Microbiol 2022; 24:158-178. [DOI: 10.1111/1462-2920.15891] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 12/14/2021] [Accepted: 12/26/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Víctor G. Tagua
- Department of Environmental Protection Estación Experimental del Zaidín, CSIC Granada Spain
| | | | - María L. Travieso
- Department of Environmental Protection Estación Experimental del Zaidín, CSIC Granada Spain
| | - Rafael Nisa‐Martínez
- Department of Environmental Protection Estación Experimental del Zaidín, CSIC Granada Spain
| | - José Miguel Quesada
- Department of Environmental Protection Estación Experimental del Zaidín, CSIC Granada Spain
| | - Manuel Espinosa‐Urgel
- Department of Environmental Protection Estación Experimental del Zaidín, CSIC Granada Spain
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5
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Leal-Morales A, Pulido-Sánchez M, López-Sánchez A, Govantes F. Transcriptional organization and regulation of the Pseudomonas putida flagellar system. Environ Microbiol 2021; 24:137-157. [PMID: 34859548 DOI: 10.1111/1462-2920.15857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 01/22/2023]
Abstract
A single region of the Pseudomonas putida genome, designated the flagellar cluster, includes 59 genes potentially involved in the biogenesis and function of the flagellar system. Here, we combine bioinformatics and in vivo gene expression analyses to clarify the transcriptional organization and regulation of the flagellar genes in the cluster. We have identified 11 flagellar operons and characterized 22 primary and internal promoter regions. Our results indicate that synthesis of the flagellar apparatus and core chemotaxis machinery is regulated by a three-tier cascade in which fleQ is a Class I gene, standing at the top of the transcriptional hierarchy. FleQ- and σ54 -dependent Class II genes encode most components of the flagellar structure, part of the chemotaxis machinery and multiple regulatory elements, including the flagellar σ factor FliA. FliA activation of Class III genes enables synthesis of the filament, one stator complex and completion of the chemotaxis apparatus. Accessory regulatory proteins and an intricate operon architecture add complexity to the regulation by providing feedback and feed-forward loops to the main circuit. Because of the high conservation of the gene arrangement and promoter motifs, we believe that the regulatory circuit presented here may also apply to other environmental pseudomonads.
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Affiliation(s)
- Antonio Leal-Morales
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Marta Pulido-Sánchez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Aroa López-Sánchez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
| | - Fernando Govantes
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/Consejo Superior de Investigaciones Científicas/Junta de Andalucía and Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Sevilla, Spain
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6
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Xu Z, Liu Z, Soteyome T, Hua J, Zhang L, Yuan L, Ye Y, Cai Z, Yang L, Chen L, Harro JM, Kjellerup BV, Liu J, Li Y. Impact of pmrA on Cronobacter sakazakii planktonic and biofilm cells: A comprehensive transcriptomic study. Food Microbiol 2021; 98:103785. [PMID: 33875213 DOI: 10.1016/j.fm.2021.103785] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 12/30/2020] [Accepted: 03/05/2021] [Indexed: 10/21/2022]
Abstract
Cronobacter sakazakii is an emerging opportunistic foodborne pathogen causing rare but severe infections in neonates. Furthermore, the formation of biofilm allows C. sakazakii to persist in different environments. We have demonstrated that the mutator phenotype ascribed to deficiency of the pmrA gene results in more biomass in the first 24 h but less during the post maturation stage (7-14 d) compared with BAA 894. The present study aimed to investigate the regulatory mechanism modulating biofilm formation due to pmrA mutation. The transcriptomic analyses of BAA 894 and s-3 were performed by RNA-sequencing on planktonic and biofilm cells collected at different time points. According to the results, when comparing biofilm to planktonic cells, expression of genes encoding outer membrane proteins, lysozyme, etc. were up-regulated, with LysR family transcriptional regulators, periplasmic proteins, etc. down-regulated. During biofilm formation, cellulose synthase operon genes, flagella-related genes, etc. played essential roles in different stages. Remarkably, pmrA varies the expression of a number of genes related to motility, biofilm formation, and antimicrobial resistance, including srfB, virK, mviM encoding virulence factor, flgF, fliN, etc. encoding flagellar assembly, and marA, ramA, etc. encoding AraC family transcriptional regulators in C. sakazakii. This study provides valuable insights into transcriptional regulation of C. sakazakii pmrA mutant during biofilm formation.
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Affiliation(s)
- Zhenbo Xu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China; Department of Clinical Pharmacy and Translational Science, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, 38103, USA; Home Economics Technology, Rajamangala University of Technology Phra Nakhon, Bangkok, Thailand; National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka; Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), Guangzhou, 510640, China
| | - Ziqi Liu
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China
| | - Thanapop Soteyome
- National Institute of Fundamental Studies, Hantana Road, Kandy, Sri Lanka
| | - Jingjing Hua
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China
| | - Liang Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, China.
| | - Lei Yuan
- College of Food Science and Engineering, Yangzhou University, Yangzhou, China
| | - Yanrui Ye
- School of Biological Science and Engineering, South China University of Technology, Guangzhou, 510640, China
| | - Zhao Cai
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Ling Chen
- School of Food Science and Engineering, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, South China University of Technology, Guangzhou, 510640, China
| | - Janette M Harro
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, MD, 21201, USA
| | - Birthe Veno Kjellerup
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Junyan Liu
- Department of Civil and Environmental Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Yanyan Li
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Xihu District, Hangzhou, 310024, Zhejiang Province, China.
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7
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Pseudomonas aeruginosa as a Model To Study Chemosensory Pathway Signaling. Microbiol Mol Biol Rev 2021; 85:85/1/e00151-20. [PMID: 33441490 DOI: 10.1128/mmbr.00151-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Bacteria have evolved a variety of signal transduction mechanisms that generate different outputs in response to external stimuli. Chemosensory pathways are widespread in bacteria and are among the most complex signaling mechanisms, requiring the participation of at least six proteins. These pathways mediate flagellar chemotaxis, in addition to controlling alternative functions such as second messenger levels or twitching motility. The human pathogen Pseudomonas aeruginosa has four different chemosensory pathways that carry out different functions and are stimulated by signal binding to 26 chemoreceptors. Recent research employing a diverse range of experimental approaches has advanced enormously our knowledge on these four pathways, establishing P. aeruginosa as a primary model organism in this field. In the first part of this article, we review data on the function and physiological relevance of chemosensory pathways as well as their involvement in virulence, whereas the different transcriptional and posttranscriptional regulatory mechanisms that govern pathway function are summarized in the second part. The information presented will be of help to advance the understanding of pathway function in other organisms.
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8
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Muok AR, Ortega DR, Kurniyati K, Yang W, Maschmann ZA, Sidi Mabrouk A, Li C, Crane BR, Briegel A. Atypical chemoreceptor arrays accommodate high membrane curvature. Nat Commun 2020; 11:5763. [PMID: 33188180 PMCID: PMC7666581 DOI: 10.1038/s41467-020-19628-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022] Open
Abstract
The prokaryotic chemotaxis system is arguably the best-understood signaling pathway in biology. In all previously described species, chemoreceptors organize into a hexagonal (P6 symmetry) extended array. Here, we report an alternative symmetry (P2) of the chemotaxis apparatus that emerges from a strict linear organization of the histidine kinase CheA in Treponema denticola cells, which possesses arrays with the highest native curvature investigated thus far. Using cryo-ET, we reveal that Td chemoreceptor arrays assume an unusual arrangement of the supra-molecular protein assembly that has likely evolved to accommodate the high membrane curvature. The arrays have several atypical features, such as an extended dimerization domain of CheA and a variant CheW-CheR-like fusion protein that is critical for maintaining an ordered chemosensory apparatus. Furthermore, the previously characterized Td oxygen sensor ODP influences CheA ordering. These results suggest a greater diversity of the chemotaxis signaling system than previously thought.
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Affiliation(s)
- Alise R Muok
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Davi R Ortega
- Department of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, USA
| | - Kurni Kurniyati
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Wen Yang
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Zachary A Maschmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Adam Sidi Mabrouk
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands
| | - Chunhao Li
- Department of Oral and Craniofacial Molecular Biology, Philips Research Institute for Oral Health, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Ariane Briegel
- Institute for Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands.
- Centre for Microbial Cell Biology, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands.
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9
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Matilla MA, Martín-Mora D, Krell T. The use of isothermal titration calorimetry to unravel chemotactic signalling mechanisms. Environ Microbiol 2020; 22:3005-3019. [PMID: 32329116 DOI: 10.1111/1462-2920.15035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022]
Abstract
Chemotaxis is based on the action of chemosensory pathways and is typically initiated by the recognition of chemoeffectors at chemoreceptor ligand-binding domains (LBD). Chemosensory signalling is highly complex; aspect that is not only reflected in the intricate interaction between many signalling proteins but also in the fact that bacteria frequently possess multiple chemosensory pathways and often a large number of chemoreceptors, which are mostly of unknown function. We review here the usefulness of isothermal titration calorimetry (ITC) to study this complexity. ITC is the gold standard for studying binding processes due to its precision and sensitivity, as well as its capability to determine simultaneously the association equilibrium constant, enthalpy change and stoichiometry of binding. There is now evidence that members of all major LBD families can be produced as individual recombinant proteins that maintain their ligand-binding properties. High-throughput screening of these proteins using thermal shift assays offer interesting initial information on chemoreceptor ligands, providing the basis for microcalorimetric analyses and microbiological experimentation. ITC has permitted the identification and characterization of many chemoreceptors with novel specificities. This ITC-based approach can also be used to identify signal molecules that stimulate members of other families of sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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10
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Alvarado A, Behrens W, Josenhans C. Protein Activity Sensing in Bacteria in Regulating Metabolism and Motility. Front Microbiol 2020; 10:3055. [PMID: 32010106 PMCID: PMC6978683 DOI: 10.3389/fmicb.2019.03055] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/18/2019] [Indexed: 01/24/2023] Open
Abstract
Bacteria have evolved complex sensing and signaling systems to react to their changing environments, most of which are present in all domains of life. Canonical bacterial sensing and signaling modules, such as membrane-bound ligand-binding receptors and kinases, are very well described. However, there are distinct sensing mechanisms in bacteria that are less studied. For instance, the sensing of internal or external cues can also be mediated by changes in protein conformation, which can either be implicated in enzymatic reactions, transport channel formation or other important cellular functions. These activities can then feed into pathways of characterized kinases, which translocate the information to the DNA or other response units. This type of bacterial sensory activity has previously been termed protein activity sensing. In this review, we highlight the recent findings about this non-canonical sensory mechanism, as well as its involvement in metabolic functions and bacterial motility. Additionally, we explore some of the specific proteins and protein-protein interactions that mediate protein activity sensing and their downstream effects. The complex sensory activities covered in this review are important for bacterial navigation and gene regulation in their dynamic environment, be it host-associated, in microbial communities or free-living.
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Affiliation(s)
- Alejandra Alvarado
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany
| | - Wiebke Behrens
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
| | - Christine Josenhans
- Max von Pettenkofer-Institute, Ludwig Maximilian University of Munich, Munich, Germany.,German Center for Infection Research (DZIF) Partner Site Munich, Munich, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hanover, Germany
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11
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Molina L, Segura A, Duque E, Ramos JL. The versatility of Pseudomonas putida in the rhizosphere environment. ADVANCES IN APPLIED MICROBIOLOGY 2019; 110:149-180. [PMID: 32386604 DOI: 10.1016/bs.aambs.2019.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
This article addresses the lifestyle of Pseudomonas and focuses on how Pseudomonas putida can be used as a model system for biotechnological processes in agriculture, and in the removal of pollutants from soils. In this chapter we aim to show how a deep analysis using genetic information and experimental tests has helped to reveal insights into the lifestyle of Pseudomonads. Pseudomonas putida is a Plant Growth Promoting Rhizobacteria (PGPR) that establishes commensal relationships with plants. The interaction involves a series of functions encoded by core genes which favor nutrient mobilization, prevention of pathogen development and efficient niche colonization. Certain Pseudomonas putida strains harbor accessory genes that confer specific biodegradative properties and because these microorganisms can thrive on the roots of plants they can be exploited to remove pollutants via rhizoremediation, making the consortium plant/Pseudomonas a useful tool to combat pollution.
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Affiliation(s)
- Lázaro Molina
- CSIC- Estación Experimental del Zaidín, Granada, Spain
| | - Ana Segura
- CSIC- Estación Experimental del Zaidín, Granada, Spain
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12
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López-Farfán D, Reyes-Darias JA, Matilla MA, Krell T. Concentration Dependent Effect of Plant Root Exudates on the Chemosensory Systems of Pseudomonas putida KT2440. Front Microbiol 2019; 10:78. [PMID: 30761113 PMCID: PMC6363813 DOI: 10.3389/fmicb.2019.00078] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/15/2019] [Indexed: 12/28/2022] Open
Abstract
Plant root colonization by rhizobacteria can protect plants against pathogens and promote plant growth, and chemotaxis to root exudates was shown to be an essential prerequisite for efficient root colonization. Since many chemoattractants control the transcript levels of their cognate chemoreceptor genes, we have studied here the transcript levels of the 27 Pseudomonas putida KT2440 chemoreceptor genes in the presence of different maize root exudate (MRE) concentrations. Transcript levels were increased for 10 chemoreceptor genes at low MRE concentrations, whereas almost all receptor genes showed lower transcript levels at high MRE concentrations. The exposure of KT2440 to different MRE concentrations did not alter c-di-GMP levels, indicating that changes in chemoreceptor transcripts are not mediated by this second messenger. Data suggest that rhizosphere colonization unfolds in a temporal fashion. Whereas at a distance to the root, exudates enhance chemoreceptor gene transcript levels promoting in turn chemotaxis, this process is reversed in root vicinity, where the necessity of chemotaxis toward the root may be less important. Insight into KT2440 signaling processes were obtained by analyzing mutants defective in the three cheA paralogous genes. Whereas a mutant in cheA1 showed reduced c-di-GMP levels and impaired biofilm formation, a cheA2 mutant was entirely deficient in MRE chemotaxis, indicating the existence of homologs of the P. aeruginosawsp and che (chemotaxis) pathways. Signaling through both pathways was important for efficient maize root colonization. Future studies will show whether the MRE concentration dependent effect on chemoreceptor gene transcript levels is a feature shared by other species.
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Affiliation(s)
- Diana López-Farfán
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José A Reyes-Darias
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A Matilla
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas, Granada, Spain
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13
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Ongpipattanakul C, Nair SK. Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis. ACS Chem Biol 2018; 13:2989-2999. [PMID: 30204409 DOI: 10.1021/acschembio.8b00668] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
N-methylation of nucleic acids, proteins, and peptides is a chemical modification with significant impact on biological regulation. Despite the simplicity of the structural change, N-methylation can influence diverse functions including epigenetics, protein complex formation, and microtubule stability. While there are limited examples of N-methylation of the α-amino group of bacterial and eukaryotic proteins, there are no examples of catalysts that carry out post-translation methylation of backbone amides in proteins or peptides. Recent studies have identified enzymes that catalyze backbone N-methylation on a peptide substrate, a reaction with little biochemical precedent, in a family of ribosomally synthesized natural products produced in basidiomycetes. Here, we describe the crystal structures of Dendrothele bispora dbOphMA, a methyltransferase that catalyzes multiple N-methylations on the peptide backbone. We further carry out biochemical studies of this catalyst to determine the molecular details that promote this unusual chemical transformation. The structural and biochemical framework described here could facilitate biotechnological applications of catalysts for the rapid production of backbone N-methylated peptides.
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14
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The activity of the C4-dicarboxylic acid chemoreceptor of Pseudomonas aeruginosa is controlled by chemoattractants and antagonists. Sci Rep 2018; 8:2102. [PMID: 29391435 PMCID: PMC5795001 DOI: 10.1038/s41598-018-20283-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/15/2018] [Indexed: 11/10/2022] Open
Abstract
Chemotaxis toward organic acids has been associated with colonization fitness and virulence and the opportunistic pathogen Pseudomonas aeruginosa exhibits taxis toward several tricarboxylic acid intermediates. In this study, we used high-throughput ligand screening and isothermal titration calorimetry to demonstrate that the ligand binding domain (LBD) of the chemoreceptor PA2652 directly recognizes five C4-dicarboxylic acids with KD values ranging from 23 µM to 1.24 mM. In vivo experimentation showed that three of the identified ligands act as chemoattractants whereas two of them behave as antagonists by inhibiting the downstream chemotaxis signalling cascade. In vitro and in vivo competition assays showed that antagonists compete with chemoattractants for binding to PA2652-LBD, thereby decreasing the affinity for chemoattractants and the subsequent chemotactic response. Two chemosensory pathways encoded in the genome of P. aeruginosa, che and che2, have been associated to chemotaxis but we found that only the che pathway is involved in PA2652-mediated taxis. The receptor PA2652 is predicted to contain a sCACHE LBD and analytical ultracentrifugation analyses showed that PA2652-LBD is dimeric in the presence and the absence of ligands. Our results indicate the feasibility of using antagonists to interfere specifically with chemotaxis, which may be an alternative strategy to fight bacterial pathogens.
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15
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Yan XF, Xin L, Yen JT, Zeng Y, Jin S, Cheang QW, Fong RACY, Chiam KH, Liang ZX, Gao YG. Structural analyses unravel the molecular mechanism of cyclic di-GMP regulation of bacterial chemotaxis via a PilZ adaptor protein. J Biol Chem 2017; 293:100-111. [PMID: 29146598 DOI: 10.1074/jbc.m117.815704] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/10/2017] [Indexed: 01/09/2023] Open
Abstract
The bacterial second messenger cyclic di-GMP (c-di-GMP) has emerged as a prominent mediator of bacterial physiology, motility, and pathogenicity. c-di-GMP often regulates the function of its protein targets through a unique mechanism that involves a discrete PilZ adaptor protein. However, the molecular mechanism for PilZ protein-mediated protein regulation is unclear. Here, we present the structure of the PilZ adaptor protein MapZ cocrystallized in complex with c-di-GMP and its protein target CheR1, a chemotaxis-regulating methyltransferase in Pseudomonas aeruginosa This cocrystal structure, together with the structure of free CheR1, revealed that the binding of c-di-GMP induces dramatic structural changes in MapZ that are crucial for CheR1 binding. Importantly, we found that restructuring and repositioning of two C-terminal helices enable MapZ to disrupt the CheR1 active site by dislodging a structural domain. The crystallographic observations are reinforced by protein-protein binding and single cell-based flagellar motor switching analyses. Our studies further suggest that the regulation of chemotaxis by c-di-GMP through MapZ orthologs/homologs is widespread in proteobacteria and that the use of allosterically regulated C-terminal motifs could be a common mechanism for PilZ adaptor proteins. Together, the findings provide detailed structural insights into how c-di-GMP controls the activity of an enzyme target indirectly through a PilZ adaptor protein.
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Affiliation(s)
- Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore
| | - Lingyi Xin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Jackie Tan Yen
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore
| | - Yukai Zeng
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, Number 07-01, S138671 Singapore, Singapore
| | - Shengyang Jin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | | | - Keng-Hwee Chiam
- Bioinformatics Institute (A*STAR), 30 Biopolis Street, Number 07-01, S138671 Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, Singapore 639798, Singapore; Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), 61 Biopolis Drive, Singapore 138673, Singapore.
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16
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Assigning chemoreceptors to chemosensory pathways in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2017; 114:12809-12814. [PMID: 29133402 DOI: 10.1073/pnas.1708842114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In contrast to Escherichia coli, a model organism for chemotaxis that has 5 chemoreceptors and a single chemosensory pathway, Pseudomonas aeruginosa PAO1 has a much more complex chemosensory network, which consists of 26 chemoreceptors feeding into four chemosensory pathways. While several chemoreceptors were rigorously linked to specific pathways in a series of experimental studies, for most of them this information is not available. Thus, we addressed the problem computationally. Protein-protein interaction network prediction, coexpression data mining, and phylogenetic profiling all produced incomplete and uncertain assignments of chemoreceptors to pathways. However, comparative sequence analysis specifically targeting chemoreceptor regions involved in pathway interactions revealed conserved sequence patterns that enabled us to unambiguously link all 26 chemoreceptors to four pathways. Placing computational evidence in the context of experimental data allowed us to conclude that three chemosensory pathways in P. aeruginosa utilize one chemoreceptor per pathway, whereas the fourth pathway, which is the main system controlling chemotaxis, utilizes the other 23 chemoreceptors. Our results show that while only a very few amino acid positions in receptors, kinases, and adaptors determine their pathway specificity, assigning receptors to pathways computationally is possible. This requires substantial knowledge about interacting partners on a molecular level and focusing comparative sequence analysis on the pathway-specific regions. This general principle should be applicable to resolving many other receptor-pathway interactions.
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17
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Abstract
Chemoreceptors in bacteria detect a variety of signals and feed this information into chemosensory pathways that represent a major mode of signal transduction. The five chemoreceptors from Escherichia coli have served as traditional models in the study of this protein family. Genome analyses revealed that many bacteria contain much larger numbers of chemoreceptors with broader sensory capabilities. Chemoreceptors differ in topology, sensing mode, cellular location, and, above all, the type of ligand binding domain (LBD). Here, we highlight LBD diversity using well-established and emerging model organisms as well as genomic surveys. Nearly a hundred different types of protein domains that are found in chemoreceptor sequences are known or predicted LBDs, but only a few of them are ubiquitous. LBDs of the same class recognize different ligands, and conversely, the same ligand can be recognized by structurally different LBDs; however, recent studies began to reveal common characteristics in signal-LBD relationships. Although signals can stimulate chemoreceptors in a variety of different ways, diverse LBDs appear to employ a universal transmembrane signaling mechanism. Current and future studies aim to establish relationships between LBD types, the nature of signals that they recognize, and the mechanisms of signal recognition and transduction.
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18
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Fernández M, Matilla MA, Ortega Á, Krell T. Metabolic Value Chemoattractants Are Preferentially Recognized at Broad Ligand Range Chemoreceptor of Pseudomonas putida KT2440. Front Microbiol 2017; 8:990. [PMID: 28620365 PMCID: PMC5449446 DOI: 10.3389/fmicb.2017.00990] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 05/17/2017] [Indexed: 12/18/2022] Open
Abstract
Bacteria have evolved a wide range of chemoreceptors with different ligand specificities. Typically, chemoreceptors bind ligands with elevated specificity and ligands serve as growth substrates. However, there is a chemoreceptor family that has a broad ligand specificity including many compounds that are not of metabolic value. To advance the understanding of this family, we have used the PcaY_PP (PP2643) chemoreceptor of Pseudomonas putida KT2440 as a model. Using Isothermal Titration Calorimetry we showed here that the recombinant ligand binding domain (LBD) of PcaY_PP recognizes 17 different C6-ring containing carboxylic acids with KD values between 3.7 and 138 μM and chemoeffector affinity correlated with the magnitude of the chemotactic response. Mutation of the pcaY_PP gene abolished chemotaxis to these compounds; phenotype that was restored following gene complementation. Growth experiments using PcaY_PP ligands as sole C-sources revealed functional relationships between their metabolic potential and affinity for the chemoreceptor. Thus, only 7 PcaY_PP ligands supported growth and their KD values correlated with the length of the bacterial lag phase. Furthermore, PcaY_PP ligands that did not support growth had significantly higher KD values than those that did. The receptor has thus binds preferentially compounds that serve as C-sources and amongst them those that rapidly promote growth. Tightest binding compounds were quinate, shikimate, 3-dehydroshikimate and protocatechuate, which are at the interception of the biosynthetic shikimate and catabolic quinate pathways. Analytical ultracentrifugation studies showed that ligand free PcaY_PP-LBD is present in a monomer-dimer equilibrium (KD = 57.5 μM). Ligand binding caused a complete shift to the dimeric state, which appears to be a general feature of four-helix bundle LBDs. This study indicates that the metabolic potential of compounds is an important parameter in the molecular recognition by broad ligand range chemoreceptors.
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Affiliation(s)
- Matilde Fernández
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas,Granada, Spain
| | - Miguel A Matilla
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas,Granada, Spain
| | - Álvaro Ortega
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas,Granada, Spain
| | - Tino Krell
- Estación Experimental del Zaidín, Department of Environmental Protection, Consejo Superior de Investigaciones Científicas,Granada, Spain
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19
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Xu L, Xin L, Zeng Y, Yam JKH, Ding Y, Venkataramani P, Cheang QW, Yang X, Tang X, Zhang LH, Chiam KH, Yang L, Liang ZX. A cyclic di-GMP-binding adaptor protein interacts with a chemotaxis methyltransferase to control flagellar motor switching. Sci Signal 2016; 9:ra102. [PMID: 27811183 DOI: 10.1126/scisignal.aaf7584] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The bacterial messenger cyclic diguanylate monophosphate (c-di-GMP) binds to various effectors, the most common of which are single-domain PilZ proteins. These c-di-GMP effectors control various cellular functions and multicellular behaviors at the transcriptional or posttranslational level. We found that MapZ (methyltransferase-associated PilZ; formerly known as PA4608), a single-domain PilZ protein from the opportunistic pathogen Pseudomonas aeruginosa, directly interacted with the methyltransferase CheR1 and that this interaction was enhanced by c-di-GMP. In vitro assays indicated that, in the presence of c-di-GMP, MapZ inhibited CheR1 from methylating the chemoreceptor PctA, which would be expected to increase its affinity for chemoattractants and promote chemotaxis. MapZ localized to the poles of P. aeruginosa cells, where the flagellar motor and other chemotactic proteins, including PctA and CheR1, are also located. P. aeruginosa cells exhibit a random walk behavior by frequently switching the direction of flagellar rotation in a uniform solution. We showed that binding of c-di-GMP to MapZ decreased the frequency of flagellar motor switching and that MapZ was essential for generating the heterogeneous motility typical of P. aeruginosa cell populations and for efficient surface attachment during biofilm formation. Collectively, the studies revealed that c-di-GMP affects flagellar motor output by regulating the methylation of chemoreceptors through a single-domain PilZ adaptor protein.
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Affiliation(s)
- Linghui Xu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Lingyi Xin
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Yukai Zeng
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Singapore 138671, Singapore
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551, Singapore
| | - Yichen Ding
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.,Interdisciplinary Graduate School, Nanyang Technological University, Singapore 637551, Singapore
| | - Prabhadevi Venkataramani
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Qing Wei Cheang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Xiaobei Yang
- Guangdong Innovative and Entrepreneurial Research Team of Sociomicrobiology Basic Science and Frontier Technology, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Xuhua Tang
- Institute of Molecular and Cell Biology, A*STAR, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Lian-Hui Zhang
- Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Keng-Hwee Chiam
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01, Singapore 138671, Singapore
| | - Liang Yang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore. .,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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20
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Lee K, Ha GS, Veeranagouda Y, Seo YS, Hwang I. A CHASE3/GAF sensor hybrid histidine kinase BmsA modulates biofilm formation and motility in Pseudomonas alkylphenolica. MICROBIOLOGY-SGM 2016; 162:1945-1954. [PMID: 27655385 DOI: 10.1099/mic.0.000373] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pseudomonas alkylphenolica is an important strain in the biodegradation of toxic alkylphenols and mass production of bioactive polymannuronate polymers. This strain forms a diverse, 3D biofilm architecture, including mushroom-like aerial structures, circular pellicles and surface spreading, depending on culture conditions. A mutagenesis and complementation study showed that a predicted transmembrane kinase, PSAKL28_21690 (1164 aa), harbouring a periplasmic CHASE3 domain flanked by two transmembrane helices in addition to its cytoplasmic GAF, histidine kinase and three CheY-like response regulator domains, plays a positive role in the formation of the special biofilm architecture and a negative role in swimming activity. In addition, the gene, named here as bmsA, is co-transcribed with three genes encoding proteins with CheR (PSAKL28_21700) and CheB (PSAKL28_21710) domains and response regulator and histidine kinase domains (PSAKL28_21720). This gene cluster is thus named bmsABCD and is found widely distributed in pseudomonads and other bacteria. Deletion of the genes in the cluster, except forbmsA, did not result in changes in biofilm-related phenotypes. The RNA-seq analysis showed that the expression of genes coding for flagellar synthesis was increased when bmsA was mutated. In addition, the expression of rsmZ, which is one of final targets of the Gac regulon, was not significantly altered in the bmsA mutant, and overexpression of bmsA in the gacA mutant did not produce the WT phenotype. These results indicate that the sensory Bms regulon does not affect the upper cascade of the Gac signal transduction pathway for the biofilm-related phenotypes in P. alkylphenolica.
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Affiliation(s)
- Kyoung Lee
- Department of Bio Health Science, Changwon National University, Changwon-si, Kyongnam 51140, Republic of Korea
| | - Gwang Su Ha
- Department of Bio Health Science, Changwon National University, Changwon-si, Kyongnam 51140, Republic of Korea
| | - Yaligara Veeranagouda
- Department of Bio Health Science, Changwon National University, Changwon-si, Kyongnam 51140, Republic of Korea
| | - Young-Su Seo
- Department of Microbiology, Pusan National University, Busan 46241, Republic of Korea
| | - Ingyu Hwang
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
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21
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López-Farfán D, Reyes-Darias JA, Krell T. The expression of many chemoreceptor genes depends on the cognate chemoeffector as well as on the growth medium and phase. Curr Genet 2016; 63:457-470. [DOI: 10.1007/s00294-016-0646-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/24/2016] [Accepted: 08/31/2016] [Indexed: 01/03/2023]
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22
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Ramos-González MI, Travieso ML, Soriano MI, Matilla MA, Huertas-Rosales Ó, Barrientos-Moreno L, Tagua VG, Espinosa-Urgel M. Genetic Dissection of the Regulatory Network Associated with High c-di-GMP Levels in Pseudomonas putida KT2440. Front Microbiol 2016; 7:1093. [PMID: 27489550 PMCID: PMC4951495 DOI: 10.3389/fmicb.2016.01093] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 06/30/2016] [Indexed: 11/24/2022] Open
Abstract
Most bacteria grow in nature forming multicellular structures named biofilms. The bacterial second messenger cyclic diguanosine monophosphate (c-di-GMP) is a key player in the regulation of the transition from planktonic to sessile lifestyles and this regulation is crucial in the development of biofilms. In Pseudomonas putida KT2440, Rup4959, a multidomain response regulator with diguanylate cyclase activity, when overexpressed causes an increment in the intracellular levels of c-di-GMP that gives rise to a pleiotropic phenotype consisting of increased biofilm formation and crinkly colony morphology. In a broad genomic screen we have isolated mutant derivatives that lose the crinkly morphology, designed as cfc (crinkle free colony). A total of 19 different genes have been identified as being related with the emergence of the cfc phenotype either because the expression or functionality of Rup4959 is compromised, or due to a lack of transduction of the c-di-GMP signal to downstream elements involved in the acquisition of the phenotype. Discernment between these possibilities was investigated by using a c-di-GMP biosensor and by HPLC-MS quantification of the second messenger. Interestingly five of the identified genes encode proteins with AAA+ ATPase domain. Among the bacterial determinants found in this screen are the global transcriptional regulators GacA, AlgU and FleQ and two enzymes involved in the arginine biosynthesis pathway. We present evidences that this pathway seems to be an important element to both the availability of the free pool of the second messenger c-di-GMP and to its further transduction as a signal for biosynthesis of biopolimers. In addition we have identified an uncharacterized hybrid sensor histidine kinase whose phosphoaceptor conserved histidine residue has been shown in this work to be required for in vivo activation of the orphan response regulator Rup4959, which suggests these two elements constitute a two-component phosphorelay system.
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Affiliation(s)
- María Isabel Ramos-González
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - María L Travieso
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - María I Soriano
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Óscar Huertas-Rosales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Laura Barrientos-Moreno
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Víctor G Tagua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
| | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas Granada, Spain
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23
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Corral-Lugo A, De la Torre J, Matilla MA, Fernández M, Morel B, Espinosa-Urgel M, Krell T. Assessment of the contribution of chemoreceptor-based signalling to biofilm formation. Environ Microbiol 2016; 18:3355-3372. [PMID: 26662997 DOI: 10.1111/1462-2920.13170] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 11/30/2015] [Indexed: 12/01/2022]
Abstract
Although it is well established that one- and two-component regulatory systems participate in regulating biofilm formation, there also exists evidence suggesting that chemosensory pathways are also involved. However, little information exists about which chemoreceptors and signals modulate this process. Here we report the generation of the complete set of chemoreceptor mutants of Pseudomonas putida KT2440 and the identification of four mutants with significantly altered biofilm phenotypes. These receptors are a WspA homologue of Pseudomonas aeruginosa, previously identified to control biofilm formation by regulating c-di-GMP levels, and three uncharacterized chemoreceptors. One of these receptors, named McpU, was found to mediate chemotaxis towards different polyamines. The functional annotation of McpU was initiated by high-throughput thermal shift assays of the receptor ligand binding domain (LBD). Isothermal titration calorimetry showed that McpU-LBD specifically binds putrescine, cadaverine and spermidine, indicating that McpU represents a novel chemoreceptor type. Another uncharacterized receptor, named McpA, specifically binds 12 different proteinogenic amino acids and mediates chemotaxis towards these compounds. We also show that mutants in McpU and WspA-Pp have a significantly reduced ability to colonize plant roots. Data agree with other reports showing that polyamines are signal molecules involved in the regulation of bacteria-plant communication and biofilm formation.
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Affiliation(s)
- Andrés Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Jesús De la Torre
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Bertrand Morel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Manuel Espinosa-Urgel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, C/Prof. Albareda 1, 18008, Granada, Spain.
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24
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Owings JP, Kuiper EG, Prezioso SM, Meisner J, Varga JJ, Zelinskaya N, Dammer EB, Duong DM, Seyfried NT, Albertí S, Conn GL, Goldberg JB. Pseudomonas aeruginosa EftM Is a Thermoregulated Methyltransferase. J Biol Chem 2015; 291:3280-90. [PMID: 26677219 DOI: 10.1074/jbc.m115.706853] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Indexed: 11/06/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen that trimethylates elongation factor-thermo-unstable (EF-Tu) on lysine 5. Lysine 5 methylation occurs in a temperature-dependent manner and is generally only seen when P. aeruginosa is grown at temperatures close to ambient (25 °C) but not at higher temperatures (37 °C). We have previously identified the gene, eftM (for EF-Tu-modifying enzyme), responsible for this modification and shown its activity to be associated with increased bacterial adhesion to and invasion of respiratory epithelial cells. Bioinformatic analyses predicted EftM to be a Class I S-adenosyl-l-methionine (SAM)-dependent methyltransferase. An in vitro methyltransferase assay was employed to show that, in the presence of SAM, EftM directly trimethylates EF-Tu. A natural variant of EftM, with a glycine to arginine substitution at position 50 in the predicted SAM-binding domain, lacks both SAM binding and enzyme activity. Mass spectrometry analysis of the in vitro methyltransferase reaction products revealed that EftM exclusively methylates at lysine 5 of EF-Tu in a distributive manner. Consistent with the in vivo temperature dependence of methylation of EF-Tu, preincubation of EftM at 37 °C abolished methyltransferase activity, whereas this activity was retained when EftM was preincubated at 25 °C. Irreversible protein unfolding at 37 °C was observed, and we propose that this instability is the molecular basis for the temperature dependence of EftM activity. Collectively, our results show that EftM is a thermolabile, SAM-dependent methyltransferase that directly trimethylates lysine 5 of EF-Tu in P. aeruginosa.
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Affiliation(s)
- Joshua P Owings
- From the Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep and the Emory-Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, the Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia 22908
| | - Emily G Kuiper
- the Department of Biochemistry and the Biochemistry, Cell, and Developmental Biology Program and
| | - Samantha M Prezioso
- From the Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep and the Emory-Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Emory University School of Medicine, Atlanta, Georgia 30322, and
| | - Jeffrey Meisner
- From the Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep and the Emory-Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322
| | - John J Varga
- From the Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep and the Emory-Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, the Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia 22908
| | | | | | | | | | - Sebastián Albertí
- the Instituto Universitario de Investigación en Ciencias de la Salud, Universidad de las Islas Baleares, Palma de Mallorca, 07122 Spain
| | | | - Joanna B Goldberg
- From the Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep and the Emory-Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322, the Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, Virginia 22908,
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25
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Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses. Appl Environ Microbiol 2015; 82:51-61. [PMID: 26452555 DOI: 10.1128/aem.02602-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 10/07/2015] [Indexed: 01/06/2023] Open
Abstract
Enzymes of the denitrification pathway play an important role in the global nitrogen cycle, including release of nitrous oxide, an ozone-depleting greenhouse gas. In addition, nitric oxide reductase, maturation factors, and proteins associated with nitric oxide detoxification are used by pathogens to combat nitric oxide release by host immune systems. While the core reductases that catalyze the conversion of nitrate to dinitrogen are well understood at a mechanistic level, there are many peripheral proteins required for denitrification whose basic function is unclear. A bar-coded transposon DNA library from Pseudomonas stutzeri strain RCH2 was grown under denitrifying conditions, using nitrate or nitrite as an electron acceptor, and also under molybdenum limitation conditions, with nitrate as the electron acceptor. Analysis of sequencing results from these growths yielded gene fitness data for 3,307 of the 4,265 protein-encoding genes present in strain RCH2. The insights presented here contribute to our understanding of how peripheral proteins contribute to a fully functioning denitrification pathway. We propose a new low-affinity molybdate transporter, OatABC, and show that differential regulation is observed for two MoaA homologs involved in molybdenum cofactor biosynthesis. We also propose that NnrS may function as a membrane-bound NO sensor. The dominant HemN paralog involved in heme biosynthesis is identified, and a CheR homolog is proposed to function in nitrate chemotaxis. In addition, new insights are provided into nitrite reductase redundancy, nitric oxide reductase maturation, nitrous oxide reductase maturation, and regulation.
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26
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Abstract
Pseudomonads sense changes in the concentration of chemicals in their environment and exhibit a behavioral response mediated by flagella or pili coupled with a chemosensory system. The two known chemotaxis pathways, a flagella-mediated pathway and a putative pili-mediated system, are described in this review. Pseudomonas shows chemotaxis response toward a wide range of chemicals, and this review includes a summary of them organized by chemical structure. The assays used to measure positive and negative chemotaxis swimming and twitching Pseudomonas as well as improvements to those assays and new assays are also described. This review demonstrates that there is ample research and intellectual space for future investigators to elucidate the role of chemotaxis in important processes such as pathogenesis, bioremediation, and the bioprotection of plants and animals.
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Affiliation(s)
| | - Rebecca E Parales
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, CA, USA
| | - Tino Krell
- Department of Environmental Protection, CSIC, Estacion Experimental del Zaidin, Granada, Spain
| | - Jane E Hill
- Thayer School of Engineering, Dartmouth College, Hanover, NH, USA
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27
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Prol García MJ, D'Alvise PW, Rygaard AM, Gram L. Biofilm formation is not a prerequisite for production of the antibacterial compound tropodithietic acid in Phaeobacter inhibens DSM17395. J Appl Microbiol 2014; 117:1592-600. [PMID: 25284322 DOI: 10.1111/jam.12659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 09/18/2014] [Accepted: 09/30/2014] [Indexed: 01/06/2023]
Abstract
AIMS The goal of this study was to investigate if biofilm formation on population level is a physiological requirement for antagonism in Phaeobacter inhibens DSM17395, since the antibiotic compound tropodithietic acid (TDA) is produced by several Roseobacter clade species during growth as multicellular aggregates or biofilms at the air-liquid interface and is induced on single cell level upon attachment. METHODS AND RESULTS A mutant library was created by Tn5 transposon insertion and 22 TDA-positive (brown) mutants with decreased biofilm formation or adhesion, and eight TDA-negative (white) mutants with increased biofilm formation or adhesion were selected. None of the selected biofilm-overproducing white mutants showed any antibiotic activity, while all brown mutants with reduced or disabled biofilm formation produced the antibacterial compound. Sequencing analysis indicated that genes that are likely involved in EPS/LPS production, motility and chemotaxis, and redox regulation play a role in biofilm formation and/or adhesion in P. inhibens DSM17395. CONCLUSIONS Cell aggregation and biofilm formation are not physiological prerequisites for TDA production. SIGNIFICANCE AND IMPACT OF THE STUDY This study contributes to the understanding of TDA production in P. inhibens, which has great potential as a probiotic in marine larviculture.
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Affiliation(s)
- M J Prol García
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
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28
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Sarikaya-Bayram O, Bayram O, Feussner K, Kim JH, Kim HS, Kaever A, Feussner I, Chae KS, Han DM, Han KH, Braus GH. Membrane-bound methyltransferase complex VapA-VipC-VapB guides epigenetic control of fungal development. Dev Cell 2014; 29:406-20. [PMID: 24871947 DOI: 10.1016/j.devcel.2014.03.020] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2013] [Revised: 02/26/2014] [Accepted: 03/25/2014] [Indexed: 12/16/2022]
Abstract
Epigenetic and transcriptional control of gene expression must be coordinated in response to external signals to promote alternative multicellular developmental programs. The membrane-associated trimeric complex VapA-VipC-VapB controls a signal transduction pathway for fungal differentiation. The VipC-VapB methyltransferases are tethered to the membrane by the FYVE-like zinc finger protein VapA, allowing the nuclear VelB-VeA-LaeA complex to activate transcription for sexual development. Once the release from VapA is triggered, VipC-VapB is transported into the nucleus. VipC-VapB physically interacts with VeA and reduces its nuclear import and protein stability, thereby reducing the nuclear VelB-VeA-LaeA complex. Nuclear VapB methyltransferase diminishes the establishment of facultative heterochromatin by decreasing histone 3 lysine 9 trimethylation (H3K9me3). This favors activation of the regulatory genes brlA and abaA, which promote the asexual program. The VapA-VipC-VapB methyltransferase pathway combines control of nuclear import and stability of transcription factors with histone modification to foster appropriate differentiation responses.
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Affiliation(s)
- Ozlem Sarikaya-Bayram
- Department of Molecular Microbiology and Genetics, Georg August University, Grisebachstrasse 8, Göttingen 37077, Germany
| | - Ozgür Bayram
- Department of Molecular Microbiology and Genetics, Georg August University, Grisebachstrasse 8, Göttingen 37077, Germany
| | - Kirstin Feussner
- Department of Plant Biochemistry, Georg August University, Justus-von-Liebig-Weg 11, Göttingen 37077, Germany
| | - Jong-Hwa Kim
- Department of Pharmaceutical Engineering, Woosuk University, Wanju 565-701, Korea
| | - Hee-Seo Kim
- Department of Pharmaceutical Engineering, Woosuk University, Wanju 565-701, Korea; Department of Molecular Biology, Chonbuk National University, Jeonju 561-756, Korea
| | - Alexander Kaever
- Department of Bioinformatics, Georg August University, Goldschmidtstrasse 1, Göttingen 37077, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Georg August University, Justus-von-Liebig-Weg 11, Göttingen 37077, Germany
| | - Keon-Sang Chae
- Department of Molecular Biology, Chonbuk National University, Jeonju 561-756, Korea
| | - Dong-Min Han
- Division of Life Sciences, Wonkwang University, Iksan 570-749, Korea
| | - Kap-Hoon Han
- Department of Pharmaceutical Engineering, Woosuk University, Wanju 565-701, Korea
| | - Gerhard H Braus
- Department of Molecular Microbiology and Genetics, Georg August University, Grisebachstrasse 8, Göttingen 37077, Germany.
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